Daily Papers

Graph In-Context Learning, with the ability to adapt pre-trained graph models to novel and diverse downstream graphs without updating any parameters, has gained much attention in the community. The key to graph in-context learning is to perform downstream graphs conditioned on chosen prompt examples. Existing methods randomly select subgraphs or edges as prompts, leading to noisy graph prompts and inferior model performance. Additionally, due to the gap between pre-training and testing graphs, when the number of classes in the testing graphs is much greater than that in the training, the in-context learning ability will also significantly deteriorate. To tackle the aforementioned challenges, we develop a multi-stage adaptive prompt optimization method GraphPrompter, which optimizes the entire process of generating, selecting, and using graph prompts for better in-context learning capabilities. Firstly, Prompt Generator introduces a reconstruction layer to highlight the most informative edges and reduce irrelevant noise for graph prompt construction. Furthermore, in the selection stage, Prompt Selector employs the k-nearest neighbors algorithm and pre-trained selection layers to dynamically choose appropriate samples and minimize the influence of irrelevant prompts. Finally, we leverage a Prompt Augmenter with a cache replacement strategy to enhance the generalization capability of the pre-trained model on new datasets. Extensive experiments show that GraphPrompter effectively enhances the in-context learning ability of graph models. On average across all the settings, our approach surpasses the state-of-the-art baselines by over 8%. Our code is released at https://github.com/karin0018/GraphPrompter.

Large Language Models (LLMs) have gained the ability to assimilate human knowledge and facilitate natural language interactions with both humans and other LLMs. However, despite their impressive achievements, LLMs have not made significant advancements in the realm of graph machine learning. This limitation arises because graphs encapsulate distinct relational data, making it challenging to transform them into natural language that LLMs understand. In this paper, we bridge this gap with a novel framework, GraphText, that translates graphs into natural language. GraphText derives a graph-syntax tree for each graph that encapsulates both the node attributes and inter-node relationships. Traversal of the tree yields a graph text sequence, which is then processed by an LLM to treat graph tasks as text generation tasks. Notably, GraphText offers multiple advantages. It introduces training-free graph reasoning: even without training on graph data, GraphText with ChatGPT can achieve on par with, or even surpassing, the performance of supervised-trained graph neural networks through in-context learning (ICL). Furthermore, GraphText paves the way for interactive graph reasoning, allowing both humans and LLMs to communicate with the model seamlessly using natural language. These capabilities underscore the vast, yet-to-be-explored potential of LLMs in the domain of graph machine learning.

Large language models (LLMs) are increasingly adopted for a variety of tasks with implicit graphical structures, such as planning in robotics, multi-hop question answering or knowledge probing, structured commonsense reasoning, and more. While LLMs have advanced the state-of-the-art on these tasks with structure implications, whether LLMs could explicitly process textual descriptions of graphs and structures, map them to grounded conceptual spaces, and perform structured operations remains underexplored. To this end, we propose NLGraph (Natural Language Graph), a comprehensive benchmark of graph-based problem solving designed in natural language. NLGraph contains 29,370 problems, covering eight graph reasoning tasks with varying complexity from simple tasks such as connectivity and shortest path up to complex problems such as maximum flow and simulating graph neural networks. We evaluate LLMs (GPT-3/4) with various prompting approaches on the NLGraph benchmark and find that 1) language models do demonstrate preliminary graph reasoning abilities, 2) the benefit of advanced prompting and in-context learning diminishes on more complex graph problems, while 3) LLMs are also (un)surprisingly brittle in the face of spurious correlations in graph and problem settings. We then propose Build-a-Graph Prompting and Algorithmic Prompting, two instruction-based approaches to enhance LLMs in solving natural language graph problems. Build-a-Graph and Algorithmic prompting improve the performance of LLMs on NLGraph by 3.07% to 16.85% across multiple tasks and settings, while how to solve the most complicated graph reasoning tasks in our setup with language models remains an open research question. The NLGraph benchmark and evaluation code are available at https://github.com/Arthur-Heng/NLGraph.

Large language models (LLMs) have demonstrated remarkable in-context reasoning capabilities across a wide range of tasks, particularly with unstructured inputs such as language or images. However, LLMs struggle to handle structured data, such as graphs, due to their lack of understanding of non-Euclidean structures. As a result, without additional fine-tuning, their performance significantly lags behind that of graph neural networks (GNNs) in graph learning tasks. In this paper, we show that learning on graph data can be conceptualized as a retrieval-augmented generation (RAG) process, where specific instances (e.g., nodes or edges) act as queries, and the graph itself serves as the retrieved context. Building on this insight, we propose a series of RAG frameworks to enhance the in-context learning capabilities of LLMs for graph learning tasks. Comprehensive evaluations demonstrate that our proposed RAG frameworks significantly improve LLM performance on graph-based tasks, particularly in scenarios where a pretrained LLM must be used without modification or accessed via an API.

Conversational Recommender Systems (CRSs) have emerged as a transformative paradigm for offering personalized recommendations through natural language dialogue. However, they face challenges with knowledge sparsity, as users often provide brief, incomplete preference statements. While recent methods have integrated external knowledge sources to mitigate this, they still struggle with semantic understanding and complex preference reasoning. Recent Large Language Models (LLMs) demonstrate promising capabilities in natural language understanding and reasoning, showing significant potential for CRSs. Nevertheless, due to the lack of domain knowledge, existing LLM-based CRSs either produce hallucinated recommendations or demand expensive domain-specific training, which largely limits their applicability. In this work, we present G-CRS (Graph Retrieval-Augmented Large Language Model for Conversational Recommender Systems), a novel training-free framework that combines graph retrieval-augmented generation and in-context learning to enhance LLMs' recommendation capabilities. Specifically, G-CRS employs a two-stage retrieve-and-recommend architecture, where a GNN-based graph reasoner first identifies candidate items, followed by Personalized PageRank exploration to jointly discover potential items and similar user interactions. These retrieved contexts are then transformed into structured prompts for LLM reasoning, enabling contextually grounded recommendations without task-specific training. Extensive experiments on two public datasets show that G-CRS achieves superior recommendation performance compared to existing methods without requiring task-specific training.

Recent work has demonstrated that semantics specified by pretraining data influence how representations of different concepts are organized in a large language model (LLM). However, given the open-ended nature of LLMs, e.g., their ability to in-context learn, we can ask whether models alter these pretraining semantics to adopt alternative, context-specified ones. Specifically, if we provide in-context exemplars wherein a concept plays a different role than what the pretraining data suggests, do models reorganize their representations in accordance with these novel semantics? To answer this question, we take inspiration from the theory of conceptual role semantics and define a toy "graph tracing" task wherein the nodes of the graph are referenced via concepts seen during training (e.g., apple, bird, etc.) and the connectivity of the graph is defined via some predefined structure (e.g., a square grid). Given exemplars that indicate traces of random walks on the graph, we analyze intermediate representations of the model and find that as the amount of context is scaled, there is a sudden re-organization from pretrained semantic representations to in-context representations aligned with the graph structure. Further, we find that when reference concepts have correlations in their semantics (e.g., Monday, Tuesday, etc.), the context-specified graph structure is still present in the representations, but is unable to dominate the pretrained structure. To explain these results, we analogize our task to energy minimization for a predefined graph topology, providing evidence towards an implicit optimization process to infer context-specified semantics. Overall, our findings indicate scaling context-size can flexibly re-organize model representations, possibly unlocking novel capabilities.

Large language models (LLMs) have shown remarkable in-context learning (ICL) capabilities on textual data. We explore whether these capabilities can be extended to continuous vectors from diverse domains, obtained from black-box pretrained encoders. By aligning input data with an LLM's embedding space through lightweight projectors, we observe that LLMs can effectively process and learn from these projected vectors, which we term Vector-ICL. In particular, we find that pretraining projectors with general language modeling objectives enables Vector-ICL, while task-specific finetuning further enhances performance. In our experiments across various tasks and modalities, including text reconstruction, numerical function regression, text classification, summarization, molecule captioning, time-series classification, graph classification, and fMRI decoding, Vector-ICL often surpasses both few-shot ICL and domain-specific model or tuning. We further conduct analyses and case studies, indicating the potential of LLMs to process vector representations beyond traditional token-based paradigms.

Extensive knowledge graphs (KGs) have been constructed to facilitate knowledge-driven tasks across various scenarios. However, existing work usually develops separate reasoning models for different KGs, lacking the ability to generalize and transfer knowledge across diverse KGs and reasoning settings. In this paper, we propose a prompt-based KG foundation model via in-context learning, namely KG-ICL, to achieve a universal reasoning ability. Specifically, we introduce a prompt graph centered with a query-related example fact as context to understand the query relation. To encode prompt graphs with the generalization ability to unseen entities and relations in queries, we first propose a unified tokenizer that maps entities and relations in prompt graphs to predefined tokens. Then, we propose two message passing neural networks to perform prompt encoding and KG reasoning, respectively. We conduct evaluation on 43 different KGs in both transductive and inductive settings. Results indicate that the proposed KG-ICL outperforms baselines on most datasets, showcasing its outstanding generalization and universal reasoning capabilities. The source code is accessible on GitHub: https://github.com/nju-websoft/KG-ICL.

Recent progress in diffusion models significantly advances various image generation tasks. However, the current mainstream approach remains focused on building task-specific models, which have limited efficiency when supporting a wide range of different needs. While universal models attempt to address this limitation, they face critical challenges, including generalizable task instruction, appropriate task distributions, and unified architectural design. To tackle these challenges, we propose VisualCloze, a universal image generation framework, which supports a wide range of in-domain tasks, generalization to unseen ones, unseen unification of multiple tasks, and reverse generation. Unlike existing methods that rely on language-based task instruction, leading to task ambiguity and weak generalization, we integrate visual in-context learning, allowing models to identify tasks from visual demonstrations. Meanwhile, the inherent sparsity of visual task distributions hampers the learning of transferable knowledge across tasks. To this end, we introduce Graph200K, a graph-structured dataset that establishes various interrelated tasks, enhancing task density and transferable knowledge. Furthermore, we uncover that our unified image generation formulation shared a consistent objective with image infilling, enabling us to leverage the strong generative priors of pre-trained infilling models without modifying the architectures.

Large language models present opportunities for innovative Question Answering over Knowledge Graphs (KGQA). However, they are not inherently designed for query generation. To bridge this gap, solutions have been proposed that rely on fine-tuning or ad-hoc architectures, achieving good results but limited out-of-domain distribution generalization. In this study, we introduce a novel approach called Dynamic Few-Shot Learning (DFSL). DFSL integrates the efficiency of in-context learning and semantic similarity and provides a generally applicable solution for KGQA with state-of-the-art performance. We run an extensive evaluation across multiple benchmark datasets and architecture configurations.

Designing a single model to address multiple tasks has been a long-standing objective in artificial intelligence. Recently, large language models have demonstrated exceptional capability in solving different tasks within the language domain. However, a unified model for various graph tasks remains underexplored, primarily due to the challenges unique to the graph learning domain. First, graph data from different areas carry distinct attributes and follow different distributions. Such discrepancy makes it hard to represent graphs in a single representation space. Second, tasks on graphs diversify into node, link, and graph tasks, requiring distinct embedding strategies. Finally, an appropriate graph prompting paradigm for in-context learning is unclear. We propose One for All (OFA), the first general framework that can use a single graph model to address the above challenges. Specifically, OFA proposes text-attributed graphs to unify different graph data by describing nodes and edges with natural language and uses language models to encode the diverse and possibly cross-domain text attributes to feature vectors in the same embedding space. Furthermore, OFA introduces the concept of nodes-of-interest to standardize different tasks with a single task representation. For in-context learning on graphs, OFA introduces a novel graph prompting paradigm that appends prompting substructures to the input graph, which enables it to address varied tasks without fine-tuning. We train the OFA model using graph data from multiple domains (including citation networks, molecular graphs, knowledge graphs, etc.) simultaneously and evaluate its ability in supervised, few-shot, and zero-shot learning scenarios. OFA performs well across different tasks, making it the first general-purpose across-domains classification model on graphs.

Temporal Knowledge Graph Question Answering (TKGQA) aims to answer questions with temporal intent over Temporal Knowledge Graphs (TKGs). The core challenge of this task lies in understanding the complex semantic information regarding multiple types of time constraints (e.g., before, first) in questions. Existing end-to-end methods implicitly model the time constraints by learning time-aware embeddings of questions and candidate answers, which is far from understanding the question comprehensively. Motivated by semantic-parsing-based approaches that explicitly model constraints in questions by generating logical forms with symbolic operators, we design fundamental temporal operators for time constraints and introduce a novel self-improvement Programming method for TKGQA (Prog-TQA). Specifically, Prog-TQA leverages the in-context learning ability of Large Language Models (LLMs) to understand the combinatory time constraints in the questions and generate corresponding program drafts with a few examples given. Then, it aligns these drafts to TKGs with the linking module and subsequently executes them to generate the answers. To enhance the ability to understand questions, Prog-TQA is further equipped with a self-improvement strategy to effectively bootstrap LLMs using high-quality self-generated drafts. Extensive experiments demonstrate the superiority of the proposed Prog-TQA on MultiTQ and CronQuestions datasets, especially in the Hits@1 metric.

Large language models (LLMs) demonstrate impressive performance on a wide variety of tasks, but they often struggle with tasks that require multi-step reasoning or goal-directed planning. To address this, we take inspiration from the human brain, in which planning is accomplished via the recurrent interaction of specialized modules in the prefrontal cortex (PFC). These modules perform functions such as conflict monitoring, state prediction, state evaluation, task decomposition, and task coordination. We find that LLMs are sometimes capable of carrying out these functions in isolation, but struggle to autonomously coordinate them in the service of a goal. Therefore, we propose a black box architecture with multiple LLM-based (GPT-4) modules. The architecture improves planning through the interaction of specialized PFC-inspired modules that break down a larger problem into multiple brief automated calls to the LLM. We evaluate the combined architecture on two challenging planning tasks -- graph traversal and Tower of Hanoi -- finding that it yields significant improvements over standard LLM methods (e.g., zero-shot prompting or in-context learning). These results demonstrate the benefit of utilizing knowledge from cognitive neuroscience to improve planning in LLMs.

Building a general-purpose agent is a long-standing vision in the field of artificial intelligence. Existing agents have made remarkable progress in many domains, yet they still struggle to complete long-horizon tasks in an open world. We attribute this to the lack of necessary world knowledge and multimodal experience that can guide agents through a variety of long-horizon tasks. In this paper, we propose a Hybrid Multimodal Memory module to address the above challenges. It 1) transforms knowledge into Hierarchical Directed Knowledge Graph that allows agents to explicitly represent and learn world knowledge, and 2) summarises historical information into Abstracted Multimodal Experience Pool that provide agents with rich references for in-context learning. On top of the Hybrid Multimodal Memory module, a multimodal agent, Optimus-1, is constructed with dedicated Knowledge-guided Planner and Experience-Driven Reflector, contributing to a better planning and reflection in the face of long-horizon tasks in Minecraft. Extensive experimental results show that Optimus-1 significantly outperforms all existing agents on challenging long-horizon task benchmarks, and exhibits near human-level performance on many tasks. In addition, we introduce various Multimodal Large Language Models (MLLMs) as the backbone of Optimus-1. Experimental results show that Optimus-1 exhibits strong generalization with the help of the Hybrid Multimodal Memory module, outperforming the GPT-4V baseline on many tasks.

Many recent approaches to natural language tasks are built on the remarkable abilities of large language models. Large language models can perform in-context learning, where they learn a new task from a few task demonstrations, without any parameter updates. This work examines the implications of in-context learning for the creation of datasets for new natural language tasks. Departing from recent in-context learning methods, we formulate an annotation-efficient, two-step framework: selective annotation that chooses a pool of examples to annotate from unlabeled data in advance, followed by prompt retrieval that retrieves task examples from the annotated pool at test time. Based on this framework, we propose an unsupervised, graph-based selective annotation method, voke-k, to select diverse, representative examples to annotate. Extensive experiments on 10 datasets (covering classification, commonsense reasoning, dialogue, and text/code generation) demonstrate that our selective annotation method improves the task performance by a large margin. On average, vote-k achieves a 12.9%/11.4% relative gain under an annotation budget of 18/100, as compared to randomly selecting examples to annotate. Compared to state-of-the-art supervised finetuning approaches, it yields similar performance with 10-100x less annotation cost across 10 tasks. We further analyze the effectiveness of our framework in various scenarios: language models with varying sizes, alternative selective annotation methods, and cases where there is a test data domain shift. We hope that our studies will serve as a basis for data annotations as large language models are increasingly applied to new tasks. Our code is available at https://github.com/HKUNLP/icl-selective-annotation.

In task-oriented dialogue, a system often needs to follow a sequence of actions, called a workflow, that complies with a set of guidelines in order to complete a task. In this paper, we propose the novel problem of multi-step workflow action prediction, in which the system predicts multiple future workflow actions. Accurate prediction of multiple steps allows for multi-turn automation, which can free up time to focus on more complex tasks. We propose three modeling approaches that are simple to implement yet lead to more action automation: 1) fine-tuning on a training dataset, 2) few-shot in-context learning leveraging retrieval and large language model prompting, and 3) zero-shot graph traversal, which aggregates historical action sequences into a graph for prediction. We show that multi-step action prediction produces features that improve accuracy on downstream dialogue tasks like predicting task success, and can increase automation of steps by 20% without requiring as much feedback from a human overseeing the system.

Graphs can be leveraged to model polyphonic multitrack symbolic music, where notes, chords and entire sections may be linked at different levels of the musical hierarchy by tonal and rhythmic relationships. Nonetheless, there is a lack of works that consider graph representations in the context of deep learning systems for music generation. This paper bridges this gap by introducing a novel graph representation for music and a deep Variational Autoencoder that generates the structure and the content of musical graphs separately, one after the other, with a hierarchical architecture that matches the structural priors of music. By separating the structure and content of musical graphs, it is possible to condition generation by specifying which instruments are played at certain times. This opens the door to a new form of human-computer interaction in the context of music co-creation. After training the model on existing MIDI datasets, the experiments show that the model is able to generate appealing short and long musical sequences and to realistically interpolate between them, producing music that is tonally and rhythmically consistent. Finally, the visualization of the embeddings shows that the model is able to organize its latent space in accordance with known musical concepts.

Persistent homology, a technique from computational topology, has recently shown strong empirical performance in the context of graph classification. Being able to capture long range graph properties via higher-order topological features, such as cycles of arbitrary length, in combination with multi-scale topological descriptors, has improved predictive performance for data sets with prominent topological structures, such as molecules. At the same time, the theoretical properties of persistent homology have not been formally assessed in this context. This paper intends to bridge the gap between computational topology and graph machine learning by providing a brief introduction to persistent homology in the context of graphs, as well as a theoretical discussion and empirical analysis of its expressivity for graph learning tasks.

Weakly-Supervised Scene Graph Generation (WSSGG) research has recently emerged as an alternative to the fully-supervised approach that heavily relies on costly annotations. In this regard, studies on WSSGG have utilized image captions to obtain unlocalized triplets while primarily focusing on grounding the unlocalized triplets over image regions. However, they have overlooked the two issues involved in the triplet formation process from the captions: 1) Semantic over-simplification issue arises when extracting triplets from captions, where fine-grained predicates in captions are undesirably converted into coarse-grained predicates, resulting in a long-tailed predicate distribution, and 2) Low-density scene graph issue arises when aligning the triplets in the caption with entity/predicate classes of interest, where many triplets are discarded and not used in training, leading to insufficient supervision. To tackle the two issues, we propose a new approach, i.e., Large Language Model for weakly-supervised SGG (LLM4SGG), where we mitigate the two issues by leveraging the LLM's in-depth understanding of language and reasoning ability during the extraction of triplets from captions and alignment of entity/predicate classes with target data. To further engage the LLM in these processes, we adopt the idea of Chain-of-Thought and the in-context few-shot learning strategy. To validate the effectiveness of LLM4SGG, we conduct extensive experiments on Visual Genome and GQA datasets, showing significant improvements in both Recall@K and mean Recall@K compared to the state-of-the-art WSSGG methods. A further appeal is that LLM4SGG is data-efficient, enabling effective model training with a small amount of training images.

Rationale discovery is defined as finding a subset of the input data that maximally supports the prediction of downstream tasks. In graph machine learning context, graph rationale is defined to locate the critical subgraph in the given graph topology, which fundamentally determines the prediction results. In contrast to the rationale subgraph, the remaining subgraph is named the environment subgraph. Graph rationalization can enhance the model performance as the mapping between the graph rationale and prediction label is viewed as invariant, by assumption. To ensure the discriminative power of the extracted rationale subgraphs, a key technique named "intervention" is applied. The core idea of intervention is that given any changing environment subgraphs, the semantics from the rationale subgraph is invariant, which guarantees the correct prediction result. However, most, if not all, of the existing rationalization works on graph data develop their intervention strategies on the graph level, which is coarse-grained. In this paper, we propose well-tailored intervention strategies on graph data. Our idea is driven by the development of Transformer models, whose self-attention module provides rich interactions between input nodes. Based on the self-attention module, our proposed invariant graph Transformer (IGT) can achieve fine-grained, more specifically, node-level and virtual node-level intervention. Our comprehensive experiments involve 7 real-world datasets, and the proposed IGT shows significant performance advantages compared to 13 baseline methods.

