Daily Papers

Hallucinations, outputs that sound plausible but are factually incorrect, remain an open challenge for deployed LLMs. In code generation, models frequently hallucinate non-existent software packages, recommending imports and installation commands for fictional libraries. This creates a critical supply-chain vulnerability: an attacker can proactively register such packages on public registries with malicious payloads that are subsequently installed and executed by developers or autonomous agents, a class of package confusion attack known as slopsquatting. Once a model is deployed, mitigating this failure mode is difficult: full retraining is costly, and existing approaches either cause severe degradation of model utility or rely on a pre-specified forget-set, an assumption that does not apply to the unbounded space of hallucinations. To address this problem, we present Adaptive Unlearning (AU), a post-deployment framework that surgically suppresses hallucinations while preserving general model utility. AU introduces a hybrid token-level objective that simultaneously reinforces valid outputs and suppresses hallucinated ones. Combined with an adaptive discovery loop that continuously surfaces new hallucination-inducing contexts without human supervision, AU enables generalization to unseen prompts and hallucinations. We demonstrate that AU reduces package hallucination rates by 81%, corresponding to a substantial reduction in slopsquatting attack surface, while maintaining performance on standard coding benchmarks. Our analysis shows that distributional changes are concentrated on package-related generations, leaving general coding behavior largely unaffected and confirming that AU's effect is isolated to the targeted distribution. AU operates entirely on model-generated data, requires no human annotation, and generalizes across domains.

Language models are increasingly used in scientific discovery to generate hypotheses, propose candidate solutions, implement systems, and iteratively refine them. At the core of these trial-and-error loops lies evaluation: the process of obtaining feedback on candidate solutions via verifiers, simulators, or task-specific scoring functions. While prior work has highlighted the importance of evaluation, it has not explicitly formulated the problem of how evaluation-driven discovery loops can be scaled up in a principled and effective manner to push the boundaries of scientific discovery, a problem this paper seeks to address. We introduce Simple Test-time Evaluation-driven Scaling (SimpleTES), a general framework that strategically combines parallel exploration, feedback-driven refinement, and local selection, revealing substantial gains unlocked by scaling evaluation-driven discovery loops along the right dimensions. Across 21 scientific problems spanning six domains, SimpleTES discovers state-of-the-art solutions using gpt-oss models, consistently outperforming both frontier-model baselines and sophisticated optimization pipelines. Particularly, we sped up the widely used LASSO algorithm by over 2x, designed quantum circuit routing policies that reduce gate overhead by 24.5%, and discovered new Erdos minimum overlap constructions that surpass the best-known results. Beyond novel discoveries, SimpleTES produces trajectory-level histories that naturally supervise feedback-driven learning. When post-trained on successful trajectories, models not only improve efficiency on seen problems but also generalize to unseen problems, discovering solutions that base models fail to uncover. Together, our results establish effective evaluation-driven loop scaling as a central axis for advancing LLM-driven scientific discovery, and provide a simple yet practical framework for realizing these gains.

Traditional scientific discovery relies on an iterative hypothesise-experiment-refine cycle that has driven progress for centuries, but its intuitive, ad-hoc implementation often wastes resources, yields inefficient designs, and misses critical insights. This tutorial presents Bayesian Optimisation (BO), a principled probability-driven framework that formalises and automates this core scientific cycle. BO uses surrogate models (e.g., Gaussian processes) to model empirical observations as evolving hypotheses, and acquisition functions to guide experiment selection, balancing exploitation of known knowledge and exploration of uncharted domains to eliminate guesswork and manual trial-and-error. We first frame scientific discovery as an optimisation problem, then unpack BO's core components, end-to-end workflows, and real-world efficacy via case studies in catalysis, materials science, organic synthesis, and molecule discovery. We also cover critical technical extensions for scientific applications, including batched experimentation, heteroscedasticity, contextual optimisation, and human-in-the-loop integration. Tailored for a broad audience, this tutorial bridges AI advances in BO with practical natural science applications, offering tiered content to empower cross-disciplinary researchers to design more efficient experiments and accelerate principled scientific discovery.

Discovering causal regularities and applying them to build functional systems--the discovery-to-application loop--is a hallmark of general intelligence, yet evaluating this capacity has been hindered by the vast complexity gap between scientific discovery and real-world engineering. We introduce SciCrafter, a Minecraft-based benchmark that operationalizes this loop through parameterized redstone circuit tasks. Agents must ignite lamps in specified patterns (e.g., simultaneously or in timed sequences); scaling target parameters substantially increases construction complexity and required knowledge, forcing genuine discovery rather than reliance on memorized solutions. Evaluating frontier models including GPT-5.2, Gemini-3-Pro, and Claude-Opus-4.5 under a general-purpose code agent scaffold, we find that all plateau at approximately 26% success rate. To diagnose these failures, we decompose the loop into four capacities--knowledge gap identification, experimental discovery, knowledge consolidation, and knowledge application--and design targeted interventions whose marginal contributions serve as proxies for corresponding gaps. Our analysis reveals that although the general knowledge application capability still remains as the biggest gap across all models, for frontier models the knowledge gap identification starts to become a major hurdle--indicating the bottleneck is shifting from solving problems right to raising the right problems for current AI. We release SciCrafter as a diagnostic probe for future research on AI systems that navigate the full discovery-to-application loop.

The cycle of scientific discovery is frequently bottlenecked by the slow, manual creation of software to support computational experiments. To address this, we present an AI system that creates expert-level scientific software whose goal is to maximize a quality metric. The system uses a Large Language Model (LLM) and Tree Search (TS) to systematically improve the quality metric and intelligently navigate the large space of possible solutions. The system achieves expert-level results when it explores and integrates complex research ideas from external sources. The effectiveness of tree search is demonstrated across a wide range of benchmarks. In bioinformatics, it discovered 40 novel methods for single-cell data analysis that outperformed the top human-developed methods on a public leaderboard. In epidemiology, it generated 14 models that outperformed the CDC ensemble and all other individual models for forecasting COVID-19 hospitalizations. Our method also produced state-of-the-art software for geospatial analysis, neural activity prediction in zebrafish, time series forecasting and numerical solution of integrals. By devising and implementing novel solutions to diverse tasks, the system represents a significant step towards accelerating scientific progress.

This work proposes a procedure for designing algorithms for specific adaptive data collection tasks like active learning and pure-exploration multi-armed bandits. Unlike the design of traditional adaptive algorithms that rely on concentration of measure and careful analysis to justify the correctness and sample complexity of the procedure, our adaptive algorithm is learned via adversarial training over equivalence classes of problems derived from information theoretic lower bounds. In particular, a single adaptive learning algorithm is learned that competes with the best adaptive algorithm learned for each equivalence class. Our procedure takes as input just the available queries, set of hypotheses, loss function, and total query budget. This is in contrast to existing meta-learning work that learns an adaptive algorithm relative to an explicit, user-defined subset or prior distribution over problems which can be challenging to define and be mismatched to the instance encountered at test time. This work is particularly focused on the regime when the total query budget is very small, such as a few dozen, which is much smaller than those budgets typically considered by theoretically derived algorithms. We perform synthetic experiments to justify the stability and effectiveness of the training procedure, and then evaluate the method on tasks derived from real data including a noisy 20 Questions game and a joke recommendation task.

We introduce ShinkaEvolve: a new open-source framework leveraging large language models (LLMs) to advance scientific discovery with state-of-the-art performance and unprecedented efficiency. Recent advances in scaling inference time compute of LLMs have enabled significant progress in generalized scientific discovery. These approaches rely on evolutionary agentic harnesses that leverage LLMs as mutation operators to generate candidate solutions. However, current code evolution methods suffer from critical limitations: they are sample inefficient, requiring thousands of samples to identify effective solutions, and remain closed-source, hindering broad adoption and extension. ShinkaEvolve addresses these limitations, introducing three key innovations: a parent sampling technique balancing exploration and exploitation, code novelty rejection-sampling for efficient search space exploration, and a bandit-based LLM ensemble selection strategy. We evaluate ShinkaEvolve across diverse tasks, demonstrating consistent improvements in sample efficiency and solution quality. ShinkaEvolve discovers a new state-of-the-art circle packing solution using only 150 samples, designs high-performing agentic harnesses for AIME mathematical reasoning tasks, identifies improvements to ALE-Bench competitive programming solutions, and discovers novel mixture-of-expert load balancing loss functions that illuminate the space of optimization strategies. Our results demonstrate that ShinkaEvolve achieves broad applicability with exceptional sample efficiency. By providing open-source accessibility and cost-efficiency, this work democratizes open-ended discovery across diverse computational problems.

We introduce InternAgent-1.5, a unified system designed for end-to-end scientific discovery across computational and empirical domains. The system is built on a structured architecture composed of three coordinated subsystems for generation, verification, and evolution. These subsystems are supported by foundational capabilities for deep research, solution optimization, and long horizon memory. The architecture allows InternAgent-1.5 to operate continuously across extended discovery cycles while maintaining coherent and improving behavior. It also enables the system to coordinate computational modeling and laboratory experimentation within a single unified system. We evaluate InternAgent-1.5 on scientific reasoning benchmarks such as GAIA, HLE, GPQA, and FrontierScience, and the system achieves leading performance that demonstrates strong foundational capabilities. Beyond these benchmarks, we further assess two categories of discovery tasks. In algorithm discovery tasks, InternAgent-1.5 autonomously designs competitive methods for core machine learning problems. In empirical discovery tasks, it executes complete computational or wet lab experiments and produces scientific findings in earth, life, biological, and physical domains. Overall, these results show that InternAgent-1.5 provides a general and scalable framework for autonomous scientific discovery.

We introduce the STATION, an open-world multi-agent environment that models a miniature scientific ecosystem. Leveraging their extended context windows, agents in the Station can engage in long scientific journeys that include reading papers from peers, formulating hypotheses, submitting code, performing analyses, and publishing results. Importantly, there is no centralized system coordinating their activities - agents are free to choose their own actions and develop their own narratives within the Station. Experiments demonstrate that AI agents in the Station achieve new state-of-the-art performance on a wide range of benchmarks, spanning from mathematics to computational biology to machine learning, notably surpassing AlphaEvolve in circle packing. A rich tapestry of narratives emerges as agents pursue independent research, interact with peers, and build upon a cumulative history. From these emergent narratives, novel methods arise organically, such as a new density-adaptive algorithm for scRNA-seq batch integration. The Station marks a first step towards autonomous scientific discovery driven by emergent behavior in an open-world environment, representing a new paradigm that moves beyond rigid optimization.

While previous AI Scientist systems can generate novel findings, they often lack the focus to produce scientifically valuable contributions that address pressing human-defined challenges. We introduce DeepScientist, a system designed to overcome this by conducting goal-oriented, fully autonomous scientific discovery over month-long timelines. It formalizes discovery as a Bayesian Optimization problem, operationalized through a hierarchical evaluation process consisting of "hypothesize, verify, and analyze". Leveraging a cumulative Findings Memory, this loop intelligently balances the exploration of novel hypotheses with exploitation, selectively promoting the most promising findings to higher-fidelity levels of validation. Consuming over 20,000 GPU hours, the system generated about 5,000 unique scientific ideas and experimentally validated approximately 1100 of them, ultimately surpassing human-designed state-of-the-art (SOTA) methods on three frontier AI tasks by 183.7\%, 1.9\%, and 7.9\%. This work provides the first large-scale evidence of an AI achieving discoveries that progressively surpass human SOTA on scientific tasks, producing valuable findings that genuinely push the frontier of scientific discovery. To facilitate further research into this process, we will open-source all experimental logs and system code at https://github.com/ResearAI/DeepScientist/.

We study the problem of adaptively identifying patient subpopulations that benefit from a given treatment during a confirmatory clinical trial. This type of adaptive clinical trial has been thoroughly studied in biostatistics, but has been allowed only limited adaptivity so far. Here, we aim to relax classical restrictions on such designs and investigate how to incorporate ideas from the recent machine learning literature on adaptive and online experimentation to make trials more flexible and efficient. We find that the unique characteristics of the subpopulation selection problem -- most importantly that (i) one is usually interested in finding subpopulations with any treatment benefit (and not necessarily the single subgroup with largest effect) given a limited budget and that (ii) effectiveness only has to be demonstrated across the subpopulation on average -- give rise to interesting challenges and new desiderata when designing algorithmic solutions. Building on these findings, we propose AdaGGI and AdaGCPI, two meta-algorithms for subpopulation construction. We empirically investigate their performance across a range of simulation scenarios and derive insights into their (dis)advantages across different settings.

We propose a method for adapting neural networks to distribution shifts at test-time. In contrast to training-time robustness mechanisms that attempt to anticipate and counter the shift, we create a closed-loop system and make use of a test-time feedback signal to adapt a network on the fly. We show that this loop can be effectively implemented using a learning-based function, which realizes an amortized optimizer for the network. This leads to an adaptation method, named Rapid Network Adaptation (RNA), that is notably more flexible and orders of magnitude faster than the baselines. Through a broad set of experiments using various adaptation signals and target tasks, we study the efficiency and flexibility of this method. We perform the evaluations using various datasets (Taskonomy, Replica, ScanNet, Hypersim, COCO, ImageNet), tasks (depth, optical flow, semantic segmentation, classification), and distribution shifts (Cross-datasets, 2D and 3D Common Corruptions) with promising results. We end with a discussion on general formulations for handling distribution shifts and our observations from comparing with similar approaches from other domains.

Protein fitness optimization involves finding a protein sequence that maximizes desired quantitative properties in a combinatorially large design space of possible sequences. Recent developments in steering protein generative models (e.g diffusion models, language models) offer a promising approach. However, by and large, past studies have optimized surrogate rewards and/or utilized large amounts of labeled data for steering, making it unclear how well existing methods perform and compare to each other in real-world optimization campaigns where fitness is measured by low-throughput wet-lab assays. In this study, we explore fitness optimization using small amounts (hundreds) of labeled sequence-fitness pairs and comprehensively evaluate strategies such as classifier guidance and posterior sampling for guiding generation from different discrete diffusion models of protein sequences. We also demonstrate how guidance can be integrated into adaptive sequence selection akin to Thompson sampling in Bayesian optimization, showing that plug-and-play guidance strategies offer advantages compared to alternatives such as reinforcement learning with protein language models.

Humans have the ability to adapt the type of information they use, the procedure they employ, and the amount of time they spend when solving problems. However, most standard neural networks have a fixed function type and computation budget regardless of the sample's nature or difficulty. Adaptivity is a powerful paradigm as it not only imbues practitioners with flexibility pertaining to the downstream usage of these models but can also serve as a powerful inductive bias for solving certain challenging classes of problems. In this work, we introduce a new approach called AdaTape, which allows for dynamic computation in neural networks through adaptive tape tokens. AdaTape utilizes an elastic input sequence by equipping an architecture with a dynamic read-and-write tape. Specifically, we adaptively generate input sequences using tape tokens obtained from a tape bank which can be either trainable or derived from input data. We examine the challenges and requirements to obtain dynamic sequence content and length, and propose the Adaptive Tape Reading (ATR) algorithm to achieve both goals. Through extensive experiments on image recognition tasks, we show that AdaTape can achieve better performance while maintaining the computational cost. To facilitate further research, we have released code at https://github.com/google-research/scenic.

Automating scientific discovery in complex, experiment-driven domains requires more than iterative mutation of programs; it demands structured hypothesis management, environment interaction, and principled reflection. We present OR-Agent, a configurable multi-agent research framework designed for automated exploration in rich experimental environments. OR-Agent organizes research as a structured tree-based workflow that explicitly models branching hypothesis generation and systematic backtracking, enabling controlled management of research trajectories beyond simple mutation-crossover loops. At its core, we introduce an evolutionary-systematic ideation mechanism that unifies evolutionary selection of research starting points, comprehensive research plan generation, and coordinated exploration within a research tree. We introduce a hierarchical optimization-inspired reflection system in which short-term reflections act as verbal gradients, long-term reflections as verbal momentum, and memory compression as semantic weight decay, collectively forming a principled mechanism for governing research dynamics. We conduct extensive experiments across classical combinatorial optimization benchmarks as well as simulation-based cooperative driving scenarios. Results demonstrate that OR-Agent outperforms strong evolutionary baselines while providing a general, extensible, and inspectable framework for AI-assisted scientific discovery. All code and experimental data are publicly available at https://github.com/qiliuchn/OR-Agent.

