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Apr 1

Does your model understand genes? A benchmark of gene properties for biological and text models

The application of deep learning methods, particularly foundation models, in biological research has surged in recent years. These models can be text-based or trained on underlying biological data, especially omics data of various types. However, comparing the performance of these models consistently has proven to be a challenge due to differences in training data and downstream tasks. To tackle this problem, we developed an architecture-agnostic benchmarking approach that, instead of evaluating the models directly, leverages entity representation vectors from each model and trains simple predictive models for each benchmarking task. This ensures that all types of models are evaluated using the same input and output types. Here we focus on gene properties collected from professionally curated bioinformatics databases. These gene properties are categorized into five major groups: genomic properties, regulatory functions, localization, biological processes, and protein properties. Overall, we define hundreds of tasks based on these databases, which include binary, multi-label, and multi-class classification tasks. We apply these benchmark tasks to evaluate expression-based models, large language models, protein language models, DNA-based models, and traditional baselines. Our findings suggest that text-based models and protein language models generally outperform expression-based models in genomic properties and regulatory functions tasks, whereas expression-based models demonstrate superior performance in localization tasks. These results should aid in the development of more informed artificial intelligence strategies for biological understanding and therapeutic discovery. To ensure the reproducibility and transparency of our findings, we have made the source code and benchmark data publicly accessible for further investigation and expansion at github.com/BiomedSciAI/gene-benchmark.

  • 5 authors
·
Dec 5, 2024

Autoregressive Entity Retrieval

Entities are at the center of how we represent and aggregate knowledge. For instance, Encyclopedias such as Wikipedia are structured by entities (e.g., one per Wikipedia article). The ability to retrieve such entities given a query is fundamental for knowledge-intensive tasks such as entity linking and open-domain question answering. Current approaches can be understood as classifiers among atomic labels, one for each entity. Their weight vectors are dense entity representations produced by encoding entity meta information such as their descriptions. This approach has several shortcomings: (i) context and entity affinity is mainly captured through a vector dot product, potentially missing fine-grained interactions; (ii) a large memory footprint is needed to store dense representations when considering large entity sets; (iii) an appropriately hard set of negative data has to be subsampled at training time. In this work, we propose GENRE, the first system that retrieves entities by generating their unique names, left to right, token-by-token in an autoregressive fashion. This mitigates the aforementioned technical issues since: (i) the autoregressive formulation directly captures relations between context and entity name, effectively cross encoding both; (ii) the memory footprint is greatly reduced because the parameters of our encoder-decoder architecture scale with vocabulary size, not entity count; (iii) the softmax loss is computed without subsampling negative data. We experiment with more than 20 datasets on entity disambiguation, end-to-end entity linking and document retrieval tasks, achieving new state-of-the-art or very competitive results while using a tiny fraction of the memory footprint of competing systems. Finally, we demonstrate that new entities can be added by simply specifying their names. Code and pre-trained models at https://github.com/facebookresearch/GENRE.

  • 4 authors
·
Oct 2, 2020

Efficient and Interpretable Neural Models for Entity Tracking

What would it take for a natural language model to understand a novel, such as The Lord of the Rings? Among other things, such a model must be able to: (a) identify and record new characters (entities) and their attributes as they are introduced in the text, and (b) identify subsequent references to the characters previously introduced and update their attributes. This problem of entity tracking is essential for language understanding, and thus, useful for a wide array of downstream applications in NLP such as question-answering, summarization. In this thesis, we focus on two key problems in relation to facilitating the use of entity tracking models: (i) scaling entity tracking models to long documents, such as a novel, and (ii) integrating entity tracking into language models. Applying language technologies to long documents has garnered interest recently, but computational constraints are a significant bottleneck in scaling up current methods. In this thesis, we argue that computationally efficient entity tracking models can be developed by representing entities with rich, fixed-dimensional vector representations derived from pretrained language models, and by exploiting the ephemeral nature of entities. We also argue for the integration of entity tracking into language models as it will allow for: (i) wider application given the current ubiquitous use of pretrained language models in NLP applications, and (ii) easier adoption since it is much easier to swap in a new pretrained language model than to integrate a separate standalone entity tracking model.