Dictionary learning is a key tool for representation learning, that explains the data as linear combination of few basic elements. Yet, this analysis is not amenable in the context of graph learning, as graphs usually belong to different metric spaces. We fill this gap by proposing a new online Graph Dictionary Learning approach, which uses the Gromov Wasserstein divergence for the data fitting term. In our work, graphs are encoded through their nodes' pairwise relations and modeled as convex combination of graph atoms, i.e. dictionary elements, estimated thanks to an online stochastic algorithm, which operates on a dataset of unregistered graphs with potentially different number of nodes. Our approach naturally extends to labeled graphs, and is completed by a novel upper bound that can be used as a fast approximation of Gromov Wasserstein in the embedding space. We provide numerical evidences showing the interest of our approach for unsupervised embedding of graph datasets and for online graph subspace estimation and tracking.

Text-attributed graphs have recently garnered significant attention due to their wide range of applications in web domains. Existing methodologies employ word embedding models for acquiring text representations as node features, which are subsequently fed into Graph Neural Networks (GNNs) for training. Recently, the advent of Large Language Models (LLMs) has introduced their powerful capabilities in information retrieval and text generation, which can greatly enhance the text attributes of graph data. Furthermore, the acquisition and labeling of extensive datasets are both costly and time-consuming endeavors. Consequently, few-shot learning has emerged as a crucial problem in the context of graph learning tasks. In order to tackle this challenge, we propose a lightweight paradigm called LLM4NG, which adopts a plug-and-play approach to empower text-attributed graphs through node generation using LLMs. Specifically, we utilize LLMs to extract semantic information from the labels and generate samples that belong to these categories as exemplars. Subsequently, we employ an edge predictor to capture the structural information inherent in the raw dataset and integrate the newly generated samples into the original graph. This approach harnesses LLMs for enhancing class-level information and seamlessly introduces labeled nodes and edges without modifying the raw dataset, thereby facilitating the node classification task in few-shot scenarios. Extensive experiments demonstrate the outstanding performance of our proposed paradigm, particularly in low-shot scenarios. For instance, in the 1-shot setting of the ogbn-arxiv dataset, LLM4NG achieves a 76% improvement over the baseline model.

Graph Neural Networks (GNNs) have demonstrated state-of-the-art performance in various graph representation learning tasks. Recently, studies revealed their vulnerability to adversarial attacks. In this work, we theoretically define the concept of expected robustness in the context of attributed graphs and relate it to the classical definition of adversarial robustness in the graph representation learning literature. Our definition allows us to derive an upper bound of the expected robustness of Graph Convolutional Networks (GCNs) and Graph Isomorphism Networks subject to node feature attacks. Building on these findings, we connect the expected robustness of GNNs to the orthonormality of their weight matrices and consequently propose an attack-independent, more robust variant of the GCN, called the Graph Convolutional Orthonormal Robust Networks (GCORNs). We further introduce a probabilistic method to estimate the expected robustness, which allows us to evaluate the effectiveness of GCORN on several real-world datasets. Experimental experiments showed that GCORN outperforms available defense methods. Our code is publicly available at: https://github.com/Sennadir/GCORN{https://github.com/Sennadir/GCORN}.

Task planning in language agents is emerging as an important research topic alongside the development of large language models (LLMs). It aims to break down complex user requests in natural language into solvable sub-tasks, thereby fulfilling the original requests. In this context, the sub-tasks can be naturally viewed as a graph, where the nodes represent the sub-tasks, and the edges denote the dependencies among them. Consequently, task planning is a decision-making problem that involves selecting a connected path or subgraph within the corresponding graph and invoking it. In this paper, we explore graph learning-based methods for task planning, a direction that is orthogonal to the prevalent focus on prompt design. Our interest in graph learning stems from a theoretical discovery: the biases of attention and auto-regressive loss impede LLMs' ability to effectively navigate decision-making on graphs, which is adeptly addressed by graph neural networks (GNNs). This theoretical insight led us to integrate GNNs with LLMs to enhance overall performance. Extensive experiments demonstrate that GNN-based methods surpass existing solutions even without training, and minimal training can further enhance their performance. The performance gain increases with a larger task graph size.

We introduce Graph-Induced Sum-Product Networks (GSPNs), a new probabilistic framework for graph representation learning that can tractably answer probabilistic queries. Inspired by the computational trees induced by vertices in the context of message-passing neural networks, we build hierarchies of sum-product networks (SPNs) where the parameters of a parent SPN are learnable transformations of the a-posterior mixing probabilities of its children's sum units. Due to weight sharing and the tree-shaped computation graphs of GSPNs, we obtain the efficiency and efficacy of deep graph networks with the additional advantages of a probabilistic model. We show the model's competitiveness on scarce supervision scenarios, under missing data, and for graph classification in comparison to popular neural models. We complement the experiments with qualitative analyses on hyper-parameters and the model's ability to answer probabilistic queries.

Multimodal learning combines multiple data modalities, broadening the types and complexity of data our models can utilize: for example, from plain text to image-caption pairs. Most multimodal learning algorithms focus on modeling simple one-to-one pairs of data from two modalities, such as image-caption pairs, or audio-text pairs. However, in most real-world settings, entities of different modalities interact with each other in more complex and multifaceted ways, going beyond one-to-one mappings. We propose to represent these complex relationships as graphs, allowing us to capture data with any number of modalities, and with complex relationships between modalities that can flexibly vary from one sample to another. Toward this goal, we propose Multimodal Graph Learning (MMGL), a general and systematic framework for capturing information from multiple multimodal neighbors with relational structures among them. In particular, we focus on MMGL for generative tasks, building upon pretrained Language Models (LMs), aiming to augment their text generation with multimodal neighbor contexts. We study three research questions raised by MMGL: (1) how can we infuse multiple neighbor information into the pretrained LMs, while avoiding scalability issues? (2) how can we infuse the graph structure information among multimodal neighbors into the LMs? and (3) how can we finetune the pretrained LMs to learn from the neighbor context in a parameter-efficient manner? We conduct extensive experiments to answer these three questions on MMGL and analyze the empirical results to pave the way for future MMGL research.

Predicting drug efficacy and safety in vivo requires information on biological responses (e.g., cell morphology and gene expression) to small molecule perturbations. However, current molecular representation learning methods do not provide a comprehensive view of cell states under these perturbations and struggle to remove noise, hindering model generalization. We introduce the Information Alignment (InfoAlign) approach to learn molecular representations through the information bottleneck method in cells. We integrate molecules and cellular response data as nodes into a context graph, connecting them with weighted edges based on chemical, biological, and computational criteria. For each molecule in a training batch, InfoAlign optimizes the encoder's latent representation with a minimality objective to discard redundant structural information. A sufficiency objective decodes the representation to align with different feature spaces from the molecule's neighborhood in the context graph. We demonstrate that the proposed sufficiency objective for alignment is tighter than existing encoder-based contrastive methods. Empirically, we validate representations from InfoAlign in two downstream tasks: molecular property prediction against up to 19 baseline methods across four datasets, plus zero-shot molecule-morphology matching.

Pre-trained sequence-to-sequence language models have led to widespread success in many natural language generation tasks. However, there has been relatively less work on analyzing their ability to generate structured outputs such as graphs. Unlike natural language, graphs have distinct structural and semantic properties in the context of a downstream NLP task, e.g., generating a graph that is connected and acyclic can be attributed to its structural constraints, while the semantics of a graph can refer to how meaningfully an edge represents the relation between two node concepts. In this work, we study pre-trained language models that generate explanation graphs in an end-to-end manner and analyze their ability to learn the structural constraints and semantics of such graphs. We first show that with limited supervision, pre-trained language models often generate graphs that either violate these constraints or are semantically incoherent. Since curating large amount of human-annotated graphs is expensive and tedious, we propose simple yet effective ways of graph perturbations via node and edge edit operations that lead to structurally and semantically positive and negative graphs. Next, we leverage these graphs in different contrastive learning models with Max-Margin and InfoNCE losses. Our methods lead to significant improvements in both structural and semantic accuracy of explanation graphs and also generalize to other similar graph generation tasks. Lastly, we show that human errors are the best negatives for contrastive learning and also that automatically generating more such human-like negative graphs can lead to further improvements. Our code and models are publicly available at https://github.com/swarnaHub/ExplagraphGen

Efficient numerical solvers for partial differential equations empower science and engineering. One of the commonly employed numerical solvers is the preconditioned conjugate gradient (PCG) algorithm which can solve large systems to a given precision level. One challenge in PCG solvers is the selection of preconditioners, as different problem-dependent systems can benefit from different preconditioners. We present a new method to introduce inductive bias in preconditioning conjugate gradient algorithm. Given a system matrix and a set of solution vectors arise from an underlying distribution, we train a graph neural network to obtain an approximate decomposition to the system matrix to be used as a preconditioner in the context of PCG solvers. We conduct extensive experiments to demonstrate the efficacy and generalizability of our proposed approach in solving various 2D and 3D linear second-order PDEs.

Examining Drug-Drug Interactions (DDIs) is a pivotal element in the process of drug development. DDIs occur when one drug's properties are affected by the inclusion of other drugs. Detecting favorable DDIs has the potential to pave the way for creating and advancing innovative medications applicable in practical settings. However, existing DDI prediction models continue to face challenges related to generalization in extreme cases, robust feature extraction, and real-life application possibilities. We aim to address these challenges by leveraging the effectiveness of context-aware deep graph learning by introducing a novel framework named CADGL. Based on a customized variational graph autoencoder (VGAE), we capture critical structural and physio-chemical information using two context preprocessors for feature extraction from two different perspectives: local neighborhood and molecular context, in a heterogeneous graphical structure. Our customized VGAE consists of a graph encoder, a latent information encoder, and an MLP decoder. CADGL surpasses other state-of-the-art DDI prediction models, excelling in predicting clinically valuable novel DDIs, supported by rigorous case studies.

Aspect-based sentiment analysis (ABSA) is a fine-grained task of sentiment analysis. To better comprehend long complicated sentences and obtain accurate aspect-specific information, linguistic and commonsense knowledge are generally required in this task. However, most current methods employ complicated and inefficient approaches to incorporate external knowledge, e.g., directly searching the graph nodes. Additionally, the complementarity between external knowledge and linguistic information has not been thoroughly studied. To this end, we propose a knowledge graph augmented network KGAN, which aims to effectively incorporate external knowledge with explicitly syntactic and contextual information. In particular, KGAN captures the sentiment feature representations from multiple different perspectives, i.e., context-, syntax- and knowledge-based. First, KGAN learns the contextual and syntactic representations in parallel to fully extract the semantic features. Then, KGAN integrates the knowledge graphs into the embedding space, based on which the aspect-specific knowledge representations are further obtained via an attention mechanism. Last, we propose a hierarchical fusion module to complement these multi-view representations in a local-to-global manner. Extensive experiments on five popular ABSA benchmarks demonstrate the effectiveness and robustness of our KGAN. Notably, with the help of the pretrained model of RoBERTa, KGAN achieves a new record of state-of-the-art performance among all datasets.

Software vulnerabilities present a persistent security challenge, with over 25,000 new vulnerabilities reported in the Common Vulnerabilities and Exposures (CVE) database in 2024 alone. While deep learning based approaches show promise for vulnerability detection, recent studies reveal critical limitations in terms of accuracy and robustness: accuracy drops by up to 45% on rigorously verified datasets, and performance degrades significantly under simple code modifications. This paper presents LLMxCPG, a novel framework integrating Code Property Graphs (CPG) with Large Language Models (LLM) for robust vulnerability detection. Our CPG-based slice construction technique reduces code size by 67.84 to 90.93% while preserving vulnerability-relevant context. Our approach's ability to provide a more concise and accurate representation of code snippets enables the analysis of larger code segments, including entire projects. This concise representation is a key factor behind the improved detection capabilities of our method, as it can now identify vulnerabilities that span multiple functions. Empirical evaluation demonstrates LLMxCPG's effectiveness across verified datasets, achieving 15-40% improvements in F1-score over state-of-the-art baselines. Moreover, LLMxCPG maintains high performance across function-level and multi-function codebases while exhibiting robust detection efficacy under various syntactic code modifications.

A key component of deep learning (DL) for natural language processing (NLP) is word embeddings. Word embeddings that effectively capture the meaning and context of the word that they represent can significantly improve the performance of downstream DL models for various NLP tasks. Many existing word embeddings techniques capture the context of words based on word co-occurrence in documents and text; however, they often cannot capture broader domain-specific relationships between concepts that may be crucial for the NLP task at hand. In this paper, we propose a method to integrate external knowledge from medical terminology ontologies into the context captured by word embeddings. Specifically, we use a medical knowledge graph, such as the unified medical language system (UMLS), to find connections between clinical terms in cancer pathology reports. This approach aims to minimize the distance between connected clinical concepts. We evaluate the proposed approach using a Multitask Convolutional Neural Network (MT-CNN) to extract six cancer characteristics -- site, subsite, laterality, behavior, histology, and grade -- from a dataset of ~900K cancer pathology reports. The results show that the MT-CNN model which uses our domain informed embeddings outperforms the same MT-CNN using standard word2vec embeddings across all tasks, with an improvement in the overall micro- and macro-F1 scores by 4.97\%and 22.5\%, respectively.

Named Entity Disambiguation (NED) refers to the task of resolving multiple named entity mentions in a document to their correct references in a knowledge base (KB) (e.g., Wikipedia). In this paper, we propose a novel embedding method specifically designed for NED. The proposed method jointly maps words and entities into the same continuous vector space. We extend the skip-gram model by using two models. The KB graph model learns the relatedness of entities using the link structure of the KB, whereas the anchor context model aims to align vectors such that similar words and entities occur close to one another in the vector space by leveraging KB anchors and their context words. By combining contexts based on the proposed embedding with standard NED features, we achieved state-of-the-art accuracy of 93.1% on the standard CoNLL dataset and 85.2% on the TAC 2010 dataset.

In-context learning (ICL) is one of the most powerful and most unexpected capabilities to emerge in recent transformer-based large language models (LLMs). Yet the mechanisms that underlie it are poorly understood. In this paper, we demonstrate that comparable ICL capabilities can be acquired by an alternative sequence prediction learning method using clone-structured causal graphs (CSCGs). Moreover, a key property of CSCGs is that, unlike transformer-based LLMs, they are {\em interpretable}, which considerably simplifies the task of explaining how ICL works. Specifically, we show that it uses a combination of (a) learning template (schema) circuits for pattern completion, (b) retrieving relevant templates in a context-sensitive manner, and (c) rebinding of novel tokens to appropriate slots in the templates. We go on to marshall evidence for the hypothesis that similar mechanisms underlie ICL in LLMs. For example, we find that, with CSCGs as with LLMs, different capabilities emerge at different levels of overparameterization, suggesting that overparameterization helps in learning more complex template (schema) circuits. By showing how ICL can be achieved with small models and datasets, we open up a path to novel architectures, and take a vital step towards a more general understanding of the mechanics behind this important capability.

Retrosynthetic planning aims to devise a complete multi-step synthetic route from starting materials to a target molecule. Current strategies use a decoupled approach of single-step retrosynthesis models and search algorithms, taking only the product as the input to predict the reactants for each planning step and ignoring valuable context information along the synthetic route. In this work, we propose a novel framework that utilizes context information for improved retrosynthetic planning. We view synthetic routes as reaction graphs and propose to incorporate context through three principled steps: encode molecules into embeddings, aggregate information over routes, and readout to predict reactants. Our approach is the first attempt to utilize in-context learning for retrosynthesis prediction in retrosynthetic planning. The entire framework can be efficiently optimized in an end-to-end fashion and produce more practical and accurate predictions. Comprehensive experiments demonstrate that by fusing in the context information over routes, our model significantly improves the performance of retrosynthetic planning over baselines that are not context-aware, especially for long synthetic routes. Code is available at https://github.com/SongtaoLiu0823/FusionRetro.

Answering Questions over Knowledge Graphs (KGQA) is key to well-functioning autonomous language agents in various real-life applications. To improve the neural-symbolic reasoning capabilities of language agents powered by Large Language Models (LLMs) in KGQA, we propose the DecompositionAlignment-Reasoning Agent (DARA) framework. DARA effectively parses questions into formal queries through a dual mechanism: high-level iterative task decomposition and low-level task grounding. Importantly, DARA can be efficiently trained with a small number of high-quality reasoning trajectories. Our experimental results demonstrate that DARA fine-tuned on LLMs (e.g. Llama-2-7B, Mistral) outperforms both in-context learning-based agents with GPT-4 and alternative fine-tuned agents, across different benchmarks in zero-shot evaluation, making such models more accessible for real-life applications. We also show that DARA attains performance comparable to state-of-the-art enumerating-and-ranking-based methods for KGQA.

Recently, an intriguing class of non-convex optimization problems has emerged in the context of learning directed acyclic graphs (DAGs). These problems involve minimizing a given loss or score function, subject to a non-convex continuous constraint that penalizes the presence of cycles in a graph. In this work, we delve into the optimization challenges associated with this class of non-convex programs. To address these challenges, we propose a bi-level algorithm that leverages the non-convex constraint in a novel way. The outer level of the algorithm optimizes over topological orders by iteratively swapping pairs of nodes within the topological order of a DAG. A key innovation of our approach is the development of an effective method for generating a set of candidate swapping pairs for each iteration. At the inner level, given a topological order, we utilize off-the-shelf solvers that can handle linear constraints. The key advantage of our proposed algorithm is that it is guaranteed to find a local minimum or a KKT point under weaker conditions compared to previous work and finds solutions with lower scores. Extensive experiments demonstrate that our method outperforms state-of-the-art approaches in terms of achieving a better score. Additionally, our method can also be used as a post-processing algorithm to significantly improve the score of other algorithms. Code implementing the proposed method is available at https://github.com/duntrain/topo.

Learning sparse coordination graphs adaptive to the coordination dynamics among agents is a long-standing problem in cooperative multi-agent learning. This paper studies this problem and proposes a novel method using the variance of payoff functions to construct context-aware sparse coordination topologies. We theoretically consolidate our method by proving that the smaller the variance of payoff functions is, the less likely action selection will change after removing the corresponding edge. Moreover, we propose to learn action representations to effectively reduce the influence of payoff functions' estimation errors on graph construction. To empirically evaluate our method, we present the Multi-Agent COordination (MACO) benchmark by collecting classic coordination problems in the literature, increasing their difficulty, and classifying them into different types. We carry out a case study and experiments on the MACO and StarCraft II micromanagement benchmark to demonstrate the dynamics of sparse graph learning, the influence of graph sparseness, and the learning performance of our method. (The MACO benchmark and codes are publicly available at https://github.com/TonghanWang/CASEC-MACO-benchmark.)

Digital Twins (DT) are a promising concept in cyber-physical systems research due to their advanced features including monitoring and automated reasoning. Semantic technologies such as Knowledge Graphs (KG) are recently being utilized in DTs especially for information modelling. Building on this move, this paper proposes a pipeline for semantic association rule learning in DTs using KGs and time series data. In addition to this initial pipeline, we also propose new semantic association rule criterion. The approach is evaluated on an industrial water network scenario. Initial evaluation shows that the proposed approach is able to learn a high number of association rules with semantic information which are more generalizable. The paper aims to set a foundation for further work on using semantic association rule learning especially in the context of industrial applications.

Large Language Models (LLMs) have exhibited impressive proficiency in various natural language processing (NLP) tasks, which involve increasingly complex reasoning. Knowledge reasoning, a primary type of reasoning, aims at deriving new knowledge from existing one.While it has been widely studied in the context of knowledge graphs (KGs), knowledge reasoning in LLMs remains underexplored. In this paper, we introduce Chain-of-Knowledge, a comprehensive framework for knowledge reasoning, including methodologies for both dataset construction and model learning. For dataset construction, we create KnowReason via rule mining on KGs. For model learning, we observe rule overfitting induced by naive training. Hence, we enhance CoK with a trial-and-error mechanism that simulates the human process of internal knowledge exploration. We conduct extensive experiments with KnowReason. Our results show the effectiveness of CoK in refining LLMs in not only knowledge reasoning, but also general reasoning benchmarkms.

Recently, knowledge-enhanced pre-trained language models (KEPLMs) improve context-aware representations via learning from structured relations in knowledge graphs, and/or linguistic knowledge from syntactic or dependency analysis. Unlike English, there is a lack of high-performing open-source Chinese KEPLMs in the natural language processing (NLP) community to support various language understanding applications. In this paper, we revisit and advance the development of Chinese natural language understanding with a series of novel Chinese KEPLMs released in various parameter sizes, namely CKBERT (Chinese knowledge-enhanced BERT).Specifically, both relational and linguistic knowledge is effectively injected into CKBERT based on two novel pre-training tasks, i.e., linguistic-aware masked language modeling and contrastive multi-hop relation modeling. Based on the above two pre-training paradigms and our in-house implemented TorchAccelerator, we have pre-trained base (110M), large (345M) and huge (1.3B) versions of CKBERT efficiently on GPU clusters. Experiments demonstrate that CKBERT outperforms strong baselines for Chinese over various benchmark NLP tasks and in terms of different model sizes.

