Sample Efficient Generative Optimization for Molecular Design

Molecular optimization in drug discovery, materials design, and catalysis requires searching vast chemical spaces under tight evaluation budgets, since high-fidelity oracles and experimental measurements are costly. The practical impact of an optimization method therefore hinges on its sample efficiency: how few evaluations it needs to find strong candidates. We introduce Sample Efficient Generative Optimization (SEGO), a framework for Bayesian optimization on adaptively generated molecules. In SEGO, a probabilistic surrogate model forms a hypothesis about where hits lie in chemical space, a generative model is steered to propose candidates in that region, the most promising candidate is selected via an acquisition function, and the resulting oracle call is used both to sharpen the surrogate and to anchor the generator in real reward. SEGO attains state-of-the-art performance on the practical molecular optimization (PMO) benchmark using only one tenth of the oracle calls consumed by other methods, and on a multiparameter docking task it reaches ten hits in roughly half the oracle calls of existing approaches. These gains move molecular optimization closer to campaigns driven by direct experimental feedback.

Agentic generation of verifiable rules for deterministic, self-expanding reaction classification

Computer-assisted synthesis planning breaks target molecules into accessible precursors using large libraries of reaction rules that assign each transformation a deterministic, interpretable label. But chemistry is long-tailed, making manual encoding intractable, and existing tools rely on fixed rulesets that cannot adapt to new chemistries. Here we present a fully automated pipeline in which a multi-agent framework of large language models (LLMs) classifies reactions and writes the rules themselves across 665,901 US patent reactions, generating each rule under a verification loop that tests it against the corpus. It expands a standard taxonomy from 68 to 14,073 classes without human curation. With a lightweight fingerprint classifier, it classifies 97.7\% of unseen reactions, matching a leading proprietary classifier while resolving chemistry more finely and extending on demand to chemistry outside its training distribution. The result is a living reactivity database and a general route to turning generative models into reliable, self-expanding symbolic systems.

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.

From Knowledge to Action: Outcomes of the 2025 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry

Large language models (LLMs) are rapidly changing how researchers in materials science and chemistry discover, organize, and act on scientific knowledge. This paper analyzes a broad set of community-developed LLM applications in an effort to identify emerging patterns in how these systems can be used across the scientific research lifecycle. We organize the projects into two complementary categories: Knowledge Infrastructure, systems that structure, retrieve, synthesize, and validate scientific information; and Action Systems, systems that execute, coordinate, or automate scientific work across computational and experimental environments. The submissions reveal a shift from single-purpose LLM tools toward integrated, multi-agent workflows that combine retrieval, reasoning, tool use, and domain-specific validation. Prominent themes include retrieval-augmented generation as grounding infrastructure, persistent structured knowledge representations, multimodal and multilingual scientific inputs, and early progress toward laboratory-integrated closed-loop systems. Together, these results suggest that LLMs are evolving from general-purpose assistants into composable infrastructure for scientific reasoning and action. This work provides a community snapshot of that transition and a practical taxonomy for understanding emerging LLM-enabled workflows in materials science and chemistry.

CASCADE: Cumulative Agentic Skill Creation through Autonomous Development and Evolution

Large language model (LLM) agents currently depend on predefined tools or brittle tool generation, constraining their capability and adaptability to complex scientific tasks. We introduce CASCADE, a self-evolving agentic framework representing an early instantiation of the transition from "LLM + tool use" to "LLM + skill acquisition". CASCADE enables agents to master complex external tools and codify knowledge through two meta-skills: continuous learning via web search and code extraction, and self-reflection via introspection and knowledge graph exploration, among others. We evaluate CASCADE on SciSkillBench, a benchmark of 116 materials science and chemistry research tasks. CASCADE achieves a 93.3% success rate using GPT-5, compared to 35.4% without evolution mechanisms. We further demonstrate real-world applications in computational analysis, autonomous laboratory experiments, and selective reproduction of published papers. Along with human-agent collaboration and memory consolidation, CASCADE accumulates executable skills that can be shared across agents and scientists, moving toward scalable AI-assisted scientific research.

MiST: Understanding the Role of Mid-Stage Scientific Training in Developing Chemical Reasoning Models

Large Language Models can develop reasoning capabilities through online fine-tuning with rule-based rewards. However, recent studies reveal a critical constraint: reinforcement learning succeeds only when the base model already assigns non-negligible probability to correct answers -- a property we term 'latent solvability'. This work investigates the emergence of chemical reasoning capabilities and what these prerequisites mean for chemistry. We identify two necessary conditions for RL-based chemical reasoning: 1) Symbolic competence, and 2) Latent chemical knowledge. We propose mid-stage scientific training (MiST): a set of mid-stage training techniques to satisfy these, including data-mixing with SMILES/CIF-aware pre-processing, continued pre-training on 2.9B tokens, and supervised fine-tuning on 1B tokens. These steps raise the latent-solvability score on 3B and 7B models by up to 1.8x, and enable RL to lift top-1 accuracy from 10.9 to 63.9% on organic reaction naming, and from 40.6 to 67.4% on inorganic material generation. Similar results are observed for other challenging chemical tasks, while producing interpretable reasoning traces. Our results define clear prerequisites for chemical reasoning training and highlight the broader role of mid-stage training in unlocking reasoning capabilities.

