chemical engineering teams

Abstract: Early-stage computational drug discovery requires coordinating heterogeneous scientific tools across multi-step workflows. We present a lightweight, tool-augmented framework in which a locally deployable compact language model plans calls to 18 modular tools. A Unified Molecular Schema maintains shared molecular records, while a plug-in interface supports tool replacement and extension. We construct 1,263 manually refined query-plan pairs through workflow-graph path coverage and apply LoRA fine-tuning to three compact model families. Under the query-level split, all fine-tuned models generate fully parseable and schema-compliant plans on 47 held-out cross-group queries. Llama 3.2-3B achieves a tool-selection F1 of 0.998, sequence exact match of 0.979, and argument F1 of 0.960. Under the stricter workflow-grouped split, which excludes identical ordered tool sequences across partitions, sequence exact match reaches 0.452 to 0.548, highlighting the remaining difficulty for compact models in generating complete workflow paths unseen during training. These results demonstrate the feasibility of compact, locally deployable planning while identifying compositional generalization as an important direction for further improvement.

Abstract: De novo crystal generation (DNG) models decide where to search in composition space and how to generate structures with one set of weights. We argue that discovery is better served by separating the two. A crystal structure prediction (CSP) model is a physical prior that should be improved by likelihood training, while rewards, including novelty measured against the search's own history, should act on a search over compositions. We introduce ANCHOR, a GRPO composition policy trained with multi-objective rewards around a frozen CSP model, and continuous adaptive novelty (CAN), a graded novelty score against known structures and a growing discovery history. Using the frozen CSP model as a fixed ruler under one evaluator, we test where adaptation should act. Replacing DNG compositions with ANCHOR's policy on the same CSP backbone raises MSUN from 11.4% to 47.6% and SUN from 1.1% to 22.1% at 99.9% formula uniqueness. Fine-tuning DNG models directly on the same rewards instead moves their composition marginal without raising their on-hull fraction. We show that KL-regularized fine-tuning of a DNG model can only reweight chemistry the pretrained model already supports by a bounded factor, while unregularized DNG fine-tunes move toward known or less stable chemistry. Even a stability-only reward routed into ANCHOR's CSP backbone roughly halves SUN relative to the frozen backbone, whereas likelihood training on structures found during search can improve a CSP backbone. Under MatterGen's evaluation pipeline, ANCHOR raises state-of-the-art MSUN from 29.2% to 41.3%, transfers without retraining to two further CSP backbones, and reaches 47.1% after distillation into Crystalite-CSP. As with any model optimised against a potential, its on-hull rate depends on that potential.

Abstract: Large language models (LLMs) are increasingly used to drive scientific discovery. Understanding how LLMs make decisions from new data and memory of the literature is vital before trusting them to design experiments under tight experimental budgets. However, their decision strategies are invisible in the current performance scores used to evaluate research agents. Here, we benchmark five frontier LLMs in a Bayesian Optimization setting against published statistical baselines on seven combinatorial datasets spanning protein engineering, reaction optimization, molecular design, peptide self-assembly, and catalysis. Performance is paired with direct measurements of model beliefs and actions, enabling highly resolved behavior analysis. A prompt ablation that progressively strips context separates memorization from chemical reasoning and from bare categorical optimization. Prior chemical knowledge helps in expectation, but with high variance and occasionally even harms performance. No configuration tested decisively beats a mean statistical baseline across domains. Belief-movement and Martingale diagnostics, corrected here for a measurement-noise bias that mislabels rational agents as irrational, show that models overreact to incoming data rather than entrenching on their priors in the contexts studied here. Interestingly, while LLM actions are exploitative, models sincerely intend to explore and consistently act on that intent. This failure is a competence gap arising from context-stickiness. Removing in-context history restores exploration, indicating that priors and data must be decoupled to achieve effective LLM-driven discovery.

Abstract: Achieving precise control over multiple properties without sacrificing chemical validity remains a central challenge in molecular inverse design. Existing reinforcement learning (RL) methods fine-tune graph diffusion models by treating **reverse** sampling as a sequential policy, using a single terminal reward to optimize hundreds of coupled decisions. They often suffer from instability, validity collapse, and limited property gains. We introduce GraphFDM (Graph Forward Distribution Matching), a new online RL paradigm for graph diffusion that performs optimization through the **forward** process. GraphFDM uses valid generations to define a reward-tilted target distribution jointly optimized over graph size and molecular structure for each property condition, incorporating reinforcement signals into supervised learning without storing reverse trajectories. We derive the unique optimal target, prove a condition-wise improvement guarantee, and show that the fixed graph-size prior of standard graph diffusion leaves an irreducible matching gap. In multi-conditional polymer and small-molecule generation, GraphFDM achieves the lowest MAE on every target property, with reductions of up to 53.0\% relative to the strongest baselines and chemical validity above 0.99. It further generalizes to out-of-distribution property combinations.

Abstract: Molecular property prediction is often limited by the small size of labeled downstream datasets, motivating pretraining on large corpora of unlabeled molecules. In this work, we ask whether useful inductive biases can instead be learned from abstract, procedurally generated data before a model sees any molecular data. We introduce a three-stage training pipeline consisting of procedural pretraining, molecular pretraining on SMILES, and downstream fine-tuning, and evaluate several procedural tasks spanning sequence structure, cellular automata, and graph reasoning. We find that procedural pretraining can improve molecular property prediction even after subsequent molecular pretraining: on Lipophilicity, \textsc{Reverse} reduces test error by 4.8\%. For context, the magnitude of this improvement is roughly 90\% of the performance difference between our 250K-molecule baseline and the publicly released MoLFormer checkpoint pretrained on approximately 100M molecules. Our analysis shows that the benefit is strongest under downstream data scarcity, depends on the structure of the procedural data rather than only surface-level statistics, and does not increase monotonically with additional procedural training. Instead, transfer typically peaks at an intermediate procedural budget and deteriorates as the model approaches convergence on the procedural task. We further find that, for several tasks, much of the transferable information is localized in the attention layers, while feed-forward layers can contribute to over-specialization. These results show that procedural data can provide transferable structure for molecular learning and offer a complementary route to improving performance when labeled molecular data are limited.