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From Rules to Reasoning: A Survey of Large Language Model-Based Approaches to Scientific Hypothesis and Idea Generation

Scientific hypothesis generation represents a fundamental challenge in contemporary research due to exponentially expanding literature volumes and increasing disciplinary specialization. Large language models (LLMs) have emerged as transformative tools for automated scientific discovery, moving beyond traditional rule-based and literature-mining approaches. Four paradigmatic approaches define current LLM-driven hypothesis generation: direct prompting and fine-tuning methods, knowledge-enhanced frameworks integrating retrieval-augmented generation (RAG), multi-agent collaborative systems simulating research teams, and reasoning-focused approaches implementing cognitive architectures. Domain-specific applications demonstrate statistical equivalence to human expert performance in social psychology, experimental validation in biomedical research, and near-expert quality in astronomy. Evaluation methodologies encompass human expert assessment, LLM-as-judge frameworks, and comprehensive benchmarking systems. Technical challenges include hallucination management, knowledge integration limitations, and balancing novelty with feasibility. Future directions emphasize hybrid neural-symbolic architectures and sophisticated human-AI collaboration models for responsible scientific discovery acceleration.

AI-driven discovery

32 examples of LLM applications in materials science and chemistry: towards automation, assistants, agents, and accelerated scientific discovery

Abstract Large language models (LLMs) are reshaping many aspects of materials science and chemistry research, enabling advances in molecular property prediction, materials design, scientific automation, knowledge extraction, and more. Recent developments demonstrate that the latest class of models are able to integrate structured and unstructured data, assist in hypothesis generation, and streamline research workflows. To explore the frontier of LLM capabilities across the research lifecycle, we review applications of LLMs through 32 total projects developed during the second annual LLM hackathon for applications in materials science and chemistry, a global hybrid event. These projects spanned seven key research areas: (1) molecular and material property prediction, (2) molecular and material design, (3) automation and novel interfaces, (4) scientific communication and education, (5) research data management and automation, (6) hypothesis generation and evaluation, and (7) knowledge extraction and reasoning from the scientific literature. Collectively, these applications illustrate how LLMs serve as versatile predictive models, platforms for rapid prototyping of domain-specific tools, and much more. In particular, improvements in both open source and proprietary LLM performance through the addition of reasoning, additional training data, and new techniques have expanded effectiveness, particularly in low-data environments and interdisciplinary research. As LLMs continue to improve, their integration into scientific workflows presents both new opportunities and new challenges, requiring ongoing exploration, continued refinement, and further research to address reliability, interpretability, and reproducibility.

Computer Science

Hierarchical Multi-agent Large Language Model Reasoning for Autonomous Heterogeneous Catalyst Discovery

Artificial intelligence is reshaping scientific exploration, but most methods automate procedural tasks without engaging in scientific reasoning, limiting autonomy in discovery. We demonstrate that hierarchical agentic large language model reasoning can efficiently drive simulation and scientific exploration. Across two chemical applications, CO adsorption on Cu surface transition metal adatoms and on M–N–C catalysts, reasoning-guided exploration reduces required atomistic simulations by up to 90% relative to heuristic or random selection. Comparisons across single-agent, multi-agent, and stochastic baselines show that hierarchical strategies yield more coherent and information-efficient search trajectories. Reasoning traces reveal chemically grounded decisions that cannot be explained by semantic bias or stochastic sampling. We realize these agentic reasoning strategies in Materials Agents for Simulation and Theory in Electronic-structure Reasoning (MASTER), a multimodal system that translates natural language into density functional theory workflows. Altogether, multi-agent collaboration accelerates heterogeneous catalyst discovery and marks a step toward more autonomous, reasoning-guided scientific exploration.

