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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Jun 21, 2026cs.AI

ARIA: A Causal-Aware Framework for Rescuing LLM Reasoning in Trustworthy Materials Discovery

Generative models have revolutionized the process of materials discovery, yet they often fail to satisfy underlying physical causality. Through an analysis of Large Language Models (LLMs) augmented with knowledge graphs derived from current literature, we uncover a phenomenon termed contextual tunneling, where models "over-anchor" on narrow, retrieved evidence while suppressing global physical reasoning. To address this problem, we introduce ARIA, a causal-aware framework that conditions knowledge use on mechanistic completeness. ARIA routes each query through a three-tier cascade: (i) direct causal reasoning when complete evidence chains of Process-Structure-Property (PSP) are available, (ii) physics-informed analogical transfer for sparse or novel material systems, and (iii) explicit parametric fallback when external evidence is incomplete. As a proof of concept, we construct a Knowledge Graph (KG) containing 2,839 extracted PSP relations from peer-reviewed articles in the materials literature and evaluate ARIA on forward prediction and inverse design tasks for two-dimensional (2D) materials. ARIA mitigates contextual tunneling, improves over unaugmented and naive KG-augmented baselines, and provides further gains when an online literature search is used for evidence enrichment. Crucially, ARIA produces auditable causal traces, enabling physically grounded and trustworthy AI-assisted materials discovery.

Yi Cao, Liaoyaqi Wang, Jieneng Chen +3

Knowledge Augmentation for Language Models Materials Property Prediction Causal Reasoning in Language Models Materials Science Large Language Model-Guided Scientific Discovery Inverse Design

Jun 20, 2026cs.AI

Learning the ARTS of Search for Automated Discovery

Scientific discovery can be formulated as an iterative search process over the space of hypotheses and experiments. Contemporary methods navigate this space using heuristics such as MCTS. These algorithms conflate the merit of a hypothesis with the quality of its experimental execution. A promising hypothesis with preliminary execution is therefore ranked below a modest hypothesis whose execution is refined. Moreover, prior methods prune the search logs as the search progresses because the accumulated history outgrows the context window. We propose Agentic Reasoning for Tree Search (ARTS), where we deploy a reasoning language model to navigate this space. The model inspects prior execution logs, diagnoses whether earlier failures arose from faulty implementations or bad hypotheses, and selects the hypothesis to build on next. To mitigate challenges with context length, ARTS uses test-time training to instill the knowledge of search tree in the model weights. Across 22 tasks from MLGym and MLEBench, we show that ARTS outperforms leading algorithms, with over 15.3% relative improvement in the normalized score. With test-time training we show that a Qwen3-4B agent can match performance with closed-source frontier models like Gemini-3 Pro and GPT o3-reasoning with upto 5x lower inference cost. We further observe that on partially observable RL tasks, the test-time trained Qwen3-4B scientist surpasses ARTS with the o3 scientist by rediscovering the human-best recurrent-memory solution that heuristic methods prune away.

Gurusha Juneja, Arnav Kumar Jain, Deepak Nathani +2

University of California, Santa Barbara · Université de Montréal and Mila- Quebec AI Institute

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

Jun 17, 2026cond-mat.mtrl-sci

AdsMind: A Physics-Grounded Multi-Agent System for Self-Correcting Discovery of Adsorption Configurations on Heterogeneous Catalyst Surfaces

Identifying the lowest-energy surface-adsorbate configuration is critical for modeling heterogeneous catalysis, yet exhaustive exploration with ab initio calculations is computationally prohibitive. Machine-learning force fields (MLFFs) accelerate structural relaxation but leave the search over the vast configurational space a major bottleneck, and open-loop large language model (LLM) agents lack a physics-grounded feedback mechanism to correct erroneous initial guesses. We propose AdsMind (Adsorption configuration discovery with Machine intelligence and relaxation feedback), a closed-loop multi-agent framework that enables autonomous error correction through MLFF relaxation feedback. Across four LLM backends, AdsMind achieves consistently high search reliability, with success rates of 100% and 98.8% on the benchmarks AA20 and OCD-GMAE62. Relative to its single-pass (1-Shot) ablation it reduces cross-backend energy dispersion, and it uses only 4.11 and 4.67 MLFF relaxations per case, respectively -- an approximately 14-fold reduction over heuristic enumeration baselines. Density functional theory (DFT) validation using VASP/PBE on six representative AA20 systems shows that the reported open-loop Adsorb-Agent outputs exhibit qualitative adsorption-energy sign errors for molecular adsorbates, whereas AdsMind preserves the correct sign in all tested cases with closer quantitative agreement. AdsMind thus delivers reliability, self-reflection, and interpretability simultaneously, supporting more DFT-informed autonomous chemistry workflows.

Zongmin Zhang, Yuyang Lou, Bowen Zhang +6

Department of Computer Science and Engineering, Hong Kong University of Science and Technology, Jun Kowloon, Hong Kong 999077, China · Department of Chemistry, Hong Kong University of Science and Technology, Kowloon, Hong Kong 999077, China · Laboratory of Artificial Chemical Intelligence (LIAC), EPFL, Lausanne, Switzerland +2

Multi-Agent LLM Systems Materials Science Large Language Model-Guided Scientific Discovery

Jun 17, 2026physics.chem-ph

LLM-Guided Test-Time Discovery of Quantum-Chemical Approximation Algorithms

Quantum chemistry simulations underpin modern materials discovery, yet their impact is limited by steep computational cost and dependence on fixed approximation schemes. Foundation models, such as machine-learned interatomic potentials, have accelerated parts of this workflow, but their reliance on large-scale pretraining restricts adaptability at the frontier of chemical space, where methodological innovation and sparse data are the norm. Agentic AI systems can automate existing simulation pipelines, yet they remain constrained by the predefined tools and algorithms they orchestrate. In response, we introduce LADeQ, an LLM-guided workflow that discovers, implements, and benchmarks candidate approximation algorithms at test-time within existing quantum chemistry codes. Rather than selecting from a predefined repertoire, LADeQ constructs candidate approximation schemes on demand, drawing on techniques from disciplines such as spatial statistics, circuit simulation, and kernel methods that have had little prior presence in electronic-structure theory. Because it builds on an out-of-the-box language model, LADeQ requires no task-specific pretraining or curated data, and the resulting implementations are transparent and inspectable, with explicitly traceable approximation errors that enable principled control of accuracy--efficiency trade-offs. We show that LADeQ accelerates coupled cluster singles and doubles (CCSD) and configuration interaction singles and doubles (CISD) calculations while keeping correlation-energy errors within user-specified tolerances, demonstrating autonomous, objective-driven discovery of approximation algorithms inside existing electronic-structure solvers.