Heterogeneous graph contrastive learning has received wide attention recently. Some existing methods use meta-paths, which are sequences of object types that capture semantic relationships between objects, to construct contrastive views. However, most of them ignore the rich meta-path context information that describes how two objects are connected by meta-paths. Further, they fail to distinguish negative samples, which could adversely affect the model performance. To address the problems, we propose MEOW, which considers both meta-path contexts and weighted negative samples. Specifically, MEOW constructs a coarse view and a fine-grained view for contrast. The former reflects which objects are connected by meta-paths, while the latter uses meta-path contexts and characterizes details on how the objects are connected. Then, we theoretically analyze the InfoNCE loss and recognize its limitations for computing gradients of negative samples. To better distinguish negative samples, we learn hard-valued weights for them based on node clustering and use prototypical contrastive learning to pull close embeddings of nodes in the same cluster. In addition, we propose a variant model AdaMEOW that adaptively learns soft-valued weights of negative samples to further improve node representation. Finally, we conduct extensive experiments to show the superiority of MEOW and AdaMEOW against other state-of-the-art methods.

In recent years, graph representation learning has undergone a paradigm shift, driven by the emergence and proliferation of graph neural networks (GNNs) and their heterogeneous counterparts. Heterogeneous GNNs have shown remarkable success in extracting low-dimensional embeddings from complex graphs that encompass diverse entity types and relationships. While meta-path-based techniques have long been recognized for their ability to capture semantic affinities among nodes, their dependence on manual specification poses a significant limitation. In contrast, matrix-focused methods accelerate processing by utilizing structural cues but often overlook contextual richness. In this paper, we challenge the current paradigm by introducing ontology as a fundamental semantic primitive within complex graphs. Our goal is to integrate the strengths of both matrix-centric and meta-path-based approaches into a unified framework. We propose perturbation Ontology-based Graph Attention Networks (POGAT), a novel methodology that combines ontology subgraphs with an advanced self-supervised learning paradigm to achieve a deep contextual understanding. The core innovation of POGAT lies in our enhanced homogeneous perturbing scheme designed to generate rigorous negative samples, encouraging the model to explore minimal contextual features more thoroughly. Through extensive empirical evaluations, we demonstrate that POGAT significantly outperforms state-of-the-art baselines, achieving a groundbreaking improvement of up to 10.78\% in F1-score for the critical task of link prediction and 12.01\% in Micro-F1 for the critical task of node classification.

Graph representation learning nowadays becomes fundamental in analyzing graph-structured data. Inspired by recent success of contrastive methods, in this paper, we propose a novel framework for unsupervised graph representation learning by leveraging a contrastive objective at the node level. Specifically, we generate two graph views by corruption and learn node representations by maximizing the agreement of node representations in these two views. To provide diverse node contexts for the contrastive objective, we propose a hybrid scheme for generating graph views on both structure and attribute levels. Besides, we provide theoretical justification behind our motivation from two perspectives, mutual information and the classical triplet loss. We perform empirical experiments on both transductive and inductive learning tasks using a variety of real-world datasets. Experimental experiments demonstrate that despite its simplicity, our proposed method consistently outperforms existing state-of-the-art methods by large margins. Moreover, our unsupervised method even surpasses its supervised counterparts on transductive tasks, demonstrating its great potential in real-world applications.

Executing actions in a correlated manner is a common strategy for human coordination that often leads to better cooperation, which is also potentially beneficial for cooperative multi-agent reinforcement learning (MARL). However, the recent success of MARL relies heavily on the convenient paradigm of purely decentralized execution, where there is no action correlation among agents for scalability considerations. In this work, we introduce a Bayesian network to inaugurate correlations between agents' action selections in their joint policy. Theoretically, we establish a theoretical justification for why action dependencies are beneficial by deriving the multi-agent policy gradient formula under such a Bayesian network joint policy and proving its global convergence to Nash equilibria under tabular softmax policy parameterization in cooperative Markov games. Further, by equipping existing MARL algorithms with a recent method of differentiable directed acyclic graphs (DAGs), we develop practical algorithms to learn the context-aware Bayesian network policies in scenarios with partial observability and various difficulty. We also dynamically decrease the sparsity of the learned DAG throughout the training process, which leads to weakly or even purely independent policies for decentralized execution. Empirical results on a range of MARL benchmarks show the benefits of our approach.

AutoML systems build machine learning models automatically by performing a search over valid data transformations and learners, along with hyper-parameter optimization for each learner. Many AutoML systems use meta-learning to guide search for optimal pipelines. In this work, we present a novel meta-learning system called KGpip which, (1) builds a database of datasets and corresponding pipelines by mining thousands of scripts with program analysis, (2) uses dataset embeddings to find similar datasets in the database based on its content instead of metadata-based features, (3) models AutoML pipeline creation as a graph generation problem, to succinctly characterize the diverse pipelines seen for a single dataset. KGpip's meta-learning is a sub-component for AutoML systems. We demonstrate this by integrating KGpip with two AutoML systems. Our comprehensive evaluation using 126 datasets, including those used by the state-of-the-art systems, shows that KGpip significantly outperforms these systems.

Attention mechanisms have been widely used to capture long-range dependencies among nodes in Graph Transformers. Bottlenecked by the quadratic computational cost, attention mechanisms fail to scale in large graphs. Recent improvements in computational efficiency are mainly achieved by attention sparsification with random or heuristic-based graph subsampling, which falls short in data-dependent context reasoning. State space models (SSMs), such as Mamba, have gained prominence for their effectiveness and efficiency in modeling long-range dependencies in sequential data. However, adapting SSMs to non-sequential graph data presents a notable challenge. In this work, we introduce Graph-Mamba, the first attempt to enhance long-range context modeling in graph networks by integrating a Mamba block with the input-dependent node selection mechanism. Specifically, we formulate graph-centric node prioritization and permutation strategies to enhance context-aware reasoning, leading to a substantial improvement in predictive performance. Extensive experiments on ten benchmark datasets demonstrate that Graph-Mamba outperforms state-of-the-art methods in long-range graph prediction tasks, with a fraction of the computational cost in both FLOPs and GPU memory consumption. The code and models are publicly available at https://github.com/bowang-lab/Graph-Mamba.

Modeling dynamic graphs, such as those found in social networks, recommendation systems, and e-commerce platforms, is crucial for capturing evolving relationships and delivering relevant insights over time. Traditional approaches primarily rely on graph neural networks with temporal components or sequence generation models, which often focus narrowly on the historical context of target nodes. This limitation restricts the ability to adapt to new and emerging patterns in dynamic graphs. To address this challenge, we propose a novel framework, Retrieval-Augmented Generation for Dynamic Graph modeling (RAG4DyG), which enhances dynamic graph predictions by incorporating contextually and temporally relevant examples from broader graph structures. Our approach includes a time- and context-aware contrastive learning module to identify high-quality demonstrations and a graph fusion strategy to effectively integrate these examples with historical contexts. The proposed framework is designed to be effective in both transductive and inductive scenarios, ensuring adaptability to previously unseen nodes and evolving graph structures. Extensive experiments across multiple real-world datasets demonstrate the effectiveness of RAG4DyG in improving predictive accuracy and adaptability for dynamic graph modeling. The code and datasets are publicly available at https://github.com/YuxiaWu/RAG4DyG.

Given a graph with textual attributes, we enable users to `chat with their graph': that is, to ask questions about the graph using a conversational interface. In response to a user's questions, our method provides textual replies and highlights the relevant parts of the graph. While existing works integrate large language models (LLMs) and graph neural networks (GNNs) in various ways, they mostly focus on either conventional graph tasks (such as node, edge, and graph classification), or on answering simple graph queries on small or synthetic graphs. In contrast, we develop a flexible question-answering framework targeting real-world textual graphs, applicable to multiple applications including scene graph understanding, common sense reasoning, and knowledge graph reasoning. Toward this goal, we first develop a Graph Question Answering (GraphQA) benchmark with data collected from different tasks. Then, we propose our G-Retriever method, introducing the first retrieval-augmented generation (RAG) approach for general textual graphs, which can be fine-tuned to enhance graph understanding via soft prompting. To resist hallucination and to allow for textual graphs that greatly exceed the LLM's context window size, G-Retriever performs RAG over a graph by formulating this task as a Prize-Collecting Steiner Tree optimization problem. Empirical evaluations show that our method outperforms baselines on textual graph tasks from multiple domains, scales well with larger graph sizes, and mitigates hallucination.~Our codes and datasets are available at: \url{https://github.com/XiaoxinHe/G-Retriever}

Graph retrieval-augmented generation (GraphRAG) has emerged as a powerful paradigm for enhancing large language models (LLMs) with external knowledge. It leverages graphs to model the hierarchical structure between specific concepts, enabling more coherent and effective knowledge retrieval for accurate reasoning.Despite its conceptual promise, recent studies report that GraphRAG frequently underperforms vanilla RAG on many real-world tasks. This raises a critical question: Is GraphRAG really effective, and in which scenarios do graph structures provide measurable benefits for RAG systems? To address this, we propose GraphRAG-Bench, a comprehensive benchmark designed to evaluate GraphRAG models onboth hierarchical knowledge retrieval and deep contextual reasoning. GraphRAG-Bench features a comprehensive dataset with tasks of increasing difficulty, coveringfact retrieval, complex reasoning, contextual summarization, and creative generation, and a systematic evaluation across the entire pipeline, from graph constructionand knowledge retrieval to final generation. Leveraging this novel benchmark, we systematically investigate the conditions when GraphRAG surpasses traditional RAG and the underlying reasons for its success, offering guidelines for its practical application. All related resources and analyses are collected for the community at https://github.com/GraphRAG-Bench/GraphRAG-Benchmark.

The rapidly growing number and variety of Large Language Models (LLMs) present significant challenges in efficiently selecting the appropriate LLM for a given query, especially considering the trade-offs between performance and computational cost. Current LLM selection methods often struggle to generalize across new LLMs and different tasks because of their limited ability to leverage contextual interactions among tasks, queries, and LLMs, as well as their dependence on a transductive learning framework. To address these shortcomings, we introduce a novel inductive graph framework, named as GraphRouter, which fully utilizes the contextual information among tasks, queries, and LLMs to enhance the LLM selection process. GraphRouter constructs a heterogeneous graph comprising task, query, and LLM nodes, with interactions represented as edges, which efficiently captures the contextual information between the query's requirements and the LLM's capabilities. Through an innovative edge prediction mechanism, GraphRouter is able to predict attributes (the effect and cost of LLM response) of potential edges, allowing for optimized recommendations that adapt to both existing and newly introduced LLMs without requiring retraining. Comprehensive experiments across three distinct effect-cost weight scenarios have shown that GraphRouter substantially surpasses existing routers, delivering a minimum performance improvement of 12.3%. In addition, it achieves enhanced generalization across new LLMs settings and supports diverse tasks with at least a 9.5% boost in effect and a significant reduction in computational demands. This work endeavors to apply a graph-based approach for the contextual and adaptive selection of LLMs, offering insights for real-world applications. Our codes for GraphRouter is released at https://github.com/ulab-uiuc/GraphRouter.

Graph-structured data are the commonly used and have wide application scenarios in the real world. For these diverse applications, the vast variety of learning tasks, graph domains, and complex graph learning procedures present challenges for human experts when designing versatile graph learning approaches. Facing these challenges, large language models (LLMs) offer a potential solution due to the extensive knowledge and the human-like intelligence. This paper proposes a novel conceptual prototype for designing versatile graph learning methods with LLMs, with a particular focus on the "where" and "how" perspectives. From the "where" perspective, we summarize four key graph learning procedures, including task definition, graph data feature engineering, model selection and optimization, deployment and serving. We then explore the application scenarios of LLMs in these procedures across a wider spectrum. In the "how" perspective, we align the abilities of LLMs with the requirements of each procedure. Finally, we point out the promising directions that could better leverage the strength of LLMs towards versatile graph learning methods.

Knowledge graph (KG) link prediction aims to infer new facts based on existing facts in the KG. Recent studies have shown that using the graph neighborhood of a node via graph neural networks (GNNs) provides more useful information compared to just using the query information. Conventional GNNs for KG link prediction follow the standard message-passing paradigm on the entire KG, which leads to superfluous computation, over-smoothing of node representations, and also limits their expressive power. On a large scale, it becomes computationally expensive to aggregate useful information from the entire KG for inference. To address the limitations of existing KG link prediction frameworks, we propose a novel retrieve-and-read framework, which first retrieves a relevant subgraph context for the query and then jointly reasons over the context and the query with a high-capacity reader. As part of our exemplar instantiation for the new framework, we propose a novel Transformer-based GNN as the reader, which incorporates graph-based attention structure and cross-attention between query and context for deep fusion. This simple yet effective design enables the model to focus on salient context information relevant to the query. Empirical results on two standard KG link prediction datasets demonstrate the competitive performance of the proposed method. Furthermore, our analysis yields valuable insights for designing improved retrievers within the framework.

Graph learning has become indispensable for interpreting and harnessing relational data in diverse fields, ranging from recommendation systems to social network analysis. In this context, a variety of GNNs have emerged as promising methodologies for encoding the structural information of graphs. By effectively capturing the graph's underlying structure, these GNNs have shown great potential in enhancing performance in graph learning tasks, such as link prediction and node classification. However, despite their successes, a significant challenge persists: these advanced methods often face difficulties in generalizing to unseen graph data that significantly differs from the training instances. In this work, our aim is to advance the graph learning paradigm by developing a general graph foundation model. This model is designed to understand the complex topological patterns present in diverse graph data, enabling it to excel in zero-shot graph learning tasks across different downstream datasets. To achieve this goal, we address several key technical challenges in our OpenGraph model. Firstly, we propose a unified graph tokenizer to adapt our graph model to generalize well on unseen graph data, even when the underlying graph properties differ significantly from those encountered during training. Secondly, we develop a scalable graph transformer as the foundational encoder, which effectively captures node-wise dependencies within the global topological context. Thirdly, we introduce a data augmentation mechanism enhanced by a LLM to alleviate the limitations of data scarcity in real-world scenarios. Extensive experiments validate the effectiveness of our framework. By adapting our OpenGraph to new graph characteristics and comprehending the nuances of diverse graphs, our approach achieves remarkable zero-shot graph learning performance across various settings and domains.

Research question answering requires accurate retrieval and contextual understanding of scientific literature. However, current Retrieval-Augmented Generation (RAG) methods often struggle to balance complex document relationships with precise information retrieval. In this paper, we introduce Contextualized Graph Retrieval-Augmented Generation (CG-RAG), a novel framework that integrates sparse and dense retrieval signals within graph structures to enhance retrieval efficiency and subsequently improve generation quality for research question answering. First, we propose a contextual graph representation for citation graphs, effectively capturing both explicit and implicit connections within and across documents. Next, we introduce Lexical-Semantic Graph Retrieval (LeSeGR), which seamlessly integrates sparse and dense retrieval signals with graph encoding. It bridges the gap between lexical precision and semantic understanding in citation graph retrieval, demonstrating generalizability to existing graph retrieval and hybrid retrieval methods. Finally, we present a context-aware generation strategy that utilizes the retrieved graph-structured information to generate precise and contextually enriched responses using large language models (LLMs). Extensive experiments on research question answering benchmarks across multiple domains demonstrate that our CG-RAG framework significantly outperforms RAG methods combined with various state-of-the-art retrieval approaches, delivering superior retrieval accuracy and generation quality.

Large language models (LLMs) have demonstrated remarkable success across a wide range of tasks; however, they still encounter challenges in reasoning tasks that require understanding and inferring relationships between distinct pieces of information within text sequences. This challenge is particularly pronounced in tasks involving multi-step processes, such as logical reasoning and multi-hop question answering, where understanding implicit relationships between entities and leveraging multi-hop connections in the given context are crucial. Graphs, as fundamental data structures, explicitly represent pairwise relationships between entities, thereby offering the potential to enhance LLMs' reasoning capabilities. External graphs have proven effective in supporting LLMs across multiple tasks. However, in many reasoning tasks, no pre-existing graph structure is provided. Can we structure implicit knowledge derived from context into graphs to assist LLMs in reasoning? In this paper, we propose Reasoning with Graphs (RwG) by first constructing explicit graphs from the context and then leveraging these graphs to enhance LLM reasoning performance on reasoning tasks. Extensive experiments demonstrate the effectiveness of the proposed method in improving both logical reasoning and multi-hop question answering tasks.

In-context learning is a promising paradigm that utilizes in-context examples as prompts for the predictions of large language models. These prompts are crucial for achieving strong performance. However, since the prompts need to be sampled from a large volume of annotated examples, finding the right prompt may result in high annotation costs. To address this challenge, this paper introduces an influence-driven selective annotation method that aims to minimize annotation costs while improving the quality of in-context examples. The essence of our method is to select a pivotal subset from a large-scale unlabeled data pool to annotate for the subsequent sampling of prompts. Specifically, a directed graph is first constructed to represent unlabeled data. Afterward, the influence of candidate unlabeled subsets is quantified with a diffusion process. A simple yet effective greedy algorithm for unlabeled data selection is lastly introduced. It iteratively selects the data if it provides a maximum marginal gain with respect to quantified influence. Compared with previous efforts on selective annotations, our influence-driven method works in an end-to-end manner, avoids an intractable explicit balance between data diversity and representativeness, and enjoys theoretical support. Experiments confirm the superiority of the proposed method on various benchmarks, achieving better performance under lower time consumption during subset selection. The project page is available at https://skzhang1.github.io/IDEAL/.

We tackle NED by comparing entities in short sentences with graphs. Creating a context vector from graphs through deep learning is a challenging problem that has never been applied to NED. Our main contribution is to present an experimental study of recent neural techniques, as well as a discussion about which graph features are most important for the disambiguation task. In addition, a new dataset () is created to allow a clean and scalable evaluation of NED with entries, and to be used as a reference in future research. In the end our results show that a Bi-LSTM encoding of the graph triplets performs best, improving upon the baseline models and scoring an F1 value of 91.6% on the test set

Language Models (LMs) are increasingly challenging the dominance of domain-specific models, including Graph Neural Networks (GNNs) and Graph Transformers (GTs), in graph learning tasks. Following this trend, we propose a novel approach that empowers off-the-shelf LMs to achieve performance comparable to state-of-the-art GNNs on node classification tasks, without requiring any architectural modification. By preserving the LM's original architecture, our approach retains a key benefit of LM instruction tuning: the ability to jointly train on diverse datasets, fostering greater flexibility and efficiency. To achieve this, we introduce two key augmentation strategies: (1) Enriching LMs' input using topological and semantic retrieval methods, which provide richer contextual information, and (2) guiding the LMs' classification process through a lightweight GNN classifier that effectively prunes class candidates. Our experiments on real-world datasets show that backbone Flan-T5 models equipped with these augmentation strategies outperform state-of-the-art text-output node classifiers and are comparable to top-performing vector-output node classifiers. By bridging the gap between specialized task-specific node classifiers and general LMs, this work paves the way for more versatile and widely applicable graph learning models. We will open-source the code upon publication.

Recent advances in representation learning on graphs, mainly leveraging graph convolutional networks, have brought a substantial improvement on many graph-based benchmark tasks. While novel approaches to learning node embeddings are highly suitable for node classification and link prediction, their application to graph classification (predicting a single label for the entire graph) remains mostly rudimentary, typically using a single global pooling step to aggregate node features or a hand-designed, fixed heuristic for hierarchical coarsening of the graph structure. An important step towards ameliorating this is differentiable graph coarsening---the ability to reduce the size of the graph in an adaptive, data-dependent manner within a graph neural network pipeline, analogous to image downsampling within CNNs. However, the previous prominent approach to pooling has quadratic memory requirements during training and is therefore not scalable to large graphs. Here we combine several recent advances in graph neural network design to demonstrate that competitive hierarchical graph classification results are possible without sacrificing sparsity. Our results are verified on several established graph classification benchmarks, and highlight an important direction for future research in graph-based neural networks.

The goal of this paper is to detect objects by exploiting their interrelationships. Contrary to existing methods, which learn objects and relations separately, our key idea is to learn the object-relation distribution jointly. We first propose a novel way of creating a graphical representation of an image from inter-object relation priors and initial class predictions, we call a context-likelihood graph. We then learn the joint distribution with an energy-based modeling technique which allows to sample and refine the context-likelihood graph iteratively for a given image. Our formulation of jointly learning the distribution enables us to generate a more accurate graph representation of an image which leads to a better object detection performance. We demonstrate the benefits of our context-likelihood graph formulation and the energy-based graph refinement via experiments on the Visual Genome and MS-COCO datasets where we achieve a consistent improvement over object detectors like DETR and Faster-RCNN, as well as alternative methods modeling object interrelationships separately. Our method is detector agnostic, end-to-end trainable, and especially beneficial for rare object classes.

