Large Language Model-Guided Scientific Discovery

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18 papers in the last four weeks, up 80% on the four weeks before. 0.2% of all new papers.

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Aug 31, 2026cs.CL

COGTRL: Training LLMs for Scientific Discovery Assistance using Cognitive Traces via Reinforcement Learning

Large Language Models (LLMs) trained on extensive scientific research are increasingly integrated as assistants for scientific discovery. However, most research papers omit the fine-grained cognitive process of examining constraints, failed alternatives, and iterative decisions required to achieve the desired goal. Such cognitive processes are vital for real-world scientists working toward specific goals under constraints. In this paper, we show that LLMs, when trained to produce such cognitive traces, perform better as scientific discovery assistants than when trained solely on scientific literature. We propose COGTRL, a trajectory-level reinforcement learning framework that trains LLMs to emulate cognitively grounded reasoning by jointly optimizing cognitive traces and the scientific steps produced in an interleaved manner. Across two 3B-parameter models and two scientific domains (AI and Materials Science), COGTRL improves method quality by an average of 7.85 points over comparable 3B model baselines and achieves competitive performance relative to 70B parameter models. Moreover, analysis by domain experts shows a preference for methods generated by COGTRL over the baselines.

Shrinidhi Kumbhar Santosh Mashetty Divij Handa Kevin Coutinho, Siddharth Sambhaji Ghule, Chitta Baral

Arizona State University

RL for Language Model Reasoning LLM Post-Training Large Language Model-Guided Scientific Discovery

Aug 20, 2026cs.CL

FormalTCS: Benchmarking End-to-End Frontier Formal Theoretical Computer Science Research of Large Language Models

Large language models (LLMs) have shown growing potential for automated theoretical computer science (TCS) research, yet existing benchmarks remain far from realistic research settings. We introduce \ourbenchmark, an expert-validated benchmark for evaluating LLMs on frontier, end-to-end TCS research. \ourbenchmark contains

143

instances drawn from papers accepted to STOC, FOCS, SODA, and COLT in 2025-2026, preserving paper-specific definitions, assumptions, and proof dependencies, with expert-verified Lean formalizations and proofs. Evaluations of leading LLMs reveal that current models remain far from reliably completing the full research pipeline. In particular, autoformalization is the sharpest bottleneck: the best model achieves only

11.5

on translating natural-language claims into formal theorem statements, compared with

28.6

Pass@8 when proving human-provided formal statements. Building on \ourbenchmark, we further develop an automated TCS research framework that generates, formalizes, filters, and proves new claims. Of

64

generated claims, only

6

ultimately pass expert evaluation and proof verification, indicating that beyond formalization, limited research taste remains another major barrier to autonomous TCS research.

Dingzirui Wang, Xuanliang Zhang, Keyan Xu +2

Harbin Institute of Technology

LLM Evaluation Automated Theorem Proving Autoformalization Large Language Model-Guided Scientific Discovery

Aug 16, 2026cs.LG

Large Discovery Models: Empirically-grounded Model-Based Open-Ended Search

Scientific discovery often involves optimising expensive-to-evaluate objectives over vast, structured, and open-ended hypothesis spaces, such as molecules, protein sequences, and computer programs. Generative models such as large language models (LLMs) provide expressive priors over such spaces, but their likelihoods and self-assessments are unreliable proxies for the objectives and calibrated epistemic uncertainty, especially for novel candidates outside the observed data distribution. We introduce the Large Discovery Model (LDM), an empirically grounded recurrent architecture that couples a generative model with a Bayesian non-parametric reward surrogate model. The generative model proposes and refines candidate designs, while the surrogate predicts their performance and quantifies uncertainty, yielding an uncertainty-aware value that guides candidate generation, refinement, and selection. The discovery memory and the surrogate model are continually updated as each new experimental observation arrives. We evaluate LDM on three scenarios spanning different design modalities and objectives, including neural-network training, antibody design, and molecular optimisation. Compared to LLM-only reflection or traditional statistical search across these domains, LDM achieves a

2.4\times

greater reduction in validation BPB, an

18.2\%

relative decrease in binding energy, and more than

60\%

relative gains in molecular multi-objective performance. These results suggests that LDM could serve as a general-purpose discovery engine for effective search over open-ended hypothesis spaces.

Zhongwei Yu, Yan Song, Xue Yan +9

The Hong Kong University of Science and Technology (GZ) · University College London · AI Lab, The Yangtze River Delta +3

Bayesian Optimization Large Language Model-Guided Optimization Large Language Model-Guided Scientific Discovery

Aug 13, 2026cs.AI

Beyond the Best Guess: Improving LLM Solution Coverage with Evolution Strategies

Large Language Models (LLMs) are increasingly deployed in discovery domains such as math and science. The usual approach is to present the problem to the model and use its answer as the proposed solution. However, beyond this best guess, discovery can be enhanced by increasing test-time compute. In a process called pass@k, the model is allowed to explore the solution space and generate diverse candidate solutions. Unfortunately, the standard approach to post-training LLMs through Reinforcement Learning (RL) may limit pass@k: the model's output distribution narrows around high-reward outputs, causing the solution coverage to collapse. The alternative is to use Evolution Strategies (ES), a population-based, gradient-free post-training method that optimizes directly in weight space through random perturbations. As this paper shows, ES achieves consistently higher pass@k than RL and produces a broader output distribution with greater solution coverage. This coverage in turn makes it possible to achieve better results in e.g. standard math benchmarks. Thus, ES provides a better foundation for post-training in discovery problems and other domains where diverse solution coverage is critical.