  • 1 authors
·
Aug 30, 2022

NERetrieve: Dataset for Next Generation Named Entity Recognition and Retrieval

Recognizing entities in texts is a central need in many information-seeking scenarios, and indeed, Named Entity Recognition (NER) is arguably one of the most successful examples of a widely adopted NLP task and corresponding NLP technology. Recent advances in large language models (LLMs) appear to provide effective solutions (also) for NER tasks that were traditionally handled with dedicated models, often matching or surpassing the abilities of the dedicated models. Should NER be considered a solved problem? We argue to the contrary: the capabilities provided by LLMs are not the end of NER research, but rather an exciting beginning. They allow taking NER to the next level, tackling increasingly more useful, and increasingly more challenging, variants. We present three variants of the NER task, together with a dataset to support them. The first is a move towards more fine-grained -- and intersectional -- entity types. The second is a move towards zero-shot recognition and extraction of these fine-grained types based on entity-type labels. The third, and most challenging, is the move from the recognition setup to a novel retrieval setup, where the query is a zero-shot entity type, and the expected result is all the sentences from a large, pre-indexed corpus that contain entities of these types, and their corresponding spans. We show that all of these are far from being solved. We provide a large, silver-annotated corpus of 4 million paragraphs covering 500 entity types, to facilitate research towards all of these three goals.

  • 4 authors
·
Oct 22, 2023 6

Inductive Entity Representations from Text via Link Prediction

Knowledge Graphs (KG) are of vital importance for multiple applications on the web, including information retrieval, recommender systems, and metadata annotation. Regardless of whether they are built manually by domain experts or with automatic pipelines, KGs are often incomplete. Recent work has begun to explore the use of textual descriptions available in knowledge graphs to learn vector representations of entities in order to preform link prediction. However, the extent to which these representations learned for link prediction generalize to other tasks is unclear. This is important given the cost of learning such representations. Ideally, we would prefer representations that do not need to be trained again when transferring to a different task, while retaining reasonable performance. In this work, we propose a holistic evaluation protocol for entity representations learned via a link prediction objective. We consider the inductive link prediction and entity classification tasks, which involve entities not seen during training. We also consider an information retrieval task for entity-oriented search. We evaluate an architecture based on a pretrained language model, that exhibits strong generalization to entities not observed during training, and outperforms related state-of-the-art methods (22% MRR improvement in link prediction on average). We further provide evidence that the learned representations transfer well to other tasks without fine-tuning. In the entity classification task we obtain an average improvement of 16% in accuracy compared with baselines that also employ pre-trained models. In the information retrieval task, we obtain significant improvements of up to 8.8% in NDCG@10 for natural language queries. We thus show that the learned representations are not limited KG-specific tasks, and have greater generalization properties than evaluated in previous work.

  • 3 authors
·
Oct 7, 2020

High-Throughput Vector Similarity Search in Knowledge Graphs

There is an increasing adoption of machine learning for encoding data into vectors to serve online recommendation and search use cases. As a result, recent data management systems propose augmenting query processing with online vector similarity search. In this work, we explore vector similarity search in the context of Knowledge Graphs (KGs). Motivated by the tasks of finding related KG queries and entities for past KG query workloads, we focus on hybrid vector similarity search (hybrid queries for short) where part of the query corresponds to vector similarity search and part of the query corresponds to predicates over relational attributes associated with the underlying data vectors. For example, given past KG queries for a song entity, we want to construct new queries for new song entities whose vector representations are close to the vector representation of the entity in the past KG query. But entities in a KG also have non-vector attributes such as a song associated with an artist, a genre, and a release date. Therefore, suggested entities must also satisfy query predicates over non-vector attributes beyond a vector-based similarity predicate. While these tasks are central to KGs, our contributions are generally applicable to hybrid queries. In contrast to prior works that optimize online queries, we focus on enabling efficient batch processing of past hybrid query workloads. We present our system, HQI, for high-throughput batch processing of hybrid queries. We introduce a workload-aware vector data partitioning scheme to tailor the vector index layout to the given workload and describe a multi-query optimization technique to reduce the overhead of vector similarity computations. We evaluate our methods on industrial workloads and demonstrate that HQI yields a 31x improvement in throughput for finding related KG queries compared to existing hybrid query processing approaches.

