Organizations: Dept. of Energy Conversion and Storage, Technical University of Denmark, Denmark · Dept. of Applied Mathematics and Computer Science, Technical University of Denmark, Denmark · Pioneer Center for Accelerating P2X Materials Discovery (CAPeX), Kgs. Lyngby, Denmark
Abstract
Discovering novel stable molecules without training data remains a grand scientific challenge. Current molecular generative models are trained on large, pre-curated datasets, which introduce biases and limit exploration of novel chemistry. In contrast, we propose a new paradigm: autonomous, generalized agents capable of mapping vast, unknown chemical spaces without any pretraining. For the first time, we present AtomComposer, a self-guided agent that autonomously constructs valid 3D isomers under stoichiometric constraints and is trained exclusively online using reinforcement learning. Unlike existing approaches that generally overfit to a specific chemical formula, we establish a multi-composition training scheme that enables a broad generalization across diverse chemistry, guided by energy- and validity-based rewards. Our agent can discover up to an order of magnitude more valid isomers on unseen test formulas than existing single-composition reinforcement-learning baselines trained with per-step energy rewards. These results fulfill the promise of online reinforcement learning as a powerful paradigm for scalable, from-scratch exploration of chemical configuration space.
Despite the success of foundation models in language and vision, molecular graph generation still lacks a unified framework for heterogeneous design tasks with reliable controllability. While reinforcement learning (RL) offers a natural post-training mechanism for task-specific optimization, applying it to graph generative models is hindered by the vast atom-wise action spaces and chemically invalid intermediate states. We propose \textbf{Co}ntrollable \textbf{Mole}cular Generative Foundation Models (CoMole), built with a unified motif-aware graph diffusion pipeline. By learning a motif-aware graph space, CoMole transfers pretrained structural priors into controllable generation, where RL optimizes conditional reverse policies over chemically meaningful decisions. We theoretically characterize the bottleneck of atom-level RL and justify motif-aware policy optimization. Across three heterogeneous benchmarks spanning materials and drug discovery, CoMole ranks first in controllability on all nine targets, reduces MAE by up to 48.2% relative to the strongest baselines, and maintains validity above 0.94 without rule-based correction or post-hoc filtering. We further show that CoMole transfers controllability to unseen properties by optimizing only task embeddings with the generator frozen, achieving performance competitive with strong task-specific baselines.
A major bottleneck in scientific discovery consists of narrowing an exponentially large set of objects, such as proteins or molecules, to a small set of promising candidates with desirable properties. While this process can rely on expert knowledge, recent methods leverage reinforcement learning (RL) guided by a proxy reward function to enable this filtering. By employing various forms of entropy regularization, these methods aim to learn samplers that generate diverse candidates that are highly rated by the proxy function. In this work, we make two main contributions. First, we show that these methods are liable to generate overly diverse, suboptimal candidates in large search spaces. To address this issue, we introduce a novel unified operator that combines several regularized RL operators into a general framework that better targets peakier sampling distributions. Secondly, we offer a novel, robust RL perspective of this filtering process. The regularization can be interpreted as robustness to a compositional form of uncertainty in the proxy function (i.e., the true evaluation of a candidate differs from the proxy's evaluation). Our analysis leads us to a novel, easy-to-use algorithm we name trajectory general mellowmax (TGM): we show it identifies higher quality, diverse candidates than baselines in both synthetic and real-world tasks. Code: https://github.com/marcojira/tgm.
Marco Jiralerspong, Esther Derman, Danilo Vucetic +5
Autoresearch offers a flexible paradigm for automating scientific tasks, in which an AI agent proposes, implements, evaluates, and refines candidate solutions against a quantitative objective. Here, we use composition-based materials-property prediction to test whether such agents can perform a task beyond model selection and hyperparameter optimization: the design of input descriptors. We introduce Automat, an autoresearch framework where a coding agent based on a large language model generates composition-only descriptors for chemical compounds and evaluates them using a random forest workflow. The agent is restricted to information derivable from chemical formulas and iteratively proposes, implements, and tests chemically motivated descriptor strategies. We apply Automat, with OpenAI Codex using GPT-5.5 as the coding agent, to the prediction of experimental band gaps in inorganic materials and Curie temperatures in ferromagnetic compounds. In both tasks, Automat improves over fractional-composition, Magpie, and combined fractional-composition/Magpie baselines, while producing descriptor families that are chemically interpretable. These results provide a demonstration that autoresearch agents can generate competitive, task-specific materials descriptors without manual feature engineering during the run. They also reveal current limitations, including descriptor redundancy, sensitivity to greedy feature expansion, and the need for explicit complexity control, descriptor pruning, and more sophisticated search strategies.