Conor F. Hayes, Elliot Meyerson, Kajetan Schweighofer +4

1Cognizant AI Lab, San Francisco · 2The University of Texas at Austin, Austin

Evolution Strategies LLM Post-Training Large Language Model-Guided Scientific Discovery

Aug 12, 2026cs.AI

Mechanist: AI as a Scientific Instrument for Discovering the Mechanisms of Intelligence

AI models have achieved remarkable success across diverse domains, yet the mechanisms underlying their capabilities and the risks they may pose remain poorly understood. As AI development becomes faster and increasingly automated, mechanistic exploration remains largely manual, widening the gap between what models can do and our ability to understand and control them. To bridge this gap, we introduce Mechanist, an agentic system that uses AI as a scientific instrument for the autonomous discovery of mechanisms underlying AI intelligence. To support autonomous mechanistic discovery, we construct an interpretability-focused knowledge graph of approximately 13,000 papers and integrate it with a multidisciplinary database of 43 million papers spanning 26 fields. We further curate a library of 32 foundational methods for mechanism analysis, causal intervention, and validation. Compared with Claude Code and existing AI-scientist systems, Mechanist generates more valuable mechanism hypotheses and executes experiments more reliably. Mechanist also demonstrates a progression from discovering model behaviors to explaining and controlling AI models. Specifically, Mechanist first uncovers a counterintuitive safety risk in scientific laboratories, showing that unsafe traits can transfer across modalities through apparently safe training data. Mechanist then develops a mechanism theory of belief, revealing how models represent world knowledge, form beliefs, infer the beliefs of others, and how these mechanisms emerge during pretraining. Finally, Mechanist translates these mechanistic insights into practical interventions that improve model performance across diverse scenarios and steer scientific foundation models toward generating DNA sequences with specified properties.

Mengru Wang, Junfeng Fang, Shuofei Qiao +16

Zhejiang University · National University of Singapore · Heriot-Watt University +3

AI Agents for Scientific Discovery Mechanistic Interpretability Large Language Model-Guided Scientific Discovery Autonomous Research Agents

Aug 11, 2026cs.AI

Tree-of-Ideas: Automated Research Ideation via Cross-Trajectory Reasoning over Scholarly Evolution

Effective research ideation requires moving beyond a static understanding of prior work to trace how research problems and solutions evolve across the literature. Existing methods either treat papers as unstructured context or model scholarly evolution as isolated citation chains, overlooking interactions among research trajectories. We propose Tree-of-Ideas (ToI), a two-stage framework. EvoTrace reconstructs branching scholarly trajectories from citations, tracking evolving methods, resolved problems, and gaps. EvoAgent then reasons across trajectories to identify convergent problems and complementary solutions, generating grounded research ideas. Across six AI research topics, ToI achieves the highest score among automatic methods (6.27 vs. 5.36 for the strongest baseline on a 10-point scale), with strong Novelty (6.36) and Groundedness (7.00). Also, its score approaches that of human-paper references (6.29), demonstrating the value of cross-path evolutionary reasoning.

Xun Li, Yiying Yang, Pengtao Li +8

Guangdong Laboratory of Artificial Intelligence and Digital Economy (SZ) · University of Melbourne · University of Sydney +4

AI Agents for Scientific Discovery Research Idea Generation Large Language Model-Guided Scientific Discovery

Aug 10, 2026cs.AI

Model Discovery Agent: LLM-assisted Bayesian experiment design for data-efficient discovery of mechanistic world models

A primary goal of science is to learn mechanistic world models from limited experimental data, both to explain observations and to predict novel interventions. We introduce the Model Discovery Agent (MDA), which combines LLM proposals for

\mathcal M

-open model discovery, experiment design based on Value of Information, and approximate Bayesian inference over model structures, parameters, and stochastic latent trajectories. We apply MDA to learn symbolic reaction rate laws for ChemBench \citep{kabra2026autoscilab}, partially observed ODE models for GlucoseBench \citep{xie2018simglucose,kovatchev2009insilico}, and partially observed SDE models for a new stochastic single-neuron simulator we create. In the appendix, we also show results on various other domains from BoxingGym \citep{gandhi2025boxinggym}. We show that MDA has improved sample efficiency compared to various baseline methods, and the learned models are good predictors but also provide interpretable abstractions of each domain.

Kevin Murphy

Dept. Computer Science Univ. British Columbia, Canada.

Dynamical Systems AI Agents for Scientific Discovery Bayesian Experimental Design Large Language Model-Guided Scientific Discovery

Aug 9, 2026cs.LG

Idea Search: Guiding Tree Search with Ideas to Explore Diverse Scientific Methods

Tree Search-based test-time scaling of LLMs is a powerful tool for automated scientific coding. However, pure Tree Search sometimes struggles with systematic exploration, becoming trapped in local optima, or unproductive loops, especially in the vast search space of scientific methods. To address this limitation, we propose Idea Search, a framework that systematically integrates a dynamic "Idea Bank" into Tree Search. Idea Search involves three steps: (1) decomposing existing methods into atomic ideas, (2) sampling from this bank of ideas to guide branches of code mutations, and (3) dynamically updating the bank with new ideas discovered through execution. On single-cell RNA-sequencing (scRNA-seq) batch integration, Idea Search reliably breaks the plateau of a strong pure Tree Search baseline, improving the mean score from 0.678 to 0.697 and reaching a best score of 0.728. We then characterize which design choices drive these gains: bank augmentation helps bandit sampling but not random sampling, "Exploratory" prompting that prioritizes new ideas surfaces the rare best-performing solutions, while increasing sampling-level exploration is counterproductive.