Large Language Model (LLM)-based multi-agent systems (MAS) demonstrate remarkable potential for scientific discovery. Existing approaches, however, often automate scientific discovery using predefined workflows that lack rationality constraints. This often leads to aimless hypothesizing and a failure to consistently link hypotheses with evidence, thereby hindering systematic uncertainty reduction. Overcoming these limitations fundamentally requires systematic uncertainty reduction. We introduce PiFlow, an information-theoretical framework, treating automated scientific discovery as a structured uncertainty reduction problem guided by principles (e.g., scientific laws). In evaluations across three distinct scientific domains -- discovering nanomaterial structures, bio-molecules, and superconductor candidates with targeted properties -- our method significantly improves discovery efficiency, reflected by a 73.55\% increase in the Area Under the Curve (AUC) of property values versus exploration steps, and enhances solution quality by 94.06\% compared to a vanilla agent system. Overall, PiFlow serves as a Plug-and-Play method, establishing a novel paradigm shift in highly efficient automated scientific discovery, paving the way for more robust and accelerated AI-driven research. Code is publicly available at our https://github.com/amair-lab/PiFlow{GitHub}.

Scientific discovery relies on scientists generating novel hypotheses that undergo rigorous experimental validation. To augment this process, we introduce an AI co-scientist, a multi-agent system built on Gemini 2.0. The AI co-scientist is intended to help uncover new, original knowledge and to formulate demonstrably novel research hypotheses and proposals, building upon prior evidence and aligned to scientist-provided research objectives and guidance. The system's design incorporates a generate, debate, and evolve approach to hypothesis generation, inspired by the scientific method and accelerated by scaling test-time compute. Key contributions include: (1) a multi-agent architecture with an asynchronous task execution framework for flexible compute scaling; (2) a tournament evolution process for self-improving hypotheses generation. Automated evaluations show continued benefits of test-time compute, improving hypothesis quality. While general purpose, we focus development and validation in three biomedical areas: drug repurposing, novel target discovery, and explaining mechanisms of bacterial evolution and anti-microbial resistance. For drug repurposing, the system proposes candidates with promising validation findings, including candidates for acute myeloid leukemia that show tumor inhibition in vitro at clinically applicable concentrations. For novel target discovery, the AI co-scientist proposed new epigenetic targets for liver fibrosis, validated by anti-fibrotic activity and liver cell regeneration in human hepatic organoids. Finally, the AI co-scientist recapitulated unpublished experimental results via a parallel in silico discovery of a novel gene transfer mechanism in bacterial evolution. These results, detailed in separate, co-timed reports, demonstrate the potential to augment biomedical and scientific discovery and usher an era of AI empowered scientists.

Large language models (LLMs) have shown promise in automating scientific hypothesis generation, yet existing approaches primarily yield coarse-grained hypotheses lacking critical methodological and experimental details. We introduce and formally define the novel task of fine-grained scientific hypothesis discovery, which entails generating detailed, experimentally actionable hypotheses from coarse initial research directions. We frame this as a combinatorial optimization problem and investigate the upper limits of LLMs' capacity to solve it when maximally leveraged. Specifically, we explore four foundational questions: (1) how to best harness an LLM's internal heuristics to formulate the fine-grained hypothesis it itself would judge as the most promising among all the possible hypotheses it might generate, based on its own internal scoring-thus defining a latent reward landscape over the hypothesis space; (2) whether such LLM-judged better hypotheses exhibit stronger alignment with ground-truth hypotheses; (3) whether shaping the reward landscape using an ensemble of diverse LLMs of similar capacity yields better outcomes than defining it with repeated instances of the strongest LLM among them; and (4) whether an ensemble of identical LLMs provides a more reliable reward landscape than a single LLM. To address these questions, we propose a hierarchical search method that incrementally proposes and integrates details into the hypothesis, progressing from general concepts to specific experimental configurations. We show that this hierarchical process smooths the reward landscape and enables more effective optimization. Empirical evaluations on a new benchmark of expert-annotated fine-grained hypotheses from recent chemistry literature show that our method consistently outperforms strong baselines.

Despite long-standing efforts in accelerating scientific discovery with AI, building AI co-scientists remains challenging due to limited high-quality data for training and evaluation. To tackle this data scarcity issue, we present AutoSDT, an automatic pipeline that collects high-quality coding tasks in real-world data-driven discovery workflows. AutoSDT leverages the coding capabilities and parametric knowledge of LLMs to search for diverse sources, select ecologically valid tasks, and synthesize accurate task instructions and code solutions. Using our pipeline, we construct AutoSDT-5K, a dataset of 5,404 coding tasks for data-driven discovery that covers four scientific disciplines and 756 unique Python packages. To the best of our knowledge, AutoSDT-5K is the only automatically collected and the largest open dataset for data-driven scientific discovery. Expert feedback on a subset of 256 tasks shows the effectiveness of AutoSDT: 93% of the collected tasks are ecologically valid, and 92.2% of the synthesized programs are functionally correct. Trained on AutoSDT-5K, the Qwen2.5-Coder-Instruct LLM series, dubbed AutoSDT-Coder, show substantial improvement on two challenging data-driven discovery benchmarks, ScienceAgentBench and DiscoveryBench. Most notably, AutoSDT-Coder-32B reaches the same level of performance as GPT-4o on ScienceAgentBench with a success rate of 7.8%, doubling the performance of its base model. On DiscoveryBench, it lifts the hypothesis matching score to 8.1, bringing a 17.4% relative improvement and closing the gap between open-weight models and GPT-4o.

Molecular discovery, when formulated as an optimization problem, presents significant computational challenges because optimization objectives can be non-differentiable. Evolutionary Algorithms (EAs), often used to optimize black-box objectives in molecular discovery, traverse chemical space by performing random mutations and crossovers, leading to a large number of expensive objective evaluations. In this work, we ameliorate this shortcoming by incorporating chemistry-aware Large Language Models (LLMs) into EAs. Namely, we redesign crossover and mutation operations in EAs using LLMs trained on large corpora of chemical information. We perform extensive empirical studies on both commercial and open-source models on multiple tasks involving property optimization, molecular rediscovery, and structure-based drug design, demonstrating that the joint usage of LLMs with EAs yields superior performance over all baseline models across single- and multi-objective settings. We demonstrate that our algorithm improves both the quality of the final solution and convergence speed, thereby reducing the number of required objective evaluations. Our code is available at http://github.com/zoom-wang112358/MOLLEO

Discovering effective predictive signals, or ``alphas,'' from financial data with high dimensionality and extremely low signal-to-noise ratio remains a difficult open problem. Despite progress in deep learning, genetic programming, and, more recently, large language model (LLM)--based factor generation, existing approaches still explore only a narrow region of the vast alpha search space. Neural models tend to produce opaque and fragile patterns, while symbolic or formula-based methods often yield redundant or economically ungrounded expressions that generalize poorly. Although different in form, these paradigms share a key limitation: none can conduct broad, structured, and human-like exploration that balances logical consistency with creative leaps. To address this gap, we introduce the Cognitive Alpha Mining Framework (CogAlpha), which combines code-level alpha representation with LLM-driven reasoning and evolutionary search. Treating LLMs as adaptive cognitive agents, our framework iteratively refines, mutates, and recombines alpha candidates through multi-stage prompts and financial feedback. This synergistic design enables deeper thinking, richer structural diversity, and economically interpretable alpha discovery, while greatly expanding the effective search space. Experiments on A-share equities demonstrate that CogAlpha consistently discovers alphas with superior predictive accuracy, robustness, and generalization over existing methods. Our results highlight the promise of aligning evolutionary optimization with LLM-based reasoning for automated and explainable alpha discovery. All source code will be released.

Motivated by the need to efficiently identify multiple candidates in high trial-and-error cost tasks such as drug discovery, we propose a near-optimal algorithm to identify all ε-best arms (i.e., those at most ε worse than the optimum). Specifically, we introduce LinFACT, an algorithm designed to optimize the identification of all ε-best arms in linear bandits. We establish a novel information-theoretic lower bound on the sample complexity of this problem and demonstrate that LinFACT achieves instance optimality by matching this lower bound up to a logarithmic factor. A key ingredient of our proof is to integrate the lower bound directly into the scaling process for upper bound derivation, determining the termination round and thus the sample complexity. We also extend our analysis to settings with model misspecification and generalized linear models. Numerical experiments, including synthetic and real drug discovery data, demonstrate that LinFACT identifies more promising candidates with reduced sample complexity, offering significant computational efficiency and accelerating early-stage exploratory experiments.

We present a novel method for symbolic regression (SR), the task of searching for compact programmatic hypotheses that best explain a dataset. The problem is commonly solved using genetic algorithms; we show that we can enhance such methods by inducing a library of abstract textual concepts. Our algorithm, called LaSR, uses zero-shot queries to a large language model (LLM) to discover and evolve concepts occurring in known high-performing hypotheses. We discover new hypotheses using a mix of standard evolutionary steps and LLM-guided steps (obtained through zero-shot LLM queries) conditioned on discovered concepts. Once discovered, hypotheses are used in a new round of concept abstraction and evolution. We validate LaSR on the Feynman equations, a popular SR benchmark, as well as a set of synthetic tasks. On these benchmarks, LaSR substantially outperforms a variety of state-of-the-art SR approaches based on deep learning and evolutionary algorithms. Moreover, we show that LaSR can be used to discover a novel and powerful scaling law for LLMs.

Automated AI research holds great potential to accelerate scientific discovery. However, current LLMs often generate plausible-looking but ineffective ideas. Execution grounding may help, but it is unclear whether automated execution is feasible and whether LLMs can learn from the execution feedback. To investigate these, we first build an automated executor to implement ideas and launch large-scale parallel GPU experiments to verify their effectiveness. We then convert two realistic research problems - LLM pre-training and post-training - into execution environments and demonstrate that our automated executor can implement a large fraction of the ideas sampled from frontier LLMs. We analyze two methods to learn from the execution feedback: evolutionary search and reinforcement learning. Execution-guided evolutionary search is sample-efficient: it finds a method that significantly outperforms the GRPO baseline (69.4% vs 48.0%) on post-training, and finds a pre-training recipe that outperforms the nanoGPT baseline (19.7 minutes vs 35.9 minutes) on pre-training, all within just ten search epochs. Frontier LLMs often generate meaningful algorithmic ideas during search, but they tend to saturate early and only occasionally exhibit scaling trends. Reinforcement learning from execution reward, on the other hand, suffers from mode collapse. It successfully improves the average reward of the ideator model but not the upper-bound, due to models converging on simple ideas. We thoroughly analyze the executed ideas and training dynamics to facilitate future efforts towards execution-grounded automated AI research.

The ARC-AGI benchmark series serves as a critical measure of few-shot generalization on novel tasks, a core aspect of intelligence. The ARC Prize 2025 global competition targeted the newly released ARC-AGI-2 dataset, which features greater task complexity compared to its predecessor. The Kaggle competition attracted 1,455 teams and 15,154 entries, with the top score reaching 24% on the ARC-AGI-2 private evaluation set. Paper submissions nearly doubled year-over-year to 90 entries, reflecting the growing research interest in fluid intelligence and abstract reasoning. The defining theme of 2025 is the emergence of the refinement loop -- a per-task iterative program optimization loop guided by a feedback signal. Refinement loops come in a variety of forms, in particular evolutionary program synthesis approaches and application-layer refinements to commercial AI systems. Such refinement loops are also possible in weight space, as evidenced by zero-pretraining deep learning methods which are now achieving competitive performance with remarkably small networks (7M parameters). In parallel, four frontier AI labs (Anthropic, Google DeepMind, OpenAI, and xAI) reported ARC-AGI performance in public model cards in 2025, establishing ARC-AGI as an industry standard benchmark for AI reasoning. However, our analysis indicates that current frontier AI reasoning performance remains fundamentally constrained to knowledge coverage, giving rise to new forms of benchmark contamination. In this paper, we survey the top-performing methods, examine the role of refinement loops in AGI progress, discuss knowledge-dependent overfitting, and preview ARC-AGI-3, which introduces interactive reasoning challenges that require exploration, planning, memory, goal acquisition, and alignment capabilities.

The transcriptional response to genetic perturbation reveals fundamental insights into complex cellular systems. While current approaches have made progress in predicting genetic perturbation responses, they provide limited biological understanding and cannot systematically refine existing knowledge. Overcoming these limitations requires an end-to-end integration of data-driven learning and existing knowledge. However, this integration is challenging due to inconsistencies between data and knowledge bases, such as noise, misannotation, and incompleteness. To address this challenge, we propose ALIGNED (Adaptive aLignment for Inconsistent Genetic kNowledgE and Data), a neuro-symbolic framework based on the Abductive Learning (ABL) paradigm. This end-to-end framework aligns neural and symbolic components and performs systematic knowledge refinement. We introduce a balanced consistency metric to evaluate the predictions' consistency against both data and knowledge. Our results show that ALIGNED outperforms state-of-the-art methods by achieving the highest balanced consistency, while also re-discovering biologically meaningful knowledge. Our work advances beyond existing methods to enable both the transparency and the evolution of mechanistic biological understanding.

We introduce a novel score-based diffusion framework named Twigs that incorporates multiple co-evolving flows for enriching conditional generation tasks. Specifically, a central or trunk diffusion process is associated with a primary variable (e.g., graph structure), and additional offshoot or stem processes are dedicated to dependent variables (e.g., graph properties or labels). A new strategy, which we call loop guidance, effectively orchestrates the flow of information between the trunk and the stem processes during sampling. This approach allows us to uncover intricate interactions and dependencies, and unlock new generative capabilities. We provide extensive experiments to demonstrate strong performance gains of the proposed method over contemporary baselines in the context of conditional graph generation, underscoring the potential of Twigs in challenging generative tasks such as inverse molecular design and molecular optimization.

Sampling is ubiquitous in machine learning methodologies. Due to the growth of large datasets and model complexity, we want to learn and adapt the sampling process while training a representation. Towards achieving this grand goal, a variety of sampling techniques have been proposed. However, most of them either use a fixed sampling scheme or adjust the sampling scheme based on simple heuristics. They cannot choose the best sample for model training in different stages. Inspired by "Think, Fast and Slow" (System 1 and System 2) in cognitive science, we propose a reward-guided sampling strategy called Adaptive Sample with Reward (ASR) to tackle this challenge. To the best of our knowledge, this is the first work utilizing reinforcement learning (RL) to address the sampling problem in representation learning. Our approach optimally adjusts the sampling process to achieve optimal performance. We explore geographical relationships among samples by distance-based sampling to maximize overall cumulative reward. We apply ASR to the long-standing sampling problems in similarity-based loss functions. Empirical results in information retrieval and clustering demonstrate ASR's superb performance across different datasets. We also discuss an engrossing phenomenon which we name as "ASR gravity well" in experiments.

Autonomous scientific discovery with large language model (LLM)-based agents has recently made substantial progress, demonstrating the ability to automate end-to-end research workflows. However, existing systems largely rely on runtime-centric execution paradigms, repeatedly reading, summarizing, and reasoning over large volumes of scientific literature online. This on-the-spot computation strategy incurs high computational cost, suffers from context window limitations, and often leads to brittle reasoning and hallucination. We propose Idea2Story, a pre-computation-driven framework for autonomous scientific discovery that shifts literature understanding from online reasoning to offline knowledge construction. Idea2Story continuously collects peer-reviewed papers together with their review feedback, extracts core methodological units, composes reusable research patterns, and organizes them into a structured methodological knowledge graph. At runtime, underspecified user research intents are aligned to established research paradigms, enabling efficient retrieval and reuse of high-quality research patterns instead of open-ended generation and trial-and-error. By grounding research planning and execution in a pre-built knowledge graph, Idea2Story alleviates the context window bottleneck of LLMs and substantially reduces repeated runtime reasoning over literature. We conduct qualitative analyses and preliminary empirical studies demonstrating that Idea2Story can generate coherent, methodologically grounded, and novel research patterns, and can produce several high-quality research demonstrations in an end-to-end setting. These results suggest that offline knowledge construction provides a practical and scalable foundation for reliable autonomous scientific discovery.

Optimizing large-scale machine learning systems, such as recommendation models for global video platforms, requires navigating a massive hyperparameter search space and, more critically, designing sophisticated optimizers, architectures, and reward functions to capture nuanced user behaviors. Achieving substantial improvements in these areas is a non-trivial task, traditionally relying on extensive manual iterations to test new hypotheses. We propose a self-evolving system that leverages Large Language Models (LLMs), specifically those from Google's Gemini family, to autonomously generate, train, and deploy high-performing, complex model changes within an end-to-end automated workflow. The self-evolving system is comprised of an Offline Agent (Inner Loop) that performs high-throughput hypothesis generation using proxy metrics, and an Online Agent (Outer Loop) that validates candidates against delayed north star business metrics in live production. Our agents act as specialized Machine Learning Engineers (MLEs): they exhibit deep reasoning capabilities, discovering novel improvements in optimization algorithms and model architecture, and formulating innovative reward functions that target long-term user engagement. The effectiveness of this approach is demonstrated through several successful production launches at YouTube, confirming that autonomous, LLM-driven evolution can surpass traditional engineering workflows in both development velocity and model performance.