Masaya Hagai, Yuta Suzuki, Tomoya Murata +2

Lattice Lab, Toyota Motor Corporation · Department of Chemistry, Graduate School of Science, Nagoya University · National Institute of Informatics

Automated Algorithm Discovery Quantum Chemistry Large Language Model-Guided Scientific Discovery

Jun 16, 2026cs.AI

Learning Cardiac Electrophysiology Digital Twins Through Agentic Discovery of Hybrid Structure

Building personalized cardiac electrophysiology (EP) digital twins requires identifying the appropriate model structure for each patient, not merely fitting parameters. Traditional methods rely on experts to manually prescribe hybrid physics-neural architectures, which requires deep domain expertise and does not transfer across patients. Recent works have applied large language models (LLMs) to generate or act as hybrid models. However, despite their promising generalization capacity, these LLM-based methods lack the structural priors needed for stable cardiac simulations. Hence, we propose LEADS, a framework that formulates cardiac EP domain knowledge as a structured action space and utilizes an LLM agent to discover hybrid models. The agent follows an iterative reasoning-and-action loop to select, combine, and refine hybrid models, whilst gradient descent handles parameter fitting. The proposed LEADS designs every candidate model towards physically grounded, interpretable, and numerically stable, while allowing open-ended architectural discovery. We validate LEADS on synthetic data with three ground-truth reaction models and on real cardiac EP data, demonstrating that it outperforms both human-designed hybrid models and other LLM-based hybrid modeling.

Ziqi Zhou, Yubo Ye, Sumeet Atul Vadhavka +2

Rochester Institute of Technology, Rochester, NY, 14623, USA

Scientific Discovery Digital Twins Large Language Model-Guided Scientific Discovery

Jun 14, 2026cs.CL

SciOrch: Learning to Orchestrate Expert LLMs for Solving Frontier Multimodal Scientific Reasoning Tasks

Frontier scientific reasoning remains a major challenge for large language models (LLMs), where even the strongest commercial systems fall short of expert-level performance. A closer look at model behavior reveals substantial complementarity that single-model evaluation hides: different frontier models excel on different question types, and no single model captures the full picture. We present SciOrch, a framework that trains a lightweight 8B model to orchestrate frontier LLMs for scientific reasoning. The orchestrator decomposes each question, delegates sub-problems to selected commercial models through API calls, and synthesizes a final answer. Training such an orchestrator is fundamentally harder than conventional agentic RL: each action triggers an API call that is expensive in both dollar cost and latency, making standard online rollouts infeasible. We address this with MCTS-based approach, producing diverse orchestration trajectories, extracting per-node single-turn samples, and optimizing the orchestrator with GRPO-style training. On a 240-question test set spanning SGI-Reasoning and Scientists' First Exam, SciOrch reaches 56.66% average accuracy, outperforming the strongest single commercial model by 3.74% and the strongest multi-agent baseline by 3.33%. It also attains the best accuracy on both SGI and SFE with less than half the API cost of typical multi-agent methods.

Jingru Guo, Xiangyuan Xue, Lian Zhang +6

1Imperial College London · 2The Chinese University of Hong Kong · University of Illinois Urbana-Champaign +4

LLM Agent Orchestration Multimodal Reasoning Scientific Reasoning in Language Models Large Language Model-Guided Scientific Discovery RL for LLM Agents

Jun 12, 2026cs.LG

Discovery under Hypothesis Redundancy: A Geometric Theory of Discovery Bottlenecks

Scientific discovery saturates when new hypotheses cease to provide independent information, even if the nominal hypothesis space remains large. We study hybrid discovery systems that combine structured local search with LLM-generated non-local proposals and pose the Search Compression Hypothesis: non-local exploration helps only when three geometric conditions co-occur: spectral compression, orthogonal escape from the explored span, and residual signal alignment with the target. We formalize these conditions, derive necessary conditions for hybrid advantage, and test the mechanism in controlled synthetic environments, large-scale A-share factor discovery, and symbolic-regression benchmarks; a public tabular operational sanity check tests the associated budget-allocation implication. Signal-planting and directed-versus-random experiments show that novelty alone is insufficient: random orthogonal jumps expand coverage but do not improve yield without predictive alignment. Across compression sweeps, real factor archives, and LLM-SRBench tasks, hybrid gains concentrate in weakly represented but target-bearing directions and vanish as the hypothesis space approaches full rank. The framework turns LLM-guided discovery from generic novelty search into a diagnostic procedure for deciding when directed non-local exploration is warranted.

Li Xia, Baoxun Wang

School of Economics and Management, Tsinghua University · Platform & Content Group, Tencent

Scientific Hypothesis Generation Large Language Model-Guided Scientific Discovery

Jun 11, 2026quant-ph

An LLM System for Autonomous Variational Quantum Circuit Design

The design of high performing quantum circuits remains largely dependent on human expertise. We introduce an autonomous agentic framework that employs large language models (LLMs) to conduct iterative quantum circuit designs under explicit design constraints. Our system integrates seven components: Exploration, Generation, Discussion, Validation, Storage, Evaluation, and Review. These components form a closed-loop workflow that combines web-based knowledge acquisition, literature-grounded critique, executable code generation, and experimental feedback. We evaluate the framework on two tasks: quantum feature map construction for quantum machine learning and ansatz generation for variational quantum eigensolver applications in quantum chemistry. In image classification benchmarks, the best generated feature map outperforms representative quantum feature maps and, when scaled to larger qubit counts, surpasses the classical radial basis function kernel. In molecular ground state estimation across seven molecules, the generated ansatz attains competitive accuracy with widely used chemically inspired and hardware-efficient constructions while satisfying the imposed scaling constraints. These results establish LLM driven agentic system as a viable paradigm for automated quantum circuit design and illustrate how AI systems can participate in iterative scientific optimization workflows across scientific domains.