Xuefei Julie Wang, Hao Cui, Michael P. Brenner +1

California Institute of Technology · *Work done during an internship at Google Research. · Google Research +1

Inference-Time Search Automated Algorithm Discovery Scientific Code Generation Large Language Model-Guided Scientific Discovery

Aug 8, 2026cs.AI

Janus: An Algorithm-Evaluator Co-Evolution Framework for LLM-Driven Discovery under Expensive Evaluation Budgets

LLM-driven program discovery relies on rapid evaluator feedback, but many scientific and engineering tasks require high-fidelity simulations, hardware execution, or physical experiments, making each evaluation expensive. Cheap surrogate evaluators can reduce this cost, yet fixed surrogates are vulnerable to search-induced distribution shift and are difficult to fit reliably from sparse, search-biased labels. We introduce Janus, a framework that uses LLMs to co-evolve target programs and executable proxy evaluators. To address label scarcity, Janus leverages domain knowledge encoded in LLMs to generate task-specific evaluator programs and calibrates them using real outcomes. To mitigate distribution shift, Janus evolves evaluators alongside target programs, selects them using a promotion-aligned objective, and maintains region-conditioned portfolios with online credit updates. Because proxy predictions remain fallible, Janus uses them only to prioritize candidates and requires real validation before candidates can enter the target-program population or update the incumbent. Across five scientific and engineering design tasks, Janus achieves a larger area under the best-so-far improvement curve over the real-evaluation budget and higher final performance than a matched baseline that evolves only target programs. On average, Janus reaches 99/% of the baseline's final improvement with 59.1/% fewer real evaluations. Evolved proxy evaluators also rank promising candidates more accurately than their seed versions. Together, these results extend evaluator-guided LLM discovery from tasks with cheap, scalable feedback to scientific domains where trustworthy evaluation is scarce and expensive.

Ximeng Liu, Qianlong Wang, Yingming Mao +6

Shanghai Jiao Tong University, Shanghai, China · Baidu Inc., Beijing, China · Xi’an Jiaotong University, Xi’an, China +1

Surrogate-Assisted Optimization Large Language Model-Guided Optimization LLM-Based Program Synthesis Automated Evaluation Large Language Model-Guided Scientific Discovery

Aug 8, 2026cs.AI

Neurosymbolic Discovery of Algebraic Graph Constructions

There are several methods for searching for graphs with prescribed properties, such as SAT solvers and specialized generators. These methods return the result as raw data: an adjacency matrix or a string encoding. The raw data certifies that the graph exists, but it does not reveal any structural properties of the graph. We ask whether one can automatically discover a short algebraic description if only this raw data is provided. We look for a description such as a Cayley graph

\mathrm{Cay}(Γ, S)

or a lexicographic product

C_5[K_3]

. We address this question with a neurosymbolic approach. We propose an agent that runs on a general-purpose large language model with no fine-tuning or per-target training. The model interleaves reasoning with calls to the computer algebra system SageMath: it analyzes the target graph, proposes and tests candidate constructions, and revises them until the output matches the target. The agent communicates with SageMath through a Model Context Protocol (MCP) server, which we release as a general-purpose bridge. Whether a construction matches the target is checked by a single exact isomorphism test, and therefore rests on the symbolic side and not on the model. We test the approach on a benchmark of 100 highly symmetric graphs, namely two-orbit graphs on up to 25 vertices; the benchmark was fixed in advance. Our agent could find verified algebraic constructions for all of them, without falling back to raw encodings. A strong template-enumeration baseline reaches only about

20\%

, and a catalog lookup could not identify any of these graphs. However, construction quality declines when symmetry is removed. As a concrete application, we identify the smallest known counterexample to the Bernhart-Kainen dispersability conjecture, a

16

-vertex graph that enumeration found as raw data. For this graph, our agent found an explicit algebraic construction.

David Seka, Stefan Szeider

Algorithms and Complexity Group TU Wien, Vienna, Austria

Neuro-Symbolic Reasoning Large Language Model-Guided Scientific Discovery

Aug 7, 2026physics.acc-ph

Autonomous discovery of accelerator commissioning algorithms

Simulated commissioning has become essential for de-risking modern light-source design and commissioning, but the procedures being simulated are still designed entirely by human experts. Their labor-intensive redevelopment after lattice changes makes such studies hard to repeat and limits their use during early design iteration. This Letter demonstrates a closed research loop in which a language-model agent writes commissioning code, tests it in simulation, and improves the algorithm from the results. Applied to RF beam capture in the ALS-U accumulator-ring model, the loop substantially improves a working expert procedure and can construct a working one from a minimal starting point, with more capable models succeeding from less initial code. Extending the same framework to multiple objectives produces 16 non-dominated algorithms spanning physically distinct trade-offs between rapid beam capture and correction of seeded machine errors. This reframes commissioning studies from evaluating human-designed procedures toward a mode in which agents participate directly in discovering accelerator algorithms.

Thorsten Hellert

Lawrence Berkeley National Laboratory · Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

Automated Algorithm Discovery Large Language Model-Guided Scientific Discovery Autonomous Experimentation

Aug 5, 2026cs.LG

DASyR-LLM: Domain-Aware Symbolic Regression with LLMs for Kinetic Model Discovery

Kinetic model discovery is a central challenge in chemical engineering, as accurate rate expressions are essential for understanding and controlling chemical and biological processes. Symbolic regression (SR) has emerged as a powerful data-driven approach for identifying interpretable kinetic models, but usually operates without domain knowledge, often exploring physicochemically implausible models. Large language models (LLMs) offer a promising avenue for injecting domain expertise into this search. Here, we introduce an LLM-guided SR framework, embedding an LLM module within an iterative SR algorithm for automated kinetic model discovery. The LLM performs two roles at each iteration: (1) a qualitative physicochemical critique of the best SR candidates, and (2) the proposal of new candidate rate expressions guided by the SR-generated models and embedded chemical knowledge. Our framework is evaluated on four in silico case studies of increasing complexity, spanning heterogeneous catalysis and bioprocess systems. Results show the LLM-guided framework reduces iterations to identify the ground-truth model by

41.7-79.3\%

versus a state-of-the-art SR framework, with the LLM directly proposing the correct model structure in over half of the guided runs. In practical settings, where each iteration typically requires a new wet-lab experiment, this translates into a substantial reduction in experimental effort. Predictive performance on an independent validation set is equivalent between both approaches, with

R^2>0.98

in all case studies. Ablation studies indicate that both the SR component and the LLM scale contribute to this performance, with a reduced-size LLM largely retaining discovery efficiency. These findings demonstrate that LLMs can effectively inject domain knowledge into scientific model discovery, paving the way toward fully automated, domain-aware kinetic modelling pipelines.