Decision trees are a crucial class of models offering robust predictive performance and inherent interpretability across various domains, including healthcare, finance, and logistics. However, current tree induction methods often face limitations such as suboptimal solutions from greedy methods or prohibitive computational costs and limited applicability of exact optimization approaches. To address these challenges, we propose an evolutionary optimization method for decision tree induction based on genetic programming (GP). Our key innovation is the integration of semantic priors and domain-specific knowledge about the search space into the optimization algorithm. To this end, we introduce LLEGO, a framework that incorporates semantic priors into genetic search operators through the use of Large Language Models (LLMs), thereby enhancing search efficiency and targeting regions of the search space that yield decision trees with superior generalization performance. This is operationalized through novel genetic operators that work with structured natural language prompts, effectively utilizing LLMs as conditional generative models and sources of semantic knowledge. Specifically, we introduce fitness-guided crossover to exploit high-performing regions, and diversity-guided mutation for efficient global exploration of the search space. These operators are controlled by corresponding hyperparameters that enable a more nuanced balance between exploration and exploitation across the search space. Empirically, we demonstrate across various benchmarks that LLEGO evolves superior-performing trees compared to existing tree induction methods, and exhibits significantly more efficient search performance compared to conventional GP approaches.

In the realm of machine learning, traditional model development and automated approaches like AutoML typically rely on layers of abstraction, such as tree-based or Cartesian genetic programming. Our study introduces "Guided Evolution" (GE), a novel framework that diverges from these methods by utilizing Large Language Models (LLMs) to directly modify code. GE leverages LLMs for a more intelligent, supervised evolutionary process, guiding mutations and crossovers. Our unique "Evolution of Thought" (EoT) technique further enhances GE by enabling LLMs to reflect on and learn from the outcomes of previous mutations. This results in a self-sustaining feedback loop that augments decision-making in model evolution. GE maintains genetic diversity, crucial for evolutionary algorithms, by leveraging LLMs' capability to generate diverse responses from expertly crafted prompts and modulate model temperature. This not only accelerates the evolution process but also injects expert like creativity and insight into the process. Our application of GE in evolving the ExquisiteNetV2 model demonstrates its efficacy: the LLM-driven GE autonomously produced variants with improved accuracy, increasing from 92.52% to 93.34%, without compromising model compactness. This underscores the potential of LLMs to accelerate the traditional model design pipeline, enabling models to autonomously evolve and enhance their own designs.

Large language models are emerging as powerful tools for scientific law discovery, a foundational challenge in AI-driven science. However, existing benchmarks for this task suffer from a fundamental methodological trilemma, forcing a trade-off between scientific relevance, scalability, and resistance to memorization. Furthermore, they oversimplify discovery as static function fitting, failing to capture the authentic scientific process of uncovering embedded laws through the interactive exploration of complex model systems. To address these critical gaps, we introduce NewtonBench, a benchmark comprising 324 scientific law discovery tasks across 12 physics domains. Our design mitigates the evaluation trilemma by using metaphysical shifts - systematic alterations of canonical laws - to generate a vast suite of problems that are scalable, scientifically relevant, and memorization-resistant. Moreover, we elevate the evaluation from static function fitting to interactive model discovery, requiring agents to experimentally probe simulated complex systems to uncover hidden principles. Our extensive experiment reveals a clear but fragile capability for discovery in frontier LLMs: this ability degrades precipitously with increasing system complexity and exhibits extreme sensitivity to observational noise. Notably, we uncover a paradoxical effect of tool assistance: providing a code interpreter can hinder more capable models by inducing a premature shift from exploration to exploitation, causing them to satisfice on suboptimal solutions. These results demonstrate that robust, generalizable discovery in complex, interactive environments remains the core challenge. By providing a scalable, robust, and scientifically authentic testbed, NewtonBench offers a crucial tool for measuring true progress and guiding the development of next-generation AI agents capable of genuine scientific discovery.

As Large Multimodal Models (LMMs) scale up and reinforcement learning (RL) methods mature, LMMs have made notable progress in complex reasoning and decision making. Yet training still relies on static data and fixed recipes, making it difficult to diagnose capability blind spots or provide dynamic, targeted reinforcement. Motivated by findings that test driven error exposure and feedback based correction outperform repetitive practice, we propose Diagnostic-driven Progressive Evolution (DPE), a spiral loop where diagnosis steers data generation and reinforcement, and each iteration re-diagnoses the updated model to drive the next round of targeted improvement. DPE has two key components. First, multiple agents annotate and quality control massive unlabeled multimodal data, using tools such as web search and image editing to produce diverse, realistic samples. Second, DPE attributes failures to specific weaknesses, dynamically adjusts the data mixture, and guides agents to generate weakness focused data for targeted reinforcement. Experiments on Qwen3-VL-8B-Instruct and Qwen2.5-VL-7B-Instruct show stable, continual gains across eleven benchmarks, indicating DPE as a scalable paradigm for continual LMM training under open task distributions. Our code, models, and data are publicly available at https://github.com/hongruijia/DPE.

Reward-based optimization algorithms require both exploration, to find rewards, and exploitation, to maximize performance. The need for efficient exploration is even more significant in sparse reward settings, in which performance feedback is given sparingly, thus rendering it unsuitable for guiding the search process. In this work, we introduce the SparsE Reward Exploration via Novelty and Emitters (SERENE) algorithm, capable of efficiently exploring a search space, as well as optimizing rewards found in potentially disparate areas. Contrary to existing emitters-based approaches, SERENE separates the search space exploration and reward exploitation into two alternating processes. The first process performs exploration through Novelty Search, a divergent search algorithm. The second one exploits discovered reward areas through emitters, i.e. local instances of population-based optimization algorithms. A meta-scheduler allocates a global computational budget by alternating between the two processes, ensuring the discovery and efficient exploitation of disjoint reward areas. SERENE returns both a collection of diverse solutions covering the search space and a collection of high-performing solutions for each distinct reward area. We evaluate SERENE on various sparse reward environments and show it compares favorably to existing baselines.

A great deal of effort has been devoted to reducing the risk of spurious scientific discoveries, from the use of sophisticated validation techniques, to deep statistical methods for controlling the false discovery rate in multiple hypothesis testing. However, there is a fundamental disconnect between the theoretical results and the practice of data analysis: the theory of statistical inference assumes a fixed collection of hypotheses to be tested, or learning algorithms to be applied, selected non-adaptively before the data are gathered, whereas in practice data is shared and reused with hypotheses and new analyses being generated on the basis of data exploration and the outcomes of previous analyses. In this work we initiate a principled study of how to guarantee the validity of statistical inference in adaptive data analysis. As an instance of this problem, we propose and investigate the question of estimating the expectations of m adaptively chosen functions on an unknown distribution given n random samples. We show that, surprisingly, there is a way to estimate an exponential in n number of expectations accurately even if the functions are chosen adaptively. This gives an exponential improvement over standard empirical estimators that are limited to a linear number of estimates. Our result follows from a general technique that counter-intuitively involves actively perturbing and coordinating the estimates, using techniques developed for privacy preservation. We give additional applications of this technique to our question.

Can we leverage LLMs to model the process of discovering novel language model (LM) architectures? Inspired by real research, we propose a multi-agent LLM approach that simulates the conventional stages of research, from ideation and literature search (proposal stage) to design implementation (code generation), generative pre-training, and downstream evaluation (verification). Using ideas from scaling laws, our system, Genesys, employs a Ladder of Scales approach; new designs are proposed, adversarially reviewed, implemented, and selectively verified at increasingly larger model scales (14Msim350M parameters) with a narrowing budget (the number of models we can train at each scale). To help make discovery efficient and factorizable, Genesys uses a novel genetic programming backbone, which we show has empirical advantages over commonly used direct prompt generation workflows (e.g., sim86\% percentage point improvement in successful design generation, a key bottleneck). We report experiments involving 1,162 newly discovered designs (1,062 fully verified through pre-training) and find the best designs to be highly competitive with known architectures (e.g., outperform GPT2, Mamba2, etc., on 6/9 common benchmarks). We couple these results with comprehensive system-level ablations and formal results, which give broader insights into the design of effective autonomous discovery systems.

Can AI accelerate the development of AI itself? While recent agentic systems have shown strong performance on well-scoped tasks with rapid feedback, it remains unclear whether they can tackle the costly, long-horizon, and weakly supervised research loops that drive real AI progress. We present ASI-Evolve, an agentic framework for AI-for-AI research that closes this loop through a learn-design-experiment-analyze cycle. ASI-Evolve augments standard evolutionary agents with two key components: a cognition base that injects accumulated human priors into each round of exploration, and a dedicated analyzer that distills complex experimental outcomes into reusable insights for future iterations. To our knowledge, ASI-Evolve is the first unified framework to demonstrate AI-driven discovery across three central components of AI development: data, architectures, and learning algorithms. In neural architecture design, it discovered 105 SOTA linear attention architectures, with the best discovered model surpassing DeltaNet by +0.97 points, nearly 3x the gain of recent human-designed improvements. In pretraining data curation, the evolved pipeline improves average benchmark performance by +3.96 points, with gains exceeding 18 points on MMLU. In reinforcement learning algorithm design, discovered algorithms outperform GRPO by up to +12.5 points on AMC32, +11.67 points on AIME24, and +5.04 points on OlympiadBench. We further provide initial evidence that this AI-for-AI paradigm can transfer beyond the AI stack through experiments in mathematics and biomedicine. Together, these results suggest that ASI-Evolve represents a promising step toward enabling AI to accelerate AI across the foundational stages of development, offering early evidence for the feasibility of closed-loop AI research.

Public repositories host millions of fine-tuned models, yet community usage remains disproportionately concentrated on a small number of foundation checkpoints. We investigate whether this concentration reflects efficient market selection or if superior models are systematically overlooked. Through an extensive evaluation of over 2,000 models, we show the prevalence of "hidden gems", unpopular fine-tunes that significantly outperform their popular counterparts. Notably, within the Llama-3.1-8B family, we find rarely downloaded checkpoints that improve math performance from 83.2% to 96.0% without increasing inference costs. However, discovering these models through exhaustive evaluation of every uploaded model is computationally infeasible. We therefore formulate model discovery as a Multi-Armed Bandit problem and accelerate the Sequential Halving search algorithm by using shared query sets and aggressive elimination schedules. Our method retrieves top models with as few as 50 queries per candidate, accelerating discovery by over 50x.

Recent advances in LLM-guided evolutionary computation, particularly AlphaEvolve (Novikov et al., 2025; Georgiev et al., 2025), have demonstrated remarkable success in discovering novel mathematical constructions and solving challenging optimization problems. However, the high-level descriptions in published work leave many implementation details unspecified, hindering reproducibility and further research. In this report we present GigaEvo, an extensible open-source framework that enables researchers to study and experiment with hybrid LLM-evolution approaches inspired by AlphaEvolve. Our system provides modular implementations of key components: MAP-Elites quality-diversity algorithms, asynchronous DAG-based evaluation pipelines, LLM-driven mutation operators with insight generation and bidirectional lineage tracking, and flexible multi-island evolutionary strategies. In order to assess reproducibility and validate our implementation we evaluate GigaEvo on challenging problems from the AlphaEvolve paper: Heilbronn triangle placement, circle packing in squares, and high-dimensional kissing numbers. The framework emphasizes modularity, concurrency, and ease of experimentation, enabling rapid prototyping through declarative configuration. We provide detailed descriptions of system architecture, implementation decisions, and experimental methodology to support further research in LLM driven evolutionary methods. The GigaEvo framework and all experimental code are available at https://github.com/AIRI-Institute/gigaevo-core.

Large language models hold promise as scientific assistants, yet existing agents either rely solely on algorithm evolution or on deep research in isolation, both of which face critical limitations. Pure algorithm evolution, as in AlphaEvolve, depends only on the internal knowledge of LLMs and quickly plateaus in complex domains, while pure deep research proposes ideas without validation, resulting in unrealistic or unimplementable solutions. We present DeepEvolve, an agent that integrates deep research with algorithm evolution, uniting external knowledge retrieval, cross-file code editing, and systematic debugging under a feedback-driven iterative loop. Each iteration not only proposes new hypotheses but also refines, implements, and tests them, avoiding both shallow improvements and unproductive over-refinements. Across nine benchmarks in chemistry, mathematics, biology, materials, and patents, DeepEvolve consistently improves the initial algorithm, producing executable new algorithms with sustained gains. By bridging the gap between unguided evolution and research without grounding, DeepEvolve provides a reliable framework for advancing scientific algorithm discovery. Our code is available at https://github.com/liugangcode/deepevolve.

Large Language Models (LLMs) are transforming scientific hypothesis generation and validation by enabling information synthesis, latent relationship discovery, and reasoning augmentation. This survey provides a structured overview of LLM-driven approaches, including symbolic frameworks, generative models, hybrid systems, and multi-agent architectures. We examine techniques such as retrieval-augmented generation, knowledge-graph completion, simulation, causal inference, and tool-assisted reasoning, highlighting trade-offs in interpretability, novelty, and domain alignment. We contrast early symbolic discovery systems (e.g., BACON, KEKADA) with modern LLM pipelines that leverage in-context learning and domain adaptation via fine-tuning, retrieval, and symbolic grounding. For validation, we review simulation, human-AI collaboration, causal modeling, and uncertainty quantification, emphasizing iterative assessment in open-world contexts. The survey maps datasets across biomedicine, materials science, environmental science, and social science, introducing new resources like AHTech and CSKG-600. Finally, we outline a roadmap emphasizing novelty-aware generation, multimodal-symbolic integration, human-in-the-loop systems, and ethical safeguards, positioning LLMs as agents for principled, scalable scientific discovery.

The paradigm of automated program generation is shifting from one-shot generation to inference-time search, where Large Language Models (LLMs) function as semantic mutation operators within evolutionary loops. While effective, these systems are currently governed by static schedules that fail to account for the non-stationary dynamics of the search process. This rigidity results in substantial computational waste, as resources are indiscriminately allocated to stagnating populations while promising frontiers remain under-exploited. We introduce AdaEvolve, a framework that reformulates LLM-driven evolution as a hierarchical adaptive optimization problem. AdaEvolve uses an "accumulated improvement signal" to unify decisions across three levels: Local Adaptation, which dynamically modulates the exploration intensity within a population of solution candidates; Global Adaptation, which routes the global resource budget via bandit-based scheduling across different solution candidate populations; and Meta-Guidance which generates novel solution tactics based on the previously generated solutions and their corresponding improvements when the progress stalls. We demonstrate that AdaEvolve consistently outperforms the open-sourced baselines across 185 different open-ended optimization problems including combinatorial, systems optimization and algorithm design problems.

Large language models have made significant progress in complex but easy-to-verify problems, yet they still struggle with discovering the unknown. In this paper, we present AlphaResearch, an autonomous research agent designed to discover new algorithms on open-ended problems. To synergize the feasibility and innovation of the discovery process, we construct a novel dual research environment by combining the execution-based verify and simulated real-world peer review environment. AlphaResearch discovers new algorithm by iteratively running the following steps: (1) propose new ideas (2) verify the ideas in the dual research environment (3) optimize the research proposals for better performance. To promote a transparent evaluation process, we construct AlphaResearchComp, a new evaluation benchmark that includes an eight open-ended algorithmic problems competition, with each problem carefully curated and verified through executable pipelines, objective metrics, and reproducibility checks. AlphaResearch gets a 2/8 win rate in head-to-head comparison with human researchers, demonstrate the possibility of accelerating algorithm discovery with LLMs. Notably, the algorithm discovered by AlphaResearch on the ``packing circles'' problem achieves the best-of-known performance, surpassing the results of human researchers and strong baselines from recent work (e.g., AlphaEvolve). Additionally, we conduct a comprehensive analysis of the remaining challenges of the 6/8 failure cases, providing valuable insights for future research.

To fully leverage the capabilities of diffusion models, we are often interested in optimizing downstream reward functions during inference. While numerous algorithms for reward-guided generation have been recently proposed due to their significance, current approaches predominantly focus on single-shot generation, transitioning from fully noised to denoised states. We propose a novel framework for inference-time reward optimization with diffusion models inspired by evolutionary algorithms. Our approach employs an iterative refinement process consisting of two steps in each iteration: noising and reward-guided denoising. This sequential refinement allows for the gradual correction of errors introduced during reward optimization. Besides, we provide a theoretical guarantee for our framework. Finally, we demonstrate its superior empirical performance in protein and cell-type-specific regulatory DNA design. The code is available at https://github.com/masa-ue/ProDifEvo-Refinement{https://github.com/masa-ue/ProDifEvo-Refinement}.