  • 8 authors
·
Apr 4, 2023

ReLiK: Retrieve and LinK, Fast and Accurate Entity Linking and Relation Extraction on an Academic Budget

Entity Linking (EL) and Relation Extraction (RE) are fundamental tasks in Natural Language Processing, serving as critical components in a wide range of applications. In this paper, we propose ReLiK, a Retriever-Reader architecture for both EL and RE, where, given an input text, the Retriever module undertakes the identification of candidate entities or relations that could potentially appear within the text. Subsequently, the Reader module is tasked to discern the pertinent retrieved entities or relations and establish their alignment with the corresponding textual spans. Notably, we put forward an innovative input representation that incorporates the candidate entities or relations alongside the text, making it possible to link entities or extract relations in a single forward pass and to fully leverage pre-trained language models contextualization capabilities, in contrast with previous Retriever-Reader-based methods, which require a forward pass for each candidate. Our formulation of EL and RE achieves state-of-the-art performance in both in-domain and out-of-domain benchmarks while using academic budget training and with up to 40x inference speed compared to competitors. Finally, we show how our architecture can be used seamlessly for Information Extraction (cIE), i.e. EL + RE, and setting a new state of the art by employing a shared Reader that simultaneously extracts entities and relations.

  • 4 authors
·
Jul 31, 2024 2

Vector representations of text data in deep learning

In this dissertation we report results of our research on dense distributed representations of text data. We propose two novel neural models for learning such representations. The first model learns representations at the document level, while the second model learns word-level representations. For document-level representations we propose Binary Paragraph Vector: a neural network models for learning binary representations of text documents, which can be used for fast document retrieval. We provide a thorough evaluation of these models and demonstrate that they outperform the seminal method in the field in the information retrieval task. We also report strong results in transfer learning settings, where our models are trained on a generic text corpus and then used to infer codes for documents from a domain-specific dataset. In contrast to previously proposed approaches, Binary Paragraph Vector models learn embeddings directly from raw text data. For word-level representations we propose Disambiguated Skip-gram: a neural network model for learning multi-sense word embeddings. Representations learned by this model can be used in downstream tasks, like part-of-speech tagging or identification of semantic relations. In the word sense induction task Disambiguated Skip-gram outperforms state-of-the-art models on three out of four benchmarks datasets. Our model has an elegant probabilistic interpretation. Furthermore, unlike previous models of this kind, it is differentiable with respect to all its parameters and can be trained with backpropagation. In addition to quantitative results, we present qualitative evaluation of Disambiguated Skip-gram, including two-dimensional visualisations of selected word-sense embeddings.

  • 1 authors
·
Jan 7, 2019

On the Theoretical Limitations of Embedding-Based Retrieval

Vector embeddings have been tasked with an ever-increasing set of retrieval tasks over the years, with a nascent rise in using them for reasoning, instruction-following, coding, and more. These new benchmarks push embeddings to work for any query and any notion of relevance that could be given. While prior works have pointed out theoretical limitations of vector embeddings, there is a common assumption that these difficulties are exclusively due to unrealistic queries, and those that are not can be overcome with better training data and larger models. In this work, we demonstrate that we may encounter these theoretical limitations in realistic settings with extremely simple queries. We connect known results in learning theory, showing that the number of top-k subsets of documents capable of being returned as the result of some query is limited by the dimension of the embedding. We empirically show that this holds true even if we restrict to k=2, and directly optimize on the test set with free parameterized embeddings. We then create a realistic dataset called LIMIT that stress tests models based on these theoretical results, and observe that even state-of-the-art models fail on this dataset despite the simple nature of the task. Our work shows the limits of embedding models under the existing single vector paradigm and calls for future research to develop methods that can resolve this fundamental limitation.