Kenya Sakka, Wataru Mizukami, Kosuke Mitarai

Center for Quantum Information and Quantum Biology, The University of Osaka, 1-2 Machikaneyama, Toyonaka 560-0043, Japan · Graduate School of Engineering Science, The University of Osaka 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan

Quantum Chemistry Quantum Kernel Methods Variational Quantum Circuits Large Language Model-Guided Scientific Discovery

Jun 9, 2026cs.LG

Towards Diverse Scientific Hypothesis Search with Large Language Models

Large language models (LLMs) are on the rise for accelerating scientific discovery, most recently in advanced tasks such as generating valid scientific hypotheses. Yet in many discovery settings, the goal is not to identify a single best hypothesis since validation can be noisy and expensive, and scientists benefit from a set of high-quality alternative hypotheses that hedge against downstream uncertainty for the best solutions. Nevertheless, commonly used evolutionary search recipes tend to prioritize optimization over exploration in hypothesis generation, and the resulting selection pressure during the search process leads to diversity collapse. Motivated by these limitations, we formulate hypothesis search as a sampling problem, where the objective is to efficiently produce diverse, high-quality hypotheses under a fixed validation budget. Building on this perspective, we propose \ours, an evolutionary framework inspired by the classical parallel tempering algorithm that searches hypotheses at multiple temperature levels and enables principled information exchange across temperatures to improve exploration without disrupting convergence. Across domains including molecular discovery, equation discovery, and algorithm discovery, our approach consistently improves both hypothesis quality and diversity under the same validation budget, and produces candidates that remain robust under more expensive downstream computational validations.

Haorui Wang, Parshin Shojaee, Kazem Meidani +7

Georgia Institute of Technology · Virginia Tech · Carnegie Mellon University +3

Automated Algorithm Discovery Scientific Hypothesis Generation Large Language Model-Guided Scientific Discovery Parallel Tempering

Jun 8, 2026cs.AI

MASS: Deep Research for Social Sciences with Memory-Augmented Social Simulation

Deep Research agents powered by Large Language Models (LLMs) have exhibited extraordinary potential in automated paper writing tasks. However, existing systems rely heavily on literature retrieval and synthesis through internet and local knowledge bases, often resulting research in lacking insight and creativity in social science. To address this issue, we propose "Memory-Augmented Social Simulation (MASS)", an innovative paradigm that leverages highly realistic and research-oriented social simulations to enhance the creativity and empirical founding of LLMs-generated research. Specifically, MASS integrates three core components: dynamic goal-path planning with multi-level social norm restraint to guide the simulation, a multi-disciplinary behavior dataset for agent memory cold-start, and a structured forgetting mechanism inspired by the Ebbinghaus curve. Together, these ensure simulation authenticity and provide a robust empirical foundation for generating innovative scholarly papers. Experimental results demonstrate the effectiveness of our method, showing a 6.81% improvement in generation overall quality over foundation LLMs and 17.19% gain in Insight over strong baselines.

Yongrui Liu, Deyi Xiong

The International Joint Institute of Tianjin University, Fuzhou, Tianjin University, China · TJUNLP Lab, School of Computer Science and Technology, Tianjin University, China

Human Behavior Simulation Large Language Model-Based Social Simulation Large Language Model-Guided Scientific Discovery Memory-Augmented Agents Autonomous Research Agents

Jun 8, 2026cs.AI

Graph2Idea:Retrieval-Augmented Scientific Idea Generation with Graph-Structured Contexts

Generating novel, feasible, and high-quality research ideas is an important yet challenging task in scientific discovery. Recent Large Language Model (LLM)-based methods often ground idea generation with retrieved literature, but the retrieved evidence is usually provided as flat text, such as titles, abstracts, or summaries. Such flat contexts may contain redundant or weakly relevant information, while making cross-paper relations among problems, methods, mechanisms, and findings difficult to identify and trace. To address this challenge, we propose Graph2Idea, a knowledge graph-guided framework for retrieval-augmented scientific idea generation.Graph2Idea first retrieves papers according to the input topic, transforms them into structured knowledge triples, and dynamically constructs a target-centered knowledge graph to make literature relations explicit. It then extracts compact graph-derived contexts that retain target-relevant relational evidence while reducing noisy textual input. Based on these contexts, a two-stage generation process first identifies promising research directions and then guides the LLM to synthesize candidate ideas from graph-grounded evidence. Experiments on a scientific idea generation benchmark show that Graph2Idea outperforms representative baselines under the automatic evaluation protocol. Compared with the strongest baseline scores, it improves Novelty from 0.45 to 0.52, Quality from 0.24 to 0.29, and Feasibility from 0.22 to 0.28. These results suggest that graph-structured evidence helps LLMs generate research ideas through more explicit, compact, and traceable recombination of prior scientific knowledge.