The saturation of high-quality pre-training data has shifted research focus toward evolutionary systems capable of continuously generating novel artifacts, leading to the success of AlphaEvolve. However, the progress of such systems is hindered by the lack of rigorous, quantitative evaluation. To tackle this challenge, we introduce CreativeBench, a benchmark for evaluating machine creativity in code generation, grounded in a classical cognitive framework. Comprising two subsets -- CreativeBench-Combo and CreativeBench-Explore -- the benchmark targets combinatorial and exploratory creativity through an automated pipeline utilizing reverse engineering and self-play. By leveraging executable code, CreativeBench objectively distinguishes creativity from hallucination via a unified metric defined as the product of quality and novelty. Our analysis of state-of-the-art models reveals distinct behaviors: (1) scaling significantly improves combinatorial creativity but yields diminishing returns for exploration; (2) larger models exhibit ``convergence-by-scaling,'' becoming more correct but less divergent; and (3) reasoning capabilities primarily benefit constrained exploration rather than combination. Finally, we propose EvoRePE, a plug-and-play inference-time steering strategy that internalizes evolutionary search patterns to consistently enhance machine creativity.

The rapid advancements in large language models (LLMs) have demonstrated their potential to accelerate scientific discovery, particularly in automating the process of research ideation. LLM-based systems have shown promise in generating hypotheses and research ideas. However, current approaches predominantly rely on prompting-based pre-trained models, limiting their ability to optimize generated content effectively. Moreover, they also lack the capability to deal with the complex interdependence and inherent restrictions among novelty, feasibility, and effectiveness, which remains challenging due to the inherent trade-offs among these dimensions, such as the innovation-feasibility conflict. To address these limitations, we for the first time propose fine-tuning LLMs to be better idea proposers and introduce a novel framework that employs a two-stage approach combining Supervised Fine-Tuning (SFT) and controllable Reinforcement Learning (RL). In the SFT stage, the model learns foundational patterns from pairs of research papers and follow-up ideas. In the RL stage, multi-dimensional reward modeling, guided by fine-grained feedback, evaluates and optimizes the generated ideas across key metrics. Dimensional controllers enable dynamic adjustment of generation, while a sentence-level decoder ensures context-aware emphasis during inference. Our framework provides a balanced approach to research ideation, achieving high-quality outcomes by dynamically navigating the trade-offs among novelty, feasibility, and effectiveness.

Supervised Fine-Tuning (SFT) Large Language Models (LLM) fundamentally rely on high-quality training data. While data selection and data synthesis are two common strategies to improve data quality, existing approaches often face limitations in static dataset curation that fail to adapt to evolving model capabilities. In this paper, we introduce Middo, a self-evolving Model-informed dynamic data optimization framework that uses model-aware data selection and context-preserving data refinement. Unlike conventional one-off filtering/synthesis methods, our framework establishes a closed-loop optimization system: (1) A self-referential diagnostic module proactively identifies suboptimal samples through tri-axial model signals - loss patterns (complexity), embedding cluster dynamics (diversity), and self-alignment scores (quality); (2) An adaptive optimization engine then transforms suboptimal samples into pedagogically valuable training points while preserving semantic integrity; (3) This optimization process continuously evolves with model capability through dynamic learning principles. Experiments on multiple benchmarks demonstrate that our \method consistently enhances the quality of seed data and boosts LLM's performance with improving accuracy by 7.15% on average while maintaining the original dataset scale. This work establishes a new paradigm for sustainable LLM training through dynamic human-AI co-evolution of data and models. Our datasets, models, and code are coming soon.

Offline model-based optimization aims to maximize a black-box objective function with a static dataset of designs and their scores. In this paper, we focus on biological sequence design to maximize some sequence score. A recent approach employs bidirectional learning, combining a forward mapping for exploitation and a backward mapping for constraint, and it relies on the neural tangent kernel (NTK) of an infinitely wide network to build a proxy model. Though effective, the NTK cannot learn features because of its parametrization, and its use prevents the incorporation of powerful pre-trained Language Models (LMs) that can capture the rich biophysical information in millions of biological sequences. We adopt an alternative proxy model, adding a linear head to a pre-trained LM, and propose a linearization scheme. This yields a closed-form loss and also takes into account the biophysical information in the pre-trained LM. In addition, the forward mapping and the backward mapping play different roles and thus deserve different weights during sequence optimization. To achieve this, we train an auxiliary model and leverage its weak supervision signal via a bi-level optimization framework to effectively learn how to balance the two mappings. Further, by extending the framework, we develop the first learning rate adaptation module Adaptive-eta, which is compatible with all gradient-based algorithms for offline model-based optimization. Experimental results on DNA/protein sequence design tasks verify the effectiveness of our algorithm. Our code is available~https://anonymous.4open.science/r/BIB-ICLR2023-Submission/README.md{here.}

We study auto research as a closed empirical loop driven by external measurement. Each submitted trial carries a hypothesis, an executable code edit, an evaluator-owned outcome, and feedback that shapes the next proposal. The output is not a generated paper or a single model checkpoint, but an auditable trajectory of proposals, code diffs, experiments, scores, and failure labels. We instantiate this loop with specialist agents that partition recipe surfaces and share measured lineage across trials. The central empirical finding is that lineage feedback lets agents turn evaluator outcomes, including crashes, budget overruns, size failures, and accuracy-gate misses, into later program-level recipe edits rather than one-shot suggestions. Across 1,197 headline-run trials plus 600 Parameter Golf control trials after one-time setup and launch, humans did not choose proposals, edit recipes, override scores, or repair failed trials during the search. In the three headline runs, the same submitted-trial loop reduces Parameter Golf validation bpb by 0.81%, raises NanoChat-D12 CORE by 38.7%, and reduces CIFAR-10 Airbench96 wallclock by 4.59%, with each task measured by its own external evaluator and legality checks. The trace includes a strict architecture-domain audit of 157 headline-run submissions and program rewrites such as a NanoChat attention-kernel path change. Within this scope the loop autonomously writes code, submits experiments, absorbs feedback, applies and combines known techniques inside each environment, and improves public starting recipes.

Small language models are attractive for production deployment due to their low cost, fast inference, and ease of specialization. However, adapting them to a specific task remains a challenging engineering loop, driven not by training itself but by surrounding decisions: data curation, failure diagnosis, regression avoidance, and iteration control. We present Pioneer Agent, a closed-loop system that automates this lifecycle. In cold-start mode, given only a natural-language task description, the agent acquires data, constructs evaluation sets, and iteratively trains models by jointly optimizing data, hyperparameters, and learning strategy. In production mode, given a deployed model with labeled failures, it diagnoses error patterns, constructs targeted training data, and retrains under explicit regression constraints. To evaluate this setting, we introduce AdaptFT-Bench, a benchmark of synthetic inference logs with progressively increasing noise, designed to test the full adaptation loop: diagnosis, curriculum synthesis, retraining, and verification. Across eight cold-start benchmarks spanning reasoning, math, code generation, summarization, and classification, Pioneer Agent improves over base models by 1.6-83.8 points. On AdaptFT-Bench, it improves or preserves performance in all seven scenarios, while naive retraining degrades by up to 43 points. On two production-style deployments built from public benchmark tasks, it raises intent classification from 84.9% to 99.3% and Entity F1 from 0.345 to 0.810. Beyond performance gains, the agent often discovers effective training strategies, including chain-of-thought supervision, task-specific optimization, and quality-focused data curation, purely from downstream feedback.

Literature-Based Discovery (LBD) aims to discover new scientific knowledge by mining papers and generating hypotheses. Standard LBD is limited to predicting pairwise relations between discrete concepts (e.g., drug-disease links), and ignores critical contexts like experimental settings (e.g., a specific patient population where a drug is evaluated) and background motivations (e.g., to find drugs without specific side effects). We address these limitations with a novel formulation of contextualized-LBD (C-LBD): generating scientific hypotheses in natural language, while grounding them in a context that controls the hypothesis search space. We present a modeling framework using retrieval of ``inspirations'' from past scientific papers. Our evaluations reveal that GPT-4 tends to generate ideas with overall low technical depth and novelty, while our inspiration prompting approaches partially mitigate this issue. Our work represents a first step toward building language models that generate new ideas derived from scientific literature.

Today's AI systems have human-designed, fixed architectures and cannot autonomously and continuously improve themselves. The advance of AI could itself be automated. If done safely, that would accelerate AI development and allow us to reap its benefits much sooner. Meta-learning can automate the discovery of novel algorithms, but is limited by first-order improvements and the human design of a suitable search space. The G\"odel machine proposed a theoretical alternative: a self-improving AI that repeatedly modifies itself in a provably beneficial manner. Unfortunately, proving that most changes are net beneficial is impossible in practice. We introduce the Darwin G\"odel Machine (DGM), a self-improving system that iteratively modifies its own code (thereby also improving its ability to modify its own codebase) and empirically validates each change using coding benchmarks. Inspired by Darwinian evolution and open-endedness research, the DGM maintains an archive of generated coding agents. It grows the archive by sampling an agent from it and using a foundation model to create a new, interesting, version of the sampled agent. This open-ended exploration forms a growing tree of diverse, high-quality agents and allows the parallel exploration of many different paths through the search space. Empirically, the DGM automatically improves its coding capabilities (e.g., better code editing tools, long-context window management, peer-review mechanisms), increasing performance on SWE-bench from 20.0% to 50.0%, and on Polyglot from 14.2% to 30.7%. Furthermore, the DGM significantly outperforms baselines without self-improvement or open-ended exploration. All experiments were done with safety precautions (e.g., sandboxing, human oversight). The DGM is a significant step toward self-improving AI, capable of gathering its own stepping stones along paths that unfold into endless innovation.

Traditional methods for automating recommender system design, such as Neural Architecture Search (NAS), are often constrained by a fixed search space defined by human priors, limiting innovation to pre-defined operators. While recent LLM-driven code evolution frameworks shift fixed search space target to open-ended program spaces, they primarily rely on scalar metrics (e.g., NDCG, Hit Ratio) that fail to provide qualitative insights into model failures or directional guidance for improvement. To address this, we propose Self-EvolveRec, a novel framework that establishes a directional feedback loop by integrating a User Simulator for qualitative critiques and a Model Diagnosis Tool for quantitative internal verification. Furthermore, we introduce a Diagnosis Tool - Model Co-Evolution strategy to ensure that evaluation criteria dynamically adapt as the recommendation architecture evolves. Extensive experiments demonstrate that Self-EvolveRec significantly outperforms state-of-the-art NAS and LLM-driven code evolution baselines in both recommendation performance and user satisfaction. Our code is available at https://github.com/Sein-Kim/self_evolverec.

Recent work such as AlphaEvolve has shown that combining LLM-driven optimization with evolutionary search can effectively improve programs, prompts, and algorithms across domains. In this paradigm, previously evaluated solutions are reused to guide the model toward new candidate solutions. Crucially, the effectiveness of this evolution process depends on the search strategy: how prior solutions are selected and varied to generate new candidates. However, most existing methods rely on fixed search strategies with predefined knobs (e.g., explore-exploit ratios) that remain static throughout execution. While effective in some settings, these approaches often fail to adapt across tasks, or even within the same task as the search space changes over time. We introduce EvoX, an adaptive evolution method that optimizes its own evolution process. EvoX jointly evolves candidate solutions and the search strategies used to generate them, continuously updating how prior solutions are selected and varied based on progress. This enables the system to dynamically shift between different search strategies during the optimization process. Across nearly 200 real-world optimization tasks, EvoX outperforms existing AI-driven evolutionary methods including AlphaEvolve, OpenEvolve, GEPA, and ShinkaEvolve on the majority of tasks.

Scientific idea generation (SIG) is critical to AI-driven autonomous research, yet existing approaches are often constrained by a static retrieval-then-generation paradigm, leading to homogeneous and insufficiently divergent ideas. In this work, we propose FlowPIE, a tightly coupled retrieval-generation framework that treats literature exploration and idea generation as a co-evolving process. FlowPIE expands literature trajectories via a flow-guided Monte Carlo Tree Search (MCTS) inspired by GFlowNets, using the quality of current ideas assessed by an LLM-based generative reward model (GRM) as a supervised signal to guide adaptive retrieval and construct a diverse, high-quality initial population. Based on this population, FlowPIE models idea generation as a test-time idea evolution process, applying selection, crossover, and mutation with the isolation island paradigm and GRM-based fitness computation to incorporate cross-domain knowledge. It effectively mitigates the information cocoons arising from over-reliance on parametric knowledge and static literature. Extensive evaluations demonstrate that FlowPIE consistently produces ideas with higher novelty, feasibility and diversity compared to strong LLM-based and agent-based frameworks, while enabling reward scaling during test time.

There has been unprecedented interest in developing agents that expand the boundary of scientific discovery, primarily by optimizing quantitative objective functions specified by scientists. However, for grand challenges in science, these objectives may only be imperfect proxies. We argue that automating objective function design is a central, yet unmet need for scientific discovery agents. In this work, we introduce the Scientific Autonomous Goal-evolving Agent (SAGA) to address this challenge. SAGA employs a bi-level architecture in which an outer loop of LLM agents analyzes optimization outcomes, proposes new objectives, and converts them into computable scoring functions, while an inner loop performs solution optimization under the current objectives. This bi-level design enables systematic exploration of the space of objectives and their trade-offs, rather than treating them as fixed inputs. We demonstrate the framework through a wide range of design applications, including antibiotics, nanobodies, functional DNA sequences, inorganic materials, and chemical processes. Notably, our experimental validation identifies a structurally novel hit with promising potency and safety profiles for E. coli in the antibiotic design task, and three de novo PD-L1 binders in the nanobody design task. These results suggest that automating objective formulation can substantially improve the effectiveness of scientific discovery agents.

Recent advances in LLMs have made automated scientific research the next frontline in the path to artificial superintelligence. However, these systems are bound either to tasks of narrow scope or the limited creative capabilities of LLMs. We propose Spacer, a scientific discovery system that develops creative and factually grounded concepts without external intervention. Spacer attempts to achieve this via 'deliberate decontextualization,' an approach that disassembles information into atomic units - keywords - and draws creativity from unexplored connections between them. Spacer consists of (i) Nuri, an inspiration engine that builds keyword sets, and (ii) the Manifesting Pipeline that refines these sets into elaborate scientific statements. Nuri extracts novel, high-potential keyword sets from a keyword graph built with 180,000 academic publications in biological fields. The Manifesting Pipeline finds links between keywords, analyzes their logical structure, validates their plausibility, and ultimately drafts original scientific concepts. According to our experiments, the evaluation metric of Nuri accurately classifies high-impact publications with an AUROC score of 0.737. Our Manifesting Pipeline also successfully reconstructs core concepts from the latest top-journal articles solely from their keyword sets. An LLM-based scoring system estimates that this reconstruction was sound for over 85% of the cases. Finally, our embedding space analysis shows that outputs from Spacer are significantly more similar to leading publications compared with those from SOTA LLMs.

Agents based on large language models have shown great potential in accelerating scientific discovery by leveraging their rich background knowledge and reasoning capabilities. In this paper, we introduce BioDiscoveryAgent, an agent that designs new experiments, reasons about their outcomes, and efficiently navigates the hypothesis space to reach desired solutions. We demonstrate our agent on the problem of designing genetic perturbation experiments, where the aim is to find a small subset out of many possible genes that, when perturbed, result in a specific phenotype (e.g., cell growth). Utilizing its biological knowledge, BioDiscoveryAgent can uniquely design new experiments without the need to train a machine learning model or explicitly design an acquisition function as in Bayesian optimization. Moreover, BioDiscoveryAgent, using Claude 3.5 Sonnet, achieves an average of 21% improvement in predicting relevant genetic perturbations across six datasets, and a 46% improvement in the harder task of non-essential gene perturbation, compared to existing Bayesian optimization baselines specifically trained for this task. Our evaluation includes one dataset that is unpublished, ensuring it is not part of the language model's training data. Additionally, BioDiscoveryAgent predicts gene combinations to perturb more than twice as accurately as a random baseline, a task so far not explored in the context of closed-loop experiment design. The agent also has access to tools for searching the biomedical literature, executing code to analyze biological datasets, and prompting another agent to critically evaluate its predictions. Overall, BioDiscoveryAgent is interpretable at every stage, representing an accessible new paradigm in the computational design of biological experiments with the potential to augment scientists' efficacy.