30 DIRECT ENERGY CONVERSION

MEAD In-situ Sampling and Testing at Haughton Crater

The Mars Exploration through Analog-site Drilling (MEAD) project is designed to demonstrate the feasibility and scientific value of robotic drilling missions to Mars in the search for evidence of past or extant life. MEAD conducts high-fidelity field simulations integrating drilling, autonomous operations, and in-situ life-detection and mineralogical instruments. The project tests the Signs of Life Detector (SOLID), proposed for the 2019 Discovery Mars Icebreaker mission, and ARIA (Astronaut Raman Instrument for ISRU and Astrobiology), which provides mineral identification and detects trace organics and volatiles, including indicators of organic thermal maturity. Because current and planned Mars drilling missions operate largely “blind,” MEAD also evaluates the use of drill-induced vibrations recorded by deployed geophones to enable local subsurface mapping for improved targeting of drilling and sampling. In August 2025, MEAD completed its first-year field deployment to Haughton Crater in the Canadian High Arctic, an established Mars impact-crater terrestrial analog site, bringing a Honeybee Robotics TRIDENT drill with applied automation, alongside ARIA, SOLID, and FleetSpace geophones.

Haughton Crater

Next-Generation Energy Technologies for Connected and Automated On-Road Vehicles (NEXTCAR) - Predictive Data-Driven Vehicle Dynamics and Powertrain Control: from ECU to the Cloud (Final Scientific/Technical Report)

This project developed and demonstrated a predictive, data-driven vehicle control system designed to improve energy efficiency and driving performance. The team created intelligent self-driving car technology that optimizes fuel and electricity use by proactively planning vehicle actions. By combining Level 4 autonomous driving capabilities with vehicle-to-everything (V2X) connectivity, the system enables vehicles to adjust speed and change lanes in response to traffic signals, surrounding vehicles, and road conditions, reducing unnecessary stops and delays. In testing, the system improved vehicle fuel economy by more than 30% and reduced travel time by approximately 10%, compared to a conventional adaptive cruise control baseline. These results demonstrate the technical effectiveness of using predictive, V2X-enabled strategies, such as traffic light timing and surrounding traffic awareness, to inform real-time vehicle powertrain control and driving behavior. Additionally, a supporting cloud platform was developed to provide dispatch and route recommendations as well as to log vehicle data, demonstrating the economic feasibility of this approach at the fleet level. By optimizing dispatching and routing operations, this technology enables electric fleet operators to use their vehicles more efficiently and reduce reliance on diesel backups, lowering both operating costs and energy consumption. Overall, this project’s technology advances the future of clean, energy-efficient transportation, enabling vehicles and fleets to reduce energy waste, cut costs, and lower emissions through intelligent automation and connectivity.

33 ADVANCED PROPULSION SYSTEMS

An Automated Probabilistic Asteroid Prediscovery Pipeline

We present an automated and probabilistic method to make prediscovery detections of near-Earth asteroids (NEAs) in archival survey images, with the goal of reducing orbital uncertainty immediately after discovery. We refit the Minor Planet Center's astrometry and propagate the full six-parameter covariance to survey epochs to define search regions. We build low-threshold source catalogs for viable images and evaluate every detected source in a search region as a candidate prediscovery. We eliminate false positives by refitting a new orbit to each candidate and probabilistically linking detections across images using a likelihood ratio. Applied to the Zwicky Transient Facility's (ZTF) imaging, we identify approximately 3000 recently discovered NEAs with prediscovery potential, including a doubling of the observational arc for about 500. We use archival ZTF imaging to make prediscovery detections of the potentially hazardous asteroid 2021 DG1, extending its arc by 2.5 yr and reducing future apparition sky plane uncertainty from many degrees to arcseconds. We also recover 2025 FU24 nearly 7 yr before its first known observation, when its sky plane uncertainty covers hundreds of square degrees across thousands of ZTF images. The method is survey agnostic and scalable, enabling rapid orbit refinement for new discoveries from Rubin, NEO Surveyor, and NEOMIR.