Xu Li, Hanzhe Tu, Xun Han

Southwest Petroleum University, Chengdu, Sichuan, China · Sichuan Police College, Luzhou, Sichuan, China

Graph Retrieval-Augmented Generation Scientific Hypothesis Generation Research Idea Generation Large Language Model-Guided Scientific Discovery

Jun 7, 2026cs.AI

DN-Hypo-Pipeline: An AI-Driven Workflow for Generating Hypotheses using Large Language Models and Scientific Explanations

Modern artificial intelligence excels at prediction but cannot explain. From large language models to AI-for-science systems, today's machines answer what by recombining patterns already present in the human literature, yet they cannot reason out why a phenomenon must arise from underlying principles even though explanation, not prediction, lies at the heart of scientific discovery. Here we ask whether the structure of scientific explanation can be operationalized to guide how a machine generates hypotheses. We introduce DN-Hypo-Pipeline, a hypothesis-generation framework that adopts a layered, explanation-theoretic scaffold: Hempel's deductive-nomological (DN) model supplies the output form and deductive validity of a hypothesis, Salmon's causal-process account supplies an organizing constraint on where to search for the governing laws, and Armstrong's view of laws as relations between universals supplies the bridge from a phenomenon's constituent processes to the laws that may be associated with it. Rather than searching the space of what has been written, the framework searches the space of what principles govern a phenomenon: given an explanandum, it abstracts the universals instantiated in the phenomenon's formation process, retrieves the laws relating those universals, and deductively reconstructs a new, testable explanation. Evaluated in data-science modeling and judged by both LLMs and human experts, hypotheses generated through this principled reasoning significantly outperform those from direct prompting. Crucially, we translated the two highest-scoring hypotheses into novel algorithms one that reduces the Transformer's theoretical complexity with only minimal performance loss, and another that achieves competitive accuracy with substantially fewer parameters.

Lei Lin, Ronghao Wang, Chunbao Zhou +2

Computer Network Information Center, Chinese Academy of Sciences, China

Scientific Reasoning Scientific Hypothesis Generation Research Idea Generation Scientific Reasoning in Language Models Large Language Model-Guided Scientific Discovery

Jun 6, 2026cs.LG

GPT-Micro: A large language paradigm for accelerated, inexpensive, and thermodynamics-consistent discovery of constitutive models in manufacturing

Constitutive modeling of the relationship between process-imposed material states and fundamental material properties is critical to control of material microstructure in manufacturing processes. The limited accuracy resulting from the typical reliance on fallible human expertise and intuition for postulation and revision of the models functional form results in incremental and time consuming model discovery. Conventional Machine Learning (ML) incurs significant cost and time of data generation. Model discovery using Large Language Models (LLMs) suffers from the above issues and/or ignores the inviolability of fundamental thermodynamics laws. This work creates a novel GPT-Micro paradigm for autonomous, data sparse, and thermodynamics-compliant discovery of de-novo constitutive models. This framework seamlessly integrates semantic knowledge extraction from literature, enforcement of thermodynamics-based conservation laws, and sparse datasets, with LLM-driven generation and refinement of model hypotheses. Validation is performed for a long-intractable constitutive modeling problem in a printed electronics process testbed. This reveals significant and simultaneous advantages over the state-of-the-art including: (a) More than 70 percent reduction in data burden relative to ML-based modeling without loss in accuracy; (b) 400X reduction in discovery time after data generation, from months to hours, relative to human-driven modeling; (c) Discovery of models with novel functional forms without subjective human choice of a starting hypothesis; (d) Enhanced physics-rooted trustworthiness, human interpretability, and mechanistic insight via synthesis of compact, conservation-compliant, and physically complete analytical models. The potential of GPT-Micro to realize rapid, low-cost, physically trustworthy, and interpretable microstructure modeling across the manufacturing landscape is discussed.

Soumik Dutta, Kiarash Naghavi Khanghah, Sania Shree +4

Department of Mechanical and Aerospace Engineering, Rutgers University, USA · Department of Mechanical, Aerospace & Manufacturing Engineering, University of Connecticut, USA · Edison Welding Institute, USA +2

Manufacturing Materials Property Prediction Physics-Informed ML Large Language Model-Guided Scientific Discovery

Jun 5, 2026cs.LG

FunctionEvolve: Structure-Guided Symbolic Regression with LLMs

Symbolic regression aims to uncover explicit scientific laws from data. Recent methods use LLMs to guide mutation from background text, which is more directed than random genetic programming. However, exact symbolic recovery requires both semantic guidance and explicit structure, so that domain-informed search are carried out through valid symbolic representation. Current LLM-driven systems remain structure-blind: they select among opaque candidates, lack explicit mechanisms for local mutation, and rely on brittle coefficient fitting that can undervalue correct skeletons. We propose FunctionEvolve, an evolutionary framework using expression trees to organize the whole search: structural summaries promote diverse parent selection, local tree edits preserve useful subexpressions, and structure-aware fitting decomposes, constrains, and simplifies coefficients for more reliable scoring. It uses only elementary function families, without additional domain-specific rules limiting generalization. On the 129-task synthetic subset of LLM-SRBench, FunctionEvolve with \emph{Claude Opus 4.6} recovers 107 exact forms, reaching 82.9% SA@50, 4.5x above same-backbone baselines, and 55.8% SA@1, 3.6x above the strongest previously published top-1 result. Ablations show that structure-visible search is central to reliable recovery, with LLM-guided refinements and structure-aware coefficient optimization serving as essential proposal and scoring mechanisms. We also audit the benchmark and show that collinearity in its materials-science subset creates identifiability issues.

Zeyu Xia, Jun Zhu, Dong Yan

Bosch Center for Artificial Intelligence · Department of Computer Science and Technology, Tsinghua University · Department of Computer Science and Technology +1

Genetic Programming Large Language Model-Guided Scientific Discovery Symbolic Regression

Jun 3, 2026cs.CL

Deliberate Evolution: Agentic Reasoning for Sample-Efficient Symbolic Regression with LLMs

Symbolic regression (SR) discovers compact mathematical expressions from data, yet recent LLM-based evolutionary methods remain sample-inefficient because they rely mainly on scalar feedback such as MSE. We identify a core limitation: existing methods conflate candidate proposal with search guidance, requiring the LLM to infer how to evolve an expression, diagnose its errors, and reuse past experience from a single score. To address this, we propose Deliberate Evolution (DE), an agentic framework that decouples symbolic generation from search control. DE guides LLM proposals with adaptive operators for search direction, analytical tools for structural diagnosis, and reflective memory for trajectory-level experience. Experiments on LLM-SRBench show that DE consistently outperforms representative LLM-based SR baselines across diverse scientific domains while using only 40% of the standard sample budget.