Large language models (LLMs) are increasingly applied to scientific research, yet prevailing science benchmarks probe decontextualized knowledge and overlook the iterative reasoning, hypothesis generation, and observation interpretation that drive scientific discovery. We introduce a scenario-grounded benchmark that evaluates LLMs across biology, chemistry, materials, and physics, where domain experts define research projects of genuine interest and decompose them into modular research scenarios from which vetted questions are sampled. The framework assesses models at two levels: (i) question-level accuracy on scenario-tied items and (ii) project-level performance, where models must propose testable hypotheses, design simulations or experiments, and interpret results. Applying this two-phase scientific discovery evaluation (SDE) framework to state-of-the-art LLMs reveals a consistent performance gap relative to general science benchmarks, diminishing return of scaling up model sizes and reasoning, and systematic weaknesses shared across top-tier models from different providers. Large performance variation in research scenarios leads to changing choices of the best performing model on scientific discovery projects evaluated, suggesting all current LLMs are distant to general scientific "superintelligence". Nevertheless, LLMs already demonstrate promise in a great variety of scientific discovery projects, including cases where constituent scenario scores are low, highlighting the role of guided exploration and serendipity in discovery. This SDE framework offers a reproducible benchmark for discovery-relevant evaluation of LLMs and charts practical paths to advance their development toward scientific discovery.

There has been a surge of interest in harnessing the reasoning capabilities of Large Language Models (LLMs) to accelerate scientific discovery. While existing approaches rely on grounding the discovery process within the relevant literature, effectiveness varies significantly with the quality and nature of the retrieved literature. We address the challenge of retrieving prior work whose concepts can inspire solutions for a given research problem, a task we define as Methodology Inspiration Retrieval (MIR). We construct a novel dataset tailored for training and evaluating retrievers on MIR, and establish baselines. To address MIR, we build the Methodology Adjacency Graph (MAG); capturing methodological lineage through citation relationships. We leverage MAG to embed an "intuitive prior" into dense retrievers for identifying patterns of methodological inspiration beyond superficial semantic similarity. This achieves significant gains of +5.4 in Recall@3 and +7.8 in Mean Average Precision (mAP) over strong baselines. Further, we adapt LLM-based re-ranking strategies to MIR, yielding additional improvements of +4.5 in Recall@3 and +4.8 in mAP. Through extensive ablation studies and qualitative analyses, we exhibit the promise of MIR in enhancing automated scientific discovery and outline avenues for advancing inspiration-driven retrieval.

To build effective therapeutics, biologists iteratively mutate antibody sequences to improve binding and stability. Proposed mutations can be informed by previous measurements or by learning from large antibody databases to predict only typical antibodies. Unfortunately, the space of typical antibodies is enormous to search, and experiments often fail to find suitable antibodies on a budget. We introduce Clone-informed Bayesian Optimization (CloneBO), a Bayesian optimization procedure that efficiently optimizes antibodies in the lab by teaching a generative model how our immune system optimizes antibodies. Our immune system makes antibodies by iteratively evolving specific portions of their sequences to bind their target strongly and stably, resulting in a set of related, evolving sequences known as a clonal family. We train a large language model, CloneLM, on hundreds of thousands of clonal families and use it to design sequences with mutations that are most likely to optimize an antibody within the human immune system. We propose to guide our designs to fit previous measurements with a twisted sequential Monte Carlo procedure. We show that CloneBO optimizes antibodies substantially more efficiently than previous methods in realistic in silico experiments and designs stronger and more stable binders in in vitro wet lab experiments.

Automated Machine Learning (AutoML) systems have been shown to efficiently build good models for new datasets. However, it is often not clear how well they can adapt when the data evolves over time. The main goal of this study is to understand the effect of data stream challenges such as concept drift on the performance of AutoML methods, and which adaptation strategies can be employed to make them more robust. To that end, we propose 6 concept drift adaptation strategies and evaluate their effectiveness on different AutoML approaches. We do this for a variety of AutoML approaches for building machine learning pipelines, including those that leverage Bayesian optimization, genetic programming, and random search with automated stacking. These are evaluated empirically on real-world and synthetic data streams with different types of concept drift. Based on this analysis, we propose ways to develop more sophisticated and robust AutoML techniques.

Discovering efficient algorithms for solving complex problems has been an outstanding challenge in mathematics and computer science, requiring substantial human expertise over the years. Recent advancements in evolutionary search with large language models (LLMs) have shown promise in accelerating the discovery of algorithms across various domains, particularly in mathematics and optimization. However, existing approaches treat the LLM as a static generator, missing the opportunity to update the model with the signal obtained from evolutionary exploration. In this work, we propose to augment LLM-based evolutionary search by continuously refining the search operator - the LLM - through reinforcement learning (RL) fine-tuning. Our method leverages evolutionary search as an exploration strategy to discover improved algorithms, while RL optimizes the LLM policy based on these discoveries. Our experiments on three combinatorial optimization tasks - bin packing, traveling salesman, and the flatpack problem - show that combining RL and evolutionary search improves discovery efficiency of improved algorithms, showcasing the potential of RL-enhanced evolutionary strategies to assist computer scientists and mathematicians for more efficient algorithm design.

Many critical applications, from autonomous scientific discovery to personalized medicine, demand systems that can both strategically acquire the most informative data and instantaneously perform inference based upon it. While amortized methods for Bayesian inference and experimental design offer part of the solution, neither approach is optimal in the most general and challenging task, where new data needs to be collected for instant inference. To tackle this issue, we introduce the Amortized Active Learning and Inference Engine (ALINE), a unified framework for amortized Bayesian inference and active data acquisition. ALINE leverages a transformer architecture trained via reinforcement learning with a reward based on self-estimated information gain provided by its own integrated inference component. This allows it to strategically query informative data points while simultaneously refining its predictions. Moreover, ALINE can selectively direct its querying strategy towards specific subsets of model parameters or designated predictive tasks, optimizing for posterior estimation, data prediction, or a mixture thereof. Empirical results on regression-based active learning, classical Bayesian experimental design benchmarks, and a psychometric model with selectively targeted parameters demonstrate that ALINE delivers both instant and accurate inference along with efficient selection of informative points.

The transition from static Large Language Models (LLMs) to self-improving agents is hindered by the lack of structured reasoning in traditional evolutionary approaches. Existing methods often struggle with premature convergence and inefficient exploration in high-dimensional code spaces. To address these challenges, we introduce LoongFlow, a self-evolving agent framework that achieves state-of-the-art solution quality with significantly reduced computational costs. Unlike "blind" mutation operators, LoongFlow integrates LLMs into a cognitive "Plan-Execute-Summarize" (PES) paradigm, effectively mapping the evolutionary search to a reasoning-heavy process. To sustain long-term architectural coherence, we incorporate a hybrid evolutionary memory system. By synergizing Multi-Island models with MAP-Elites and adaptive Boltzmann selection, this system theoretically balances the exploration-exploitation trade-off, maintaining diverse behavioral niches to prevent optimization stagnation. We instantiate LoongFlow with a General Agent for algorithmic discovery and an ML Agent for pipeline optimization. Extensive evaluations on the AlphaEvolve benchmark and Kaggle competitions demonstrate that LoongFlow outperforms leading baselines (e.g., OpenEvolve, ShinkaEvolve) by up to 60% in evolutionary efficiency while discovering superior solutions. LoongFlow marks a substantial step forward in autonomous scientific discovery, enabling the generation of expert-level solutions with reduced computational overhead.

Multi-agent systems have emerged as a powerful paradigm for automating scientific discovery. To differentiate agent behavior in the multi-agent system, current frameworks typically assign generic role-based personas such as ''reviewer'' or ''writer'' or rely on coarse grained keyword-based personas. While functional, this approach oversimplifies how human scientists operate, whose contributions are shaped by their unique research trajectories. In response, we propose INDIBATOR, a framework for molecular discovery that grounds agents in individualized scientist profiles constructed from two modalities: publication history for literature-derived knowledge and molecular history for structural priors. These agents engage in multi-turn debate through proposal, critique, and voting phases. Our evaluation demonstrates that these fine-grained individuality-grounded agents consistently outperform systems relying on coarse-grained personas, achieving competitive or state-of-the-art performance. These results validate that capturing the ``scientific DNA'' of individual agents is essential for high-quality discovery.

This paper introduces a novel Deep Researcher architecture designed to generate detailed research reports on complex PhD level topics by addressing the inherent limitations of the Parallel Scaling paradigm. Our system utilizes two key innovations: Sequential Research Plan Refinement via Reflection and a Candidates Crossover algorithm. The sequential refinement process is demonstrated as an efficient method that allows the agent to maintain a centralized Global Research Context, enabling it to look back at current progress, reason about the research plan, and intelligently make changes at runtime. This dynamic adaptation contrasts with parallel approaches, which often suffer from siloed knowledge. The Candidates Crossover algorithm further enhances search efficiency by deploying multiple LLM candidates with varied parameters to explore a larger search space, with their findings synthesized to curate a comprehensive final research response. The process concludes with One Shot Report Generation, ensuring the final document is informed by a unified narrative and high fact density. Powered by the Gemini 2.5 Pro model, our Deep Researcher was evaluated on the DeepResearch Bench, a globally recognized benchmark of 100 doctoral level research tasks. Our architecture achieved an overall score of 46.21, demonstrating superior performance by surpassing leading deep research agents such as Claude Researcher, Nvidia AIQ Research Assistant, Perplexity Research, Kimi Researcher and Grok Deeper Search present on the DeepResearch Bench actively running leaderboard. This performance marginally exceeds our previous work, Static DRA, and reinforces the finding that sequential scaling consistently outperforms the parallel self consistency paradigm.

In this white paper, we present AlphaEvolve, an evolutionary coding agent that substantially enhances capabilities of state-of-the-art LLMs on highly challenging tasks such as tackling open scientific problems or optimizing critical pieces of computational infrastructure. AlphaEvolve orchestrates an autonomous pipeline of LLMs, whose task is to improve an algorithm by making direct changes to the code. Using an evolutionary approach, continuously receiving feedback from one or more evaluators, AlphaEvolve iteratively improves the algorithm, potentially leading to new scientific and practical discoveries. We demonstrate the broad applicability of this approach by applying it to a number of important computational problems. When applied to optimizing critical components of large-scale computational stacks at Google, AlphaEvolve developed a more efficient scheduling algorithm for data centers, found a functionally equivalent simplification in the circuit design of hardware accelerators, and accelerated the training of the LLM underpinning AlphaEvolve itself. Furthermore, AlphaEvolve discovered novel, provably correct algorithms that surpass state-of-the-art solutions on a spectrum of problems in mathematics and computer science, significantly expanding the scope of prior automated discovery methods (Romera-Paredes et al., 2023). Notably, AlphaEvolve developed a search algorithm that found a procedure to multiply two 4 times 4 complex-valued matrices using 48 scalar multiplications; offering the first improvement, after 56 years, over Strassen's algorithm in this setting. We believe AlphaEvolve and coding agents like it can have a significant impact in improving solutions of problems across many areas of science and computation.

Intervention-based model steering offers a lightweight and interpretable alternative to prompting and fine-tuning. However, by adapting strong optimization objectives from fine-tuning, current methods are susceptible to overfitting and often underperform, sometimes generating unnatural outputs. We hypothesize that this is because effective steering requires the faithful identification of internal model mechanisms, not the enforcement of external preferences. To this end, we build on the principles of distributed alignment search (DAS), the standard for causal variable localization, to propose a new steering method: Concept DAS (CDAS). While we adopt the core mechanism of DAS, distributed interchange intervention (DII), we introduce a novel distribution matching objective tailored for the steering task by aligning intervened output distributions with counterfactual distributions. CDAS differs from prior work in two main ways: first, it learns interventions via weak-supervised distribution matching rather than probability maximization; second, it uses DIIs that naturally enable bi-directional steering and allow steering factors to be derived from data, reducing the effort required for hyperparameter tuning and resulting in more faithful and stable control. On AxBench, a large-scale model steering benchmark, we show that CDAS does not always outperform preference-optimization methods but may benefit more from increased model scale. In two safety-related case studies, overriding refusal behaviors of safety-aligned models and neutralizing a chain-of-thought backdoor, CDAS achieves systematic steering while maintaining general model utility. These results indicate that CDAS is complementary to preference-optimization approaches and conditionally constitutes a robust approach to intervention-based model steering. Our code is available at https://github.com/colored-dye/concept_das.

Diffusion models have shown promising generative capabilities across diverse domains, yet aligning their outputs with desired reward functions remains a challenge, particularly in cases where reward functions are non-differentiable. Some gradient-free guidance methods have been developed, but they often struggle to achieve optimal inference-time alignment. In this work, we newly frame inference-time alignment in diffusion as a search problem and propose Dynamic Search for Diffusion (DSearch), which subsamples from denoising processes and approximates intermediate node rewards. It also dynamically adjusts beam width and tree expansion to efficiently explore high-reward generations. To refine intermediate decisions, DSearch incorporates adaptive scheduling based on noise levels and a lookahead heuristic function. We validate DSearch across multiple domains, including biological sequence design, molecular optimization, and image generation, demonstrating superior reward optimization compared to existing approaches.

Machine learning has achieved remarkable success in many applications. However, existing studies are largely based on the closed-world assumption, which assumes that the environment is stationary, and the model is fixed once deployed. In many real-world applications, this fundamental and rather naive assumption may not hold because an open environment is complex, dynamic, and full of unknowns. In such cases, rejecting unknowns, discovering novelties, and then incrementally learning them, could enable models to be safe and evolve continually as biological systems do. This paper provides a holistic view of open-world machine learning by investigating unknown rejection, novel class discovery, and class-incremental learning in a unified paradigm. The challenges, principles, and limitations of current methodologies are discussed in detail. Finally, we discuss several potential directions for future research. This paper aims to provide a comprehensive introduction to the emerging open-world machine learning paradigm, to help researchers build more powerful AI systems in their respective fields, and to promote the development of artificial general intelligence.

Scientific discovery is a cumulative process and requires new ideas to be situated within an ever-expanding landscape of existing knowledge. An emerging and critical challenge is how to identify conceptually relevant prior work from rapidly growing literature, and assess how a new idea differentiates from existing research. Current embedding approaches typically conflate distinct conceptual aspects into single representations and cannot support fine-grained literature retrieval; meanwhile, LLM-based evaluators are subject to sycophancy biases, failing to provide discriminative novelty assessment. To tackle these challenges, we introduce the Ideation Space, a structured representation that decomposes scientific knowledge into three distinct dimensions, i.e., research problem, methodology, and core findings, each learned through contrastive training. This framework enables principled measurement of conceptual distance between ideas, and modeling of ideation transitions that capture the logical connections within a proposed idea. Building upon this representation, we propose a Hierarchical Sub-Space Retrieval framework for efficient, targeted literature retrieval, and a Decomposed Novelty Assessment algorithm that identifies which aspects of an idea are novel. Extensive experiments demonstrate substantial improvements, where our approach achieves Recall@30 of 0.329 (16.7% over baselines), our ideation transition retrieval reaches Hit Rate@30 of 0.643, and novelty assessment attains 0.37 correlation with expert judgments. In summary, our work provides a promising paradigm for future research on accelerating and evaluating scientific discovery.

Autonomous machine learning agents have revolutionized scientific discovery, yet they remain constrained by a Generate-Execute-Feedback paradigm. Previous approaches suffer from a severe Execution Bottleneck, as hypothesis evaluation relies strictly on expensive physical execution. To bypass these physical constraints, we internalize execution priors to substitute costly runtime checks with instantaneous predictive reasoning, drawing inspiration from World Models. In this work, we formalize the task of Data-centric Solution Preference and construct a comprehensive corpus of 18,438 pairwise comparisons. We demonstrate that LLMs exhibit significant predictive capabilities when primed with a Verified Data Analysis Report, achieving 61.5% accuracy and robust confidence calibration. Finally, we instantiate this framework in FOREAGENT, an agent that employs a Predict-then-Verify loop, achieving a 6x acceleration in convergence while surpassing execution-based baselines by +6%. Our code and dataset will be publicly available soon at https://github.com/zjunlp/predict-before-execute.

Recent advancements in meta-learning have enabled the automatic discovery of novel reinforcement learning algorithms parameterized by surrogate objective functions. To improve upon manually designed algorithms, the parameterization of this learned objective function must be expressive enough to represent novel principles of learning (instead of merely recovering already established ones) while still generalizing to a wide range of settings outside of its meta-training distribution. However, existing methods focus on discovering objective functions that, like many widely used objective functions in reinforcement learning, do not take into account the total number of steps allowed for training, or "training horizon". In contrast, humans use a plethora of different learning objectives across the course of acquiring a new ability. For instance, students may alter their studying techniques based on the proximity to exam deadlines and their self-assessed capabilities. This paper contends that ignoring the optimization time horizon significantly restricts the expressive potential of discovered learning algorithms. We propose a simple augmentation to two existing objective discovery approaches that allows the discovered algorithm to dynamically update its objective function throughout the agent's training procedure, resulting in expressive schedules and increased generalization across different training horizons. In the process, we find that commonly used meta-gradient approaches fail to discover such adaptive objective functions while evolution strategies discover highly dynamic learning rules. We demonstrate the effectiveness of our approach on a wide range of tasks and analyze the resulting learned algorithms, which we find effectively balance exploration and exploitation by modifying the structure of their learning rules throughout the agent's lifetime.

