CAi Copilot: Reducing Operational Workload in Molecular Design through Intent-Driven Agentic Workflows

Early-stage molecular design is an iterative process, not just a task of generating molecules. Researchers turn broad goals into design strategies, refine candidates, assess many properties, and gather evidence before synthesis and tests. AI methods can generate molecules, optimize several goals, predict properties, dock compounds, and account for synthesis. Yet these functions are spread across specialized tools. Experts must still coordinate each step, judge interim results, and integrate evidence. The central challenge is thus to turn research intent into adaptive, traceable runs grounded in scientific tools. We cast this challenge as intent-to-evidence molecular design workflow execution and present CAi Copilot, an expert-oriented agent with three linked layers. The Research Interface Layer turns intent into an executable plan. The Agent Reasoning Layer uses interim results to guide each run. The Execution Substrate supplies molecular tools, metrics, reusable utilities, and backend services. Across 45 tasks, CAi achieves the strongest overall performance, with an outcome score of 84.59, exceeding the next-best result by 18.07 points. Additional benchmarks test how CAi coordinates generation, screening, and multi-criteria evaluation, while exposing limits in long-horizon execution. These results show that CAi turns broad molecular-design intent into transparent, traceable workflows that connect interim decisions to candidate-level evidence.

Evidence-Gated LLM Priors for Multi-Objective Bayesian Optimization

Large language models (LLMs) are increasingly used as heuristic advisors for black-box optimization, yet their suggestions and self-reported confidence are not necessarily calibrated to downstream objective values. This issue becomes more pronounced in multi-objective Bayesian optimization, where different objectives may require different expert knowledge and where an LLM expert can be useful for one objective but misleading for another. We study how to use LLM-generated expert priors in discrete multi-objective Bayesian optimization without blindly trusting them. We propose an objective-wise reputation-market mechanism that treats each expert-objective pair as a falsifiable prior source. Expert weights are updated online from observed objective feedback, discounted over time, and gated by market-level trust. We then introduce a decoupled counterfactual gate that can use the LLM prior without confidence, use it with confidence, or abstain from the LLM prior entirely. Across controlled synthetic stress tests and three molecule optimization benchmarks with \qwenflash{}-generated expert priors, we find that dynamic objective-wise calibration improves robustness over fixed LLM priors. However, raw LLM confidence is not reliably beneficial: on ESOL, confidence is positively correlated with prediction error; on FreeSolv, confidence can help; and on Lipophilicity, ignoring confidence remains strongest. Our fixed three-arm counterfactual gate improves over the first counterfactual variant on ESOL and FreeSolv, while an attempted margin portfolio exposes a useful negative result: margin selection should be acquisition-aware rather than based only on one-step prior error.

AI4S-SDS: A Neuro-Symbolic Solvent Design System via Sparse MCTS and Differentiable Physics Alignment

Automated design of chemical formulations is a cornerstone of materials science, yet it requires navigating a high-dimensional combinatorial space involving discrete compositional choices and continuous geometric constraints. Existing Large Language Model (LLM) agents face significant challenges in this setting, including context window limitations during long-horizon reasoning and path-dependent exploration that may lead to mode collapse. To address these issues, we introduce AI4S-SDS, a closed-loop neuro-symbolic framework that integrates multi-agent collaboration with a tailored Monte Carlo Tree Search (MCTS) engine. We propose a Sparse State Storage mechanism with Dynamic Path Reconstruction, which decouples reasoning history from context length and enables arbitrarily deep exploration under fixed token budgets. To reduce local convergence and improve coverage, we implement a Global--Local Search Strategy: a memory-driven planning module adaptively reconfigures the search root based on historical feedback, while a Sibling-Aware Expansion mechanism promotes orthogonal exploration at the node level. Furthermore, we bridge symbolic reasoning and physical feasibility through a Differentiable Physics Engine, employing a hybrid normalized loss with sparsity-inducing regularization to optimize continuous mixing ratios under thermodynamic constraints. Empirical results show that AI4S-SDS achieves full validity under the adopted HSP-based physical constraints and substantially improves exploration diversity compared to baseline agents. In preliminary lithography experiments, the framework identifies a novel photoresist developer formulation that demonstrates competitive or superior performance relative to a commercial benchmark, highlighting the potential of diversity-driven neuro-symbolic search for scientific discovery.