  • 4 authors
·
Aug 28, 2025 3

Fine-Grained Entity Typing for Domain Independent Entity Linking

Neural entity linking models are very powerful, but run the risk of overfitting to the domain they are trained in. For this problem, a domain is characterized not just by genre of text but even by factors as specific as the particular distribution of entities, as neural models tend to overfit by memorizing properties of frequent entities in a dataset. We tackle the problem of building robust entity linking models that generalize effectively and do not rely on labeled entity linking data with a specific entity distribution. Rather than predicting entities directly, our approach models fine-grained entity properties, which can help disambiguate between even closely related entities. We derive a large inventory of types (tens of thousands) from Wikipedia categories, and use hyperlinked mentions in Wikipedia to distantly label data and train an entity typing model. At test time, we classify a mention with this typing model and use soft type predictions to link the mention to the most similar candidate entity. We evaluate our entity linking system on the CoNLL-YAGO dataset (Hoffart et al., 2011) and show that our approach outperforms prior domain-independent entity linking systems. We also test our approach in a harder setting derived from the WikilinksNED dataset (Eshel et al., 2017) where all the mention-entity pairs are unseen during test time. Results indicate that our approach generalizes better than a state-of-the-art neural model on the dataset.

  • 2 authors
·
Sep 12, 2019

Unsupervised Matching of Data and Text

Entity resolution is a widely studied problem with several proposals to match records across relations. Matching textual content is a widespread task in many applications, such as question answering and search. While recent methods achieve promising results for these two tasks, there is no clear solution for the more general problem of matching textual content and structured data. We introduce a framework that supports this new task in an unsupervised setting for any pair of corpora, being relational tables or text documents. Our method builds a fine-grained graph over the content of the corpora and derives word embeddings to represent the objects to match in a low dimensional space. The learned representation enables effective and efficient matching at different granularity, from relational tuples to text sentences and paragraphs. Our flexible framework can exploit pre-trained resources, but it does not depends on their existence and achieves better quality performance in matching content when the vocabulary is domain specific. We also introduce optimizations in the graph creation process with an "expand and compress" approach that first identifies new valid relationships across elements, to improve matching, and then prunes nodes and edges, to reduce the graph size. Experiments on real use cases and public datasets show that our framework produces embeddings that outperform word embeddings and fine-tuned language models both in results' quality and in execution times.

  • 3 authors
·
Dec 16, 2021

Fine-grained Contract NER using instruction based model

Lately, instruction-based techniques have made significant strides in improving performance in few-shot learning scenarios. They achieve this by bridging the gap between pre-trained language models and fine-tuning for specific downstream tasks. Despite these advancements, the performance of Large Language Models (LLMs) in information extraction tasks like Named Entity Recognition (NER), using prompts or instructions, still falls short of supervised baselines. The reason for this performance gap can be attributed to the fundamental disparity between NER and LLMs. NER is inherently a sequence labeling task, where the model must assign entity-type labels to individual tokens within a sentence. In contrast, LLMs are designed as a text generation task. This distinction between semantic labeling and text generation leads to subpar performance. In this paper, we transform the NER task into a text-generation task that can be readily adapted by LLMs. This involves enhancing source sentences with task-specific instructions and answer choices, allowing for the identification of entities and their types within natural language. We harness the strength of LLMs by integrating supervised learning within them. The goal of this combined strategy is to boost the performance of LLMs in extraction tasks like NER while simultaneously addressing hallucination issues often observed in LLM-generated content. A novel corpus Contract NER comprising seven frequently observed contract categories, encompassing named entities associated with 18 distinct legal entity types is released along with our baseline models. Our models and dataset are available to the community for future research * .

  • 3 authors
·
Jan 24, 2024

Knowledge-Rich Self-Supervision for Biomedical Entity Linking

Entity linking faces significant challenges such as prolific variations and prevalent ambiguities, especially in high-value domains with myriad entities. Standard classification approaches suffer from the annotation bottleneck and cannot effectively handle unseen entities. Zero-shot entity linking has emerged as a promising direction for generalizing to new entities, but it still requires example gold entity mentions during training and canonical descriptions for all entities, both of which are rarely available outside of Wikipedia. In this paper, we explore Knowledge-RIch Self-Supervision (tt KRISS) for biomedical entity linking, by leveraging readily available domain knowledge. In training, it generates self-supervised mention examples on unlabeled text using a domain ontology and trains a contextual encoder using contrastive learning. For inference, it samples self-supervised mentions as prototypes for each entity and conducts linking by mapping the test mention to the most similar prototype. Our approach can easily incorporate entity descriptions and gold mention labels if available. We conducted extensive experiments on seven standard datasets spanning biomedical literature and clinical notes. Without using any labeled information, our method produces tt KRISSBERT, a universal entity linker for four million UMLS entities that attains new state of the art, outperforming prior self-supervised methods by as much as 20 absolute points in accuracy.