AI agents increasingly operate over extended time horizons, yet their ability to retain, organize, and recall multimodal experiences remains a critical bottleneck. Building effective lifelong memory requires navigating a vast design space spanning architecture, retrieval strategies, prompt engineering, and data pipelines; this space is too large and interconnected for manual exploration or traditional AutoML to explore effectively. We deploy an autonomous research pipeline to discover Omni-SimpleMem, a unified multimodal memory framework for lifelong AI agents. Starting from a naïve baseline (F1=0.117 on LoCoMo), the pipeline autonomously executes {sim}50 experiments across two benchmarks, diagnosing failure modes, proposing architectural modifications, and repairing data pipeline bugs, all without human intervention in the inner loop. The resulting system achieves state-of-the-art on both benchmarks, improving F1 by +411% on LoCoMo (0.117to0.598) and +214% on Mem-Gallery (0.254to0.797) relative to the initial configurations. Critically, the most impactful discoveries are not hyperparameter adjustments: bug fixes (+175%), architectural changes (+44%), and prompt engineering (+188% on specific categories) each individually exceed the cumulative contribution of all hyperparameter tuning, demonstrating capabilities fundamentally beyond the reach of traditional AutoML. We provide a taxonomy of six discovery types and identify four properties that make multimodal memory particularly suited for autoresearch, offering guidance for applying autonomous research pipelines to other AI system domains. Code is available at this https://github.com/aiming-lab/SimpleMem.

AI agents are increasingly deployed on complex, domain-specific workflows -- navigating enterprise web applications that require dozens of clicks and form fills, orchestrating multi-step research pipelines that span search, extraction, and synthesis, automating code review across unfamiliar repositories, and handling customer escalations that demand nuanced domain knowledge. Each new task domain requires painstaking, expert-driven harness engineering: designing the prompts, tools, orchestration logic, and evaluation criteria that make a foundation model effective. We present a two-level framework that automates this process. At the first level, the Harness Evolution Loop optimizes a worker agent's harness H for a single task: a Worker Agent W_{H} executes the task, an Evaluator Agent V adversarially diagnoses failures and scores performance, and an Evolution Agent E modifies the harness based on the full history of prior attempts. At the second level, the Meta-Evolution Loop optimizes the evolution protocol Λ= (W_{H}, H^{(0)}, V, E) itself across diverse tasks, learning a protocol Λ^{(text{best)} that enables rapid harness convergence on any new task -- so that adapting an agent to a novel domain requires no human harness engineering at all.} We formalize the correspondence to meta-learning and present both algorithms. The framework shifts manual harness engineering into automated harness engineering, and takes one step further -- automating the design of the automation itself.

Machine learning has emerged as a powerful tool for scientific discovery, enabling researchers to extract meaningful insights from complex datasets. For instance, it has facilitated the identification of disease-predictive genes from gene expression data, significantly advancing healthcare. However, the traditional process for analyzing such datasets demands substantial human effort and expertise for the data selection, processing, and analysis. To address this challenge, we introduce a novel framework, a Team of AI-made Scientists (TAIS), designed to streamline the scientific discovery pipeline. TAIS comprises simulated roles, including a project manager, data engineer, and domain expert, each represented by a Large Language Model (LLM). These roles collaborate to replicate the tasks typically performed by data scientists, with a specific focus on identifying disease-predictive genes. Furthermore, we have curated a benchmark dataset to assess TAIS's effectiveness in gene identification, demonstrating our system's potential to significantly enhance the efficiency and scope of scientific exploration. Our findings represent a solid step towards automating scientific discovery through large language models.

Neural Architecture Search (NAS) has garnered significant research interest due to its capability to discover architectures superior to manually designed ones. Learning text representation is crucial for text classification and other language-related tasks. The NAS model used in text classification does not have a Hybrid hierarchical structure, and there is no restriction on the architecture structure, due to which the search space becomes very large and mostly redundant, so the existing RL models are not able to navigate the search space effectively. Also, doing a flat architecture search leads to an unorganised search space, which is difficult to traverse. For this purpose, we propose HHNAS-AM (Hierarchical Hybrid Neural Architecture Search with Adaptive Mutation Policies), a novel approach that efficiently explores diverse architectural configurations. We introduce a few architectural templates to search on which organise the search spaces, where search spaces are designed on the basis of domain-specific cues. Our method employs mutation strategies that dynamically adapt based on performance feedback from previous iterations using Q-learning, enabling a more effective and accelerated traversal of the search space. The proposed model is fully probabilistic, enabling effective exploration of the search space. We evaluate our approach on the database id (db_id) prediction task, where it consistently discovers high-performing architectures across multiple experiments. On the Spider dataset, our method achieves an 8% improvement in test accuracy over existing baselines.

Large language models have become drivers of evolutionary search, but most systems rely on a fixed, prompt-elicited policy to sample next candidates. This limits adaptation in practical engineering and research tasks, where evaluations are expensive, and progress depends on learning task-specific search dynamics. We introduce PACEvolve++, an advisor-model reinforcement learning framework for test-time policy adaptation in evolutionary search agents. PACEvolve++ decouples strategic search decisions from implementation: a trainable advisor generates, assesses, and selects hypotheses, while a stronger frontier model translates selected hypotheses into executable candidates. To train the advisor under non-stationary feedback, we propose a phase-adaptive approach that adapts its optimization strategy to different phases of the evolutionary process. Early in evolution, it uses group-relative feedback to learn broad search preferences; later, as reward gaps compress, it emphasizes best-of-k frontier contribution to support stable refinement. Across expert-parallel load balancing, sequential recommendation, and protein fitness extrapolation, PACEvolve++ outperforms the state-of-the-art evolutionary search framework with frontier models, achieving faster convergence and stabilizing test-time training during evolutionary search.

Despite advances in scientific AI, a coherent framework for Scientific General Intelligence (SGI)-the ability to autonomously conceive, investigate, and reason across scientific domains-remains lacking. We present an operational SGI definition grounded in the Practical Inquiry Model (PIM: Deliberation, Conception, Action, Perception) and operationalize it via four scientist-aligned tasks: deep research, idea generation, dry/wet experiments, and experimental reasoning. SGI-Bench comprises over 1,000 expert-curated, cross-disciplinary samples inspired by Science's 125 Big Questions, enabling systematic evaluation of state-of-the-art LLMs. Results reveal gaps: low exact match (10--20%) in deep research despite step-level alignment; ideas lacking feasibility and detail; high code executability but low execution result accuracy in dry experiments; low sequence fidelity in wet protocols; and persistent multimodal comparative-reasoning challenges. We further introduce Test-Time Reinforcement Learning (TTRL), which optimizes retrieval-augmented novelty rewards at inference, enhancing hypothesis novelty without reference answer. Together, our PIM-grounded definition, workflow-centric benchmark, and empirical insights establish a foundation for AI systems that genuinely participate in scientific discovery.

Recent advances in multimodal large language models (MLLMs) have shown impressive reasoning capabilities. However, further enhancing existing MLLMs necessitates high-quality vision-language datasets with carefully curated task complexities, which are both costly and challenging to scale. Although recent self-improving models that iteratively refine themselves offer a feasible solution, they still suffer from two core challenges: (i) most existing methods augment visual or textual data separately, resulting in discrepancies in data complexity (e.g., over-simplified diagrams paired with redundant textual descriptions); and (ii) the evolution of data and models is also separated, leading to scenarios where models are exposed to tasks with mismatched difficulty levels. To address these issues, we propose C2-Evo, an automatic, closed-loop self-improving framework that jointly evolves both training data and model capabilities. Specifically, given a base dataset and a base model, C2-Evo enhances them by a cross-modal data evolution loop and a data-model evolution loop. The former loop expands the base dataset by generating complex multimodal problems that combine structured textual sub-problems with iteratively specified geometric diagrams, while the latter loop adaptively selects the generated problems based on the performance of the base model, to conduct supervised fine-tuning and reinforcement learning alternately. Consequently, our method continuously refines its model and training data, and consistently obtains considerable performance gains across multiple mathematical reasoning benchmarks. Our code, models, and datasets will be released.

Repeated Sampling (RS) is a simple inference-time algorithm that has been shown to improve model performance on complex tasks. Although it is an effective way of scaling inference time, it often struggles to generate diverse solution candidates, frequently relying on the same underlying approach to solve the problem and thus producing redundant samples. To address this limitation, we propose a new inference algorithm, GuidedSampling, which decouples the exploration and generation phases during inference, increasing diversity of generated candidate solutions. The exploration phase identifies multiple concepts that can be utilized to solve the problem, while the generation phase applies a specific concept to provide final solution candidates. We first define the theoretical bounds of GuidedSampling and then empirically demonstrate that it improves the performance of base model at pass@50 by on an average ~21.6% across various benchmarks compared to RS. Furthermore, models trained on trajectories of GuidedSampling exhibit substantial performance improvements at pass@5 by on an average ~9.7%, compared to models trained on traditional RS. Additionally, models trained with GuidedSampling increases the average number of concepts per instance (1.67 -> 3.03), yielding a diverse set of candidates than traditional RS.

We present an agentic, autonomous graph expansion framework that iteratively structures and refines knowledge in situ. Unlike conventional knowledge graph construction methods relying on static extraction or single-pass learning, our approach couples a reasoning-native large language model with a continually updated graph representation. At each step, the system actively generates new concepts and relationships, merges them into a global graph, and formulates subsequent prompts based on its evolving structure. Through this feedback-driven loop, the model organizes information into a scale-free network characterized by hub formation, stable modularity, and bridging nodes that link disparate knowledge clusters. Over hundreds of iterations, new nodes and edges continue to appear without saturating, while centrality measures and shortest path distributions evolve to yield increasingly distributed connectivity. Our analysis reveals emergent patterns, such as the rise of highly connected 'hub' concepts and the shifting influence of 'bridge' nodes, indicating that agentic, self-reinforcing graph construction can yield open-ended, coherent knowledge structures. Applied to materials design problems, we present compositional reasoning experiments by extracting node-specific and synergy-level principles to foster genuinely novel knowledge synthesis, yielding cross-domain ideas that transcend rote summarization and strengthen the framework's potential for open-ended scientific discovery. We discuss other applications in scientific discovery and outline future directions for enhancing scalability and interpretability.

Multi-turn-to-single-turn (M2S) compresses iterative red-teaming into one structured prompt, but prior work relied on a handful of manually written templates. We present X-Teaming Evolutionary M2S, an automated framework that discovers and optimizes M2S templates through language-model-guided evolution. The system pairs smart sampling from 12 sources with an LLM-as-judge inspired by StrongREJECT and records fully auditable logs. Maintaining selection pressure by setting the success threshold to theta = 0.70, we obtain five evolutionary generations, two new template families, and 44.8% overall success (103/230) on GPT-4.1. A balanced cross-model panel of 2,500 trials (judge fixed) shows that structural gains transfer but vary by target; two models score zero at the same threshold. We also find a positive coupling between prompt length and score, motivating length-aware judging. Our results demonstrate that structure-level search is a reproducible route to stronger single-turn probes and underscore the importance of threshold calibration and cross-model evaluation. Code, configurations, and artifacts are available at https://github.com/hyunjun1121/M2S-x-teaming.

The rapid advancement in capabilities of large language models (LLMs) raises a pivotal question: How can LLMs accelerate scientific discovery? This work tackles the crucial first stage of research, generating novel hypotheses. While recent work on automated hypothesis generation focuses on multi-agent frameworks and extending test-time compute, none of the approaches effectively incorporate transparency and steerability through a synergistic Human-in-the-loop (HITL) approach. To address this gap, we introduce IRIS: Interactive Research Ideation System, an open-source platform designed for researchers to leverage LLM-assisted scientific ideation. IRIS incorporates innovative features to enhance ideation, including adaptive test-time compute expansion via Monte Carlo Tree Search (MCTS), fine-grained feedback mechanism, and query-based literature synthesis. Designed to empower researchers with greater control and insight throughout the ideation process. We additionally conduct a user study with researchers across diverse disciplines, validating the effectiveness of our system in enhancing ideation. We open-source our code at https://github.com/Anikethh/IRIS-Interactive-Research-Ideation-System

The development of powerful natural language models have increased the ability to learn meaningful representations of protein sequences. In addition, advances in high-throughput mutagenesis, directed evolution, and next-generation sequencing have allowed for the accumulation of large amounts of labeled fitness data. Leveraging these two trends, we introduce Regularized Latent Space Optimization (ReLSO), a deep transformer-based autoencoder which features a highly structured latent space that is trained to jointly generate sequences as well as predict fitness. Through regularized prediction heads, ReLSO introduces a powerful protein sequence encoder and novel approach for efficient fitness landscape traversal. Using ReLSO, we explicitly model the sequence-function landscape of large labeled datasets and generate new molecules by optimizing within the latent space using gradient-based methods. We evaluate this approach on several publicly-available protein datasets, including variant sets of anti-ranibizumab and GFP. We observe a greater sequence optimization efficiency (increase in fitness per optimization step) by ReLSO compared to other approaches, where ReLSO more robustly generates high-fitness sequences. Furthermore, the attention-based relationships learned by the jointly-trained ReLSO models provides a potential avenue towards sequence-level fitness attribution information.

This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential evolutionary knowledge from the universe of natural protein sequences, to acquire an immediate capability to design preferable protein sequences for given folds. We conduct a structural surgery on pLMs, where a lightweight structural adapter is implanted into pLMs and endows it with structural awareness. During inference, iterative refinement is performed to effectively optimize the generated protein sequences. Experiments show that LM-Design improves the state-of-the-art results by a large margin, leading to up to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65%/56.63% on CATH 4.2/4.3 single-chain benchmarks, and >60% when designing protein complexes). We provide extensive and in-depth analyses, which verify that LM-Design can (1) indeed leverage both structural and sequential knowledge to accurately handle structurally non-deterministic regions, (2) benefit from scaling data and model size, and (3) generalize to other proteins (e.g., antibodies and de novo proteins)

Hypothesis ranking is a crucial component of automated scientific discovery, particularly in natural sciences where wet-lab experiments are costly and throughput-limited. Existing approaches focus on pre-experiment ranking, relying solely on large language model's internal reasoning without incorporating empirical outcomes from experiments. We introduce the task of experiment-guided ranking, which aims to prioritize candidate hypotheses based on the results of previously tested ones. However, developing such strategies is challenging due to the impracticality of repeatedly conducting real experiments in natural science domains. To address this, we propose a simulator grounded in three domain-informed assumptions, modeling hypothesis performance as a function of similarity to a known ground truth hypothesis, perturbed by noise. We curate a dataset of 124 chemistry hypotheses with experimentally reported outcomes to validate the simulator. Building on this simulator, we develop a pseudo experiment-guided ranking method that clusters hypotheses by shared functional characteristics and prioritizes candidates based on insights derived from simulated experimental feedback. Experiments show that our method outperforms pre-experiment baselines and strong ablations.

Machine learning research has advanced in multiple aspects, including model structures and learning methods. The effort to automate such research, known as AutoML, has also made significant progress. However, this progress has largely focused on the architecture of neural networks, where it has relied on sophisticated expert-designed layers as building blocks---or similarly restrictive search spaces. Our goal is to show that AutoML can go further: it is possible today to automatically discover complete machine learning algorithms just using basic mathematical operations as building blocks. We demonstrate this by introducing a novel framework that significantly reduces human bias through a generic search space. Despite the vastness of this space, evolutionary search can still discover two-layer neural networks trained by backpropagation. These simple neural networks can then be surpassed by evolving directly on tasks of interest, e.g. CIFAR-10 variants, where modern techniques emerge in the top algorithms, such as bilinear interactions, normalized gradients, and weight averaging. Moreover, evolution adapts algorithms to different task types: e.g., dropout-like techniques appear when little data is available. We believe these preliminary successes in discovering machine learning algorithms from scratch indicate a promising new direction for the field.