GraphRAG addresses significant challenges in Retrieval-Augmented Generation (RAG) by leveraging graphs with embedded knowledge to enhance the reasoning capabilities of Large Language Models (LLMs). Despite its promising potential, the GraphRAG community currently lacks a unified framework for fine-grained decomposition of the graph-based knowledge retrieval process. Furthermore, there is no systematic categorization or evaluation of existing solutions within the retrieval process. In this paper, we present LEGO-GraphRAG, a modular framework that decomposes the retrieval process of GraphRAG into three interconnected modules: subgraph-extraction, path-filtering, and path-refinement. We systematically summarize and classify the algorithms and neural network (NN) models relevant to each module, providing a clearer understanding of the design space for GraphRAG instances. Additionally, we identify key design factors, such as Graph Coupling and Computational Cost, that influence the effectiveness of GraphRAG implementations. Through extensive empirical studies, we construct high-quality GraphRAG instances using a representative selection of solutions and analyze their impact on retrieval and reasoning performance. Our findings offer critical insights into optimizing GraphRAG instance design, ultimately contributing to the advancement of more accurate and contextually relevant LLM applications.

Graph-structured data plays a vital role in numerous domains, such as social networks, citation networks, commonsense reasoning graphs and knowledge graphs. While graph neural networks have been employed for graph processing, recent advancements have explored integrating large language models for graph-based tasks. In this paper, we propose a novel approach named Learnable Graph Pooling Token (LGPT), which addresses the limitations of the scalability issues in node-level projection and information loss in graph-level projection. LGPT enables flexible and efficient graph representation by introducing learnable parameters that act as tokens in large language models, balancing fine-grained and global graph information. Additionally, we investigate an Early Query Fusion technique, which fuses query context before constructing the graph representation, leading to more effective graph embeddings. Our method achieves a 4.13\% performance improvement on the GraphQA benchmark without training the large language model, demonstrating significant gains in handling complex textual-attributed graph data.

We introduce a self-supervised approach for learning node and graph level representations by contrasting structural views of graphs. We show that unlike visual representation learning, increasing the number of views to more than two or contrasting multi-scale encodings do not improve performance, and the best performance is achieved by contrasting encodings from first-order neighbors and a graph diffusion. We achieve new state-of-the-art results in self-supervised learning on 8 out of 8 node and graph classification benchmarks under the linear evaluation protocol. For example, on Cora (node) and Reddit-Binary (graph) classification benchmarks, we achieve 86.8% and 84.5% accuracy, which are 5.5% and 2.4% relative improvements over previous state-of-the-art. When compared to supervised baselines, our approach outperforms them in 4 out of 8 benchmarks. Source code is released at: https://github.com/kavehhassani/mvgrl

The ability to learn from context with novel concepts, and deliver appropriate responses are essential in human conversations. Despite current Multimodal Large Language Models (MLLMs) and Large Language Models (LLMs) being trained on mega-scale datasets, recognizing unseen images or understanding novel concepts in a training-free manner remains a challenge. In-Context Learning (ICL) explores training-free few-shot learning, where models are encouraged to ``learn to learn" from limited tasks and generalize to unseen tasks. In this work, we propose link-context learning (LCL), which emphasizes "reasoning from cause and effect" to augment the learning capabilities of MLLMs. LCL goes beyond traditional ICL by explicitly strengthening the causal relationship between the support set and the query set. By providing demonstrations with causal links, LCL guides the model to discern not only the analogy but also the underlying causal associations between data points, which empowers MLLMs to recognize unseen images and understand novel concepts more effectively. To facilitate the evaluation of this novel approach, we introduce the ISEKAI dataset, comprising exclusively of unseen generated image-label pairs designed for link-context learning. Extensive experiments show that our LCL-MLLM exhibits strong link-context learning capabilities to novel concepts over vanilla MLLMs. Code and data will be released at https://github.com/isekai-portal/Link-Context-Learning.

The remarkable capability of large language models (LLMs) for in-context learning (ICL) needs to be activated by demonstration examples. Prior work has extensively explored the selection of examples for ICL, predominantly following the "select then organize" paradigm, such approaches often neglect the internal relationships between examples and exist an inconsistency between the training and inference. In this paper, we formulate the problem as a sequential selection problem and introduce Se^2, a sequential-aware method that leverages the LLM's feedback on varying context, aiding in capturing inter-relationships and sequential information among examples, significantly enriching the contextuality and relevance of ICL prompts. Meanwhile, we utilize beam search to seek and construct example sequences, enhancing both quality and diversity. Extensive experiments across 23 NLP tasks from 8 distinct categories illustrate that Se^2 markedly surpasses competitive baselines and achieves 42% relative improvement over random selection. Further in-depth analysis show the effectiveness of proposed strategies, highlighting Se^2's exceptional stability and adaptability across various scenarios. Our code will be released to facilitate future research.

In-context Learning (ICL) empowers large language models (LLMs) to adapt to unseen tasks during inference by prefixing a few demonstration examples prior to test queries. Despite its versatility, ICL incurs substantial computational and memory overheads compared to zero-shot learning and is susceptible to the selection and order of demonstration examples. In this work, we introduce Implicit In-context Learning (I2CL), an innovative paradigm that addresses the challenges associated with traditional ICL by absorbing demonstration examples within the activation space. I2CL first generates a condensed vector representation, namely a context vector, from the demonstration examples. It then integrates the context vector during inference by injecting a linear combination of the context vector and query activations into the model's residual streams. Empirical evaluation on nine real-world tasks across three model architectures demonstrates that I2CL achieves few-shot performance with zero-shot cost and exhibits robustness against the variation of demonstration examples. Furthermore, I2CL facilitates a novel representation of "task-ids", enhancing task similarity detection and enabling effective transfer learning. We provide a comprehensive analysis of I2CL, offering deeper insights into its mechanisms and broader implications for ICL. The source code is available at: https://github.com/LzVv123456/I2CL.

In-Context Learning (ICL) is a technique by which language models make predictions based on examples provided in their input context. Previously, their context window size imposed a limit on the number of examples that can be shown, making example selection techniques crucial for identifying the maximally effective set of examples. However, the recent advent of Long Context Language Models (LCLMs) has significantly increased the number of examples that can be included in context, raising an important question of whether ICL performance in a many-shot regime is still sensitive to the method of sample selection. To answer this, we revisit these approaches in the context of LCLMs through extensive experiments on 18 datasets spanning 4 tasks. Surprisingly, we observe that sophisticated example selection techniques do not yield significant improvements over a simple random sample selection method. Instead, we find that the advent of LCLMs has fundamentally shifted the challenge of ICL from that of selecting the most effective examples to that of collecting sufficient examples to fill the context window. Specifically, in certain datasets, including all available examples does not fully utilize the context window; however, by augmenting the examples in context with a simple data augmentation approach, we substantially improve ICL performance by 5%.

The predictions of Large Language Models (LLMs) on downstream tasks often improve significantly when including examples of the input--label relationship in the context. However, there is currently no consensus about how this in-context learning (ICL) ability of LLMs works. For example, while Xie et al. (2021) liken ICL to a general-purpose learning algorithm, Min et al. (2022) argue ICL does not even learn label relationships from in-context examples. In this paper, we provide novel insights into how ICL leverages label information, revealing both capabilities and limitations. To ensure we obtain a comprehensive picture of ICL behavior, we study probabilistic aspects of ICL predictions and thoroughly examine the dynamics of ICL as more examples are provided. Our experiments show that ICL predictions almost always depend on in-context labels and that ICL can learn truly novel tasks in-context. However, we also find that ICL struggles to fully overcome prediction preferences acquired from pre-training data and, further, that ICL does not consider all in-context information equally.

Graph pooling compresses graph information into a compact representation. State-of-the-art graph pooling methods follow a hierarchical approach, which reduces the graph size step-by-step. These methods must balance memory efficiency with preserving node information, depending on whether they use node dropping or node clustering. Additionally, fixed pooling ratios or numbers of pooling layers are predefined for all graphs, which prevents personalized pooling structures from being captured for each individual graph. In this work, inspired by bottom-up grammar induction, we propose an efficient graph parsing algorithm to infer the pooling structure, which then drives graph pooling. The resulting Graph Parsing Network (GPN) adaptively learns personalized pooling structure for each individual graph. GPN benefits from the discrete assignments generated by the graph parsing algorithm, allowing good memory efficiency while preserving node information intact. Experimental results on standard benchmarks demonstrate that GPN outperforms state-of-the-art graph pooling methods in graph classification tasks while being able to achieve competitive performance in node classification tasks. We also conduct a graph reconstruction task to show GPN's ability to preserve node information and measure both memory and time efficiency through relevant tests.

In-context learning (ICL) is a type of prompting where a transformer model operates on a sequence of (input, output) examples and performs inference on-the-fly. In this work, we formalize in-context learning as an algorithm learning problem where a transformer model implicitly constructs a hypothesis function at inference-time. We first explore the statistical aspects of this abstraction through the lens of multitask learning: We obtain generalization bounds for ICL when the input prompt is (1) a sequence of i.i.d. (input, label) pairs or (2) a trajectory arising from a dynamical system. The crux of our analysis is relating the excess risk to the stability of the algorithm implemented by the transformer. We characterize when transformer/attention architecture provably obeys the stability condition and also provide empirical verification. For generalization on unseen tasks, we identify an inductive bias phenomenon in which the transfer learning risk is governed by the task complexity and the number of MTL tasks in a highly predictable manner. Finally, we provide numerical evaluations that (1) demonstrate transformers can indeed implement near-optimal algorithms on classical regression problems with i.i.d. and dynamic data, (2) provide insights on stability, and (3) verify our theoretical predictions.

In-context learning (ICL) is a new learning paradigm that has gained popularity along with the development of large language models. In this work, we adapt a recently proposed hardness metric, pointwise V-usable information (PVI), to an in-context version (in-context PVI). Compared to the original PVI, in-context PVI is more efficient in that it requires only a few exemplars and does not require fine-tuning. We conducted a comprehensive empirical analysis to evaluate the reliability of in-context PVI. Our findings indicate that in-context PVI estimates exhibit similar characteristics to the original PVI. Specific to the in-context setting, we show that in-context PVI estimates remain consistent across different exemplar selections and numbers of shots. The variance of in-context PVI estimates across different exemplar selections is insignificant, which suggests that in-context PVI are stable. Furthermore, we demonstrate how in-context PVI can be employed to identify challenging instances. Our work highlights the potential of in-context PVI and provides new insights into the capabilities of ICL.

Associating unstructured data with structured information is crucial for real-world tasks that require relevance search. However, existing graph learning benchmarks often overlook the rich semantic information associate with each node. To bridge such gap, we introduce the Multimodal Graph Benchmark (MM-GRAPH), the first comprehensive multi-modal graph benchmark that incorporates both textual and visual information. MM-GRAPH surpasses previous efforts, which have primarily focused on text-attributed graphs with various connectivity patterns. MM-GRAPH consists of five graph learning datasets of various scales that are appropriate for different learning tasks. Their multimodal node features, enabling a more comprehensive evaluation of graph learning algorithms in real-world scenarios. To facilitate research on multimodal graph learning, we further provide an extensive study on the performance of various graph neural networks in the presence of features from various modalities. MM-GRAPH aims to foster research on multimodal graph learning and drive the development of more advanced and robust graph learning algorithms. By providing a diverse set of datasets and benchmarks, MM-GRAPH enables researchers to evaluate and compare their models in realistic settings, ultimately leading to improved performance on real-world applications that rely on multimodal graph data.

In recent years, Graph Neural Networks (GNNs) have made significant advances in processing structured data. However, most of them primarily adopted a model-centric approach, which simplifies graphs by converting them into undirected formats and emphasizes model designs. This approach is inherently limited in real-world applications due to the unavoidable information loss in simple undirected graphs and the model optimization challenges that arise when exceeding the upper bounds of this sub-optimal data representational capacity. As a result, there has been a shift toward data-centric methods that prioritize improving graph quality and representation. Specifically, various types of graphs can be derived from naturally structured data, including heterogeneous graphs, hypergraphs, and directed graphs. Among these, directed graphs offer distinct advantages in topological systems by modeling causal relationships, and directed GNNs have been extensively studied in recent years. However, a comprehensive survey of this emerging topic is still lacking. Therefore, we aim to provide a comprehensive review of directed graph learning, with a particular focus on a data-centric perspective. Specifically, we first introduce a novel taxonomy for existing studies. Subsequently, we re-examine these methods from the data-centric perspective, with an emphasis on understanding and improving data representation. It demonstrates that a deep understanding of directed graphs and their quality plays a crucial role in model performance. Additionally, we explore the diverse applications of directed GNNs across 10+ domains, highlighting their broad applicability. Finally, we identify key opportunities and challenges within the field, offering insights that can guide future research and development in directed graph learning.

In this study, we focus on the graph representation learning (a.k.a. network embedding) in attributed graphs. Different from existing embedding methods that treat the incorporation of graph structure and semantic as the simple combination of two optimization objectives, we propose a novel semantic graph representation (SGR) method to formulate the joint optimization of the two heterogeneous sources into a common high-order proximity based framework. Concretely, we first construct an auxiliary weighted graph, where the complex homogeneous and heterogeneous relations among nodes and attributes in the original graph are comprehensively encoded. Conventional embedding methods that consider high-order topology proximities can then be easily applied to the newly constructed graph to learn the representations of both node and attribute while capturing the nonlinear high-order intrinsic correlation inside or among graph structure and semantic. The learned attribute embeddings can also effectively support some semantic-oriented inference tasks (e.g., semantic community detection), helping to reveal the graph's deep semantic. The effectiveness of SGR is further verified on a series of real graphs, where it achieves impressive performance over other baselines.

In-context learning (ICL) using large language models for tasks with many labels is challenging due to the limited context window, which makes it difficult to fit a sufficient number of examples in the prompt. In this paper, we use a pre-trained dense retrieval model to bypass this limitation, giving the model only a partial view of the full label space for each inference call. Testing with recent open-source LLMs (OPT, LLaMA), we set new state of the art performance in few-shot settings for three common intent classification datasets, with no finetuning. We also surpass fine-tuned performance on fine-grained sentiment classification in certain cases. We analyze the performance across number of in-context examples and different model scales, showing that larger models are necessary to effectively and consistently make use of larger context lengths for ICL. By running several ablations, we analyze the model's use of: a) the similarity of the in-context examples to the current input, b) the semantic content of the class names, and c) the correct correspondence between examples and labels. We demonstrate that all three are needed to varying degrees depending on the domain, contrary to certain recent works.

Graph representation learning has emerged as a powerful technique for addressing real-world problems. Various downstream graph learning tasks have benefited from its recent developments, such as node classification, similarity search, and graph classification. However, prior arts on graph representation learning focus on domain specific problems and train a dedicated model for each graph dataset, which is usually non-transferable to out-of-domain data. Inspired by the recent advances in pre-training from natural language processing and computer vision, we design Graph Contrastive Coding (GCC) -- a self-supervised graph neural network pre-training framework -- to capture the universal network topological properties across multiple networks. We design GCC's pre-training task as subgraph instance discrimination in and across networks and leverage contrastive learning to empower graph neural networks to learn the intrinsic and transferable structural representations. We conduct extensive experiments on three graph learning tasks and ten graph datasets. The results show that GCC pre-trained on a collection of diverse datasets can achieve competitive or better performance to its task-specific and trained-from-scratch counterparts. This suggests that the pre-training and fine-tuning paradigm presents great potential for graph representation learning.

Large language models (LLMs) can perform a new task by merely conditioning on task instructions and a few input-output examples, without optimizing any parameters. This is called In-Context Learning (ICL). In-context Information Extraction (IE) has recently garnered attention in the research community. However, the performance of In-context IE generally lags behind the state-of-the-art supervised expert models. We highlight a key reason for this shortfall: underspecified task description. The limited-length context struggles to thoroughly express the intricate IE task instructions and various edge cases, leading to misalignment in task comprehension with humans. In this paper, we propose a Guideline Learning (GL) framework for In-context IE which reflectively learns and follows guidelines. During the learning phrase, GL automatically synthesizes a set of guidelines based on a few error cases, and during inference, GL retrieves helpful guidelines for better ICL. Moreover, we propose a self-consistency-based active learning method to enhance the efficiency of GL. Experiments on event extraction and relation extraction show that GL can significantly improve the performance of in-context IE.

Heterogeneous graph learning aims to capture complex relationships and diverse relational semantics among entities in a heterogeneous graph to obtain meaningful representations for nodes and edges. Recent advancements in heterogeneous graph neural networks (HGNNs) have achieved state-of-the-art performance by considering relation heterogeneity and using specialized message functions and aggregation rules. However, existing frameworks for heterogeneous graph learning have limitations in generalizing across diverse heterogeneous graph datasets. Most of these frameworks follow the "pre-train" and "fine-tune" paradigm on the same dataset, which restricts their capacity to adapt to new and unseen data. This raises the question: "Can we generalize heterogeneous graph models to be well-adapted to diverse downstream learning tasks with distribution shifts in both node token sets and relation type heterogeneity?'' To tackle those challenges, we propose HiGPT, a general large graph model with Heterogeneous graph instruction-tuning paradigm. Our framework enables learning from arbitrary heterogeneous graphs without the need for any fine-tuning process from downstream datasets. To handle distribution shifts in heterogeneity, we introduce an in-context heterogeneous graph tokenizer that captures semantic relationships in different heterogeneous graphs, facilitating model adaptation. We incorporate a large corpus of heterogeneity-aware graph instructions into our HiGPT, enabling the model to effectively comprehend complex relation heterogeneity and distinguish between various types of graph tokens. Furthermore, we introduce the Mixture-of-Thought (MoT) instruction augmentation paradigm to mitigate data scarcity by generating diverse and informative instructions. Through comprehensive evaluations, our proposed framework demonstrates exceptional performance in terms of generalization performance.

Search is an ability foundational in many important tasks, and recent studies have shown that large language models (LLMs) struggle to perform search robustly. It is unknown whether this inability is due to a lack of data, insufficient model parameters, or fundamental limitations of the transformer architecture. In this work, we use the foundational graph connectivity problem as a testbed to generate effectively limitless high-coverage data to train small transformers and test whether they can learn to perform search. We find that, when given the right training distribution, the transformer is able to learn to search. We analyze the algorithm that the transformer has learned through a novel mechanistic interpretability technique that enables us to extract the computation graph from the trained model. We find that for each vertex in the input graph, transformers compute the set of vertices reachable from that vertex. Each layer then progressively expands these sets, allowing the model to search over a number of vertices exponential in the number of layers. However, we find that as the input graph size increases, the transformer has greater difficulty in learning the task. This difficulty is not resolved even as the number of parameters is increased, suggesting that increasing model scale will not lead to robust search abilities. We also find that performing search in-context (i.e., chain-of-thought) does not resolve this inability to learn to search on larger graphs.

Graphs or networks are a very convenient way to represent data with lots of interaction. Recently, Machine Learning on Graph data has gained a lot of traction. In particular, vertex classification and missing edge detection have very interesting applications, ranging from drug discovery to recommender systems. To achieve such tasks, tremendous work has been accomplished to learn embedding of nodes and edges into finite-dimension vector spaces. This task is called Graph Representation Learning. However, Graph Representation Learning techniques often display prohibitive time and memory complexities, preventing their use in real-time with business size graphs. In this paper, we address this issue by leveraging a degeneracy property of Graphs - the K-Core Decomposition. We present two techniques taking advantage of this decomposition to reduce the time and memory consumption of walk-based Graph Representation Learning algorithms. We evaluate the performances, expressed in terms of quality of embedding and computational resources, of the proposed techniques on several academic datasets. Our code is available at https://github.com/SBrandeis/kcore-embedding

Graph Structure Learning (GSL) has recently garnered considerable attention due to its ability to optimize both the parameters of Graph Neural Networks (GNNs) and the computation graph structure simultaneously. Despite the proliferation of GSL methods developed in recent years, there is no standard experimental setting or fair comparison for performance evaluation, which creates a great obstacle to understanding the progress in this field. To fill this gap, we systematically analyze the performance of GSL in different scenarios and develop a comprehensive Graph Structure Learning Benchmark (GSLB) curated from 20 diverse graph datasets and 16 distinct GSL algorithms. Specifically, GSLB systematically investigates the characteristics of GSL in terms of three dimensions: effectiveness, robustness, and complexity. We comprehensively evaluate state-of-the-art GSL algorithms in node- and graph-level tasks, and analyze their performance in robust learning and model complexity. Further, to facilitate reproducible research, we have developed an easy-to-use library for training, evaluating, and visualizing different GSL methods. Empirical results of our extensive experiments demonstrate the ability of GSL and reveal its potential benefits on various downstream tasks, offering insights and opportunities for future research. The code of GSLB is available at: https://github.com/GSL-Benchmark/GSLB.

Large language models (LLMs) have achieved impressive success across several fields, but their proficiency in understanding and resolving complex graph problems is less explored. To bridge this gap, we introduce GraphInstruct, a novel and comprehensive instruction-tuning dataset designed to equip language models with the ability to tackle a broad spectrum of graph problems using explicit reasoning paths. Utilizing GraphInstruct, we build GraphWiz, an open-source language model capable of resolving various graph problem types while generating clear reasoning processes. To enhance the model's capability and reliability, we incorporate the Direct Preference Optimization (DPO) framework into the graph problem-solving context. The enhanced model, GraphWiz-DPO, achieves an average accuracy of 65% across nine tasks with different complexity levels, surpassing GPT-4 which has an average accuracy of 43.8%. Moreover, our research delves into the delicate balance between training data volume and model performance, highlighting the potential for overfitting with increased data. We also explore the transferability of the model's reasoning ability across different graph tasks, indicating the model's adaptability and practical application potential. Our investigation offers a new blueprint and valuable insights for developing LLMs specialized in graph reasoning and problem-solving.