Xinyu Pang, Zhanke Zhou, Xuan Li +5

Beijing National Research Center for Information Science and Technology (BNRist), Department of Automation, Tsinghua University, Beijing, P.R. China · TMLR Group, Department of Computer Science, Hong Kong Baptist University · Lenovo Research

Large Language Model-Guided Optimization Large Language Model-Guided Scientific Discovery Symbolic Regression

Jun 1, 2026cs.AI

Iteris: Agentic Research Loops for Computational Mathematics

Recent advances in large language models and agentic AI systems have enabled significant progress in mathematical discovery, from solving competition problems to tackling research-level conjectures. However, open problems in computational mathematics have received comparatively less attention: research in this area often requires not only proofs but also numerical experimentation, adversarial constructions, and algorithm design. In this paper, we introduce an agentic research system, Iteris, designed for open problems in computational mathematics. We apply Iteris to two open problems from a recent Simons Workshop collection (arXiv:2602.05394). In these case studies, Iteris generated numerical evidence, constructions, and proof drafts that led, after expert review and correction, to verified results. The first result is a phase diagram for the asymptotic comparison between conjugate gradient and randomized coordinate descent on power-law spectra; the second is a counterexample showing that QR factorization with column pivoting can fail to select well-conditioned submatrices even under low coherence. These case studies suggest that agentic AI systems can participate meaningfully in research workflows for open problems in computational mathematics, while human validation remains essential.

Leheng Chen, Zihao Liu, Wanyi He +1

School of Mathematical Sciences, Peking University · 5Zhongguancun Academy · 2Beijing International Center for Mathematical Research and the New Cornerstone Science Laboratory, Peking University +2

Mathematical Reasoning Large Language Model-Guided Scientific Discovery Autonomous Research Agents

Jun 1, 2026quant-ph

Evolutionary Discovery of Bivariate Bicycle Codes with LLM-Guided Search

Quantum LDPC code discovery requires searching large algebraic design spaces while reliably certifying the parameters and equivalence classes of any candidates found. We introduce an LLM-guided evolutionary workflow in which language models mutate Python programs that generate bivariate-bicycle and perturbed bivariate-bicycle code ansätze. Across five campaigns, the system performed approximately 1{,}650 evolutionary iterations, screened about

2 \times 10^5

candidate codes, and required

{\sim}140

hours of computation and

{\sim}

US$400 in LLM inference cost. Candidate codes are evaluated through a staged validation pipeline combining

\mathrm{GF}(2)

rank computation, distance estimation and certification, mixed-integer linear programming, BLISS Tanner-graph deduplication, decomposability analysis, and local-Clifford equivalence checks. At block length

n \leq 360

, the workflow identifies 465 distinct candidate codes: 97 CSS bivariate-bicycle codes and 368 non-CSS perturbed variants. The CSS search recovers known high-performing codes and finds new finite-length representatives, including an indecomposable [[288,16,12]] code and higher-weight codes with up to

k = 50

at distance

d = 8

. The non-CSS search produces perturbed codes matching the gross-code figure of merit at [[144,12,12]], along with additional high-distance candidates reported as certified values or upper bounds according to MILP status. Overall, these results show that LLM-guided program evolution can serve as a practical tool for structured quantum-code discovery when paired with independent evaluation.

Juan Cruz-Benito, Andrew W. Cross, David Kremer +1

IBM Research, IBM T. J. Watson Research Center, NY, USA

Automated Algorithm Discovery Quantum Error Correction Large Language Model-Guided Scientific Discovery

May 31, 2026cs.AI

Reasoning4Sciences: Bridging Reasoning Language Models to All Scientific Branches

While Reasoning Language Models (RLMs) are rapidly emerging as powerful tools for scientific research, their impact is primarily concentrated in "hard science" fields. The slow -- or lack of -- adoption of RLMs in other branches of science is causing a widening gap in research productivity. In this survey, we provide the first comprehensive analysis of RLM adoption across 28 scientific disciplines following the classification used by the European Research Council (ERC), spanning the Social Sciences and Humanities, Physical Sciences and Engineering, and Life Sciences. We examine how RLMs are developed, evaluated, and applied across disciplines. Furthermore, we introduce a maturity-oriented assessment framework based on available domain-specific development and evaluation resources, revealing substantial disparities in RLM maturity that become even more pronounced when only publicly available resources are considered. Finally, we highlight current implementation paradigms that are gaining popularity across disciplines, current challenges, and future directions in enabling RLM adoption across science.

Teddy Ferdinan, Bartłomiej Koptyra, Mikołaj Langner +42

AI for Science Scientific Reasoning Scientific Reasoning in Language Models Large Language Model-Guided Scientific Discovery Large Reasoning Models

May 30, 2026stat.ML

Position: Prioritize Identifying Structure, Not Complex Models, for Scientific Discovery

Modern Machine Learning (ML) and Artificial Intelligence (AI) models, especially large language models (LLMs), are increasingly used to generate scientific hypotheses and mechanistic explanations from observational data. This position paper argues that in the high-dimensional proxy regimes where modern ML excels, mechanistic learning is generically underdetermined: many incompatible mechanisms induce essentially the same observational relationships on the support of the data, so predictive success and coherent explanations are insufficient evidence of mechanism discovery. This underdetermination becomes uniquely hazardous with large language models (LLMs), which tend to collapse large equivalence classes of explanations into a single fluent narrative. This paper proposes concrete standards for ``mechanistic ML,'' and argues these norms are necessary if LLM-centered workflows are to support science rather than merely simulate it.

Tyler H. McCormick

Departments of Statistics and Sociology, University of Washington, Seattle, WA, USA.