AI is increasingly playing a pivotal role in transforming how scientific discoveries are made. We introduce The AI Scientist-v2, an end-to-end agentic system capable of producing the first entirely AI generated peer-review-accepted workshop paper. This system iteratively formulates scientific hypotheses, designs and executes experiments, analyzes and visualizes data, and autonomously authors scientific manuscripts. Compared to its predecessor (v1, Lu et al., 2024 arXiv:2408.06292), The AI Scientist-v2 eliminates the reliance on human-authored code templates, generalizes effectively across diverse machine learning domains, and leverages a novel progressive agentic tree-search methodology managed by a dedicated experiment manager agent. Additionally, we enhance the AI reviewer component by integrating a Vision-Language Model (VLM) feedback loop for iterative refinement of content and aesthetics of the figures. We evaluated The AI Scientist-v2 by submitting three fully autonomous manuscripts to a peer-reviewed ICLR workshop. Notably, one manuscript achieved high enough scores to exceed the average human acceptance threshold, marking the first instance of a fully AI-generated paper successfully navigating a peer review. This accomplishment highlights the growing capability of AI in conducting all aspects of scientific research. We anticipate that further advancements in autonomous scientific discovery technologies will profoundly impact human knowledge generation, enabling unprecedented scalability in research productivity and significantly accelerating scientific breakthroughs, greatly benefiting society at large. We have open-sourced the code at https://github.com/SakanaAI/AI-Scientist-v2 to foster the future development of this transformative technology. We also discuss the role of AI in science, including AI safety.

Many fields use search algorithms, which automatically explore a search space to find high-performing solutions: chemists search through the space of molecules to discover new drugs; engineers search for stronger, cheaper, safer designs, scientists search for models that best explain data, etc. The goal of search algorithms has traditionally been to return the single highest-performing solution in a search space. Here we describe a new, fundamentally different type of algorithm that is more useful because it provides a holistic view of how high-performing solutions are distributed throughout a search space. It creates a map of high-performing solutions at each point in a space defined by dimensions of variation that a user gets to choose. This Multi-dimensional Archive of Phenotypic Elites (MAP-Elites) algorithm illuminates search spaces, allowing researchers to understand how interesting attributes of solutions combine to affect performance, either positively or, equally of interest, negatively. For example, a drug company may wish to understand how performance changes as the size of molecules and their cost-to-produce vary. MAP-Elites produces a large diversity of high-performing, yet qualitatively different solutions, which can be more helpful than a single, high-performing solution. Interestingly, because MAP-Elites explores more of the search space, it also tends to find a better overall solution than state-of-the-art search algorithms. We demonstrate the benefits of this new algorithm in three different problem domains ranging from producing modular neural networks to designing simulated and real soft robots. Because MAP- Elites (1) illuminates the relationship between performance and dimensions of interest in solutions, (2) returns a set of high-performing, yet diverse solutions, and (3) improves finding a single, best solution, it will advance science and engineering.

Foundation models (FMs), such as GPT-4 and AlphaFold, are reshaping the landscape of scientific research. Beyond accelerating tasks such as hypothesis generation, experimental design, and result interpretation, they prompt a more fundamental question: Are FMs merely enhancing existing scientific methodologies, or are they redefining the way science is conducted? In this paper, we argue that FMs are catalyzing a transition toward a new scientific paradigm. We introduce a three-stage framework to describe this evolution: (1) Meta-Scientific Integration, where FMs enhance workflows within traditional paradigms; (2) Hybrid Human-AI Co-Creation, where FMs become active collaborators in problem formulation, reasoning, and discovery; and (3) Autonomous Scientific Discovery, where FMs operate as independent agents capable of generating new scientific knowledge with minimal human intervention. Through this lens, we review current applications and emerging capabilities of FMs across existing scientific paradigms. We further identify risks and future directions for FM-enabled scientific discovery. This position paper aims to support the scientific community in understanding the transformative role of FMs and to foster reflection on the future of scientific discovery. Our project is available at https://github.com/usail-hkust/Awesome-Foundation-Models-for-Scientific-Discovery.

Modern artificial intelligence excels at statistical interpolation within seen manifolds but fundamentally fails at the exact reasoning required for theoretical physics and mathematics. We identify the "Float Wall" -- a catastrophic collapse of neural extrapolation at scales beyond 10^{16} -- caused by standard floating-point representation and linguistic tokenization (BPE). To resolve this, we introduce the Active Discoverer Framework, a digit-native neuro-symbolic architecture designed for invariant discovery. At its core is NumberNet, a Siamese Arithmetic Transformer that utilizes least-significant-bit (LSB) sequence encoding to achieve 0% precision loss and cosmic-scale extrapolation up to 10^{50}. To enforce physical grounding, we implement a Hamiltonian-based energy descent and Symmetry Grouping layer, ensuring the model respects Noether's theorem natively. The primary innovation is the Symbolic LaTeX Bottleneck: an active discovery loop where the model is forced to hypothesize unknown physical variables through an autoregressive LaTeX decoder. By reconciling numeric "hallucinations" with structurally valid mathematical expressions, the framework ensures that any discovered physics is parsimonious and human-interpretable. We evaluate this system against a 30-billion scale benchmark and the Universal Physics Pantheon, featuring 50 "Chaos Mode" systemic perturbations. Our results demonstrate that while traditional GBDT and LLM-based architectures collapse at cosmic scales, the Active Discoverer autonomously deduces universal constants such as the Gravitational Constant (G) with high fidelity. This framework establishes a path toward zero-hallucination artificial intelligence and truly autonomous scientific research agents.

State-of-the-art systems in deep question answering proceed as follows: (1) an initial document retrieval selects relevant documents, which (2) are then processed by a neural network in order to extract the final answer. Yet the exact interplay between both components is poorly understood, especially concerning the number of candidate documents that should be retrieved. We show that choosing a static number of documents -- as used in prior research -- suffers from a noise-information trade-off and yields suboptimal results. As a remedy, we propose an adaptive document retrieval model. This learns the optimal candidate number for document retrieval, conditional on the size of the corpus and the query. We report extensive experimental results showing that our adaptive approach outperforms state-of-the-art methods on multiple benchmark datasets, as well as in the context of corpora with variable sizes.

Test-Time Learning (TTL) enables language agents to iteratively refine their performance through repeated interactions with the environment at inference time. At the core of TTL is an adaptation policy that updates the actor policy based on experience from previous episodes, thereby improving future behavior. Existing methods rely on fixed, hand-crafted adaptation policies rather than optimizing them for downstream improvement. We argue that optimal adaptation policies should be learned from task environments, not hand-engineered based on human intuition. To achieve this, we introduce Meta-TTL, a framework that formulates the discovery of effective adaptation policies as a bi-level optimization problem. Within this framework, the inner loop executes the standard TTL process, measuring how effectively a candidate adaptation policy helps an agent correct errors across sequential episodes. Guided by the agent's performance, the outer loop employs evolutionary search over a diverse distribution of training tasks to iteratively refine the adaptation policy. We evaluate Meta-TTL on Jericho and WebArena-Lite across both in-distribution (ID) and out-of-distribution (OOD) settings, using multiple meta-agent backbones. Results on both benchmarks show that Meta-TTL consistently outperforms hand-crafted baselines, suggesting that the optimized adaptation policy encodes transferable strategies that generalize beyond the training task distribution.

How can we use AI to discover a new state of the art for a scientific problem? Prior work in test-time scaling, such as AlphaEvolve, performs search by prompting a frozen LLM. We perform reinforcement learning at test time, so the LLM can continue to train, but now with experience specific to the test problem. This form of continual learning is quite special, because its goal is to produce one great solution rather than many good ones on average, and to solve this very problem rather than generalize to other problems. Therefore, our learning objective and search subroutine are designed to prioritize the most promising solutions. We call this method Test-Time Training to Discover (TTT-Discover). Following prior work, we focus on problems with continuous rewards. We report results for every problem we attempted, across mathematics, GPU kernel engineering, algorithm design, and biology. TTT-Discover sets the new state of the art in almost all of them: (i) Erdős' minimum overlap problem and an autocorrelation inequality; (ii) a GPUMode kernel competition (up to 2times faster than prior art); (iii) past AtCoder algorithm competitions; and (iv) denoising problem in single-cell analysis. Our solutions are reviewed by experts or the organizers. All our results are achieved with an open model, OpenAI gpt-oss-120b, and can be reproduced with our publicly available code, in contrast to previous best results that required closed frontier models. Our test-time training runs are performed using Tinker, an API by Thinking Machines, with a cost of only a few hundred dollars per problem.

Recent studies have demonstrated the strong empirical performance of diffusion models on discrete sequences across domains from natural language to biological sequence generation. For example, in the protein inverse folding task, conditional diffusion models have achieved impressive results in generating natural-like sequences that fold back into the original structure. However, practical design tasks often require not only modeling a conditional distribution but also optimizing specific task objectives. For instance, we may prefer protein sequences with high stability. To address this, we consider the scenario where we have pre-trained discrete diffusion models that can generate natural-like sequences, as well as reward models that map sequences to task objectives. We then formulate the reward maximization problem within discrete diffusion models, analogous to reinforcement learning (RL), while minimizing the KL divergence against pretrained diffusion models to preserve naturalness. To solve this RL problem, we propose a novel algorithm, DRAKES, that enables direct backpropagation of rewards through entire trajectories generated by diffusion models, by making the originally non-differentiable trajectories differentiable using the Gumbel-Softmax trick. Our theoretical analysis indicates that our approach can generate sequences that are both natural-like and yield high rewards. While similar tasks have been recently explored in diffusion models for continuous domains, our work addresses unique algorithmic and theoretical challenges specific to discrete diffusion models, which arise from their foundation in continuous-time Markov chains rather than Brownian motion. Finally, we demonstrate the effectiveness of DRAKES in generating DNA and protein sequences that optimize enhancer activity and protein stability, respectively, important tasks for gene therapies and protein-based therapeutics.

In the Reinforcement Learning (RL) framework, the learning is guided through a reward signal. This means that in situations of sparse rewards the agent has to focus on exploration, in order to discover which action, or set of actions leads to the reward. RL agents usually struggle with this. Exploration is the focus of Quality-Diversity (QD) methods. In this thesis, we approach the problem of sparse rewards with these algorithms, and in particular with Novelty Search (NS). This is a method that only focuses on the diversity of the possible policies behaviors. The first part of the thesis focuses on learning a representation of the space in which the diversity of the policies is evaluated. In this regard, we propose the TAXONS algorithm, a method that learns a low-dimensional representation of the search space through an AutoEncoder. While effective, TAXONS still requires information on when to capture the observation used to learn said space. For this, we study multiple ways, and in particular the signature transform, to encode information about the whole trajectory of observations. The thesis continues with the introduction of the SERENE algorithm, a method that can efficiently focus on the interesting parts of the search space. This method separates the exploration of the search space from the exploitation of the reward through a two-alternating-steps approach. The exploration is performed through NS. Any discovered reward is then locally exploited through emitters. The third and final contribution combines TAXONS and SERENE into a single approach: STAX. Throughout this thesis, we introduce methods that lower the amount of prior information needed in sparse rewards settings. These contributions are a promising step towards the development of methods that can autonomously explore and find high-performance policies in a variety of sparse rewards settings.

Can the rapid advances in code generation, function calling, and data analysis using large language models (LLMs) help automate the search and verification of hypotheses purely from a set of provided datasets? To evaluate this question, we present DiscoveryBench, the first comprehensive benchmark that formalizes the multi-step process of data-driven discovery. The benchmark is designed to systematically assess current model capabilities in discovery tasks and provide a useful resource for improving them. Our benchmark contains 264 tasks collected across 6 diverse domains, such as sociology and engineering, by manually deriving discovery workflows from published papers to approximate the real-world challenges faced by researchers, where each task is defined by a dataset, its metadata, and a discovery goal in natural language. We additionally provide 903 synthetic tasks to conduct controlled evaluations across task complexity. Furthermore, our structured formalism of data-driven discovery enables a facet-based evaluation that provides useful insights into different failure modes. We evaluate several popular LLM-based reasoning frameworks using both open and closed LLMs as baselines on DiscoveryBench and find that even the best system scores only 25%. Our benchmark, thus, illustrates the challenges in autonomous data-driven discovery and serves as a valuable resource for the community to make progress.

Large Language Models (LLMs) and LLM-based agents show great promise in accelerating scientific research. Existing benchmarks for measuring this potential and guiding future development continue to evolve from pure recall and rote knowledge tasks, towards more practical work such as literature review and experimental planning. Bioinformatics is a domain where fully autonomous AI-driven discovery may be near, but no extensive benchmarks for measuring progress have been introduced to date. We therefore present the Bioinformatics Benchmark (BixBench), a dataset comprising over 50 real-world scenarios of practical biological data analysis with nearly 300 associated open-answer questions designed to measure the ability of LLM-based agents to explore biological datasets, perform long, multi-step analytical trajectories, and interpret the nuanced results of those analyses. We evaluate the performance of two frontier LLMs (GPT-4o and Claude 3.5 Sonnet) using a custom agent framework we open source. We find that even the latest frontier models only achieve 17% accuracy in the open-answer regime, and no better than random in a multiple-choice setting. By exposing the current limitations of frontier models, we hope BixBench can spur the development of agents capable of conducting rigorous bioinformatic analysis and accelerate scientific discovery.

Recent progress in autonomous code generation has fueled excitement around AI agents capable of accelerating scientific discovery by running experiments. However, there is currently no benchmark that evaluates whether such agents can implement scientific ideas when given varied amounts of code as a starting point, interpolating between reproduction (running code) and from-scratch replication (fully re-implementing and running code). We introduce AutoExperiment, a benchmark that evaluates AI agents' ability to implement and run machine learning experiments based on natural language descriptions in research papers. In each task, agents are given a research paper, a codebase with key functions masked out, and a command to run the experiment. The goal is to generate the missing code, execute the experiment in a sandboxed environment, and reproduce the results. AutoExperiment scales in difficulty by varying the number of missing functions n, ranging from partial reproduction to full replication. We evaluate state-of-the-art agents and find that performance degrades rapidly as n increases. Agents that can dynamically interact with the environment (e.g. to debug their code) can outperform agents in fixed "agentless" harnesses, and there exists a significant gap between single-shot and multi-trial success rates (Pass@1 vs. Pass@5), motivating verifier approaches to our benchmark. Our findings highlight critical challenges in long-horizon code generation, context retrieval, and autonomous experiment execution, establishing AutoExperiment as a new benchmark for evaluating progress in AI-driven scientific experimentation. Our data and code are open-sourced at https://github.com/j1mk1m/AutoExperiment .

Automated scientific discovery with large language models is transforming the research lifecycle from ideation to experimentation, yet existing agents struggle to autonomously process raw data collected from scientific experiments. We introduce SciDER, a data-centric end-to-end system that automates the research lifecycle. Unlike traditional frameworks, our specialized agents collaboratively parse and analyze raw scientific data, generate hypotheses and experimental designs grounded in specific data characteristics, and write and execute corresponding code. Evaluation on three benchmarks shows SciDER excels in specialized data-driven scientific discovery and outperforms general-purpose agents and state-of-the-art models through its self-evolving memory and critic-led feedback loop. Distributed as a modular Python package, we also provide easy-to-use PyPI packages with a lightweight web interface to accelerate autonomous, data-driven research and aim to be accessible to all researchers and developers.

Dynamic treatment regimes (DTRs) are personalized, adaptive, multi-stage treatment plans that adapt treatment decisions both to an individual's initial features and to intermediate outcomes and features at each subsequent stage, which are affected by decisions in prior stages. Examples include personalized first- and second-line treatments of chronic conditions like diabetes, cancer, and depression, which adapt to patient response to first-line treatment, disease progression, and individual characteristics. While existing literature mostly focuses on estimating the optimal DTR from offline data such as from sequentially randomized trials, we study the problem of developing the optimal DTR in an online manner, where the interaction with each individual affect both our cumulative reward and our data collection for future learning. We term this the DTR bandit problem. We propose a novel algorithm that, by carefully balancing exploration and exploitation, is guaranteed to achieve rate-optimal regret when the transition and reward models are linear. We demonstrate our algorithm and its benefits both in synthetic experiments and in a case study of adaptive treatment of major depressive disorder using real-world data.

There is a strong link between the general concept of intelligence and the ability to collect and use information. The theory of Bayes-adaptive exploration offers an attractive optimality framework for training machines to perform complex information gathering tasks. However, the computational complexity of the resulting optimal control problem has limited the diffusion of the theory to mainstream deep AI research. In this paper we exploit the inherent mathematical structure of Bayes-adaptive problems in order to dramatically simplify the problem by making the reward structure denser while simultaneously decoupling the learning of exploitation and exploration policies. The key to this simplification comes from the novel concept of cross-value (i.e. the value of being in an environment while acting optimally according to another), which we use to quantify the value of currently available information. This results in a new denser reward structure that "cashes in" all future rewards that can be predicted from the current information state. In a set of experiments we show that the approach makes it possible to learn challenging information gathering tasks without the use of shaping and heuristic bonuses in situations where the standard RL algorithms fail.