Roberto Aliaga Medina, Paulina Quintanilla, Antonio del Rio Chanona

Department of Chemical Engineering Imperial College London South Kensington, London, SW7 2AZ, UK · Department of Chemical Engineering, Biotechnology, and Materials University of Chile, Santiago, Chile · Department of Chemical Engineering University College London Gower Street, London, WC1E 6BT, UK

Large Language Model-Guided Scientific Discovery Symbolic Regression

Aug 5, 2026cs.CL

A-SR: Self-Evolving Agentic LLMs for Symbolic Regression via Hierarchical Coordination

Symbolic regression aims to discover closed-form equations from data, but existing LLM-guided methods often rely on a unified proposal loop that compresses heterogeneous search failures into a scalar score and a single prompt. We propose A-SR, a self-evolving agentic framework that shifts the control unit from expression edits to role-conditioned evidence views. A-SR coordinates formula discovery through routing among coordination protocols, an online evaluator-reward role policy, and state-routed process memory. During search, evaluator feedback characterizes reliability and productivity, updates role-level utilities, and routes elite motifs, failure traces, and validity diagnostics to different agents. The framework self-evolves at two timescales: within a run, it adapts the search process without updating LLM parameters; across runs, recorded trajectories can be distilled into open-source LLMs as role-conditioned proposal priors. Averaged over the four LSR-Synth scientific domains in LLM-SRBench, A-SR improves [email protected] over baselines from 25.79% to 48.30% with Llama3.1-8B, while A-SR-LoRA improves the corresponding Qwen3-4B result from 24.58% to 38.29%. On four real-world scientific discovery tasks, A-SR obtains the best in-distribution or out-of-distribution normalized mean squared error on 7 of 8 reported metrics.

Wenxiao Zhao, Dong Liu, Kaiyi Xu +9

Shanghai AI Laboratory · University of California at Los Angeles · Tongji University

Multi-Agent LLM Systems LLM Agent Training Large Language Model-Guided Scientific Discovery Symbolic Regression

Aug 4, 2026cs.CL

Visualizing Graph-to-Answer Mechanism Recovery in Materials-Science Hypothesis Generation

AI co-scientists can generate fluent materials-science hypotheses, but fluency does not show that an answer preserves a scientifically meaningful mechanism. We present a graph-to-answer mechanism-tracing case study for Graph-PRefLexOR-8B, a Qwen3-8B model adapted to expose distinct stages for brainstorming, graph construction, pattern extraction, and synthesis. We organize semantic backtracking, graph corruption, activation-based recovery measurements, and layer-by-token-region grids into a visual diagnostic workflow for inspecting this pathway. Across 100 open-ended materials-science questions, final answers remain closest to the model's own structured stages, especially synthesis. Under graph corruption, a full sweep over 37 residual-stream checkpoints, the embedding output and 36 transformer blocks, shows little mechanism recovery in the earlier transition region at layers 7--10, recovery instead concentrates in late synthesis and answer-start regions around layers 30 and 36. The workflow is intended to help scientists and model developers identify where a generated hypothesis loses or regains mechanism support before it is passed to downstream experimental planning.

Shashwat Sourav, Subhadeep Pal, Markus J. Buehler +4

Department of Physics, Washington University in St. Louis · Oak Ridge National Laboratory · Lawrence Berkeley National Laboratory +6

LLM Reasoning with Graphs Scientific Hypothesis Generation Mechanistic Interpretability Causal Interpretability Large Language Model-Guided Scientific Discovery

Aug 4, 2026cs.AI

Large language models for partial differential equation workflows

Partial differential equations (PDEs) become actionable in science and engineering not as isolated formulae, but as executable workflows that connect modelling assumptions, governing equations, numerical solvers, diagnostics, and decisions. Large language models (LLMs) are beginning to support such workflows by linking natural language, symbolic mathematics, code, solver outputs, and feedback. Here we examine recent advances in LLM-assisted PDE research across three stages: the discovery and formulation of governing models, the generation and revision of executable numerical solvers, and the use of simulation feedback to support control, design, and optimization. Across these stages, current systems act primarily as workflow-level interfaces. Despite this progress, the field remains limited by the scarcity of high-quality datasets and benchmarks, especially for knowledge discovery and real-world applications, where expert annotation, executable problem construction, and task-level feedback require substantial domain effort. A further challenge is the persistent gap between simulation-based results and real-world scientific and engineering systems, which limits the direct transfer of numerical simulations, control policies, and optimized designs to practical settings. These challenges make LLM-assisted PDE workflows a critical testbed for developing scientific AI systems that can connect language, computation, physical constraints, and real-world decision-making.