79 ASTRONOMY AND ASTROPHYSICS

Benchmarking Bayesian Optimization Frameworks and Acquisition Strategies for Materials Discovery and Autonomous Laboratories

Bayesian optimization (BO) can accelerate materials discovery by guiding expensive experiments toward the most promising processing conditions. We systematically compare five BO surrogate and framework combinations (Gaussian processes in Ax, Gaussian processes and Monte-Carlo neural networks in BayBE, random forests in Lolopy, and tree-structured Parzen (TPE) estimators in Hyperopt) on three benchmarks that mimic common materials design tasks (a discrete solid-electrolyte composition space, a hybrid discrete/continuous laminate-composite design problem solved with micromechanics modeling, and the continuous Ishigami analytic function which is a standard optimization benchmark). Each BO surrogate is paired with posterior mean, probability of improvement, and expected improvement acquisition functions and run for 100 trials from randomized initial samples with uniform random search providing a control. Across five random seeds per setting, BayBE’s Gaussian-process surrogate with expected improvement consistently reached ≥95 % of the known optimum in the fewest evaluations, while Lolopy’s random forest matched or exceeded GP performance on purely categorical or mixed spaces at a higher computational cost. Posterior mean alone often stagnated at local optima, underscoring the need for exploration, whereas probability and expected improvement balanced exploration and exploitation leading to better optimization in fewer trials. Execution times ranged from milliseconds for TPE to minutes for neural-network and random-forest surrogates. These results establish baseline expectations for BO in automated materials laboratories and highlight expected improvement with Gaussian processes as a reliable first choice, with random forests offering a strong alternative when categorical variables dominate. The benchmark suite and code are released to facilitate future surrogate, acquisition, and constraint-handling research in data-driven materials optimization.

Bayesian optimization

A Reflection on the Evolution of Sodium/Metal Chloride (ZEBRA) Batteries and Lithium-Ion Cathode Materials (1975–2025): A Tribute to Johan Coetzer

This narrative summarizes, in retrospect, the enormous and quietly-conducted contribution of Dr Johan Coetzer, a South African scientist and entrepreneur, to the discovery, development and implementation of the high temperature sodium—metal chloride “ZEBRA” battery (Na/β-Al 2 O 3 , NaAlCl 4 /MCl 2 (M = Ni, Fe)). Here, this research activity was initiated in the mid 1970’s at the Council for Scientific and Industrial Research (CSIR) in South Africa and subsequently developed primarily in partnership with the Atomic Energy Research Establishment (AERE, Harwell, UK), Beta R&D (Derby, UK) and Daimler Benz (Germany), before being transferred to industry worldwide for electric vehicle and energy storage applications, albeit at a relatively low production rate. Coetzer’s wide-ranging, innovative and, at times, unconventional scientific approach also laid the foundation for the discovery and implementation of manganese-based spinel and layered metal oxide cathode materials for the Li-ion battery industry.

ZEBRA Battery

The Relevance of the VIPER Mission to NASA’s Artemis Human Exploration of the Moon

NASA has ambitious plans to send astronaut crews to the south polar region of the Moon and explore this lunar terrain with humans for the first time through a series of Artemis missions. Artemis will provide economic benefits, drive technological advancement, and inspire the next generation of explorers. Simultaneously, Artemis presents a unique opportunity for humans to conduct high-priority planetary science in situ in the south polar region of the Moon. Prior to human exploration, landed robotic precursor investigations can provide valuable information to reduce risk and maximize discovery and productivity of subsequent crewed missions. NASA’s Volatiles Investigating Polar Exploration Rover (VIPER) is a robotic mission designed to explore and characterize the lunar south polar region prior to crewed Artemis landed missions. VIPER is designed to explore multiple thermal regimes to characterize the lunar polar environment and regolith properties, and to explore for surface and subsurface ices. Each of these objectives are key for both scientific investigation and to detect and assess volatile deposits to support in situ resource utilization (ISRU) and a sustained human presence on the Moon. VIPER would also operate with a real-time mission operations architecture with relevance and feed-forward to Artemis crewed operations on the lunar surface. VIPER would provide key information regarding the lunar environment, scientific exploration, technologies, and real-time operations to optimize the valuable surface exploration time of Artemis crew members while simultaneously reducing risk to crew and increasing health and human safety on the lunar surface.