  • 9 authors
·
Dec 15, 2021

VecCity: A Taxonomy-guided Library for Map Entity Representation Learning

Electronic maps consist of diverse entities, such as points of interest (POIs), road networks, and land parcels, playing a vital role in applications like ITS and LBS. Map entity representation learning (MapRL) generates versatile and reusable data representations, providing essential tools for efficiently managing and utilizing map entity data. Despite the progress in MapRL, two key challenges constrain further development. First, existing research is fragmented, with models classified by the type of map entity, limiting the reusability of techniques across different tasks. Second, the lack of unified benchmarks makes systematic evaluation and comparison of models difficult. To address these challenges, we propose a novel taxonomy for MapRL that organizes models based on functional module-such as encoders, pre-training tasks, and downstream tasks-rather than by entity type. Building on this taxonomy, we present a taxonomy-driven library, VecCity, which offers easy-to-use interfaces for encoding, pre-training, fine-tuning, and evaluation. The library integrates datasets from nine cities and reproduces 21 mainstream MapRL models, establishing the first standardized benchmarks for the field. VecCity also allows users to modify and extend models through modular components, facilitating seamless experimentation. Our comprehensive experiments cover multiple types of map entities and evaluate 21 VecCity pre-built models across various downstream tasks. Experimental results demonstrate the effectiveness of VecCity in streamlining model development and provide insights into the impact of various components on performance. By promoting modular design and reusability, VecCity offers a unified framework to advance research and innovation in MapRL. The code is available at https://github.com/Bigscity-VecCity/VecCity.

  • 4 authors
·
Oct 31, 2024

Dense Text Retrieval based on Pretrained Language Models: A Survey

Text retrieval is a long-standing research topic on information seeking, where a system is required to return relevant information resources to user's queries in natural language. From classic retrieval methods to learning-based ranking functions, the underlying retrieval models have been continually evolved with the ever-lasting technical innovation. To design effective retrieval models, a key point lies in how to learn the text representation and model the relevance matching. The recent success of pretrained language models (PLMs) sheds light on developing more capable text retrieval approaches by leveraging the excellent modeling capacity of PLMs. With powerful PLMs, we can effectively learn the representations of queries and texts in the latent representation space, and further construct the semantic matching function between the dense vectors for relevance modeling. Such a retrieval approach is referred to as dense retrieval, since it employs dense vectors (a.k.a., embeddings) to represent the texts. Considering the rapid progress on dense retrieval, in this survey, we systematically review the recent advances on PLM-based dense retrieval. Different from previous surveys on dense retrieval, we take a new perspective to organize the related work by four major aspects, including architecture, training, indexing and integration, and summarize the mainstream techniques for each aspect. We thoroughly survey the literature, and include 300+ related reference papers on dense retrieval. To support our survey, we create a website for providing useful resources, and release a code repertory and toolkit for implementing dense retrieval models. This survey aims to provide a comprehensive, practical reference focused on the major progress for dense text retrieval.

  • 4 authors
·
Nov 27, 2022

From Word Vectors to Multimodal Embeddings: Techniques, Applications, and Future Directions For Large Language Models

Word embeddings and language models have transformed natural language processing (NLP) by facilitating the representation of linguistic elements in continuous vector spaces. This review visits foundational concepts such as the distributional hypothesis and contextual similarity, tracing the evolution from sparse representations like one-hot encoding to dense embeddings including Word2Vec, GloVe, and fastText. We examine both static and contextualized embeddings, underscoring advancements in models such as ELMo, BERT, and GPT and their adaptations for cross-lingual and personalized applications. The discussion extends to sentence and document embeddings, covering aggregation methods and generative topic models, along with the application of embeddings in multimodal domains, including vision, robotics, and cognitive science. Advanced topics such as model compression, interpretability, numerical encoding, and bias mitigation are analyzed, addressing both technical challenges and ethical implications. Additionally, we identify future research directions, emphasizing the need for scalable training techniques, enhanced interpretability, and robust grounding in non-textual modalities. By synthesizing current methodologies and emerging trends, this survey offers researchers and practitioners an in-depth resource to push the boundaries of embedding-based language models.