Synthelite: Chemist-aligned and feasibility-aware synthesis planning with LLMs

Computer-aided synthesis planning (CASP) has long been envisioned as a complementary tool for synthetic chemists. However, existing frameworks often lack mechanisms to allow interaction with human experts, limiting their ability to integrate chemists' insights. In this work, we introduce Synthelite, a synthesis planning framework that uses large language models (LLMs) to directly propose retrosynthetic transformations. Synthelite can generate end-to-end synthesis routes by harnessing the intrinsic chemical knowledge and reasoning capabilities of LLMs, while allowing expert intervention through natural language prompts. Our experiments demonstrate that Synthelite can flexibly adapt its planning trajectory to diverse user-specified constraints, achieving up to 95\% success rates in both strategy-constrained and starting-material-constrained synthesis tasks. Additionally, Synthelite exhibits the ability to account for chemical feasibility during route design. We envision Synthelite to be both a useful tool and a step toward a paradigm where LLMs are the central orchestrators of synthesis planning.

DynaMate: An Autonomous Agent for Protein-Ligand Molecular Dynamics Simulations

Force field-based molecular dynamics (MD) simulations are indispensable for probing the structure, dynamics, and functions of biomolecular systems, including proteins and protein-ligand complexes. Despite their broad utility in drug discovery and protein engineering, the technical complexity of MD setup, encompassing parameterization, input preparation, and software configuration, remains a major barrier for widespread and efficient usage. Agentic LLMs have demonstrated their capacity to autonomously execute multi-step scientific processes, and to date, they have not successfully been used to automate protein-ligand MD workflows. Here, we present DynaMate, a modular multi-agent framework that autonomously designs and executes complete MD workflows for both protein and protein-ligand systems, and offers free energy binding affinity calculations with the MM/PB(GB)SA method. The framework integrates dynamic tool use, web search, PaperQA, and a self-correcting behavior. DynaMate comprises three specialized modules, interacting to plan the experiment, perform the simulation, and analyze the results. We evaluated its performance across twelve benchmark systems of varying complexity, assessing success rate, efficiency, and adaptability. DynaMate reliably performed full MD simulations, corrected runtime errors through iterative reasoning, and produced meaningful analyses of protein-ligand interactions. This automated framework paves the way toward standardized, scalable, and time-efficient molecular modeling pipelines for future biomolecular and drug design applications.

Flow-Based Fragment Identification via Binding Site-Specific Latent Representations

Fragment-based drug design is a promising strategy leveraging the binding of small chemical moieties that can efficiently guide drug discovery. The initial step of fragment identification remains challenging, as fragments often bind weakly and non-specifically. We developed a protein-fragment encoder that relies on a contrastive learning approach to map both molecular fragments and protein surfaces in a shared latent space. The encoder captures interaction-relevant features and allows to perform virtual screening as well as generative design with our new method LatentFrag. In LatentFrag, fragment embeddings and positions are generated conditioned on the protein surface while being chemically realistic by construction. Our expressive fragment and protein representations allow location of protein-fragment interaction sites with high sensitivity and we observe state-of-the-art fragment recovery rates when sampling from the learned distribution of latent fragment embeddings. Our generative method outperforms common methods such as virtual screening at a fraction of its computational cost providing a valuable starting point for fragment hit discovery. We further show the practical utility of LatentFrag and extend the workflow to full ligand design tasks. Together, these approaches contribute to advancing fragment identification and provide valuable tools for fragment-based drug discovery.

Lookup multivariate Kolmogorov-Arnold Networks

High-dimensional linear mappings, or linear layers, dominate both the parameter count and the computational cost of most modern deep-learning models. We introduce a general drop-in replacement, lookup multivariate Kolmogorov-Arnold Networks (lmKANs), which deliver a substantially better trade-off between capacity and inference cost. Our construction expresses a general high-dimensional mapping through trainable low-dimensional multivariate functions. These functions can carry dozens or hundreds of trainable parameters each, and yet it takes only a few multiplications to compute them because they are implemented as spline lookup tables. Empirically, lmKANs reduce inference FLOPs by up to 6.0x while matching the flexibility of MLPs in general high-dimensional function approximation. In another feedforward fully connected benchmark, on the tabular-like dataset of randomly displaced methane configurations, lmKANs enable more than 10x higher H100 throughput at equal accuracy. Within frameworks of Convolutional Neural Networks, lmKAN-based CNNs cut inference FLOPs at matched accuracy by 1.6-2.1x and by 1.7x on the CIFAR-10 and ImageNet-1k datasets, respectively. Our code, including dedicated CUDA kernels, is available online at https://github.com/schwallergroup/lmkan.