Causal Identifiability Scientific ML Large Language Model-Guided Scientific Discovery

May 29, 2026cs.AI

Coupling Language Models with Physics-based Simulation for Synthesis of Inorganic Materials

Modern generative machine learning (ML) models can propose novel inorganic crystalline materials with targeted properties; however, synthesis planning of these materials remains difficult due to the complexity of the associated physical processes and limited availability of computational tools. We introduce a novel hybrid framework to evaluate Large Language Models (LLMs) in inorganic synthesis planning by combining thermodynamic databases with simplified kinetics models to approximate realistic synthesis conditions. As a case study, we focus on the niobium-oxygen system, which features multiple industrially relevant oxide phases with well-characterized data. In computational simulations, we compare LLM-generated synthesis routes with classical path-planning algorithms, showing that the implicit priors in LLMs can yield more viable strategies. In our evaluation setting, classical search methods serve primarily as a foil rather than a direct competitor. This illustrates the relative complexity of the problem and highlights where the LLM's implicit priors add value.

Edward W. Staley, Tom Arbaugh, Michael Pekala +6

Johns Hopkins Applied Physics Laboratory, Laurel, MD 20723 · Johns Hopkins University, Baltimore, MD 21218

Materials Science Large Language Model-Guided Scientific Discovery Physics-Based Simulation

May 29, 2026cs.CL

EvoGens: A Population-Based Heuristic Search Framework for Scientific Idea Generation

Generating novel research ideas is fundamental to scientific progress. While Large Language Models (LLMs) show promise in assisting this process, existing approaches often exhibit semantic convergence, resulting in limited diversity and novelty. To address this, we introduce EvoGens, an evolution-inspired framework that recasts scientific idea generation as an evolutionary search over a population of ideas. EvoGens iteratively applies rank-based mutation with differentiated retrieval planning to incorporate external knowledge, and semantic-aware crossover to fuse complementary concepts for conceptual reorganization. A lightweight evaluation signal guides the selection process, encouraging sustained exploration while mitigating premature convergence. Extensive experiments demonstrate that EvoGens substantially enhances exploration capabilities compared to state-of-the-art baselines. Specifically, it improves the Novelty from 0.1 to 0.4 and the Diversity from 0.24 to 0.55, while maintaining comparable idea quality under the current automatic evaluation protocol. These findings suggest that evolutionary mechanisms can serve as a useful framework for exploration-oriented research ideation, especially for broadening the novelty and diversity of candidate ideas under a shared automatic evaluation setting.

Xu Li, Hanzhe Tu, Xinyi Li +3

Southwest Petroleum University, Chengdu, China · Sichuan Police College, Luzhou, China

Scientific Hypothesis Generation Research Idea Generation Large Language Model-Guided Scientific Discovery

May 29, 2026physics.chem-ph

MLIPilot: LLM-Driven Auto-Research for Machine-Learned Interatomic Potentials

Constructing production-quality machine-learned interatomic potentials (MLIPs) requires balancing accuracy, dynamical stability, and computational throughput under constraints that are not captured by a single training loss. We introduce MLIPilot, an auto-research framework in which tool-calling large language models propose hypotheses, edit MLIP training code, launch HPC jobs, and accept or revert changes using a fixed, physically constrained scorecard. We evaluate MLIPilot on MACE potential optimization using both commercial and open-weight LLM agents, including GPT-5.5, GPT-4.1, Mistral-24B, and Qwen3-32B. The benchmarks span molecular and periodic settings: a QM7-derived dataset for which we generated B3LYP/6-31G(d) energies and forces, and a Cu EMT dataset with periodic copper supercells labeled by ASE's Effective Medium Theory calculator. Across these benchmarks, the strongest agents move initially constraint-violating baselines to accepted models by discovering useful training strategies, including output normalization, loss-function changes, progressive training schedules, and model-capacity adjustments. These results suggest that LLM agents can serve as autonomous operators for scientific machine-learning workflows when their search is constrained by domain-specific validation criteria, shifting part of MLIP development from manual trial-and-error toward auditable, automated experimentation.

Etinosa Osaro, Santosh Adhikari, Stamatia Zavitsanou +2

PsiQuantum, 700 Hansen Way, Palo Alto, CA 94304

Machine Learning Interatomic Potentials Large Language Model-Guided Optimization Automated Machine Learning Large Language Model-Guided Scientific Discovery Autonomous Research Agents

May 28, 2026cs.AI

ProjectionBench: Evaluating Scientific Hypothesis Generation in LLMs Under Progressive Information Disclosure

Scientific discovery is an inherently creative and uncertain process, requiring reasoning beyond the recall of known knowledge. While many benchmarks have been proposed to evaluate large language model (LLM) performance on deep research tasks via multi-hop retrieval, their innovative reasoning abilities essential for true scientific discovery remain largely untested. We introduce a benchmark framework for evaluating model performance in scientific discovery and reasoning, building up from a raw problem to the classical null hypothesis test. In our framework, models initially receive only the topic and research question from a recent paper, with technical details progressively revealed. At each stage of information disclosure, the model is tasked with generating hypotheses that address the research question, which is compared with the conclusions from the original paper and evaluated via automated semantic similarity of constituent atomic claims. This progressive evaluation of semantic divergence from ground-truth conclusions enables assessment of a model's innovativeness (under minimal information) to grounded reasoning capabilities (under full experimental details), both critical for using LLMs for scientific discovery purposes. Our framework provides a foundation for systematically evaluating scientific reasoning and discovery capabilities in LLMs, crucial for advancing the development of next-generation AI scientist/co-scientist systems. Specifically, here we evaluate GPT-5, GPT-5.4, Gemini 2.5 pro, and Gemini 3.1 pro preview across 45 papers spanning bioactive materials, mechanical materials, and nanomaterials. We find that GPT-5.4 and Gemini 3.1 pro outperform their previous generation counterparts as expected, and GPT-5.4 in particular maintains 0.7 F1 score alignment with ground truth conclusions even under minimal context.