  • 15 authors
·
Nov 6, 2024

AMELI: Enhancing Multimodal Entity Linking with Fine-Grained Attributes

We propose attribute-aware multimodal entity linking, where the input consists of a mention described with a text paragraph and images, and the goal is to predict the corresponding target entity from a multimodal knowledge base (KB) where each entity is also accompanied by a text description, visual images, and a collection of attributes that present the meta-information of the entity in a structured format. To facilitate this research endeavor, we construct AMELI, encompassing a new multimodal entity linking benchmark dataset that contains 16,735 mentions described in text and associated with 30,472 images, and a multimodal knowledge base that covers 34,690 entities along with 177,873 entity images and 798,216 attributes. To establish baseline performance on AMELI, we experiment with several state-of-the-art architectures for multimodal entity linking and further propose a new approach that incorporates attributes of entities into disambiguation. Experimental results and extensive qualitative analysis demonstrate that extracting and understanding the attributes of mentions from their text descriptions and visual images play a vital role in multimodal entity linking. To the best of our knowledge, we are the first to integrate attributes in the multimodal entity linking task. The programs, model checkpoints, and the dataset are publicly available at https://github.com/VT-NLP/Ameli.

  • 8 authors
·
May 24, 2023

Contrastive Learning and Mixture of Experts Enables Precise Vector Embeddings

The advancement of transformer neural networks has significantly elevated the capabilities of sentence similarity models, particularly in creating effective vector representations of natural language inputs. However, these models face notable challenges in domain-specific contexts, especially in highly specialized scientific sub-fields. Traditional methods often struggle in this regime, either overgeneralizing similarities within a niche or being overly sensitive to minor differences, resulting in inaccurate text classification and subpar vector representation. In an era where retrieval augmentation and search are increasingly crucial, precise and concise numerical representations are essential. In this paper, we target this issue by assembling niche datasets using co-citations as a similarity metric, focusing on biomedical domains. We employ two key strategies for fine-tuning state-of-the-art models: 1. Domain-specific Fine-Tuning, which tailors pretrained models to a single domain, and 2. Universal Applicability with Mixture of Experts (MoE), adapting pretrained models with enforced routing for multiple domains simultaneously. Our training approach emphasizes the use of abstracts for faster training, incorporating Multiple Negative Rankings loss for efficient contrastive learning. Notably, our MoE variants, equipped with N experts, achieve the efficacy of N individual models, heralding a new era of versatile, One-Size-Fits-All transformer networks for various tasks. This methodology marks significant advancements in scientific text classification metrics and holds promise for enhancing vector database search and compilation.

  • 4 authors
·
Jan 28, 2024

Calibrated Seq2seq Models for Efficient and Generalizable Ultra-fine Entity Typing

Ultra-fine entity typing plays a crucial role in information extraction by predicting fine-grained semantic types for entity mentions in text. However, this task poses significant challenges due to the massive number of entity types in the output space. The current state-of-the-art approaches, based on standard multi-label classifiers or cross-encoder models, suffer from poor generalization performance or inefficient inference. In this paper, we present CASENT, a seq2seq model designed for ultra-fine entity typing that predicts ultra-fine types with calibrated confidence scores. Our model takes an entity mention as input and employs constrained beam search to generate multiple types autoregressively. The raw sequence probabilities associated with the predicted types are then transformed into confidence scores using a novel calibration method. We conduct extensive experiments on the UFET dataset which contains over 10k types. Our method outperforms the previous state-of-the-art in terms of F1 score and calibration error, while achieving an inference speedup of over 50 times. Additionally, we demonstrate the generalization capabilities of our model by evaluating it in zero-shot and few-shot settings on five specialized domain entity typing datasets that are unseen during training. Remarkably, our model outperforms large language models with 10 times more parameters in the zero-shot setting, and when fine-tuned on 50 examples, it significantly outperforms ChatGPT on all datasets. Our code, models and demo are available at https://github.com/yanlinf/CASENT.