Han Wan, Rui Zhang, Hao Sun

Gaoling School of Artificial Intelligence, Renmin University of China, Beijing 100872, China

PDE Discovery Large Language Model-Guided Optimization Large Language Model-Guided Scientific Discovery LLM Code Generation

Aug 4, 2026cs.AI

Can LLM design high-quality experiments? A Comprehensive and Systematic Benchmark on Autonomous Experimental Design

AI for Research (AI4Research) leverages AI to automate and improve scientific workflows. While experimental design is a critical stage of the research process, prior work has focused primarily on code implementation and execution, overlooking the importance of this stage, and no benchmark exists to evaluate AI's ability to conduct systematic experiment design. To bridge this gap, we propose SCOPE, a Scientific COmprehensive Planning Evaluation Benchmark constructed from 300 high-quality latest papers across 19 research domains from top-tier venues (e.g., ICML, NeurIPS, and ICLR),evaluating LLMs on two dimensions: High-Level planning completeness (main, ablation, and analysis experiments) and Low-Level configuration accuracy and rationality (datasets, baselines, and metrics). Benchmarking reveals three findings: (1) most LLMs cannot directly design high-quality experiments; (2) all LLMs exhibit a performance bottleneck in low-level configuration; and (3) search mode does not improve design quality. Furthermore, to address these challenges, we propose OptED, a novel agentic workflow to optimize LLM-based experimental design, that enhances LLM-based experimental planning through stage isolation, tool augmentation, and rule-based constraints, effectively alleviating the configuration bottleneck.

Zejun Liu, Jian Wu, Ru Peng +4

Westlake University · Zhejiang University · Nanjing University of Science and Technology +1

AI for Science Benchmark Design AI Agent Benchmarks Large Language Model-Guided Scientific Discovery Autonomous Experimentation

Aug 4, 2026cs.AI

AgentPanel: Toward a New Paradigm for Human--AI Collaboration in Exploring Scientific Questions

Identifying promising scientific ideas remains an important challenge in research practice. Researchers commonly rely on small-group discussions or one-to-one interactions with a single large language model, yet these approaches often expose them to only a limited range of perspectives and directions. We present AgentPanel, a multi-agent forum for human--AI collaboration in scientific exploration. Heterogeneous agents asynchronously discuss scientific questions in a forum-style environment, while researchers can submit questions, browse and organize candidate ideas, engage agents in follow-up interactions, and optionally generate post-hoc summary reports. We evaluate AgentPanel in terms of idea quality, exploration breadth, interaction effectiveness, candidate-selection efficiency, and practical utility. Offline experiments show that AgentPanel outperforms a centralized multi-agent debate baseline. A human study with 20 participants further shows that users value AgentPanel for perspective diversity and exploration support. In experience-based comparisons with commonly used LLM tools, 65% of participants favored AgentPanel for both breadth of research directions and overall suitability for early-stage exploration. The platform is publicly available at https://agentpanel.cc/.

Zhiyao Cui, Qianyi Wang, Haoyang Yan +26

Shanghai Artificial Intelligence Laboratory

Multi-Agent LLM Systems Scientific Hypothesis Generation Large Language Model-Guided Scientific Discovery Human-AI Collaboration

Aug 3, 2026cs.AI

Long-Horizon Autonomous Architecture Research with a Language-Model Agent: A Behavioural Case Study

We study what happens when a single general-purpose large language model acts as the sole researcher on a long-horizon neural architecture design problem. The agent receives a scientific question, an initial hypothesis and motivation, a compute budget, and research affordances (source and experiment management, experiment tracking, literature access, and persistent memory), then autonomously proposes, implements, evaluates, and records experiments over an extended period. The study comprises three phases, separated by human-declared transitions, that progressively expand the agent's tool surface or problem scale. Across approximately 100 sequential experiments, the agent improves a non-standard Vision Transformer from a weak baseline to a stronger, efficient model on small benchmarks and a usable but sub-SOTA model on ImageNet-1K, while producing a dense behavioural trace. We report four findings.(i)Productivity exhibits a clear phase structure: rapid early gains, a multi-dozen-hypothesis saturation wall, and recovery, with recovery triggered by expanding the action surface rather than changing the underlying model.(ii)A single early hypothesis contributes more to accuracy gain, with later improvements long-tailed.(iii)The preference for greedy, incremental hypotheses is largely workflow-induced: a commit-or-discard evaluation rule is isomorphic to greedy hill-climbing; the remainder reflects risk aversion after bold failures and anchoring on familiar literature. (iv)The agent independently rediscovers established results and, in the unfamiliar regime of pure channel attention, overturns a standard design choice. We conclude that workflow design was at least as influential as agent capability in this study and propose diversified search, budgeted moonshot hypotheses, explicit forks, and regime-aware re-validation as testable directions for future autonomous research.

Aon Safdar, Mohamed Saadeldin

University College Dublin, Ireland

AI Agents for Scientific Discovery Neural Architecture Search Long-Horizon LLM Agents Large Language Model-Guided Scientific Discovery Autonomous Research Agents

Jul 31, 2026cs.LG

MOT-SR: Multi-Objective Tool-Augmented Scientific Equation Discovery with Large Language Models

Symbolic Regression (SR) aims to discover analytical equations from observational data and plays a central role in scientific modeling. While recent Large Language Model (LLM) based approaches show promise, they face two limitations. First, they lack data analysis mechanisms for uncovering variable dependencies, which reduces the efficiency of equation discovery. Second, most methods rely on single-objective evaluation focused solely on fitting error. This neglect of structural complexity and generalization often causes models to converge prematurely to local optima, limiting their ability to explore the broader equation space. We propose Multi-Objective Tool-augmented Symbolic Regression (MOT-SR), a unified framework that integrates external analytical tools to extract structural priors and guide equation generation, while jointly optimizing for accuracy, complexity, and generalization via a multi-objective evaluation module that maintains a dynamic Pareto front. MOT-SR employs two collaborative LLM modules: a Meta Strategy Generator, which selects tools and synthesizes structural optimization strategies based on Pareto-optimal equations, and an Equation Generator, which produces new candidate equations accordingly. The system operates in a closed-loop manner, continuously refining both strategies and equation structures. Across 40 standard tasks, MOT-SR outperforms existing SR methods in accuracy, generalization, and efficiency. We further validate MOT-SR on extreme mass-ratio inspiral (EMRI) orbital modeling, an important problem in space-based gravitational-wave astronomy where small local errors can accumulate substantially over long-term evolution. The discovered interpretable correction achieves the lowest trajectory-level integration error on held-out configurations. These results demonstrate the potential of MOT-SR to enable reliable modeling of long-horizon scientific dynamics.