A. J. Lew, Y. Cao, M. J. Buehler

Unreasonable Labs · Unreasonable Labs Mountain View, CA 94043, USA

LLM Evaluation Scientific Reasoning Scientific Hypothesis Generation Research Idea Generation Scientific Reasoning in Language Models Large Language Model-Guided Scientific Discovery

May 28, 2026cs.CL

From Blind Guess to Informed Judgment: Teaching LLMs to Evaluate Materials by Building Knowledge-Augmented Preference Signals

As candidate generation and high-throughput experimentation advance, the primary bottleneck in materials discovery is shifting from property prediction to making reliable evaluations among massive candidate sets. We propose a Knowledge-Augmented Preference Signals Framework, MaterEval, that automatically produces, for the same candidate, two evaluations: an informed judgment that follows expert rules and provides supporting evidence, and a rule-removed blind guess. By pairing the two evaluations as preference data, we guide general-purpose large language models (LLMs), originally lacking materials-specific criteria, from intuitive judgment toward reliable evaluation supported by explicit evidence. To balance throughput, cost, and reliability, we further introduce a fast-slow reasoning scheme that decouples large-scale rapid screening from in-depth review on a small subset. Using high-entropy alloy (HEA) assessment as a case study, we show that, without external retrieval and relying solely on internalized capabilities, small open-source LLMs achieve substantial gains in accuracy, conclusion consistency, and evidence discrimination, approaching the performance of rule-based closed-source LLMs. These results demonstrate that expert rules can be systematically transformed into learnable preference signals, enabling a low-cost and deployable evaluation module for autonomous materials discovery loops.

Yeyong Yu, Wenya Hu, Xing Wu +1

School of Computer Engineering & Science, Shanghai University, Shanghai, 200444, China. · Center of Materials Informatics and Data Science, Materials Genome2026 Institute, Shanghai University, Shanghai, 200444, China. · Key Laboratory of Silicate Cultural Relics Conservation (Shanghai University), Ministry of Education, China. +1

LLM Evaluation Pairwise Preference Evaluation Materials Science Large Language Model-Guided Scientific Discovery Preference Learning

May 28, 2026cs.CL

MOOSE-Copilot: A Web-Based Interactive Assistant for Unified Exploratory and Fine-Grained Scientific Hypothesis Discovery

Large language models (LLMs) show remarkable potential in scientific hypothesis discovery. However, existing approaches face two critical limitations: they treat divergent exploratory search and convergent fine-grained refinement as isolated tasks, and they operate autonomously with little to no human guidance. We present MOOSE-Copilot, the first unified framework to bridge this abstraction gap through a formalized human-AI interaction (HAII) protocol. Our system empowers scientists to steer the generative process via three explicit signals: initial blueprints, inter-stage routing, and intra-stage feedback. Using an oracle-simulated evaluation in which an LLM provides idealized expert signals, we show that injecting these structured signals significantly outperforms purely autonomous baselines, characterizing the gains achievable under high-quality guidance. Furthermore, we build a web-based interface that turns the framework into a no-code workflow: researchers pose a question, watch the hypothesis search unfold as an interactive tree, and steer it by selecting hypotheses, routing between stages, and injecting feedback-no command-line agents required. This makes end-to-end hypothesis discovery directly accessible to interdisciplinary researchers.

Hongran An, Zonglin Yang

Central Conservatory of Music · Nanyang Technological University

Scientific Hypothesis Generation Human-in-the-Loop AI Large Language Model-Guided Scientific Discovery Human-AI Collaboration

May 27, 2026cs.LG

Influence-Guided Symbolic Regression: Scientific Discovery via LLM-Driven Equation Search with Granular Feedback

Large Language Models (LLMs) offer a promising avenue for scientific discovery, yet their application to symbolic regression is often constrained by inefficient search strategies and coarse feedback signals. Current methods typically guide LLMs using scalar metrics (e.g., global Mean Squared Error), which fail to identify which components of a proposed equation are driving performance or causing error. We introduce \textit{Influence-Guided Symbolic Regression} (IGSR), a method that frames equation discovery as an iterative two-step process combining diverse term generation with rigorous selection: an LLM generates candidate basis functions

ψ_j(\mathbf{x})

for a linear model, which are then evaluated using granular influence scores

Δ_j

. These scores quantify each term's marginal contribution to generalization accuracy, enabling an influence-guided pruning process that systematically refines the model structure. Integrating this mechanism into a Monte Carlo Tree Search (MCTS) enables navigating the combinatorial search space while balancing exploration of novel functional forms with exploitation of high-influence components. We demonstrate IGSR's effectiveness on a diverse suite of benchmarks, including LLM-SRBench, pharmacological PKPD models, an epidemiological simulation, and real-world genomic data. Notably, we validate the framework's capacity for genuine discovery in a case study using a high-dimensional biological dataset, in which IGSR identified a novel relationship between DNA methylation and RNA Polymerase II pausing; a hypothesis that was subsequently supported via wet-lab experimentation.

Evgeny S. Saveliev, Samuel Holt, Nabeel Seedat +3

University of Cambridge · Thomson Reuters Foundational Research · U. Colorado, Anschutz Medical Campus +1

Genomics Large Language Model-Guided Scientific Discovery Symbolic Regression

May 27, 2026cs.AI

MolLingo: Molecule-Native Representations for LLM-Powered Scientific Agents

We present MolLingo, a multi-agent system that emulates the reasoning process of a chemist to automate molecular design. Existing LLM-based approaches either operate as standalone generative models without access to external tools or lack the multi-agent coordination and shared memory needed for iterative, evidence-driven reasoning across the molecular design pipeline. MolLingo addresses this by coordinating a Literature Agent, a Chemist Agent, and an Orchestrator through a shared memory module, with each agent equipped with domain-specific tools. To enable effective molecular reasoning, we introduce BRICS-based Fragment Enumeration (BFE), a synthesis-aware molecular fragmentation method that decomposes molecules into chemically meaningful building blocks represented as block-based SMILES paired with common chemical names. This representation bridges molecular structure and LLM semantic space, enabling block-level reasoning and editing that is difficult with raw SMILES alone. As a case study in early-stage therapeutic design, MolLingo further grounds the Chemist Agent's reasoning in binding site geometry and residue-level protein context derived from molecular docking to optimize molecules for stronger target binding. Across four benchmarks, MolLingo consistently outperforms frontier LLMs and specialized baselines, including a fourfold docking score improvement over GPT-5.4 despite using the same underlying model, consistent drug property optimization gains across multiple LLM backbones, and state-of-the-art results on TOMG-Bench, surpassing both frontier LLMs and the RL-based optimization method RePO. Our results suggest that LLMs are already capable molecular design assistants when guided through chemically meaningful representations and biologically grounded structural context. Code is available at: https://anonymous.4open.science/status/MolLingo-7450.