In this paper, we approach an overlooked yet critical task Graph2Image: generating images from multimodal attributed graphs (MMAGs). This task poses significant challenges due to the explosion in graph size, dependencies among graph entities, and the need for controllability in graph conditions. To address these challenges, we propose a graph context-conditioned diffusion model called InstructG2I. InstructG2I first exploits the graph structure and multimodal information to conduct informative neighbor sampling by combining personalized page rank and re-ranking based on vision-language features. Then, a Graph-QFormer encoder adaptively encodes the graph nodes into an auxiliary set of graph prompts to guide the denoising process of diffusion. Finally, we propose graph classifier-free guidance, enabling controllable generation by varying the strength of graph guidance and multiple connected edges to a node. Extensive experiments conducted on three datasets from different domains demonstrate the effectiveness and controllability of our approach. The code is available at https://github.com/PeterGriffinJin/InstructG2I.

In-context learning (ICL), the ability of large language models to perform novel tasks by conditioning on a prompt with a few task examples, requires these examples to be informative about the test instance. The standard approach of independently ranking and selecting the most similar examples selects redundant examples while omitting important information. In this work, we show that BERTScore-Recall (BSR) selects better examples that demonstrate more of the salient aspects, e.g. reasoning patterns, of the test input. We further extend BSR and many standard metrics to easily optimizable set-level metrics, giving still better coverage of those salient aspects. On 15 datasets spanning 6 tasks and with 7 diverse LLMs, we show that (1) BSR is the superior metric for in-context example selection across the board, and (2) for compositional tasks, set selection using Set-BSR outperforms independent ranking by up to 17 points on average and, despite being training-free, surpasses methods that leverage task or LLM-specific training.

Graphs can model complex relationships between objects, enabling a myriad of Web applications such as online page/article classification and social recommendation. While graph neural networks(GNNs) have emerged as a powerful tool for graph representation learning, in an end-to-end supervised setting, their performance heavily rely on a large amount of task-specific supervision. To reduce labeling requirement, the "pre-train, fine-tune" and "pre-train, prompt" paradigms have become increasingly common. In particular, prompting is a popular alternative to fine-tuning in natural language processing, which is designed to narrow the gap between pre-training and downstream objectives in a task-specific manner. However, existing study of prompting on graphs is still limited, lacking a universal treatment to appeal to different downstream tasks. In this paper, we propose GraphPrompt, a novel pre-training and prompting framework on graphs. GraphPrompt not only unifies pre-training and downstream tasks into a common task template, but also employs a learnable prompt to assist a downstream task in locating the most relevant knowledge from the pre-train model in a task-specific manner. Finally, we conduct extensive experiments on five public datasets to evaluate and analyze GraphPrompt.

As model context lengths continue to increase, the number of demonstrations that can be provided in-context approaches the size of entire training datasets. We study the behavior of in-context learning (ICL) at this extreme scale on multiple datasets and models. We show that, for many datasets with large label spaces, performance continues to increase with hundreds or thousands of demonstrations. We contrast this with example retrieval and finetuning: example retrieval shows excellent performance at low context lengths but has diminished gains with more demonstrations; finetuning is more data hungry than ICL but can sometimes exceed long-context ICL performance with additional data. We use this ICL setting as a testbed to study several properties of both in-context learning and long-context models. We show that long-context ICL is less sensitive to random input shuffling than short-context ICL, that grouping of same-label examples can negatively impact performance, and that the performance boosts we see do not arise from cumulative gain from encoding many examples together. We conclude that although long-context ICL can be surprisingly effective, most of this gain comes from attending back to similar examples rather than task learning.

In-context learning is a recent paradigm in natural language understanding, where a large pre-trained language model (LM) observes a test instance and a few training examples as its input, and directly decodes the output without any update to its parameters. However, performance has been shown to strongly depend on the selected training examples (termed prompt). In this work, we propose an efficient method for retrieving prompts for in-context learning using annotated data and a LM. Given an input-output pair, we estimate the probability of the output given the input and a candidate training example as the prompt, and label training examples as positive or negative based on this probability. We then train an efficient dense retriever from this data, which is used to retrieve training examples as prompts at test time. We evaluate our approach on three sequence-to-sequence tasks where language utterances are mapped to meaning representations, and find that it substantially outperforms prior work and multiple baselines across the board.

The advancement of Large Language Models (LLMs) has remarkably pushed the boundaries towards artificial general intelligence (AGI), with their exceptional ability on understanding diverse types of information, including but not limited to images and audio. Despite this progress, a critical gap remains in empowering LLMs to proficiently understand and reason on graph data. Recent studies underscore LLMs' underwhelming performance on fundamental graph reasoning tasks. In this paper, we endeavor to unearth the obstacles that impede LLMs in graph reasoning, pinpointing the common practice of converting graphs into natural language descriptions (Graph2Text) as a fundamental bottleneck. To overcome this impediment, we introduce GraphLLM, a pioneering end-to-end approach that synergistically integrates graph learning models with LLMs. This synergy equips LLMs with the ability to proficiently interpret and reason on graph data, harnessing the superior expressive power of graph learning models. Our empirical evaluations across four fundamental graph reasoning tasks validate the effectiveness of GraphLLM. The results exhibit a substantial average accuracy enhancement of 54.44%, alongside a noteworthy context reduction of 96.45% across various graph reasoning tasks.

Artificial General Intelligence (AGI) has revolutionized numerous fields, yet its integration with graph data, a cornerstone in our interconnected world, remains nascent. This paper presents a pioneering survey on the emerging domain of graph prompts in AGI, addressing key challenges and opportunities in harnessing graph data for AGI applications. Despite substantial advancements in AGI across natural language processing and computer vision, the application to graph data is relatively underexplored. This survey critically evaluates the current landscape of AGI in handling graph data, highlighting the distinct challenges in cross-modality, cross-domain, and cross-task applications specific to graphs. Our work is the first to propose a unified framework for understanding graph prompt learning, offering clarity on prompt tokens, token structures, and insertion patterns in the graph domain. We delve into the intrinsic properties of graph prompts, exploring their flexibility, expressiveness, and interplay with existing graph models. A comprehensive taxonomy categorizes over 100 works in this field, aligning them with pre-training tasks across node-level, edge-level, and graph-level objectives. Additionally, we present, ProG, a Python library, and an accompanying website, to support and advance research in graph prompting. The survey culminates in a discussion of current challenges and future directions, offering a roadmap for research in graph prompting within AGI. Through this comprehensive analysis, we aim to catalyze further exploration and practical applications of AGI in graph data, underlining its potential to reshape AGI fields and beyond. ProG and the website can be accessed by https://github.com/WxxShirley/Awesome-Graph-Prompt, and https://github.com/sheldonresearch/ProG, respectively.

Graph Neural Networks (GNNs) have advanced graph structure understanding via recursive information exchange and aggregation among graph nodes. To improve model robustness, self-supervised learning (SSL) has emerged as a promising approach for data augmentation. However, existing methods for generating pre-trained graph embeddings often rely on fine-tuning with specific downstream task labels, which limits their usability in scenarios where labeled data is scarce or unavailable. To address this, our research focuses on advancing the generalization capabilities of graph models in challenging zero-shot learning scenarios. Inspired by the success of large language models (LLMs), we aim to develop a graph-oriented LLM that can achieve high generalization across diverse downstream datasets and tasks, even without any information available from the downstream graph data. In this work, we present the GraphGPT framework that aligns LLMs with graph structural knowledge with a graph instruction tuning paradigm. Our framework incorporates a text-graph grounding component to establish a connection between textual information and graph structures. Additionally, we propose a dual-stage instruction tuning paradigm, accompanied by a lightweight graph-text alignment projector. This paradigm explores self-supervised graph structural signals and task-specific graph instructions, to guide LLMs in understanding complex graph structures and improving their adaptability across different downstream tasks. Our framework is evaluated on supervised and zero-shot graph learning tasks, demonstrating superior generalization and outperforming state-of-the-art baselines.

Text-Attributed Graphs (TAGs) augment graph structures with natural language descriptions, facilitating detailed depictions of data and their interconnections across various real-world settings. However, existing TAG datasets predominantly feature textual information only at the nodes, with edges typically represented by mere binary or categorical attributes. This lack of rich textual edge annotations significantly limits the exploration of contextual relationships between entities, hindering deeper insights into graph-structured data. To address this gap, we introduce Textual-Edge Graphs Datasets and Benchmark (TEG-DB), a comprehensive and diverse collection of benchmark textual-edge datasets featuring rich textual descriptions on nodes and edges. The TEG-DB datasets are large-scale and encompass a wide range of domains, from citation networks to social networks. In addition, we conduct extensive benchmark experiments on TEG-DB to assess the extent to which current techniques, including pre-trained language models, graph neural networks, and their combinations, can utilize textual node and edge information. Our goal is to elicit advancements in textual-edge graph research, specifically in developing methodologies that exploit rich textual node and edge descriptions to enhance graph analysis and provide deeper insights into complex real-world networks. The entire TEG-DB project is publicly accessible as an open-source repository on Github, accessible at https://github.com/Zhuofeng-Li/TEG-Benchmark.

Structured representations like graphs and parse trees play a crucial role in many Natural Language Processing systems. In recent years, the advancements in multi-turn user interfaces necessitate the need for controlling and updating these structured representations given new sources of information. Although there have been many efforts focusing on improving the performance of the parsers that map text to graphs or parse trees, very few have explored the problem of directly manipulating these representations. In this paper, we explore the novel problem of graph modification, where the systems need to learn how to update an existing scene graph given a new user's command. Our novel models based on graph-based sparse transformer and cross attention information fusion outperform previous systems adapted from the machine translation and graph generation literature. We further contribute our large graph modification datasets to the research community to encourage future research for this new problem.

In-context learning, where pre-trained language models learn to perform tasks from task examples and instructions in their contexts, has attracted much attention in the NLP community. However, the ability of in-context learning is not fully exploited because language models are not explicitly trained to learn in context. To this end, we propose PICL (Pre-training for In-Context Learning), a framework to enhance the language models' in-context learning ability by pre-training the model on a large collection of "intrinsic tasks" in the general plain-text corpus using the simple language modeling objective. PICL encourages the model to infer and perform tasks by conditioning on the contexts while maintaining task generalization of pre-trained models. We evaluate the in-context learning performance of the model trained with PICL on seven widely-used text classification datasets and the Super-NaturalInstrctions benchmark, which contains 100+ NLP tasks formulated to text generation. Our experiments show that PICL is more effective and task-generalizable than a range of baselines, outperforming larger language models with nearly 4x parameters. The code is publicly available at https://github.com/thu-coai/PICL.

Many graph representation learning (GRL) problems are dynamic, with millions of edges added or removed per second. A fundamental workload in this setting is dynamic link prediction: using a history of graph updates to predict whether a given pair of vertices will become connected. Recent schemes for link prediction in such dynamic settings employ Transformers, modeling individual graph updates as single tokens. In this work, we propose HOT: a model that enhances this line of works by harnessing higher-order (HO) graph structures; specifically, k-hop neighbors and more general subgraphs containing a given pair of vertices. Harnessing such HO structures by encoding them into the attention matrix of the underlying Transformer results in higher accuracy of link prediction outcomes, but at the expense of increased memory pressure. To alleviate this, we resort to a recent class of schemes that impose hierarchy on the attention matrix, significantly reducing memory footprint. The final design offers a sweetspot between high accuracy and low memory utilization. HOT outperforms other dynamic GRL schemes, for example achieving 9%, 7%, and 15% higher accuracy than - respectively - DyGFormer, TGN, and GraphMixer, for the MOOC dataset. Our design can be seamlessly extended towards other dynamic GRL workloads.

Representation learning on heterogeneous graphs aims to obtain meaningful node representations to facilitate various downstream tasks, such as node classification and link prediction. Existing heterogeneous graph learning methods are primarily developed by following the propagation mechanism of node representations. There are few efforts on studying the role of relations for improving the learning of more fine-grained node representations. Indeed, it is important to collaboratively learn the semantic representations of relations and discern node representations with respect to different relation types. To this end, in this paper, we propose a novel Relation-aware Heterogeneous Graph Neural Network, namely R-HGNN, to learn node representations on heterogeneous graphs at a fine-grained level by considering relation-aware characteristics. Specifically, a dedicated graph convolution component is first designed to learn unique node representations from each relation-specific graph separately. Then, a cross-relation message passing module is developed to improve the interactions of node representations across different relations. Also, the relation representations are learned in a layer-wise manner to capture relation semantics, which are used to guide the node representation learning process. Moreover, a semantic fusing module is presented to aggregate relation-aware node representations into a compact representation with the learned relation representations. Finally, we conduct extensive experiments on a variety of graph learning tasks, and experimental results demonstrate that our approach consistently outperforms existing methods among all the tasks.

In-context learning (ICL) has shown impressive results in few-shot learning tasks, yet its underlying mechanism is still not fully understood. A recent line of work suggests that ICL performs gradient descent (GD)-based optimization implicitly. While appealing, much of the research focuses on simplified settings, where the parameters of a shallow model are optimized. In this work, we revisit evidence for ICL-GD correspondence on realistic NLP tasks and models. We find gaps in evaluation, both in terms of problematic metrics and insufficient baselines. We show that surprisingly, even untrained models achieve comparable ICL-GD similarity scores despite not exhibiting ICL. Next, we explore a major discrepancy in the flow of information throughout the model between ICL and GD, which we term Layer Causality. We propose a simple GD-based optimization procedure that respects layer causality, and show it improves similarity scores significantly.

Two lines of work are taking the central stage in AI research. On the one hand, the community is making increasing efforts to build models that discard spurious correlations and generalize better in novel test environments. Unfortunately, the bitter lesson so far is that no proposal convincingly outperforms a simple empirical risk minimization baseline. On the other hand, large language models (LLMs) have erupted as algorithms able to learn in-context, generalizing on-the-fly to eclectic contextual circumstances that users enforce by means of prompting. In this paper, we argue that context is environment, and posit that in-context learning holds the key to better domain generalization. Via extensive theory and experiments, we show that paying attention to contextx2013x2013unlabeled examples as they arrivex2013x2013allows our proposed In-Context Risk Minimization (ICRM) algorithm to zoom-in on the test environment risk minimizer, leading to significant out-of-distribution performance improvements. From all of this, two messages are worth taking home. Researchers in domain generalization should consider environment as context, and harness the adaptive power of in-context learning. Researchers in LLMs should consider context as environment, to better structure data towards generalization.

Recently, Retrieval-Augmented Generation (RAG) has achieved remarkable success in addressing the challenges of Large Language Models (LLMs) without necessitating retraining. By referencing an external knowledge base, RAG refines LLM outputs, effectively mitigating issues such as ``hallucination'', lack of domain-specific knowledge, and outdated information. However, the complex structure of relationships among different entities in databases presents challenges for RAG systems. In response, GraphRAG leverages structural information across entities to enable more precise and comprehensive retrieval, capturing relational knowledge and facilitating more accurate, context-aware responses. Given the novelty and potential of GraphRAG, a systematic review of current technologies is imperative. This paper provides the first comprehensive overview of GraphRAG methodologies. We formalize the GraphRAG workflow, encompassing Graph-Based Indexing, Graph-Guided Retrieval, and Graph-Enhanced Generation. We then outline the core technologies and training methods at each stage. Additionally, we examine downstream tasks, application domains, evaluation methodologies, and industrial use cases of GraphRAG. Finally, we explore future research directions to inspire further inquiries and advance progress in the field.

Graph Structure Learning (GSL) focuses on capturing intrinsic dependencies and interactions among nodes in graph-structured data by generating novel graph structures. Graph Neural Networks (GNNs) have emerged as promising GSL solutions, utilizing recursive message passing to encode node-wise inter-dependencies. However, many existing GSL methods heavily depend on explicit graph structural information as supervision signals, leaving them susceptible to challenges such as data noise and sparsity. In this work, we propose GraphEdit, an approach that leverages large language models (LLMs) to learn complex node relationships in graph-structured data. By enhancing the reasoning capabilities of LLMs through instruction-tuning over graph structures, we aim to overcome the limitations associated with explicit graph structural information and enhance the reliability of graph structure learning. Our approach not only effectively denoises noisy connections but also identifies node-wise dependencies from a global perspective, providing a comprehensive understanding of the graph structure. We conduct extensive experiments on multiple benchmark datasets to demonstrate the effectiveness and robustness of GraphEdit across various settings. We have made our model implementation available at: https://github.com/HKUDS/GraphEdit.

In-context learning (ICL) has emerged as a new approach to various natural language processing tasks, utilizing large language models (LLMs) to make predictions based on context that has been supplemented with a few examples or task-specific instructions. In this paper, we aim to extend this method to question answering tasks that utilize structured knowledge sources, and improve Text-to-SQL systems by exploring various prompt design strategies for employing LLMs. We conduct a systematic investigation into different demonstration selection methods and optimal instruction formats for prompting LLMs in the Text-to-SQL task. Our approach involves leveraging the syntactic structure of an example's SQL query to retrieve demonstrations, and we demonstrate that pursuing both diversity and similarity in demonstration selection leads to enhanced performance. Furthermore, we show that LLMs benefit from database-related knowledge augmentations. Our most effective strategy outperforms the state-of-the-art system by 2.5 points (Execution Accuracy) and the best fine-tuned system by 5.1 points on the Spider dataset. These results highlight the effectiveness of our approach in adapting LLMs to the Text-to-SQL task, and we present an analysis of the factors contributing to the success of our strategy.

In-context learning for vision data has been underexplored compared with that in natural language. Previous works studied image in-context learning, urging models to generate a single image guided by demonstrations. In this paper, we propose and study video in-context learning, where the model starts from an existing video clip and generates diverse potential future sequences, each semantically guided by the prompted video demonstrations. To achieve this, we provide a clear definition of the task, and train an autoregressive Transformer on video datasets. We thoroughly analyze the effect of different datasets and represent frames as discrete tokens, and then model them by next token predictions. We design various evaluation metrics, including both objective and subjective measures, to demonstrate the visual quality and semantic accuracy of generation results. Our model follows the scaling law and generates high-quality video clips that accurately align with the semantic guidance provided by in-context examples.

This work studies self-supervised graph learning for text-attributed graphs (TAGs) where nodes are represented by textual attributes. Unlike traditional graph contrastive methods that perturb the numerical feature space and alter the graph's topological structure, we aim to improve view generation through language supervision. This is driven by the prevalence of textual attributes in real applications, which complement graph structures with rich semantic information. However, this presents challenges because of two major reasons. First, text attributes often vary in length and quality, making it difficulty to perturb raw text descriptions without altering their original semantic meanings. Second, although text attributes complement graph structures, they are not inherently well-aligned. To bridge the gap, we introduce GAugLLM, a novel framework for augmenting TAGs. It leverages advanced large language models like Mistral to enhance self-supervised graph learning. Specifically, we introduce a mixture-of-prompt-expert technique to generate augmented node features. This approach adaptively maps multiple prompt experts, each of which modifies raw text attributes using prompt engineering, into numerical feature space. Additionally, we devise a collaborative edge modifier to leverage structural and textual commonalities, enhancing edge augmentation by examining or building connections between nodes. Empirical results across five benchmark datasets spanning various domains underscore our framework's ability to enhance the performance of leading contrastive methods as a plug-in tool. Notably, we observe that the augmented features and graph structure can also enhance the performance of standard generative methods, as well as popular graph neural networks. The open-sourced implementation of our GAugLLM is available at Github.

Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications where data are generated from non-Euclidean domains and are represented as graphs with complex relationships and interdependency between objects. The complexity of graph data has imposed significant challenges on existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this survey, we provide a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields. We propose a new taxonomy to divide the state-of-the-art graph neural networks into four categories, namely recurrent graph neural networks, convolutional graph neural networks, graph autoencoders, and spatial-temporal graph neural networks. We further discuss the applications of graph neural networks across various domains and summarize the open source codes, benchmark data sets, and model evaluation of graph neural networks. Finally, we propose potential research directions in this rapidly growing field.

Understanding a visual scene goes beyond recognizing individual objects in isolation. Relationships between objects also constitute rich semantic information about the scene. In this work, we explicitly model the objects and their relationships using scene graphs, a visually-grounded graphical structure of an image. We propose a novel end-to-end model that generates such structured scene representation from an input image. The model solves the scene graph inference problem using standard RNNs and learns to iteratively improves its predictions via message passing. Our joint inference model can take advantage of contextual cues to make better predictions on objects and their relationships. The experiments show that our model significantly outperforms previous methods for generating scene graphs using Visual Genome dataset and inferring support relations with NYU Depth v2 dataset.