Boxiao Wang, Runxiang Wang, Kai Li +4

National Key Laboratory of Cognition and Decision Intelligence for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China · School of Advanced Interdisciplinary Sciences, University of the Chinese Academy of Sciences, Beijing, China · School of Astronomy and Space Science, University of the Chinese Academy of Sciences, Beijing, China +2

Gravitational-Wave Astronomy Scientific ML Large Language Model-Guided Scientific Discovery Symbolic Regression

Jul 31, 2026cs.AI

Scaling Scientific Discovery Environments for Turn-Level Agentic RL

Large language model agents have shown promising capabilities in data-driven scientific discovery tasks, where an agent interacts with an execution environment and produces a statistical claim. Long-horizon scientific analysis remains constrained by the lack of process supervised environments over real-world scientific data. This paper introduces SciDisco, a scalable framework for training Scientific Discovery agents in process-verifiable environments. SciThèque compiles hypotheses, datasets, hidden evidence graphs, and verifiers into task environments where analytical progress can be checked during interaction. DAG-grounded trajectory synthesis uses these environments to construct verifier-filtered multi-turn demonstrations. DiscoPO then uses the environment as the source of training signal, assigning turn-level credit to actions that produce verifiable analytical evidence. Experiments show that SciDisco-14B reaches state-of-the-art on hypothesis-driven scientific data analysis benchmarks.

Yucheng Xu, Keyi Zhang, Yuyang Yu +4

Shanghai AI Lab

Process Supervision Large Language Model-Guided Scientific Discovery RL for LLM Agents

Jul 30, 2026cs.AI

Library Reachability in LSR-Synth: How Anti-Memorization Design Changes the Measurement of Symbolic Discovery

Existing benchmarks for scientific equation discovery are largely composed of well-known equations available in the public domain, making it difficult to determine whether a model is discovering laws from data or merely recalling answers from its training corpus. LSR-Synth mitigates this problem by introducing novel synthetic terms into established scientific mechanisms and filtering the resulting tasks for novelty, solvability, and scientific plausibility. This paper examines a narrower measurement question: can these tasks further distinguish scientific priors supplied by language models from conventional operator search that does not access task semantics? We construct a semantics-free baseline using a fixed vocabulary with publicly documented provenance, and assess the role of candidate coverage through semantic blinding, library weakening, and matched operator-family knockouts. Under the current task snapshot, search budget, and scoring protocol, the fixed vocabulary already covers most tasks, while language-model-generated candidates rarely expand the set of solvable instances. Their marginal contribution becomes substantial only when vocabulary coverage is selectively disrupted. Strict out-of-distribution evaluation lowers the absolute success rates of all methods but does not alter this relationship. These findings neither invalidate LSR-Synth's controls against memorization of complete formulas nor imply that language-model priors are generally unhelpful. Rather, they support a more limited conclusion: most current tasks remain suitable for evaluating the fitting and recombination of previously unseen expressions, but are insufficient on their own to identify contributions from priors beyond a fixed search space.

Zhan'ao Yao, Liang Yin, Zhihao Gao +9

State Key Laboratory of High Performance Ceramics, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai 200050, China · Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China · School of Advanced Interdisciplinary Sciences, University of Chinese Academy of Sciences, Beijing, China +4

Synthetic Benchmark Generation Data Contamination in Language Models Large Language Model-Guided Scientific Discovery Symbolic Regression

Jul 29, 2026cs.LG

Budget-Aware LLM Discovery via Cost-Calibrated Frontier Utility

Large language models increasingly support scientific and algorithmic discovery through inference-time search over evaluated candidates. Existing adaptive discovery controllers assign credit based only on score progress, even though prompt length, retries, and guidance calls cause search actions to incur different token costs. We prove that cost-blind credit can forfeit all but a vanishing fraction of attainable quality as frontiers multiply and costs diverge. Under a fixed search-side token budget, the controller must decide which frontier is improving and whether its gain justifies the realized cost before the budget is exhausted. We introduce \textbf{CostAda}, a cost-calibrated adaptive controller built around \emph{cost-calibrated frontier utility}. The utility values frontier progress relative to realized action cost and conditions that credit on the remaining budget. CostAda uses this signal to control local exploration intensity, frontier allocation, and budgeted tactic intervention. Cost and remaining budget therefore shape the search rather than serving only as accounting variables or a stopping rule. CostAda reaches the strongest baseline's full-budget quality with at most half the budget on twelve of sixteen benchmark--backbone pairs while achieving the strongest mean final quality on all eight benchmarks under GLM-5 and GPT-5.4.