Thao Nguyen, Heng Ji

Siebel School of Computing and Data Science, University of Illinois Urbana-Champaign

Molecular Optimization Multi-Agent LLM Systems Structure-Based Drug Design Large Language Model-Guided Scientific Discovery

May 26, 2026cs.AI

The Compressive Knowledge Graph Hypothesis: Which Graph Facts Matter for Scientific Hypothesis Generation?

Knowledge graphs (KGs) can provide structured scientific context to language models, but it remains unclear which graph facts actually shape the generated hypotheses. We study KG-guided hypothesis generation for battery materials across Mistral-7B, Llama-3.1-70B, and Gemini 2.5 Flash. We perturb local KGs by varying density, ontology richness, topology, and control structure, and evaluate outputs with both provided-graph and fixed-reference metrics. Across models, KG utility is selective and model-dependent: graph context changes outputs, but no-KG outputs also recover substantial graph content from model priors. Compact top-k subgraphs often approximate full-KG behavior, including when claimed-outcome triples are held out. At the same time, compression is not unique to one semantic ranking rule, random and topology-based subsets can also recover much of the signal. These results support a redundancy-aware Compressive KG hypothesis: useful KG signal is often recoverable from compact, scientifically structured subgraphs rather than requiring the full local graph.

Shashwat Sourav, Viktoriia Baibakova, Sanjay Das +4

1Washington University in St. Louis · 2Oak Ridge National Laboratory · 3Lawrence Berkeley National Laboratory +1

LLM Grounding LLM Reasoning with Graphs Scientific Hypothesis Generation Large Language Model-Guided Scientific Discovery Knowledge Graphs

May 25, 2026stat.ML

DiscoverPhysics: Benchmarking LLMs for Out-of-the-Box Scientific Thinking

Frontier LLMs now perform strongly across a wide range of physics evaluations, but it is hard to disentangle genuine reasoning from recall of established science. We introduce DiscoverPhysics, an interactive benchmark that asks a LLM agent to discover the laws of motion of a simulated world whose physics deliberately deviates from our own. We construct 22 worlds governed by, among others, screened and fractional-power gravity, multi-species couplings, hidden dark-matter-like particles, non-coordinate-free physics, and time-varying interactions. Each world is generated on demand by an N-body simulator, for which the agent proposes several rounds of experiments, observes raw trajectory data, and ultimately submits both a natural-language explanation of the world's physics and a Python implementation of the inferred law. Because solving a world requires the agent to design informative experiments and revise its hypotheses, the benchmark probes long-horizon reasoning over an experimental history. We evaluate submissions along two complementary axes: trajectory MSE on held-out particles and an LLM-judged explanation score following an expert-written rubric assessing conceptual understanding of each world. Across eleven frontier models, we find that the strongest agents pass only half of the worlds and consistently fail on those where latent structure must be uncovered. Open-source models lag substantially behind commercial models, both in their ability to design informative experiments and in extracting conclusions from the data. We further find that good predictive accuracy does not guarantee high explanation quality and that conceptual understanding depends on hypothesis refinement through well-chosen experiments.

Matt L. Wiemann, Lindsay M. Smith, Peter Melchior +4

Princeton University · Work done during internship at NYU/Polymathic AI. · Boston University +3

Physical Reasoning Scientific Discovery AI Agent Benchmarks System Identification Large Language Model-Guided Scientific Discovery

May 21, 2026cs.LG

LLM-AutoSciLab: Closed-Loop Scientific Discovery via Active Experimentation with LLMs

Scientific discovery is a closed-loop process in which hypotheses guide data acquisition and observations refine the hypothesis space. Yet most approaches reduce discovery to supervised learning over fixed datasets, where limited observations can support multiple plausible mechanisms that fit locally but fail to generalize. Thus, the key challenge is selecting informative observations to resolve uncertainty, shifting the focus from static inference to adaptive data acquisition. To address this, we propose LLM-AutoSciLab, a closed-loop framework that couples hypothesis generation with hypothesis-conditioned experiment selection and mechanism refinement. Rather than fitting models to passively collected data, LLM-AutoSciLab iteratively proposes plausible hypotheses, selects informative experiments to distinguish or refine them, and updates its state using the resulting evidence. To evaluate dynamic, closed-loop scientific discovery with active data acquisition, we introduce ActiveSciBench, comprising two datasets: ActiveSciBench-Chem with 57 enzyme-kinetics tasks and ActiveSciBench-GRN with 45 gene-regulatory-network tasks. These datasets model discovery as a budget-constrained process requiring adaptive experiment design, variable selection, and recovery of true mechanisms. Across NewtonBench, ActiveSciBench-Chem, and ActiveSciBench-GRN, LLM-AutoSciLab outperforms prior methods, achieving 67.6% and 35.1% symbolic accuracy on NewtonBench and ActiveSciBench-Chem, respectively, and 31.1% exact graph recovery on ActiveSciBench-GRN. Moreover, hypothesis-guided experimentation is 2-5x more sample-efficient than the strongest competing baselines. Code and data are available at: https://github.com/scientific-discovery/LLM-AutoSciLab

Sanchit Kabra, Nikhil Abhyankar, Saaketh Desai +2

1Virginia Tech · 2Sandia National Laboratories

Scientific Discovery Scientific Hypothesis Generation Large Language Model-Guided Scientific Discovery