  • 3 authors
·
Nov 1, 2023

MOFI: Learning Image Representations from Noisy Entity Annotated Images

We present MOFI, Manifold OF Images, a new vision foundation model designed to learn image representations from noisy entity annotated images. MOFI differs from previous work in two key aspects: (i) pre-training data, and (ii) training recipe. Regarding data, we introduce a new approach to automatically assign entity labels to images from noisy image-text pairs. Our approach involves employing a named entity recognition model to extract entities from the alt-text, and then using a CLIP model to select the correct entities as labels of the paired image. It's a simple, cost-effective method that can scale to handle billions of web-mined image-text pairs. Through this method, we have created Image-to-Entities (I2E), a new dataset with 1 billion images and 2 million distinct entities, covering rich visual concepts in the wild. Building upon the I2E dataset, we study different training recipes like supervised pre-training, contrastive pre-training, and multi-task learning. For contrastive pre-training, we treat entity names as free-form text, and further enrich them with entity descriptions. Experiments show that supervised pre-training with large-scale fine-grained entity labels is highly effective for image retrieval tasks, and multi-task training further improves the performance. The final MOFI model achieves 86.66% mAP on the challenging GPR1200 dataset, surpassing the previous state-of-the-art performance of 72.19% from OpenAI's CLIP model. Further experiments on zero-shot and linear probe image classification also show that MOFI outperforms a CLIP model trained on the original image-text data, demonstrating the effectiveness of the I2E dataset in learning strong image representations. We release our code and model weights at https://github.com/apple/ml-mofi.

  • 11 authors
·
Jun 13, 2023

Reverse Region-to-Entity Annotation for Pixel-Level Visual Entity Linking

Visual Entity Linking (VEL) is a crucial task for achieving fine-grained visual understanding, matching objects within images (visual mentions) to entities in a knowledge base. Previous VEL tasks rely on textual inputs, but writing queries for complex scenes can be challenging. Visual inputs like clicks or bounding boxes offer a more convenient alternative. Therefore, we propose a new task, Pixel-Level Visual Entity Linking (PL-VEL), which uses pixel masks from visual inputs to refer to objects, supplementing reference methods for VEL. To facilitate research on this task, we have constructed the MaskOVEN-Wiki dataset through an entirely automatic reverse region-entity annotation framework. This dataset contains over 5 million annotations aligning pixel-level regions with entity-level labels, which will advance visual understanding towards fine-grained. Moreover, as pixel masks correspond to semantic regions in an image, we enhance previous patch-interacted attention with region-interacted attention by a visual semantic tokenization approach. Manual evaluation results indicate that the reverse annotation framework achieved a 94.8% annotation success rate. Experimental results show that models trained on this dataset improved accuracy by 18 points compared to zero-shot models. Additionally, the semantic tokenization method achieved a 5-point accuracy improvement over the trained baseline.

  • 9 authors
·
Dec 18, 2024

MUVERA: Multi-Vector Retrieval via Fixed Dimensional Encodings

Neural embedding models have become a fundamental component of modern information retrieval (IR) pipelines. These models produce a single embedding x in R^d per data-point, allowing for fast retrieval via highly optimized maximum inner product search (MIPS) algorithms. Recently, beginning with the landmark ColBERT paper, multi-vector models, which produce a set of embedding per data point, have achieved markedly superior performance for IR tasks. Unfortunately, using these models for IR is computationally expensive due to the increased complexity of multi-vector retrieval and scoring. In this paper, we introduce MUVERA (MUlti-VEctor Retrieval Algorithm), a retrieval mechanism which reduces multi-vector similarity search to single-vector similarity search. This enables the usage of off-the-shelf MIPS solvers for multi-vector retrieval. MUVERA asymmetrically generates Fixed Dimensional Encodings (FDEs) of queries and documents, which are vectors whose inner product approximates multi-vector similarity. We prove that FDEs give high-quality epsilon-approximations, thus providing the first single-vector proxy for multi-vector similarity with theoretical guarantees. Empirically, we find that FDEs achieve the same recall as prior state-of-the-art heuristics while retrieving 2-5times fewer candidates. Compared to prior state of the art implementations, MUVERA achieves consistently good end-to-end recall and latency across a diverse set of the BEIR retrieval datasets, achieving an average of 10% improved recall with 90% lower latency.