Graph neural networks have shown significant success in the field of graph representation learning. Graph convolutions perform neighborhood aggregation and represent one of the most important graph operations. Nevertheless, one layer of these neighborhood aggregation methods only consider immediate neighbors, and the performance decreases when going deeper to enable larger receptive fields. Several recent studies attribute this performance deterioration to the over-smoothing issue, which states that repeated propagation makes node representations of different classes indistinguishable. In this work, we study this observation systematically and develop new insights towards deeper graph neural networks. First, we provide a systematical analysis on this issue and argue that the key factor compromising the performance significantly is the entanglement of representation transformation and propagation in current graph convolution operations. After decoupling these two operations, deeper graph neural networks can be used to learn graph node representations from larger receptive fields. We further provide a theoretical analysis of the above observation when building very deep models, which can serve as a rigorous and gentle description of the over-smoothing issue. Based on our theoretical and empirical analysis, we propose Deep Adaptive Graph Neural Network (DAGNN) to adaptively incorporate information from large receptive fields. A set of experiments on citation, co-authorship, and co-purchase datasets have confirmed our analysis and insights and demonstrated the superiority of our proposed methods.

In-context learning (ICL) improves language models' performance on a variety of NLP tasks by simply demonstrating a handful of examples at inference time. It is not well understood why ICL ability emerges, as the model has never been specifically trained on such demonstrations. Unlike prior work that explores implicit mechanisms behind ICL, we study ICL via investigating the pretraining data. Specifically, we first adapt an iterative, gradient-based approach to find a small subset of pretraining data that supports ICL. We observe that a continued pretraining on this small subset significantly improves the model's ICL ability, by up to 18%. We then compare the supportive subset constrastively with random subsets of pretraining data and discover: (1) The supportive pretraining data to ICL do not have a higher domain relevance to downstream tasks. (2) The supportive pretraining data have a higher mass of rarely occurring, long-tail tokens. (3) The supportive pretraining data are challenging examples where the information gain from long-range context is below average, indicating learning to incorporate difficult long-range context encourages ICL. Our work takes a first step towards understanding ICL via analyzing instance-level pretraining data. Our insights have a potential to enhance the ICL ability of language models by actively guiding the construction of pretraining data in the future.

In the era of Large Language Models (LLMs), human-computer interaction has evolved towards natural language, offering unprecedented flexibility. Despite this, LLMs are heavily reliant on well-structured prompts to function efficiently within the realm of In-Context Learning. Vanilla In-Context Learning relies on human-provided contexts, such as labeled examples, explicit instructions, or other guiding mechanisms that shape the model's outputs. To address this challenge, our study presents a universal framework named Automatic In-Context Learning. Upon receiving a user's request, we ask the model to independently generate examples, including labels, instructions, or reasoning pathways. The model then leverages this self-produced context to tackle the given problem. Our approach is universally adaptable and can be implemented in any setting where vanilla In-Context Learning is applicable. We demonstrate that our method yields strong performance across a range of tasks, standing up well when compared to existing methods.

Although Large Language Models (LLMs) have demonstrated potential in processing graphs, they struggle with comprehending graphical structure information through prompts of graph description sequences, especially as the graph size increases. We attribute this challenge to the uneven memory performance of LLMs across different positions in graph description sequences, known as ''positional biases''. To address this, we propose GraphInsight, a novel framework aimed at improving LLMs' comprehension of both macro- and micro-level graphical information. GraphInsight is grounded in two key strategies: 1) placing critical graphical information in positions where LLMs exhibit stronger memory performance, and 2) investigating a lightweight external knowledge base for regions with weaker memory performance, inspired by retrieval-augmented generation (RAG). Moreover, GraphInsight explores integrating these two strategies into LLM agent processes for composite graph tasks that require multi-step reasoning. Extensive empirical studies on benchmarks with a wide range of evaluation tasks show that GraphInsight significantly outperforms all other graph description methods (e.g., prompting techniques and reordering strategies) in understanding graph structures of varying sizes.

With the increasing ability of large language models (LLMs), in-context learning (ICL) has become a new paradigm for natural language processing (NLP), where LLMs make predictions only based on contexts augmented with a few examples. It has been a new trend to explore ICL to evaluate and extrapolate the ability of LLMs. In this paper, we aim to survey and summarize the progress and challenges of ICL. We first present a formal definition of ICL and clarify its correlation to related studies. Then, we organize and discuss advanced techniques, including training strategies, demonstration designing strategies, as well as related analysis. Finally, we discuss the challenges of ICL and provide potential directions for further research. We hope that our work can encourage more research on uncovering how ICL works and improving ICL.

In-context Learning (ICL) is an emerging few-shot learning paradigm on Language Models (LMs) with inner mechanisms un-explored. There are already existing works describing the inner processing of ICL, while they struggle to capture all the inference phenomena in large language models. Therefore, this paper proposes a comprehensive circuit to model the inference dynamics and try to explain the observed phenomena of ICL. In detail, we divide ICL inference into 3 major operations: (1) Summarize: LMs encode every input text (demonstrations and queries) into linear representation in the hidden states with sufficient information to solve ICL tasks. (2) Semantics Merge: LMs merge the encoded representations of demonstrations with their corresponding label tokens to produce joint representations of labels and demonstrations. (3) Feature Retrieval and Copy: LMs search the joint representations similar to the query representation on a task subspace, and copy the searched representations into the query. Then, language model heads capture these copied label representations to a certain extent and decode them into predicted labels. The proposed inference circuit successfully captured many phenomena observed during the ICL process, making it a comprehensive and practical explanation of the ICL inference process. Moreover, ablation analysis by disabling the proposed steps seriously damages the ICL performance, suggesting the proposed inference circuit is a dominating mechanism. Additionally, we confirm and list some bypass mechanisms that solve ICL tasks in parallel with the proposed circuit.

In-context learning (ICL) emerges as a promising capability of large language models (LLMs) by providing them with demonstration examples to perform diverse tasks. However, the underlying mechanism of how LLMs learn from the provided context remains under-explored. In this paper, we investigate the working mechanism of ICL through an information flow lens. Our findings reveal that label words in the demonstration examples function as anchors: (1) semantic information aggregates into label word representations during the shallow computation layers' processing; (2) the consolidated information in label words serves as a reference for LLMs' final predictions. Based on these insights, we introduce an anchor re-weighting method to improve ICL performance, a demonstration compression technique to expedite inference, and an analysis framework for diagnosing ICL errors in GPT2-XL. The promising applications of our findings again validate the uncovered ICL working mechanism and pave the way for future studies.

The success of deep learning notoriously requires larger amounts of costly annotated data. This has led to the development of self-supervised learning (SSL) that aims to alleviate this limitation by creating domain specific pretext tasks on unlabeled data. Simultaneously, there are increasing interests in generalizing deep learning to the graph domain in the form of graph neural networks (GNNs). GNNs can naturally utilize unlabeled nodes through the simple neighborhood aggregation that is unable to thoroughly make use of unlabeled nodes. Thus, we seek to harness SSL for GNNs to fully exploit the unlabeled data. Different from data instances in the image and text domains, nodes in graphs present unique structure information and they are inherently linked indicating not independent and identically distributed (or i.i.d.). Such complexity is a double-edged sword for SSL on graphs. On the one hand, it determines that it is challenging to adopt solutions from the image and text domains to graphs and dedicated efforts are desired. On the other hand, it provides rich information that enables us to build SSL from a variety of perspectives. Thus, in this paper, we first deepen our understandings on when, why, and which strategies of SSL work with GNNs by empirically studying numerous basic SSL pretext tasks on graphs. Inspired by deep insights from the empirical studies, we propose a new direction SelfTask to build advanced pretext tasks that are able to achieve state-of-the-art performance on various real-world datasets. The specific experimental settings to reproduce our results can be found in https://github.com/ChandlerBang/SelfTask-GNN.

Self-supervised learning of graph neural networks (GNNs) aims to learn an accurate representation of the graphs in an unsupervised manner, to obtain transferable representations of them for diverse downstream tasks. Predictive learning and contrastive learning are the two most prevalent approaches for graph self-supervised learning. However, they have their own drawbacks. While the predictive learning methods can learn the contextual relationships between neighboring nodes and edges, they cannot learn global graph-level similarities. Contrastive learning, while it can learn global graph-level similarities, its objective to maximize the similarity between two differently perturbed graphs may result in representations that cannot discriminate two similar graphs with different properties. To tackle such limitations, we propose a framework that aims to learn the exact discrepancy between the original and the perturbed graphs, coined as Discrepancy-based Self-supervised LeArning (D-SLA). Specifically, we create multiple perturbations of the given graph with varying degrees of similarity, and train the model to predict whether each graph is the original graph or the perturbed one. Moreover, we further aim to accurately capture the amount of discrepancy for each perturbed graph using the graph edit distance. We validate our D-SLA on various graph-related downstream tasks, including molecular property prediction, protein function prediction, and link prediction tasks, on which ours largely outperforms relevant baselines.

In-context learning (ICL), the remarkable ability to solve a task from only input exemplars, is often assumed to be a unique hallmark of Transformer models. By examining commonly employed synthetic ICL tasks, we demonstrate that multi-layer perceptrons (MLPs) can also learn in-context. Moreover, MLPs, and the closely related MLP-Mixer models, learn in-context competitively with Transformers given the same compute budget in this setting. We further show that MLPs outperform Transformers on a series of classical tasks from psychology designed to test relational reasoning, which are closely related to in-context classification. These results underscore a need for studying in-context learning beyond attention-based architectures, while also challenging strong prior arguments about MLPs' limited ability to solve relational tasks. Altogether, our results highlight the unexpected competence of MLPs, and support the growing interest in all-MLP alternatives to task-specific architectures.

The emergent ability of Large Language Models to use a small number of examples to learn to perform in novel domains and tasks, also called in-context learning (ICL). In this work, we show that a much smaller model can be trained to perform ICL by fine-tuning towards a specialized training objective, exemplified on the task of domain adaptation for neural machine translation. With this capacity for ICL, the model can take advantage of relevant few-shot examples to adapt its output towards the domain. We compare the quality of this domain adaptation to traditional supervised techniques and ICL with a 40B-parameter Large Language Model. Our approach allows efficient batch inference on a mix of domains and outperforms state-of-the-art baselines in terms of both translation quality and immediate adaptation rate, i.e. the ability to reproduce a specific term after being shown a single example.

The need to analyze graphs is ubiquitous across various fields, from social networks to biological research and recommendation systems. Therefore, enabling the ability of large language models (LLMs) to process graphs is an important step toward more advanced general intelligence. However, current LLM benchmarks on graph analysis require models to directly reason over the prompts describing graph topology, and are thus limited to small graphs with only a few dozens of nodes. In contrast, human experts typically write programs based on popular libraries for task solving, and can thus handle graphs with different scales. To this end, a question naturally arises: can LLMs analyze graphs like professionals? In this paper, we introduce ProGraph, a manually crafted benchmark containing 3 categories of graph tasks. The benchmark expects solutions based on programming instead of directly reasoning over raw inputs. Our findings reveal that the performance of current LLMs is unsatisfactory, with the best model achieving only 36% accuracy. To bridge this gap, we propose LLM4Graph datasets, which include crawled documents and auto-generated codes based on 6 widely used graph libraries. By augmenting closed-source LLMs with document retrieval and fine-tuning open-source ones on the codes, we show 11-32% absolute improvements in their accuracies. Our results underscore that the capabilities of LLMs in handling structured data are still under-explored, and show the effectiveness of LLM4Graph in enhancing LLMs' proficiency of graph analysis. The benchmark, datasets and enhanced open-source models are available at https://github.com/BUPT-GAMMA/ProGraph.

Recently, research on Text-Attributed Graphs (TAGs) has gained significant attention due to the prevalence of free-text node features in real-world applications and the advancements in Large Language Models (LLMs) that bolster TAG methodologies. However, current TAG approaches face two primary challenges: (i) Heavy reliance on label information and (ii) Limited cross-domain zero/few-shot transferability. These issues constrain the scaling of both data and model size, owing to high labor costs and scaling laws, complicating the development of graph foundation models with strong transferability. In this work, we propose the GraphCLIP framework to address these challenges by learning graph foundation models with strong cross-domain zero/few-shot transferability through a self-supervised contrastive graph-summary pretraining method. Specifically, we generate and curate large-scale graph-summary pair data with the assistance of LLMs, and introduce a novel graph-summary pretraining method, combined with invariant learning, to enhance graph foundation models with strong cross-domain zero-shot transferability. For few-shot learning, we propose a novel graph prompt tuning technique aligned with our pretraining objective to mitigate catastrophic forgetting and minimize learning costs. Extensive experiments show the superiority of GraphCLIP in both zero-shot and few-shot settings, while evaluations across various downstream tasks confirm the versatility of GraphCLIP. Our code is available at: https://github.com/ZhuYun97/GraphCLIP

Current Scene Graph Generation (SGG) methods explore contextual information to predict relationships among entity pairs. However, due to the diverse visual appearance of numerous possible subject-object combinations, there is a large intra-class variation within each predicate category, e.g., "man-eating-pizza, giraffe-eating-leaf", and the severe inter-class similarity between different classes, e.g., "man-holding-plate, man-eating-pizza", in model's latent space. The above challenges prevent current SGG methods from acquiring robust features for reliable relation prediction. In this paper, we claim that the predicate's category-inherent semantics can serve as class-wise prototypes in the semantic space for relieving the challenges. To the end, we propose the Prototype-based Embedding Network (PE-Net), which models entities/predicates with prototype-aligned compact and distinctive representations and thereby establishes matching between entity pairs and predicates in a common embedding space for relation recognition. Moreover, Prototype-guided Learning (PL) is introduced to help PE-Net efficiently learn such entitypredicate matching, and Prototype Regularization (PR) is devised to relieve the ambiguous entity-predicate matching caused by the predicate's semantic overlap. Extensive experiments demonstrate that our method gains superior relation recognition capability on SGG, achieving new state-of-the-art performances on both Visual Genome and Open Images datasets.

Recently, there has been an increasing interest in (supervised) learning with graph data, especially using graph neural networks. However, the development of meaningful benchmark datasets and standardized evaluation procedures is lagging, consequently hindering advancements in this area. To address this, we introduce the TUDataset for graph classification and regression. The collection consists of over 120 datasets of varying sizes from a wide range of applications. We provide Python-based data loaders, kernel and graph neural network baseline implementations, and evaluation tools. Here, we give an overview of the datasets, standardized evaluation procedures, and provide baseline experiments. All datasets are available at www.graphlearning.io. The experiments are fully reproducible from the code available at www.github.com/chrsmrrs/tudataset.

This paper introduces a new in-context learning (ICL) mechanism called In-Image Learning (I^2L) that combines demonstration examples, visual cues, and chain-of-thought reasoning into an aggregated image to enhance the capabilities of Large Multimodal Models (e.g., GPT-4V) in multimodal reasoning tasks. Unlike previous approaches that rely on converting images to text or incorporating visual input into language models, I^2L consolidates all information into an aggregated image and leverages image processing, understanding, and reasoning abilities. This has several advantages: it reduces inaccurate textual descriptions of complex images, provides flexibility in positioning demonstration examples, and avoids multiple input images and lengthy prompts. We also introduce I^2L-Hybrid, a method that combines the strengths of I^2L with other ICL methods. Specifically, it uses an automatic strategy to select the most suitable method (I^2L or another certain ICL method) for a specific task instance. We conduct extensive experiments to assess the effectiveness of I^2L and I^2L-Hybrid on MathVista, which covers a variety of complex multimodal reasoning tasks. Additionally, we investigate the influence of image resolution, the number of demonstration examples in a single image, and the positions of these demonstrations in the aggregated image on the effectiveness of I^2L. Our code is publicly available at https://github.com/AGI-Edgerunners/IIL.

Transformer models exhibit in-context learning: the ability to accurately predict the response to a novel query based on illustrative examples in the input sequence. In-context learning contrasts with traditional in-weights learning of query-output relationships. What aspects of the training data distribution and architecture favor in-context vs in-weights learning? Recent work has shown that specific distributional properties inherent in language, such as burstiness, large dictionaries and skewed rank-frequency distributions, control the trade-off or simultaneous appearance of these two forms of learning. We first show that these results are recapitulated in a minimal attention-only network trained on a simplified dataset. In-context learning (ICL) is driven by the abrupt emergence of an induction head, which subsequently competes with in-weights learning. By identifying progress measures that precede in-context learning and targeted experiments, we construct a two-parameter model of an induction head which emulates the full data distributional dependencies displayed by the attention-based network. A phenomenological model of induction head formation traces its abrupt emergence to the sequential learning of three nested logits enabled by an intrinsic curriculum. We propose that the sharp transitions in attention-based networks arise due to a specific chain of multi-layer operations necessary to achieve ICL, which is implemented by nested nonlinearities sequentially learned during training.

Although Large Language Models (LLMs) have demonstrated remarkable progress, their proficiency in graph-related tasks remains notably limited, hindering the development of truly general-purpose models. Previous attempts, including pretraining graph foundation models or employing supervised fine-tuning, often face challenges such as the scarcity of large-scale, universally represented graph data. We introduce G1, a simple yet effective approach demonstrating that Reinforcement Learning (RL) on synthetic graph-theoretic tasks can significantly scale LLMs' graph reasoning abilities. To enable RL training, we curate Erd\~os, the largest graph reasoning dataset to date comprising 50 diverse graph-theoretic tasks of varying difficulty levels, 100k training data and 5k test data, all drived from real-world graphs. With RL on Erd\~os, G1 obtains substantial improvements in graph reasoning, where our finetuned 3B model even outperforms Qwen2.5-72B-Instruct (24x size). RL-trained models also show strong zero-shot generalization to unseen tasks, domains, and graph encoding schemes, including other graph-theoretic benchmarks as well as real-world node classification and link prediction tasks, without compromising general reasoning abilities. Our findings offer an efficient, scalable path for building strong graph reasoners by finetuning LLMs with RL on graph-theoretic tasks, which combines the strengths of pretrained LLM capabilities with abundant, automatically generated synthetic data, suggesting that LLMs possess graph understanding abilities that RL can elicit successfully.

In this work, we seek new insights into the underlying challenges of the Scene Graph Generation (SGG) task. Quantitative and qualitative analysis of the Visual Genome dataset implies -- 1) Ambiguity: even if inter-object relationship contains the same object (or predicate), they may not be visually or semantically similar, 2) Asymmetry: despite the nature of the relationship that embodied the direction, it was not well addressed in previous studies, and 3) Higher-order contexts: leveraging the identities of certain graph elements can help to generate accurate scene graphs. Motivated by the analysis, we design a novel SGG framework, Local-to-Global Interaction Networks (LOGIN). Locally, interactions extract the essence between three instances of subject, object, and background, while baking direction awareness into the network by explicitly constraining the input order of subject and object. Globally, interactions encode the contexts between every graph component (i.e., nodes and edges). Finally, Attract & Repel loss is utilized to fine-tune the distribution of predicate embeddings. By design, our framework enables predicting the scene graph in a bottom-up manner, leveraging the possible complementariness. To quantify how much LOGIN is aware of relational direction, a new diagnostic task called Bidirectional Relationship Classification (BRC) is also proposed. Experimental results demonstrate that LOGIN can successfully distinguish relational direction than existing methods (in BRC task), while showing state-of-the-art results on the Visual Genome benchmark (in SGG task).

In-context learning (ICL) is a powerful paradigm emerged from large language models (LLMs). Despite its promises, ICL performance is known to be highly sensitive to input examples. In this work, we use in-context influences to analyze few-shot ICL performance directly from the in-context examples. Our proposed influence-based example selection method can identify both positive and negative examples, outperforming several baselines when evaluated on 9 SuperGLUE tasks. Our analysis uncovers up to a 16.3% performance gap between using the most negative in-context examples compared to the most positive. In a case study, we apply our influence-based framework to quantify the phenomena of recency bias in example ordering for few-shot ICL.

Machine learning on graphs has been extensively studied in both academic and industry. However, as the literature on graph learning booms with a vast number of emerging methods and techniques, it becomes increasingly difficult to manually design the optimal machine learning algorithm for different graph-related tasks. To solve this critical challenge, automated machine learning (AutoML) on graphs which combines the strength of graph machine learning and AutoML together, is gaining attention from the research community. Therefore, we comprehensively survey AutoML on graphs in this paper, primarily focusing on hyper-parameter optimization (HPO) and neural architecture search (NAS) for graph machine learning. We further overview libraries related to automated graph machine learning and in-depth discuss AutoGL, the first dedicated open-source library for AutoML on graphs. In the end, we share our insights on future research directions for automated graph machine learning. This paper is the first systematic and comprehensive review of automated machine learning on graphs to the best of our knowledge.

Learning graph generative models over latent spaces has received less attention compared to models that operate on the original data space and has so far demonstrated lacklustre performance. We present GLAD a latent space graph generative model. Unlike most previous latent space graph generative models, GLAD operates on a discrete latent space that preserves to a significant extent the discrete nature of the graph structures making no unnatural assumptions such as latent space continuity. We learn the prior of our discrete latent space by adapting diffusion bridges to its structure. By operating over an appropriately constructed latent space we avoid relying on decompositions that are often used in models that operate in the original data space. We present experiments on a series of graph benchmark datasets which clearly show the superiority of the discrete latent space and obtain state of the art graph generative performance, making GLAD the first latent space graph generative model with competitive performance. Our source code is published at: https://github.com/v18nguye/GLAD.