Yansen Zhang, Yilu Liu, Tianyu Liu +6

International Digital Economy Academy (IDEA) · City University of Hong Kong · Mohamed bin Zayed University of Artificial Intelligence (MBZUAI)

Inference-Time Search Automated Algorithm Discovery Cost-Aware Inference Large Language Model-Guided Scientific Discovery

Jul 29, 2026cs.DL

Scientific Knowledge Discovery in the Age of Large Language Models

The rapid growth of scholarly literature has made identifying relevant publications increasingly difficult, and conventional search systems still depend heavily on manually formulated queries and effortful manual inspection. Generative large language models (LLMs) offer a more flexible alternative, supporting literature retrieval and the screening of candidate studies against eligibility criteria. This chapter surveys 34 peer-reviewed papers applying generative LLMs to these two tasks, identified via a Boolean search over the OpenAIRE Graph (1,589 records screened to 34 inclusions). Reviewed studies are characterised by LLMs employed, model access and adaptation, prompting and architectural techniques, ground-truth sources, and evaluation metrics.

Eleni Adamidi, Serafeim Chatzopoulos, Thanasis Vergoulis

IMSI, ATHENA RC

AI-Assisted Scientific Research Information Retrieval Large Language Model-Guided Scientific Discovery

Jul 29, 2026cs.AI

EvoPINN: Agentic Discovery of Executable Algorithms for Physics-Informed Neural Networks

Physics-informed neural networks (PINNs) have emerged as a powerful paradigm for solving partial differential equations (PDEs), yet their performance heavily relies on the manual, trial-and-error engineering of neural representations, loss formulations, and optimization dynamics. While Large Language Models (LLMs) offer a promising avenue for automated design, unconstrained code generation often yields mathematically invalid or numerically unstable solutions under strict scientific computing constraints. To bridge this gap, we propose \textbf{EvoPINN}, an agentic framework that reformulates PINN development from labor-intensive manual design into a rigorous, execution-grounded algorithm discovery problem. EvoPINN navigates a modular search space by decoupling neural representations from training programs, utilizing an LLM agent to iteratively propose memory-conditioned programmatic modifications. To ensure scientific validity, all candidates undergo strict structural verification and budget-matched PDE evaluation. Extensive experiments across diverse PDE regimes (oscillatory, elliptic, dissipative, and nonlinear transport) demonstrate that EvoPINN discovers PDE-specialized learning algorithms that significantly reduce relative

L_{2}

error compared to baselines. Crucially, EvoPINN autonomously invented SLRC-PINN, a novel architecture whose performance gains persist under rigorous parameter-matched comparisons, establishing the viability of execution-grounded agents for discovering genuinely new scientific computing mechanisms.

Peng Yin, Kai Li, Yifan Zhang +1

School of Advanced Interdisciplinary Sciences, University of Chinese Academy of Sciences, Beijing, China · Institute of Automation, Chinese Academy of Sciences, Beijing, China

Automated Algorithm Discovery LLM-Based Program Synthesis Physics-Informed ML Large Language Model-Guided Scientific Discovery

Jul 28, 2026quant-ph

OmniQEC: discovering practical quantum error-correcting codes by an AI scientist

Quantum error correction (QEC) is indispensable for scalable fault-tolerant quantum computing. However, discovering QEC codes that remain effective is challenging, as logical performance depends on the interplay between code structure, hardware, syndrome extraction, and decoding, which often impose competing requirements. Here we introduce OmniQEC, an efficient AI scientist for discovering QEC codes suited to deployment on modern quantum processors. OmniQEC formulates QEC design as an iterative discovery process in which an orchestrator, implemented by advanced large language models (LLMs), coordinates code generation, code-level screening, syndrome-extraction synthesis, and decoder-based circuit evaluation. At its core, OmniQEC combines a self-evolving reasoning mechanism with a slow--fast synergistic workflow: a fast loop explores candidates using inexpensive code-level proxies, whereas a slow loop performs physically grounded circuit-level evaluation and feeds the resulting evidence back into the search. We evaluate OmniQEC across four qLDPC construction families, three LLM backends, and

14

total-physical-qubit budgets per backend. The discovered codes show steadily improving logical-error suppression with increasing physical-qubit budgets and outperform the BB codes with

[\![72,12,6]\!]

and

[\![144,12,12]\!]

under complete-implementation budgets of 98 and 240 physical qubits, respectively. The discovered codes are hardware-friendly and may be of independent interest for practical QEC implementation. These findings pave the way towards LLM-assisted QEC discovery grounded in physically informed code--circuit--decoder co-design.

Ge Yan, Shanchuan Li, Pengyue Ma +5

College of Computing and Data Science, Nanyang Technological University, Singapore · Department of Electrical Engineering and Computer Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan · 3Zhejiang University of Technology, China +3

AI Agents for Scientific Discovery Quantum Error Correction Large Language Model-Guided Scientific Discovery

Jul 24, 2026cs.AI

IDEAgent: Agentic Quality-Diversity Search for Research Idea Generation

Large Language Models (LLMs) have significantly automated the process of scientific discovery over the past few years. However, existing systems share one core limitation: they generate and optimize ideas independently for either Quality or Diversity. This often leads to the generation of ideas in close proximity to one another or to a large set of trivial, unsound, or unclear concepts. In this work, we instead argue that research ideation should be treated as a conjunction of both objectives and framed as a Quality-Diversity (QD) search. In line with this perspective, we introduce IDEAgent, a multi-agent framework that manages the evolution of ideas through lineages. We jointly drive Quality using multi-objective feedback for dedicated repair and refinement, while Diversity is achieved through lightweight sequential memory and explicit comparison against completed ideas, their historical ancestors, and rejected proposals. To systematically evaluate this QD conjunction, we develop Yield, a joint metric that computes the largest set of mutually diverse ideas that satisfy a predetermined quality threshold. Finally, through evaluations across 32 topics spanning 8 domains of Computer Science, we show that IDEAgent outperforms the best baseline by 3.89x on Yield, while achieving non-zero Yield on 8x more topics. We further corroborate these findings through an analysis of quality improvements, showing that repair and refinement are crucial for building logical rigor and clarity while preserving non-obviousness. To encourage future research on QD-search-based ideation, we open-source IDEAgent at https://github.com/declare-lab/IDEAgent.