Retrieval-augmented generation (RAG) and long-context language models (LCLMs) both address context limitations of LLMs in open-domain question answering (QA). However, optimal external context to retrieve remains an open problem: fixing the retrieval size risks either wasting tokens or omitting key evidence. Existing adaptive methods like Self-RAG and Self-Route rely on iterative LLM prompting and perform well on factoid QA, but struggle with aggregation QA, where the optimal context size is both unknown and variable. We present Adaptive-k retrieval, a simple and effective single-pass method that adaptively selects the number of passages based on the distribution of the similarity scores between the query and the candidate passages. It does not require model fine-tuning, extra LLM inferences or changes to existing retriever-reader pipelines. On both factoid and aggregation QA benchmarks, Adaptive-k matches or outperforms fixed-k baselines while using up to 10x fewer tokens than full-context input, yet still retrieves 70% of relevant passages. It improves accuracy across five LCLMs and two embedding models, highlighting that dynamically adjusting context size leads to more efficient and accurate QA.

Data-driven scientific discovery requires iterative cycles of literature search, hypothesis generation, and data analysis. Substantial progress has been made towards AI agents that can automate scientific research, but all such agents remain limited in the number of actions they can take before losing coherence, thus limiting the depth of their findings. Here we present Kosmos, an AI scientist that automates data-driven discovery. Given an open-ended objective and a dataset, Kosmos runs for up to 12 hours performing cycles of parallel data analysis, literature search, and hypothesis generation before synthesizing discoveries into scientific reports. Unlike prior systems, Kosmos uses a structured world model to share information between a data analysis agent and a literature search agent. The world model enables Kosmos to coherently pursue the specified objective over 200 agent rollouts, collectively executing an average of 42,000 lines of code and reading 1,500 papers per run. Kosmos cites all statements in its reports with code or primary literature, ensuring its reasoning is traceable. Independent scientists found 79.4% of statements in Kosmos reports to be accurate, and collaborators reported that a single 20-cycle Kosmos run performed the equivalent of 6 months of their own research time on average. Furthermore, collaborators reported that the number of valuable scientific findings generated scales linearly with Kosmos cycles (tested up to 20 cycles). We highlight seven discoveries made by Kosmos that span metabolomics, materials science, neuroscience, and statistical genetics. Three discoveries independently reproduce findings from preprinted or unpublished manuscripts that were not accessed by Kosmos at runtime, while four make novel contributions to the scientific literature.

Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences. However, rather than merely generating designs that are natural, we often aim to optimize downstream reward functions while preserving the naturalness of these design spaces. Existing methods for achieving this goal often require ``differentiable'' proxy models (e.g., classifier guidance or DPS) or involve computationally expensive fine-tuning of diffusion models (e.g., classifier-free guidance, RL-based fine-tuning). In our work, we propose a new method to address these challenges. Our algorithm is an iterative sampling method that integrates soft value functions, which looks ahead to how intermediate noisy states lead to high rewards in the future, into the standard inference procedure of pre-trained diffusion models. Notably, our approach avoids fine-tuning generative models and eliminates the need to construct differentiable models. This enables us to (1) directly utilize non-differentiable features/reward feedback, commonly used in many scientific domains, and (2) apply our method to recent discrete diffusion models in a principled way. Finally, we demonstrate the effectiveness of our algorithm across several domains, including image generation, molecule generation, and DNA/RNA sequence generation. The code is available at https://github.com/masa-ue/SVDD{https://github.com/masa-ue/SVDD}.

Large Language Models (LLMs) have emerged as powerful operators for evolutionary search, yet the design of efficient search scaffolds remains ad hoc. While promising, current LLM-in-the-loop systems lack a systematic approach to managing the evolutionary process. We identify three distinct failure modes: Context Pollution, where experiment history biases future candidate generation; Mode Collapse, where agents stagnate in local minima due to poor exploration-exploitation balance; and Weak Collaboration, where rigid crossover strategies fail to leverage parallel search trajectories effectively. We introduce Progress-Aware Consistent Evolution (PACEvolve), a framework designed to robustly govern the agent's context and search dynamics, to address these challenges. PACEvolve combines hierarchical context management (HCM) with pruning to address context pollution; momentum-based backtracking (MBB) to escape local minima; and a self-adaptive sampling policy that unifies backtracking and crossover for dynamic search coordination (CE), allowing agents to balance internal refinement with cross-trajectory collaboration. We demonstrate that PACEvolve provides a systematic path to consistent, long-horizon self-improvement, achieving state-of-the-art results on LLM-SR and KernelBench, while discovering solutions surpassing the record on Modded NanoGPT.

The question-answering system for Life science research, which is characterized by the rapid pace of discovery, evolving insights, and complex interactions among knowledge entities, presents unique challenges in maintaining a comprehensive knowledge warehouse and accurate information retrieval. To address these issues, we introduce BioRAG, a novel Retrieval-Augmented Generation (RAG) with the Large Language Models (LLMs) framework. Our approach starts with parsing, indexing, and segmenting an extensive collection of 22 million scientific papers as the basic knowledge, followed by training a specialized embedding model tailored to this domain. Additionally, we enhance the vector retrieval process by incorporating a domain-specific knowledge hierarchy, which aids in modeling the intricate interrelationships among each query and context. For queries requiring the most current information, BioRAG deconstructs the question and employs an iterative retrieval process incorporated with the search engine for step-by-step reasoning. Rigorous experiments have demonstrated that our model outperforms fine-tuned LLM, LLM with search engines, and other scientific RAG frameworks across multiple life science question-answering tasks.

Performing Reinforcement Learning in sparse rewards settings, with very little prior knowledge, is a challenging problem since there is no signal to properly guide the learning process. In such situations, a good search strategy is fundamental. At the same time, not having to adapt the algorithm to every single problem is very desirable. Here we introduce TAXONS, a Task Agnostic eXploration of Outcome spaces through Novelty and Surprise algorithm. Based on a population-based divergent-search approach, it learns a set of diverse policies directly from high-dimensional observations, without any task-specific information. TAXONS builds a repertoire of policies while training an autoencoder on the high-dimensional observation of the final state of the system to build a low-dimensional outcome space. The learned outcome space, combined with the reconstruction error, is used to drive the search for new policies. Results show that TAXONS can find a diverse set of controllers, covering a good part of the ground-truth outcome space, while having no information about such space.

We theoretically explore the relationship between sample-efficiency and adaptivity in reinforcement learning. An algorithm is sample-efficient if it uses a number of queries n to the environment that is polynomial in the dimension d of the problem. Adaptivity refers to the frequency at which queries are sent and feedback is processed to update the querying strategy. To investigate this interplay, we employ a learning framework that allows sending queries in K batches, with feedback being processed and queries updated after each batch. This model encompasses the whole adaptivity spectrum, ranging from non-adaptive 'offline' (K=1) to fully adaptive (K=n) scenarios, and regimes in between. For the problems of policy evaluation and best-policy identification under d-dimensional linear function approximation, we establish Omega(log log d) lower bounds on the number of batches K required for sample-efficient algorithms with n = O(poly(d)) queries. Our results show that just having adaptivity (K>1) does not necessarily guarantee sample-efficiency. Notably, the adaptivity-boundary for sample-efficiency is not between offline reinforcement learning (K=1), where sample-efficiency was known to not be possible, and adaptive settings. Instead, the boundary lies between different regimes of adaptivity and depends on the problem dimension.

The increasing adoption of Large Language Models (LLMs) has enabled AI scientists to perform complex end-to-end scientific discovery tasks requiring coordination of specialized roles, including idea generation and experimental execution. However, most state-of-the-art AI scientist systems rely on static, hand-designed pipelines and fail to adapt based on accumulated interaction histories. As a result, these systems overlook promising research directions, repeat failed experiments, and pursue infeasible ideas. To address this, we introduce EvoScientist, an evolving multi-agent AI scientist framework that continuously improves research strategies through persistent memory and self-evolution. EvoScientist comprises three specialized agents: a Researcher Agent (RA) for scientific idea generation, an Engineer Agent (EA) for experiment implementation and execution, and an Evolution Manager Agent (EMA) that distills insights from prior interactions into reusable knowledge. EvoScientist contains two persistent memory modules: (i) an ideation memory, which summarizes feasible research directions from top-ranked ideas while recording previously unsuccessful directions; and (ii) an experimentation memory, which captures effective data processing and model training strategies derived from code search trajectories and best-performing implementations. These modules enable the RA and EA to retrieve relevant prior strategies, improving idea quality and code execution success rates over time. Experiments show that EvoScientist outperforms 7 open-source and commercial state-of-the-art systems in scientific idea generation, achieving higher novelty, feasibility, relevance, and clarity via automatic and human evaluation. EvoScientist also substantially improves code execution success rates through multi-agent evolution, demonstrating persistent memory's effectiveness for end-to-end scientific discovery.

Modern AI progress has been driven by ML methods that are generalizable across settings and scalable to larger regimes. As large language models demonstrate advanced capabilities in reasoning, coding, and engineering tasks, it is increasingly important to understand whether they can discover such methods rather than only apply existing ones. We introduce MLS-Bench, a benchmark for evaluating whether AI systems can invent generalizable and scalable ML methods. MLS-Bench contains 140 tasks across 12 domains, each requiring an agent to improve one targeted component of an ML system or algorithm and demonstrate that the improvement generalizes across controlled settings and scales. We find that current agents remain far from reliably surpassing human-designed methods, and that engineering-style tuning is easier for them than genuine method invention. We further study the effects of test-time scaling, adaptive compute allocation, and context provision on agents' discovery performance, together with case studies of their behavior. Our analyses suggest that the bottleneck is not only in proposing new methods, but also in the scientific insight needed to plan, validate, and scale claims about them. More search, compute, or context alone does not remove this bottleneck. We build and maintain a community platform for cumulative and comparable iteration, and release the data and code at https://mls-bench.com.

One of the grand challenges of artificial general intelligence is developing agents capable of conducting scientific research and discovering new knowledge. While frontier models have already been used as aids to human scientists, e.g. for brainstorming ideas, writing code, or prediction tasks, they still conduct only a small part of the scientific process. This paper presents the first comprehensive framework for fully automatic scientific discovery, enabling frontier large language models to perform research independently and communicate their findings. We introduce The AI Scientist, which generates novel research ideas, writes code, executes experiments, visualizes results, describes its findings by writing a full scientific paper, and then runs a simulated review process for evaluation. In principle, this process can be repeated to iteratively develop ideas in an open-ended fashion, acting like the human scientific community. We demonstrate its versatility by applying it to three distinct subfields of machine learning: diffusion modeling, transformer-based language modeling, and learning dynamics. Each idea is implemented and developed into a full paper at a cost of less than $15 per paper. To evaluate the generated papers, we design and validate an automated reviewer, which we show achieves near-human performance in evaluating paper scores. The AI Scientist can produce papers that exceed the acceptance threshold at a top machine learning conference as judged by our automated reviewer. This approach signifies the beginning of a new era in scientific discovery in machine learning: bringing the transformative benefits of AI agents to the entire research process of AI itself, and taking us closer to a world where endless affordable creativity and innovation can be unleashed on the world's most challenging problems. Our code is open-sourced at https://github.com/SakanaAI/AI-Scientist

Increasing the thinking budget of AI models can significantly improve accuracy, but not all questions warrant the same amount of reasoning. Users may prefer to allocate different amounts of reasoning effort depending on how they value output quality versus latency and cost. To leverage this tradeoff effectively, users need fine-grained control over the amount of thinking used for a particular query, but few approaches enable such control. Existing methods require users to specify the absolute number of desired tokens, but this requires knowing the difficulty of the problem beforehand to appropriately set the token budget for a query. To address these issues, we propose Adaptive Effort Control, a self-adaptive reinforcement learning method that trains models to use a user-specified fraction of tokens relative to the current average chain-of-thought length for each query. This approach eliminates dataset- and phase-specific tuning while producing better cost-accuracy tradeoff curves compared to standard methods. Users can dynamically adjust the cost-accuracy trade-off through a continuous effort parameter specified at inference time. We observe that the model automatically learns to allocate resources proportionally to the task difficulty and, across model scales ranging from 1.5B to 32B parameters, our approach enables a 2-3x reduction in chain-of-thought length while maintaining or improving performance relative to the base model used for RL training.

The study of biological materials and bio-inspired materials science is well established; however, surprisingly little knowledge has been systematically translated to engineering solutions. To accelerate discovery and guide insights, an open-source autoregressive transformer large language model (LLM), BioinspiredLLM, is reported. The model was finetuned with a corpus of over a thousand peer-reviewed articles in the field of structural biological and bio-inspired materials and can be prompted to recall information, assist with research tasks, and function as an engine for creativity. The model has proven that it is able to accurately recall information about biological materials and is further enhanced with enhanced reasoning ability, as well as with retrieval-augmented generation to incorporate new data during generation that can also help to traceback sources, update the knowledge base, and connect knowledge domains. BioinspiredLLM also has been shown to develop sound hypotheses regarding biological materials design and remarkably so for materials that have never been explicitly studied before. Lastly, the model showed impressive promise in collaborating with other generative artificial intelligence models in a workflow that can reshape the traditional materials design process. This collaborative generative artificial intelligence method can stimulate and enhance bio-inspired materials design workflows. Biological materials are at a critical intersection of multiple scientific fields and models like BioinspiredLLM help to connect knowledge domains.

Test-time compute scaling has emerged as a new axis along which to improve model accuracy, where additional computation is used at inference time to allow the model to think longer for more challenging problems. One promising approach for test-time compute scaling is search against a process reward model, where a model generates multiple potential candidates at each step of the search, and these partial trajectories are then scored by a separate reward model in order to guide the search process. The diversity of trajectories in the tree search process affects the accuracy of the search, since increasing diversity promotes more exploration. However, this diversity comes at a cost, as divergent trajectories have less KV sharing, which means they consume more memory and slow down the search process. Previous search methods either do not perform sufficient exploration, or else explore diverse trajectories but have high latency. We address this challenge by proposing Efficient Tree Search (ETS), which promotes KV sharing by pruning redundant trajectories while maintaining necessary diverse trajectories. ETS incorporates a linear programming cost model to promote KV cache sharing by penalizing the number of nodes retained, while incorporating a semantic coverage term into the cost model to ensure that we retain trajectories which are semantically different. We demonstrate how ETS can achieve 1.8times reduction in average KV cache size during the search process, leading to 1.4times increased throughput relative to prior state-of-the-art methods, with minimal accuracy degradation and without requiring any custom kernel implementation. Code is available at: https://github.com/SqueezeAILab/ETS.

Retrieval-Augmented Large Language Models (LLMs), which incorporate the non-parametric knowledge from external knowledge bases into LLMs, have emerged as a promising approach to enhancing response accuracy in several tasks, such as Question-Answering (QA). However, even though there are various approaches dealing with queries of different complexities, they either handle simple queries with unnecessary computational overhead or fail to adequately address complex multi-step queries; yet, not all user requests fall into only one of the simple or complex categories. In this work, we propose a novel adaptive QA framework, that can dynamically select the most suitable strategy for (retrieval-augmented) LLMs from the simplest to the most sophisticated ones based on the query complexity. Also, this selection process is operationalized with a classifier, which is a smaller LM trained to predict the complexity level of incoming queries with automatically collected labels, obtained from actual predicted outcomes of models and inherent inductive biases in datasets. This approach offers a balanced strategy, seamlessly adapting between the iterative and single-step retrieval-augmented LLMs, as well as the no-retrieval methods, in response to a range of query complexities. We validate our model on a set of open-domain QA datasets, covering multiple query complexities, and show that ours enhances the overall efficiency and accuracy of QA systems, compared to relevant baselines including the adaptive retrieval approaches. Code is available at: https://github.com/starsuzi/Adaptive-RAG.

Materials discovery requires navigating vast chemical and structural spaces while satisfying multiple, often conflicting, objectives. We present LLM-guided Evolution for MAterials design (LLEMA), a unified framework that couples the scientific knowledge embedded in large language models with chemistry-informed evolutionary rules and memory-based refinement. At each iteration, an LLM proposes crystallographically specified candidates under explicit property constraints; a surrogate-augmented oracle estimates physicochemical properties; and a multi-objective scorer updates success/failure memories to guide subsequent generations. Evaluated on 14 realistic tasks spanning electronics, energy, coatings, optics, and aerospace, LLEMA discovers candidates that are chemically plausible, thermodynamically stable, and property-aligned, achieving higher hit-rates and stronger Pareto fronts than generative and LLM-only baselines. Ablation studies confirm the importance of rule-guided generation, memory-based refinement, and surrogate prediction. By enforcing synthesizability and multi-objective trade-offs, LLEMA delivers a principled pathway to accelerate practical materials discovery. Code: https://github.com/scientific-discovery/LLEMA