In-context learning (ICL) involves reasoning from given contextual examples. As more modalities comes, this procedure is becoming more challenging as the interleaved input modalities convolutes the understanding process. This is exemplified by the observation that multimodal models often struggle to effectively extrapolate from contextual examples to perform ICL. To address these challenges, we introduce MultiModal In-conteXt Tuning (M^2IXT), a lightweight module to enhance the ICL capabilities of multimodal unified models. The proposed M^2IXT module perceives an expandable context window to incorporate various labeled examples of multiple modalities (e.g., text, image, and coordinates). It can be prepended to various multimodal unified models (e.g., OFA, Unival, LLaVA) of different architectures and trained via a mixed-tasks strategy to enable rapid few-shot adaption on multiple tasks and datasets. When tuned on as little as 50K multimodal data, M^2IXT can boost the few-shot ICL performance significantly (e.g., 18\% relative increase for OFA), and obtained state-of-the-art results across an array of tasks including visual question answering, image captioning, visual grounding, and visual entailment, while being considerably small in terms of model parameters (e.g., sim20times smaller than Flamingo or MMICL), highlighting the flexibility and effectiveness of M^2IXT as a multimodal in-context learner.

Human knowledge provides a formal understanding of the world. Knowledge graphs that represent structural relations between entities have become an increasingly popular research direction towards cognition and human-level intelligence. In this survey, we provide a comprehensive review of knowledge graph covering overall research topics about 1) knowledge graph representation learning, 2) knowledge acquisition and completion, 3) temporal knowledge graph, and 4) knowledge-aware applications, and summarize recent breakthroughs and perspective directions to facilitate future research. We propose a full-view categorization and new taxonomies on these topics. Knowledge graph embedding is organized from four aspects of representation space, scoring function, encoding models, and auxiliary information. For knowledge acquisition, especially knowledge graph completion, embedding methods, path inference, and logical rule reasoning, are reviewed. We further explore several emerging topics, including meta relational learning, commonsense reasoning, and temporal knowledge graphs. To facilitate future research on knowledge graphs, we also provide a curated collection of datasets and open-source libraries on different tasks. In the end, we have a thorough outlook on several promising research directions.

Large language models (LLMs) with decoder-only architectures demonstrate remarkable in-context learning (ICL) capabilities. This feature enables them to effectively handle both familiar and novel tasks by utilizing examples provided within their input context. Recognizing the potential of this capability, we propose leveraging the ICL feature in LLMs to enhance the process of text embedding generation. To this end, we introduce a novel model bge-en-icl, which employs few-shot examples to produce high-quality text embeddings. Our approach integrates task-related examples directly into the query side, resulting in significant improvements across various tasks. Additionally, we have investigated how to effectively utilize LLMs as embedding models, including various attention mechanisms, pooling methods, etc. Our findings suggest that retaining the original framework often yields the best results, underscoring that simplicity is best. Experimental results on the MTEB and AIR-Bench benchmarks demonstrate that our approach sets new state-of-the-art (SOTA) performance. Our model, code and dataset are freely available at https://github.com/FlagOpen/FlagEmbedding .

We develop a set of methods to improve on the results of self-supervised learning using context. We start with a baseline of patch based arrangement context learning and go from there. Our methods address some overt problems such as chromatic aberration as well as other potential problems such as spatial skew and mid-level feature neglect. We prevent problems with testing generalization on common self-supervised benchmark tests by using different datasets during our development. The results of our methods combined yield top scores on all standard self-supervised benchmarks, including classification and detection on PASCAL VOC 2007, segmentation on PASCAL VOC 2012, and "linear tests" on the ImageNet and CSAIL Places datasets. We obtain an improvement over our baseline method of between 4.0 to 7.1 percentage points on transfer learning classification tests. We also show results on different standard network architectures to demonstrate generalization as well as portability. All data, models and programs are available at: https://gdo-datasci.llnl.gov/selfsupervised/.

Graphs are essential data structures for modeling complex interactions in domains such as social networks, molecular structures, and biological systems. Graph-level tasks, which predict properties or classes for the entire graph, are critical for applications, such as molecular property prediction and subgraph counting. Graph Neural Networks (GNNs) have shown promise in these tasks, but their evaluations are often limited to narrow datasets, tasks, and inconsistent experimental setups, restricting their generalizability. To address these limitations, we propose a unified evaluation framework for graph-level GNNs. This framework provides a standardized setting to evaluate GNNs across diverse datasets, various graph tasks (e.g., graph classification and regression), and challenging scenarios, including noisy, imbalanced, and few-shot graphs. Additionally, we propose a novel GNN model with enhanced expressivity and generalization capabilities. Specifically, we enhance the expressivity of GNNs through a k-path rooted subgraph approach, enabling the model to effectively count subgraphs (e.g., paths and cycles). Moreover, we introduce a unified graph contrastive learning algorithm for graphs across diverse domains, which adaptively removes unimportant edges to augment graphs, thereby significantly improving generalization performance. Extensive experiments demonstrate that our model achieves superior performance against fourteen effective baselines across twenty-seven graph datasets, establishing it as a robust and generalizable model for graph-level tasks.

Foundation models in language and vision have the ability to run inference on any textual and visual inputs thanks to the transferable representations such as a vocabulary of tokens in language. Knowledge graphs (KGs) have different entity and relation vocabularies that generally do not overlap. The key challenge of designing foundation models on KGs is to learn such transferable representations that enable inference on any graph with arbitrary entity and relation vocabularies. In this work, we make a step towards such foundation models and present ULTRA, an approach for learning universal and transferable graph representations. ULTRA builds relational representations as a function conditioned on their interactions. Such a conditioning strategy allows a pre-trained ULTRA model to inductively generalize to any unseen KG with any relation vocabulary and to be fine-tuned on any graph. Conducting link prediction experiments on 57 different KGs, we find that the zero-shot inductive inference performance of a single pre-trained ULTRA model on unseen graphs of various sizes is often on par or better than strong baselines trained on specific graphs. Fine-tuning further boosts the performance.

Existing commonsense knowledge bases often organize tuples in an isolated manner, which is deficient for commonsense conversational models to plan the next steps. To fill the gap, we curate a large-scale multi-turn human-written conversation corpus, and create the first Chinese commonsense conversation knowledge graph which incorporates both social commonsense knowledge and dialog flow information. To show the potential of our graph, we develop a graph-conversation matching approach, and benchmark two graph-grounded conversational tasks.

In-context learning (ICL) is an appealing approach for semantic parsing due to its few-shot nature and improved generalization. However, learning to parse to rare domain-specific languages (DSLs) from just a few demonstrations is challenging, limiting the performance of even the most capable LLMs. In this work, we improve the effectiveness of ICL for semantic parsing by (1) using general-purpose programming languages such as Python instead of DSLs, and (2) augmenting prompts with a structured domain description that includes, e.g., the available classes and functions. We show that both these changes significantly improve accuracy across three popular datasets. Combined, they lead to dramatic improvements (e.g. 7.9% to 66.5% on SMCalFlow compositional split), nearly closing the performance gap between easier i.i.d.\ and harder compositional splits when used with a strong model, and reducing the need for a large number of demonstrations. We find that the resemblance of the target parse language to general-purpose code is a more important factor than the language's popularity in pre-training corpora. Our findings provide an improved methodology for building semantic parsers in the modern context of ICL with LLMs.

Graph Convolutional Networks (GCNs) have shown strong performance in learning text representations for various tasks such as text classification, due to its expressive power in modeling graph structure data (e.g., a literature citation network). Most existing GCNs are limited to deal with documents included in a pre-defined graph, i.e., it cannot be generalized to out-of-graph documents. To address this issue, we propose to transform the document graph into a word graph, to decouple data samples (i.e., documents in training and test sets) and a GCN model by using a document-independent graph. Such word-level GCN could therefore naturally inference out-of-graph documents in an inductive way. The proposed Word-level Graph (WGraph) can not only implicitly learning word presentation with commonly-used word co-occurrences in corpora, but also incorporate extra global semantic dependency derived from inter-document relationships (e.g., literature citations). An inductive Word-grounded Graph Convolutional Network (WGCN) is proposed to learn word and document representations based on WGraph in a supervised manner. Experiments on text classification with and without citation networks evidence that the proposed WGCN model outperforms existing methods in terms of effectiveness and efficiency.

Hypergraphs are a powerful abstraction for representing higher-order interactions between entities of interest. To exploit these relationships in making downstream predictions, a variety of hypergraph neural network architectures have recently been proposed, in large part building upon precursors from the more traditional graph neural network (GNN) literature. Somewhat differently, in this paper we begin by presenting an expressive family of parameterized, hypergraph-regularized energy functions. We then demonstrate how minimizers of these energies effectively serve as node embeddings that, when paired with a parameterized classifier, can be trained end-to-end via a supervised bilevel optimization process. Later, we draw parallels between the implicit architecture of the predictive models emerging from the proposed bilevel hypergraph optimization, and existing GNN architectures in common use. Empirically, we demonstrate state-of-the-art results on various hypergraph node classification benchmarks. Code is available at https://github.com/yxzwang/PhenomNN.

Long-context capabilities are essential for large language models (LLMs) to tackle complex and long-input tasks. Despite numerous efforts made to optimize LLMs for long contexts, challenges persist in robustly processing long inputs. In this paper, we introduce GraphReader, a graph-based agent system designed to handle long texts by structuring them into a graph and employing an agent to explore this graph autonomously. Upon receiving a question, the agent first undertakes a step-by-step analysis and devises a rational plan. It then invokes a set of predefined functions to read node content and neighbors, facilitating a coarse-to-fine exploration of the graph. Throughout the exploration, the agent continuously records new insights and reflects on current circumstances to optimize the process until it has gathered sufficient information to generate an answer. Experimental results on the LV-Eval dataset reveal that GraphReader, using a 4k context window, consistently outperforms GPT-4-128k across context lengths from 16k to 256k by a large margin. Additionally, our approach demonstrates superior performance on four challenging single-hop and multi-hop benchmarks.

Advances in Visually Rich Document Understanding (VrDU) have enabled information extraction and question answering over documents with complex layouts. Two tropes of architectures have emerged -- transformer-based models inspired by LLMs, and Graph Neural Networks. In this paper, we introduce DocGraphLM, a novel framework that combines pre-trained language models with graph semantics. To achieve this, we propose 1) a joint encoder architecture to represent documents, and 2) a novel link prediction approach to reconstruct document graphs. DocGraphLM predicts both directions and distances between nodes using a convergent joint loss function that prioritizes neighborhood restoration and downweighs distant node detection. Our experiments on three SotA datasets show consistent improvement on IE and QA tasks with the adoption of graph features. Moreover, we report that adopting the graph features accelerates convergence in the learning process during training, despite being solely constructed through link prediction.

Recent prevailing works on graph machine learning typically follow a similar methodology that involves designing advanced variants of graph neural networks (GNNs) to maintain the superior performance of GNNs on different graphs. In this paper, we aim to streamline the GNN design process and leverage the advantages of Large Language Models (LLMs) to improve the performance of GNNs on downstream tasks. We formulate a new paradigm, coined "LLMs-as-Consultants," which integrates LLMs with GNNs in an interactive manner. A framework named LOGIN (LLM Consulted GNN training) is instantiated, empowering the interactive utilization of LLMs within the GNN training process. First, we attentively craft concise prompts for spotted nodes, carrying comprehensive semantic and topological information, and serving as input to LLMs. Second, we refine GNNs by devising a complementary coping mechanism that utilizes the responses from LLMs, depending on their correctness. We empirically evaluate the effectiveness of LOGIN on node classification tasks across both homophilic and heterophilic graphs. The results illustrate that even basic GNN architectures, when employed within the proposed LLMs-as-Consultants paradigm, can achieve comparable performance to advanced GNNs with intricate designs. Our codes are available at https://github.com/QiaoYRan/LOGIN.

Disinformation on social media poses both societal and technical challenges. While previous studies have integrated textual information into propagation networks, they have yet to fully leverage the advancements in Transformer-based language models for high-quality contextual text representations. This work investigates the impact of incorporating textual features into Graph Neural Networks (GNNs) for fake news detection. Our experiments demonstrate that contextual representations improve performance by 9.3% in Macro F1 over static ones and 33.8% over GNNs without textual features. However, noisy data augmentation degrades performance and increases instability. We expect our methodology to open avenues for further research, and all code is made publicly available.

Large language models (LLMs) such as GPT-4 have emerged as frontrunners, showcasing unparalleled prowess in diverse applications, including answering queries, code generation, and more. Parallelly, graph-structured data, an intrinsic data type, is pervasive in real-world scenarios. Merging the capabilities of LLMs with graph-structured data has been a topic of keen interest. This paper bifurcates such integrations into two predominant categories. The first leverages LLMs for graph learning, where LLMs can not only augment existing graph algorithms but also stand as prediction models for various graph tasks. Conversely, the second category underscores the pivotal role of graphs in advancing LLMs. Mirroring human cognition, we solve complex tasks by adopting graphs in either reasoning or collaboration. Integrating with such structures can significantly boost the performance of LLMs in various complicated tasks. We also discuss and propose open questions for integrating LLMs with graph-structured data for the future direction of the field.

Learning on text-attributed graphs (TAGs), in which nodes are associated with one or more texts, has been the subject of much recent work. However, most approaches tend to make strong assumptions about the downstream task of interest, are reliant on hand-labeled data, or fail to equally balance the importance of both text and graph representations. In this work, we propose Contrastive Graph-Text pretraining (ConGraT), a general, self-supervised approach for jointly learning separate representations of texts and nodes in a TAG. Our method trains a language model (LM) and a graph neural network (GNN) to align their representations in a common latent space using a batch-wise contrastive learning objective inspired by CLIP. We further propose an extension to the CLIP objective that leverages graph structure to incorporate information about inter-node similarity. Extensive experiments demonstrate that ConGraT outperforms baselines on various downstream tasks, including node and text category classification, link prediction, and language modeling. Finally, we present an application of our method to community detection in social graphs, which enables finding more textually grounded communities, rather than purely graph-based ones. Code and certain datasets are available at https://github.com/wwbrannon/congrat.

We present TabPFN, a trained Transformer that can do supervised classification for small tabular datasets in less than a second, needs no hyperparameter tuning and is competitive with state-of-the-art classification methods. TabPFN performs in-context learning (ICL), it learns to make predictions using sequences of labeled examples (x, f(x)) given in the input, without requiring further parameter updates. TabPFN is fully entailed in the weights of our network, which accepts training and test samples as a set-valued input and yields predictions for the entire test set in a single forward pass. TabPFN is a Prior-Data Fitted Network (PFN) and is trained offline once, to approximate Bayesian inference on synthetic datasets drawn from our prior. This prior incorporates ideas from causal reasoning: It entails a large space of structural causal models with a preference for simple structures. On the 18 datasets in the OpenML-CC18 suite that contain up to 1 000 training data points, up to 100 purely numerical features without missing values, and up to 10 classes, we show that our method clearly outperforms boosted trees and performs on par with complex state-of-the-art AutoML systems with up to 230times speedup. This increases to a 5 700times speedup when using a GPU. We also validate these results on an additional 67 small numerical datasets from OpenML. We provide all our code, the trained TabPFN, an interactive browser demo and a Colab notebook at https://github.com/automl/TabPFN.

Graphs are a powerful tool for representing and analyzing complex relationships in real-world applications such as social networks, recommender systems, and computational finance. Reasoning on graphs is essential for drawing inferences about the relationships between entities in a complex system, and to identify hidden patterns and trends. Despite the remarkable progress in automated reasoning with natural text, reasoning on graphs with large language models (LLMs) remains an understudied problem. In this work, we perform the first comprehensive study of encoding graph-structured data as text for consumption by LLMs. We show that LLM performance on graph reasoning tasks varies on three fundamental levels: (1) the graph encoding method, (2) the nature of the graph task itself, and (3) interestingly, the very structure of the graph considered. These novel results provide valuable insight on strategies for encoding graphs as text. Using these insights we illustrate how the correct choice of encoders can boost performance on graph reasoning tasks inside LLMs by 4.8% to 61.8%, depending on the task.

Embodied AI agents that search for objects in large environments such as households often need to make efficient decisions by predicting object locations based on partial information. We pose this as a new type of link prediction problem: link prediction on partially observable dynamic graphs. Our graph is a representation of a scene in which rooms and objects are nodes, and their relationships are encoded in the edges; only parts of the changing graph are known to the agent at each timestep. This partial observability poses a challenge to existing link prediction approaches, which we address. We propose a novel state representation -- Scene Graph Memory (SGM) -- with captures the agent's accumulated set of observations, as well as a neural net architecture called a Node Edge Predictor (NEP) that extracts information from the SGM to search efficiently. We evaluate our method in the Dynamic House Simulator, a new benchmark that creates diverse dynamic graphs following the semantic patterns typically seen at homes, and show that NEP can be trained to predict the locations of objects in a variety of environments with diverse object movement dynamics, outperforming baselines both in terms of new scene adaptability and overall accuracy. The codebase and more can be found at https://www.scenegraphmemory.com.

In-context learning is a new learning paradigm where a language model conditions on a few input-output pairs (demonstrations) and a test input, and directly outputs the prediction. It has been shown highly dependent on the provided demonstrations and thus promotes the research of demonstration retrieval: given a test input, relevant examples are retrieved from the training set to serve as informative demonstrations for in-context learning. While previous works focus on training task-specific retrievers for several tasks separately, these methods are often hard to transfer and scale on various tasks, and separately trained retrievers incur a lot of parameter storage and deployment cost. In this paper, we propose Unified Demonstration Retriever (UDR), a single model to retrieve demonstrations for a wide range of tasks. To train UDR, we cast various tasks' training signals into a unified list-wise ranking formulation by language model's feedback. Then we propose a multi-task list-wise ranking training framework, with an iterative mining strategy to find high-quality candidates, which can help UDR fully incorporate various tasks' signals. Experiments on 30+ tasks across 13 task families and multiple data domains show that UDR significantly outperforms baselines. Further analyses show the effectiveness of each proposed component and UDR's strong ability in various scenarios including different LMs (1.3B - 175B), unseen datasets, varying demonstration quantities, etc.

Information extraction (IE) is an important task in Natural Language Processing (NLP), involving the extraction of named entities and their relationships from unstructured text. In this paper, we propose a novel approach to this task by formulating it as graph structure learning (GSL). By formulating IE as GSL, we enhance the model's ability to dynamically refine and optimize the graph structure during the extraction process. This formulation allows for better interaction and structure-informed decisions for entity and relation prediction, in contrast to previous models that have separate or untied predictions for these tasks. When compared against state-of-the-art baselines on joint entity and relation extraction benchmarks, our model, GraphER, achieves competitive results.

Existing PTLM-based models for TSC can be categorized into two groups: 1) fine-tuning-based models that adopt PTLM as the context encoder; 2) prompting-based models that transfer the classification task to the text/word generation task. In this paper, we present a new perspective of leveraging PTLM for TSC: simultaneously leveraging the merits of both language modeling and explicit target-context interactions via contextual target attributes. Specifically, we design the domain- and target-constrained cloze test, which can leverage the PTLMs' strong language modeling ability to generate the given target's attributes pertaining to the review context. The attributes contain the background and property information of the target, which can help to enrich the semantics of the review context and the target. To exploit the attributes for tackling TSC, we first construct a heterogeneous information graph by treating the attributes as nodes and combining them with (1) the syntax graph automatically produced by the off-the-shelf dependency parser and (2) the semantics graph of the review context, which is derived from the self-attention mechanism. Then we propose a heterogeneous information gated graph convolutional network to model the interactions among the attribute information, the syntactic information, and the contextual information. The experimental results on three benchmark datasets demonstrate the superiority of our model, which achieves new state-of-the-art performance.

Large language models (LLMs) demonstrate emergent in-context learning capabilities, where they adapt to new tasks based on example demonstrations. However, in-context learning has seen limited effectiveness in many settings, is difficult to quantitatively control and takes up context window space. To overcome these limitations, we propose an alternative approach that recasts in-context learning as in-context vectors (ICV). Using ICV has two steps. We first use a forward pass on demonstration examples to create the in-context vector from the latent embedding of the LLM. This vector captures essential information about the intended task. On a new query, instead of adding demonstrations to the prompt, we shift the latent states of the LLM using the ICV. The ICV approach has several benefits: 1) it enables the LLM to more effectively follow the demonstration examples; 2) it's easy to control by adjusting the magnitude of the ICV; 3) it reduces the length of the prompt by removing the in-context demonstrations; 4) ICV is computationally much more efficient than fine-tuning. We demonstrate that ICV achieves better performance compared to standard in-context learning and fine-tuning on diverse tasks including safety, style transfer, role-playing and formatting. Moreover, we show that we can flexibly teach LLM to simultaneously follow different types of instructions by simple vector arithmetics on the corresponding ICVs.

In-context learning refers to the emerging ability of large language models (LLMs) to perform a target task without additional training, utilizing demonstrations of the task. Recent studies aim to enhance in-context learning performance by selecting more useful demonstrations. However, they overlook the presence of inevitable noisy labels in task demonstrations that arise during the labeling process in the real-world. In this paper, we propose a new task, in-context learning with noisy labels, which aims to solve real-world problems for in-context learning where labels in task demonstrations would be corrupted. Moreover, we propose a new method and baseline methods for the new task, inspired by studies in learning with noisy labels. Through experiments, we demonstrate that our proposed method can serve as a safeguard against performance degradation in in-context learning caused by noisy labels.