Varun Gumma, Navonil Majumder, Soumitra Sinhahajari +1

DeCLaRe Lab, Nanyang Technological University, Singapore

Multi-Agent LLM Systems Quality-Diversity Optimization Research Idea Generation Large Language Model-Guided Scientific Discovery

Jul 21, 2026cs.LG

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects

Evaluating machine learning in scientific domains requires separating correct predictions from correct reasons under realistic distribution shifts. We introduce PertReason, a knowledge-grounded benchmark and framework suite for cell-state--conditioned reasoning about perturbation effects. At its core, PertReasonQA is a benchmark that tests whether models can generate mechanistically faithful explanations while remaining robust to complex shifts, such as new cells and unseen perturbations. PertReasonQA combines single-cell genetic and chemical perturbation data across multiple cellular contexts with knowledge graphs, and dynamically conditions pathways on cell-specific basal states to avoid generic memorization. Evaluations on state-of-the-art models reveal systematic gaps between predictive accuracy and mechanistic reasoning. Specifically, these models exhibit failure modes largely invisible to standard benchmarks, such as deriving correct answers through flawed logic, ignoring cellular context, and generating directionally inconsistent mechanisms. As a reference probe of the benchmark, we present PertReasonLM, a large language model trained to align outcome predictions with context-specific mechanistic reasoning. Our model targets the identified failure modes by grounding rationales in context-specific pathways and tightening agreement between outcomes and mechanisms. Together, we provide a diagnostic framework for exposing and mitigating failures in faithful reasoning in data-rich scientific systems.

Dongkwan Kim, Yiming Gao, Yining Yang +1

Department of Electrical and Computer Engineering, Texas A&M University

LLM Grounding Single-Cell Perturbation Modeling Causal Reasoning in Language Models Large Language Model-Guided Scientific Discovery

Jul 20, 2026cs.CL

Automated Discovery Has No Universally Superior Harness

Autonomous discovery systems such as OpenEvolve and TTT-Discover are often used as general-purpose harnesses. However, in practice these are composite systems combining several design choices about archives, parent selection, exploration, and budget allocation into a single recipe. Because discovery runs are expensive and inherently stochastic, existing harnesses are often compared using too few independent trials to distinguish key methodological improvements from run-to-run variance. We systematically decompose OpenEvolve-style evolutionary search and the TTT-Discover search harness into its constituent components and systematically evaluate 30 budget-matched harnesses across 12 model-problem pairs using more than 3.1 million LLM rollouts and repeated-trial statistical analysis. Our results show that discovery harnesses have a generalization problem: No fixed harness is reliably superior across the evaluated model-problem pairs, and variants of OpenEvolve generally underperform simpler alternatives. Thus, harness choice is better viewed as a hyperparameter rather than as a universal recipe, and should be tailored to the specific problem and underlying model. We also find that early discovery progress predicts final performance, and use this property to present a budget-matched adaptive-allocation experiment that starts multiple harnesses, prunes weak partial runs, and reallocates compute to stronger survivors, outperforming both commitment to a randomly sampled fixed harness and a non-adaptive harness ensemble. Together, these results motivate shifting from fixed harness selection to online adaptation guided by early performance. We release all run pools including baseline null distributions for every model-problem pair as reusable statistical infrastructure against for future harness proposals.

Akshat Gupta, Jermaine Lei, Alexander Lu +2

UC Berkeley · MIT, MIT-IBM Watson AI Lab

Automated Algorithm Discovery Automated Heuristic Design Evolutionary Optimization Agent Harness Optimization Large Language Model-Guided Scientific Discovery Hyperparameter Optimization

Jul 20, 2026cs.IT

Autonomous Discovery of Wireless Communications Algorithms

Large language model (LLM)-driven evolutionary search is an emerging algorithm-discovery paradigm that has already produced novel results in several scientific fields. Yet its application to wireless communications remains largely unexplored. To bridge this gap, we introduce The AI Telco Engineer (AITE), a framework to autonomously design algorithms for complex communication problems, while navigating performance-complexity tradeoffs. We showcase AITE on two challenging physical-layer problems: designing an equalizer for an orthogonal time-frequency space (OTFS) system, and constructing a receiver algorithm for an orthogonal frequency-division multiplexing (OFDM) system using a custom constellation and operating without pilots. For the first task, AITE develops algorithms that outperform the best-known solutions while reducing computational latency by a factor of 3.6 compared to the strongest baseline. For the second task, it discovers the first explicit, explainable algorithms that achieve performance parity with state-of-the-art neural receivers. These results demonstrate the strong potential of LLM-driven evolutionary search for the autonomous discovery of next-generation wireless communications algorithms.

Fayçal Aït Aoudia, Jakob Hoydis, Sebastian Cammerer +4

NVIDIA, 92400 Courbevoie, France · NVIDIA, 10623 Berlin, Germany · NVIDIA, 8004 Zürich, Switzerland

Automated Algorithm Discovery Large Language Model-Guided Optimization Wireless Communications Large Language Model-Guided Scientific Discovery

Jul 19, 2026math.FA

Mathematical Discovery in the Wild: AI-Guided Proofs in Banach Space Theory

We investigate the capacity of current language models to contribute to mathematical research. In Banach space theory, AI systems generated key ideas and proofs for five new results, which were then verified and refined by humans. We also developed an automated system that searches the literature for open problems and attempts solutions at scale. Our results show both the potential of language models for mathematical discovery and the continuing importance of expert verification.

Antonio Acuaviva, Pablo Acuaviva

Automated Theorem Proving AI-Assisted Scientific Research Large Language Model-Guided Scientific Discovery LLM Mathematical Reasoning