Jennifer L Heldmann

Identification of potent inhibitors of JUN N-terminal kinases for treatment of endometriosis and associated pain

Endometriosis, defined as the ectopic growth of endometrial tissue outside of the uterine cavity, is an inflammatory and hormone-dependent disease that causes excruciating pelvic pain, infertility, and significantly decreases quality of life in affected patients. The JUN N-terminal kinases (JNKs) are a leading class of nonhormonal therapeutic targets that have been validated in preclinical models of endometriosis and in a Phase 1/2 clinical trial. Despite their therapeutic potential, JNK inhibitors with increased potency and specificity are needed to address the inflammatory pathology of endometriosis and to prevent disease progression. Leveraging a DNA-encoded chemical library collection of ~4 billion compounds, we identified lead inhibitor CDD-2428 and optimized derivatives, CDD-2728 and CDD-3013, with excellent binding affinity to JNK1-3 (K d = 0.12 to 3.7 nM), enhanced selectivity, metabolic stability, and cellular permeability. Crystallographic and biochemical studies confirmed that CDD-3013 exhibited superior kinase selectivity with improved efficacy compared to existing JNK inhibitors. In primary endometriosis cell models, CDD-2728 and CDD-3013 suppressed JNK-dependent inflammatory signaling, dampening pathways linked to pain, invasion, angiogenesis, and macrophage recruitment. In an endometriosis mouse model, both CDD-2728 and CDD-3013 reduced endometriotic lesion size, macrophage infiltration, and cellular proliferation, showing in vivo efficacy. When tested in a lipopolysaccharide-induced hyperalgesia model, CDD-2728 and CDD-3013 decreased markers of induced pain, as measured by changes in a dynamic weight bearing test and Grimace scores. These findings nominate CDD-2728 and CDD-3013 as potent, nonhormonal therapeutic candidates for endometriosis with broad anti-inflammatory and analgesic activity, addressing a critical unmet clinical need.

Madasu, Chandrashekhar [Department of Pathology an

Nuclear Isomer Discovery Database Released

Nuclear isomers correspond to excited states in nuclides with finite lifetimes. Here, after the discovery of isotopes–different nuclides of the same element–in 1913 by Frederick Soddy [Citation1], Otto Hahn postulated in 1921 [Citation2] that there are even different metastable states within one isotope. In analogy to chemical isomers, which are the same compounds with distinct structures, nuclear isomers have the same number of protons and neutrons but in different configurations.

Thoennessen, Michael [Michigan State University, E

High entropy oxides prediction and discovery by the Mixed Enthalpy-Entropy Descriptor

The vast, high-dimensional composition space of high-entropy oxides (HEOs) offers exceptional opportunities for functional materials discovery, yet it also poses a fundamental challenge: the rational and efficient prediction of stable, synthesizable compositions and the corresponding structure–property relationships. Despite growing interest, the field still lacks broadly applicable, physically grounded descriptors capable of navigating various large chemical spaces. Here, we introduce a Mixed Enthalpy–Entropy Descriptor (MEED) that enables rapid, first-principles–based prediction of HEOs synthesizability across diverse chemistries. Using MEED, we perform high-throughput screening of two distinct HEO families: rocksalt oxides and perovskite oxides. The predicted top candidates in each family were experimentally validated. MEED reveals unifying thermodynamic and structural principles governing stability across both chemical compositions and polymorphs, providing mechanistic insight into the formation of high-entropy phases. This work significantly broadens the accessible chemical design space for HEOs and establishes a data-efficient framework for accelerating the discovery of next-generation functional materials.

Yu, Liping [University of Central Florida]