In-context Learning (ICL) enables large language models (LLMs) to tackle downstream tasks through sophisticated prompting and high-quality demonstrations. However, this traditional ICL paradigm shows limitations when facing complex mathematical reasoning tasks, primarily due to its heavy dependence on example quality and the necessity for human intervention in challenging scenarios. To address these limitations, this paper presents HiAR-ICL, a High-level Automated Reasoning paradigm in ICL that shifts focus from specific examples to abstract thinking patterns, extending the conventional concept of context in ICL. HiAR-ICL introduces five atomic reasoning actions as fundamental components for constructing chain-structured patterns. Using Monte Carlo Tree Search, we explore reasoning paths and construct thought cards to guide subsequent inference. We then develop a cognitive complexity framework that dynamically matches problems with appropriate thought cards. Experimental results demonstrate HiAR-ICL's effectiveness, achieving state-of-the-art accuracy (79.6%) on the MATH benchmark with Qwen2.5-7B-Instruct, surpassing GPT-4o (76.6%) and Claude 3.5 (71.1%).

Low-dimensional embeddings of nodes in large graphs have proved extremely useful in a variety of prediction tasks, from content recommendation to identifying protein functions. However, most existing approaches require that all nodes in the graph are present during training of the embeddings; these previous approaches are inherently transductive and do not naturally generalize to unseen nodes. Here we present GraphSAGE, a general, inductive framework that leverages node feature information (e.g., text attributes) to efficiently generate node embeddings for previously unseen data. Instead of training individual embeddings for each node, we learn a function that generates embeddings by sampling and aggregating features from a node's local neighborhood. Our algorithm outperforms strong baselines on three inductive node-classification benchmarks: we classify the category of unseen nodes in evolving information graphs based on citation and Reddit post data, and we show that our algorithm generalizes to completely unseen graphs using a multi-graph dataset of protein-protein interactions.

This paper explores the elusive mechanism underpinning in-context learning in Large Language Models (LLMs). Our work provides a novel perspective by examining in-context learning via the lens of surface repetitions. We quantitatively investigate the role of surface features in text generation, and empirically establish the existence of token co-occurrence reinforcement, a principle that strengthens the relationship between two tokens based on their contextual co-occurrences. By investigating the dual impacts of these features, our research illuminates the internal workings of in-context learning and expounds on the reasons for its failures. This paper provides an essential contribution to the understanding of in-context learning and its potential limitations, providing a fresh perspective on this exciting capability.

In Large Visual Language Models (LVLMs), the efficacy of In-Context Learning (ICL) remains limited by challenges in cross-modal interactions and representation disparities. To overcome these challenges, we introduce a novel Visual In-Context Learning (VICL) method comprising Visual Demonstration Retrieval, Intent-Oriented Image Summarization, and Intent-Oriented Demonstration Composition. Our approach retrieves images via ''Retrieval & Rerank'' paradigm, summarises images with task intent and task-specific visual parsing, and composes language-based demonstrations that reduce token count and alleviate cross-modal interaction problem. Experimental evaluations on five visual reasoning datasets demonstrate the effectiveness of our method. Moreover, our extensive experiments leverage information flow analysis to elucidate the effectiveness of our method, and investigate the impact of length and position of demonstrations for LVLM. The use of in-context unlearning further shows promise in resetting specific model knowledge without retraining.

Large language models are extensively applied across a wide range of tasks, such as customer support, content creation, educational tutoring, and providing financial guidance. However, a well-known drawback is their predisposition to generate hallucinations. This damages the trustworthiness of the information these models provide, impacting decision-making and user confidence. We propose a method to detect hallucinations by looking at the structure of the latent space and finding associations within hallucinated and non-hallucinated generations. We create a graph structure that connects generations that lie closely in the embedding space. Moreover, we employ a Graph Attention Network which utilizes message passing to aggregate information from neighboring nodes and assigns varying degrees of importance to each neighbor based on their relevance. Our findings show that 1) there exists a structure in the latent space that differentiates between hallucinated and non-hallucinated generations, 2) Graph Attention Networks can learn this structure and generalize it to unseen generations, and 3) the robustness of our method is enhanced when incorporating contrastive learning. When evaluated against evidence-based benchmarks, our model performs similarly without access to search-based methods.

In-context learning (ICL) enables Large Language Models (LLMs) to perform tasks using few demonstrations, facilitating task adaptation when labeled examples are hard to obtain. However, ICL is sensitive to the choice of demonstrations, and it remains unclear which demonstration attributes enable in-context generalization. In this work, we conduct a perturbation study of in-context demonstrations for low-resource Named Entity Detection (NED). Our surprising finding is that in-context demonstrations with partially correct annotated entity mentions can be as effective for task transfer as fully correct demonstrations. Based off our findings, we propose Pseudo-annotated In-Context Learning (PICLe), a framework for in-context learning with noisy, pseudo-annotated demonstrations. PICLe leverages LLMs to annotate many demonstrations in a zero-shot first pass. We then cluster these synthetic demonstrations, sample specific sets of in-context demonstrations from each cluster, and predict entity mentions using each set independently. Finally, we use self-verification to select the final set of entity mentions. We evaluate PICLe on five biomedical NED datasets and show that, with zero human annotation, PICLe outperforms ICL in low-resource settings where limited gold examples can be used as in-context demonstrations.

Natural language understanding (NLU) is integral to various social media applications. However, existing NLU models rely heavily on context for semantic learning, resulting in compromised performance when faced with short and noisy social media content. To address this issue, we leverage in-context learning (ICL), wherein language models learn to make inferences by conditioning on a handful of demonstrations to enrich the context and propose a novel hashtag-driven in-context learning (HICL) framework. Concretely, we pre-train a model #Encoder, which employs #hashtags (user-annotated topic labels) to drive BERT-based pre-training through contrastive learning. Our objective here is to enable #Encoder to gain the ability to incorporate topic-related semantic information, which allows it to retrieve topic-related posts to enrich contexts and enhance social media NLU with noisy contexts. To further integrate the retrieved context with the source text, we employ a gradient-based method to identify trigger terms useful in fusing information from both sources. For empirical studies, we collected 45M tweets to set up an in-context NLU benchmark, and the experimental results on seven downstream tasks show that HICL substantially advances the previous state-of-the-art results. Furthermore, we conducted extensive analyzes and found that: (1) combining source input with a top-retrieved post from #Encoder is more effective than using semantically similar posts; (2) trigger words can largely benefit in merging context from the source and retrieved posts.

In-context learning is the paradigm that adapts large language models to downstream tasks by providing a few examples. Few-shot selection -- selecting appropriate examples for each test instance separately -- is important for in-context learning. In this paper, we propose Skill-KNN, a skill-based few-shot selection method for in-context learning. The key advantages of Skill-KNN include: (1) it addresses the problem that existing methods based on pre-trained embeddings can be easily biased by surface natural language features that are not important for the target task; (2) it does not require training or fine-tuning of any models, making it suitable for frequently expanding or changing example banks. The key insight is to optimize the inputs fed into the embedding model, rather than tuning the model itself. Technically, Skill-KNN generates the skill-based descriptions for each test case and candidate example by utilizing a pre-processing few-shot prompting, thus eliminating unimportant surface features. Experimental results across five cross-domain semantic parsing datasets and six backbone models show that Skill-KNN significantly outperforms existing methods.

In-Context Learning (ICL) emerges as a key feature for Large Language Models (LLMs), allowing them to adapt to new tasks by leveraging task-specific examples without updating model parameters. However, ICL faces challenges with increasing numbers of examples due to performance degradation and quadratic computational costs. In this paper, we propose Logit Arithmetic Reweighting Approach (LARA), a novel framework that enhances ICL by using logit-based ensembling of multiple demonstrations. Our approach divides long input demonstrations into parallelizable shorter inputs to significantly reduce memory requirements, and then effectively aggregate the information by reweighting logits of each group via a non-gradient optimization approach. We further introduce Binary LARA (B-LARA), a variant that constrains weights to binary values to simplify the search space and reduces memory usage by filtering out less informative demonstration groups. Experiments on BBH and MMLU demonstrate that LARA and B-LARA outperform all baseline methods in both accuracy and memory efficiency. We also conduct extensive analysis to show that LARA generalizes well to scenarios of varying numbers of examples from limited to many-shot demonstrations.

While textual information significantly enhances the performance of pre-trained language models (PLMs) in knowledge graph completion (KGC), the static and noisy nature of existing corpora collected from Wikipedia articles or synsets definitions often limits the potential of PLM-based KGC models. To surmount these challenges, we introduce the Contextualization Distillation strategy, a versatile plug-in-and-play approach compatible with both discriminative and generative KGC frameworks. Our method begins by instructing large language models (LLMs) to transform compact, structural triplets into context-rich segments. Subsequently, we introduce two tailored auxiliary tasks, reconstruction and contextualization, allowing smaller KGC models to assimilate insights from these enriched triplets. Comprehensive evaluations across diverse datasets and KGC techniques highlight the efficacy and adaptability of our approach, revealing consistent performance enhancements irrespective of underlying pipelines or architectures. Moreover, our analysis makes our method more explainable and provides insight into generating path selection, as well as the choosing of suitable distillation tasks. All the code and data in this work will be released at https://github.com/David-Li0406/Contextulization-Distillation

Contextual Text Block Detection (CTBD) is the task of identifying coherent text blocks within the complexity of natural scenes. Previous methodologies have treated CTBD as either a visual relation extraction challenge within computer vision or as a sequence modeling problem from the perspective of natural language processing. We introduce a new framework that frames CTBD as a graph generation problem. This methodology consists of two essential procedures: identifying individual text units as graph nodes and discerning the sequential reading order relationships among these units as graph edges. Leveraging the cutting-edge capabilities of DQ-DETR for node detection, our framework innovates further by integrating a novel mechanism, a Dynamic Relation Transformer (DRFormer), dedicated to edge generation. DRFormer incorporates a dual interactive transformer decoder that deftly manages a dynamic graph structure refinement process. Through this iterative process, the model systematically enhances the graph's fidelity, ultimately resulting in improved precision in detecting contextual text blocks. Comprehensive experimental evaluations conducted on both SCUT-CTW-Context and ReCTS-Context datasets substantiate that our method achieves state-of-the-art results, underscoring the effectiveness and potential of our graph generation framework in advancing the field of CTBD.

Large-scale pre-trained language models (PLMs) are well-known for being capable of solving a task simply by conditioning a few input-label pairs dubbed demonstrations on a prompt without being explicitly tuned for the desired downstream task. Such a process (i.e., in-context learning), however, naturally leads to high reliance on the demonstrations which are usually selected from external datasets. In this paper, we propose self-generated in-context learning (SG-ICL), which generates demonstrations for in-context learning from PLM itself to minimize the reliance on the external demonstration. We conduct experiments on four different text classification tasks and show SG-ICL significantly outperforms zero-shot learning and is generally worth approximately 0.6 gold training samples. Moreover, our generated demonstrations show more consistent performance with low variance compared to randomly selected demonstrations from the training dataset.

Information flows by routes inside the network via mechanisms implemented in the model. These routes can be represented as graphs where nodes correspond to token representations and edges to operations inside the network. We automatically build these graphs in a top-down manner, for each prediction leaving only the most important nodes and edges. In contrast to the existing workflows relying on activation patching, we do this through attribution: this allows us to efficiently uncover existing circuits with just a single forward pass. Additionally, the applicability of our method is far beyond patching: we do not need a human to carefully design prediction templates, and we can extract information flow routes for any prediction (not just the ones among the allowed templates). As a result, we can talk about model behavior in general, for specific types of predictions, or different domains. We experiment with Llama 2 and show that the role of some attention heads is overall important, e.g. previous token heads and subword merging heads. Next, we find similarities in Llama 2 behavior when handling tokens of the same part of speech. Finally, we show that some model components can be specialized on domains such as coding or multilingual texts.

Transferring latent structure from one environment or problem to another is a mechanism by which humans and animals generalize with very little data. Inspired by cognitive and neurobiological insights, we propose graph schemas as a mechanism of abstraction for transfer learning. Graph schemas start with latent graph learning where perceptually aliased observations are disambiguated in the latent space using contextual information. Latent graph learning is also emerging as a new computational model of the hippocampus to explain map learning and transitive inference. Our insight is that a latent graph can be treated as a flexible template -- a schema -- that models concepts and behaviors, with slots that bind groups of latent nodes to the specific observations or groundings. By treating learned latent graphs (schemas) as prior knowledge, new environments can be quickly learned as compositions of schemas and their newly learned bindings. We evaluate graph schemas on two previously published challenging tasks: the memory & planning game and one-shot StreetLearn, which are designed to test rapid task solving in novel environments. Graph schemas can be learned in far fewer episodes than previous baselines, and can model and plan in a few steps in novel variations of these tasks. We also demonstrate learning, matching, and reusing graph schemas in more challenging 2D and 3D environments with extensive perceptual aliasing and size variations, and show how different schemas can be composed to model larger and more complex environments. To summarize, our main contribution is a unified system, inspired and grounded in cognitive science, that facilitates rapid transfer learning of new environments using schemas via map-induction and composition that handles perceptual aliasing.

The arXiv has collected 1.5 million pre-print articles over 28 years, hosting literature from scientific fields including Physics, Mathematics, and Computer Science. Each pre-print features text, figures, authors, citations, categories, and other metadata. These rich, multi-modal features, combined with the natural graph structure---created by citation, affiliation, and co-authorship---makes the arXiv an exciting candidate for benchmarking next-generation models. Here we take the first necessary steps toward this goal, by providing a pipeline which standardizes and simplifies access to the arXiv's publicly available data. We use this pipeline to extract and analyze a 6.7 million edge citation graph, with an 11 billion word corpus of full-text research articles. We present some baseline classification results, and motivate application of more exciting generative graph models.

A legal knowledge graph constructed from court cases, judgments, laws and other legal documents can enable a number of applications like question answering, document similarity, and search. While the use of knowledge graphs for distant supervision in NLP tasks is well researched, using knowledge graphs for downstream graph tasks like node similarity presents challenges in selecting node types and their features. In this demo, we describe our solution for predicting similar nodes in a case graph derived from our legal knowledge graph.

Recently, there has been a surge of interest in employing neural networks for graph generation, a fundamental statistical learning problem with critical applications like molecule design and community analysis. However, most approaches encounter significant limitations when generating large-scale graphs. This is due to their requirement to output the full adjacency matrices whose size grows quadratically with the number of nodes. In response to this challenge, we introduce a new, simple, and scalable graph representation named gap encoded edge list (GEEL) that has a small representation size that aligns with the number of edges. In addition, GEEL significantly reduces the vocabulary size by incorporating the gap encoding and bandwidth restriction schemes. GEEL can be autoregressively generated with the incorporation of node positional encoding, and we further extend GEEL to deal with attributed graphs by designing a new grammar. Our findings reveal that the adoption of this compact representation not only enhances scalability but also bolsters performance by simplifying the graph generation process. We conduct a comprehensive evaluation across ten non-attributed and two molecular graph generation tasks, demonstrating the effectiveness of GEEL.

While in-context Learning (ICL) has proven to be an effective technique to improve the performance of Large Language Models (LLMs) in a variety of complex tasks, notably in translating natural language questions into Structured Query Language (NL2SQL), the question of how to select the most beneficial demonstration examples remains an open research problem. While prior works often adapted off-the-shelf encoders to retrieve examples dynamically, an inherent discrepancy exists in the representational capacities between the external retrievers and the LLMs. Further, optimizing the selection of examples is a non-trivial task, since there are no straightforward methods to assess the relative benefits of examples without performing pairwise inference. To address these shortcomings, we propose DeTriever, a novel demonstration retrieval framework that learns a weighted combination of LLM hidden states, where rich semantic information is encoded. To train the model, we propose a proxy score that estimates the relative benefits of examples based on the similarities between output queries. Experiments on two popular NL2SQL benchmarks demonstrate that our method significantly outperforms the state-of-the-art baselines on one-shot NL2SQL tasks.

In this paper, we conduct a comprehensive study of In-Context Learning (ICL) by addressing several open questions: (a) What type of ICL estimator is learned by large language models? (b) What is a proper performance metric for ICL and what is the error rate? (c) How does the transformer architecture enable ICL? To answer these questions, we adopt a Bayesian view and formulate ICL as a problem of predicting the response corresponding to the current covariate, given a number of examples drawn from a latent variable model. To answer (a), we show that, without updating the neural network parameters, ICL implicitly implements the Bayesian model averaging algorithm, which is proven to be approximately parameterized by the attention mechanism. For (b), we analyze the ICL performance from an online learning perspective and establish a O(1/T) regret bound for perfectly pretrained ICL, where T is the number of examples in the prompt. To answer (c), we show that, in addition to encoding Bayesian model averaging via attention, the transformer architecture also enables a fine-grained statistical analysis of pretraining under realistic assumptions. In particular, we prove that the error of pretrained model is bounded by a sum of an approximation error and a generalization error, where the former decays to zero exponentially as the depth grows, and the latter decays to zero sublinearly with the number of tokens in the pretraining dataset. Our results provide a unified understanding of the transformer and its ICL ability with bounds on ICL regret, approximation, and generalization, which deepens our knowledge of these essential aspects of modern language models.

In-context learning (ICL) is the ability of a model to learn a new task by observing a few exemplars in its context. While prevalent in NLP, this capability has recently also been observed in Reinforcement Learning (RL) settings. Prior in-context RL methods, however, require entire episodes in the agent's context. Given that complex environments typically lead to long episodes with sparse rewards, these methods are constrained to simple environments with short episodes. To address these challenges, we introduce Retrieval-Augmented Decision Transformer (RA-DT). RA-DT employs an external memory mechanism to store past experiences from which it retrieves only sub-trajectories relevant for the current situation. The retrieval component in RA-DT does not require training and can be entirely domain-agnostic. We evaluate the capabilities of RA-DT on grid-world environments, robotics simulations, and procedurally-generated video games. On grid-worlds, RA-DT outperforms baselines, while using only a fraction of their context length. Furthermore, we illuminate the limitations of current in-context RL methods on complex environments and discuss future directions. To facilitate future research, we release datasets for four of the considered environments.

In recent years, graphs have gained prominence across various domains, especially in recommendation systems. Within the realm of music recommendation, graphs play a crucial role in enhancing genre-based recommendations by integrating Mel-Frequency Cepstral Coefficients (MFCC) with advanced graph embeddings. This study explores the efficacy of Graph Convolutional Networks (GCN), GraphSAGE, and Graph Transformer (GT) models in learning embeddings that effectively capture intricate relationships between music items and genres represented within graph structures. Through comprehensive empirical evaluations on diverse real-world music datasets, our findings consistently demonstrate that these graph-based approaches outperform traditional methods that rely solely on MFCC features or collaborative filtering techniques. Specifically, the graph-enhanced models achieve notably higher accuracy in predicting genre-specific preferences and offering relevant music suggestions to users. These results underscore the effectiveness of utilizing graph embeddings to enrich feature representations and exploit latent associations within music data, thereby illustrating their potential to advance the capabilities of personalized and context-aware music recommendation systems. Keywords: graphs, recommendation systems, neural networks, MFCC

Large language models (LLMs) have had a huge impact on society due to their impressive capabilities and vast knowledge of the world. Various applications and tools have been created that allow users to interact with these models in a black-box scenario. However, one limitation of this scenario is that users cannot modify the internal knowledge of the model, and the only way to add or modify internal knowledge is by explicitly mentioning it to the model during the current interaction. This learning process is called in-context training, and it refers to training that is confined to the user's current session or context. In-context learning has significant applications, but also has limitations that are seldom studied. In this paper, we present a study that shows how the model can suffer from interference between information that continually flows in the context, causing it to forget previously learned knowledge, which can reduce the model's performance. Along with showing the problem, we propose an evaluation benchmark based on the bAbI dataset.

Graph Neural Networks (GNNs) have been extensively used for mining graph-structured data with impressive performance. However, because these traditional GNNs do not distinguish among various downstream tasks, embeddings embedded by them are not always effective. Intuitively, paths in a graph imply different semantics for different downstream tasks. Inspired by this, we design a novel GNN solution, namely Customized Graph Neural Network with Path Reweighting (CustomGNN for short). Specifically, the proposed CustomGNN can automatically learn the high-level semantics for specific downstream tasks to highlight semantically relevant paths as well to filter out task-irrelevant noises in a graph. Furthermore, we empirically analyze the semantics learned by CustomGNN and demonstrate its ability to avoid the three inherent problems in traditional GNNs, i.e., over-smoothing, poor robustness, and overfitting. In experiments with the node classification task, CustomGNN achieves state-of-the-art accuracies on three standard graph datasets and four large graph datasets. The source code of the proposed CustomGNN is available at https://github.com/cjpcool/CustomGNN.

We investigate novel random graph embeddings that can be computed in expected polynomial time and that are able to distinguish all non-isomorphic graphs in expectation. Previous graph embeddings have limited expressiveness and either cannot distinguish all graphs or cannot be computed efficiently for every graph. To be able to approximate arbitrary functions on graphs, we are interested in efficient alternatives that become arbitrarily expressive with increasing resources. Our approach is based on Lov\'asz' characterisation of graph isomorphism through an infinite dimensional vector of homomorphism counts. Our empirical evaluation shows competitive results on several benchmark graph learning tasks.