  • 5 authors
·
May 29, 2024

On the Robustness of Document-Level Relation Extraction Models to Entity Name Variations

Driven by the demand for cross-sentence and large-scale relation extraction, document-level relation extraction (DocRE) has attracted increasing research interest. Despite the continuous improvement in performance, we find that existing DocRE models which initially perform well may make more mistakes when merely changing the entity names in the document, hindering the generalization to novel entity names. To this end, we systematically investigate the robustness of DocRE models to entity name variations in this work. We first propose a principled pipeline to generate entity-renamed documents by replacing the original entity names with names from Wikidata. By applying the pipeline to DocRED and Re-DocRED datasets, we construct two novel benchmarks named Env-DocRED and Env-Re-DocRED for robustness evaluation. Experimental results show that both three representative DocRE models and two in-context learned large language models consistently lack sufficient robustness to entity name variations, particularly on cross-sentence relation instances and documents with more entities. Finally, we propose an entity variation robust training method which not only improves the robustness of DocRE models but also enhances their understanding and reasoning capabilities. We further verify that the basic idea of this method can be effectively transferred to in-context learning for DocRE as well.

  • 7 authors
·
Jun 11, 2024

Computer Science Named Entity Recognition in the Open Research Knowledge Graph

Domain-specific named entity recognition (NER) on Computer Science (CS) scholarly articles is an information extraction task that is arguably more challenging for the various annotation aims that can beset the task and has been less studied than NER in the general domain. Given that significant progress has been made on NER, we believe that scholarly domain-specific NER will receive increasing attention in the years to come. Currently, progress on CS NER -- the focus of this work -- is hampered in part by its recency and the lack of a standardized annotation aim for scientific entities/terms. This work proposes a standardized task by defining a set of seven contribution-centric scholarly entities for CS NER viz., research problem, solution, resource, language, tool, method, and dataset. Following which, its main contributions are: combines existing CS NER resources that maintain their annotation focus on the set or subset of contribution-centric scholarly entities we consider; further, noting the need for big data to train neural NER models, this work additionally supplies thousands of contribution-centric entity annotations from article titles and abstracts, thus releasing a cumulative large novel resource for CS NER; and, finally, trains a sequence labeling CS NER model inspired after state-of-the-art neural architectures from the general domain NER task. Throughout the work, several practical considerations are made which can be useful to information technology designers of the digital libraries.

  • 2 authors
·
Mar 28, 2022

DOM-LM: Learning Generalizable Representations for HTML Documents

HTML documents are an important medium for disseminating information on the Web for human consumption. An HTML document presents information in multiple text formats including unstructured text, structured key-value pairs, and tables. Effective representation of these documents is essential for machine understanding to enable a wide range of applications, such as Question Answering, Web Search, and Personalization. Existing work has either represented these documents using visual features extracted by rendering them in a browser, which is typically computationally expensive, or has simply treated them as plain text documents, thereby failing to capture useful information presented in their HTML structure. We argue that the text and HTML structure together convey important semantics of the content and therefore warrant a special treatment for their representation learning. In this paper, we introduce a novel representation learning approach for web pages, dubbed DOM-LM, which addresses the limitations of existing approaches by encoding both text and DOM tree structure with a transformer-based encoder and learning generalizable representations for HTML documents via self-supervised pre-training. We evaluate DOM-LM on a variety of webpage understanding tasks, including Attribute Extraction, Open Information Extraction, and Question Answering. Our extensive experiments show that DOM-LM consistently outperforms all baselines designed for these tasks. In particular, DOM-LM demonstrates better generalization performance both in few-shot and zero-shot settings, making it attractive for making it suitable for real-world application settings with limited labeled data.

  • 5 authors
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Jan 25, 2022