MoLRSI: A Recursive Self-Improving AI agent for Molecular Discovery

Yikun Zhang; Xiwei Cheng; Mingze Yuan; Yu Zhang; Brian Shim; Aarti Krishnan; Daniel Rosen; Kunyang Sun; Yingze Wang; Zhenfeng Deng; Botao Yu; Bingxu Liu; David Liu; Tianyu Liu; Yuanqi Du; Nir Hacohen; James J. Collins; Wengong Jin

arXiv · 2610.39714

MoLRSI: A Recursive Self-Improving AI agent for Molecular Discovery

Yikun Zhang·Xiwei Cheng·Mingze Yuan·Yu Zhang·Brian Shim·Aarti Krishnan·Daniel Rosen·Kunyang Sun·Yingze Wang·Zhenfeng Deng·Botao Yu·Bingxu Liu·David Liu·Tianyu Liu·Yuanqi Du·Nir Hacohen·James J. Collins·Wengong Jin

View original source ↗Read source document ↗Export metadata ↓

Abstract

Molecular discovery requires navigating vast combinatorial search spaces while balancing competing biological objectives. AI agents can automate expert-defined molecular design protocols, but automation alone does not address how to optimize workflows for new tasks or improve their development through experience. Here we introduce MoLRSI, an AI agent that combines systematic optimization of workflows and model architectures with persistent cross-task memory to recursively improve its search policy for molecular discovery. Workflow performance, refinement outcomes, and execution feedback guide subsequent searches, allowing the agent to improve both its workflows and its strategy for developing them. We evaluate MoLRSI in two challenging molecular discovery settings that require balancing competing properties. In antibiotic discovery, MoLRSI developed a screening workflow balancing antibacterial activity, cytotoxicity and structural novelty, achieving an experimental hit rate of 15.9%, compared with 8.7% for a previous expert-led workflow using the same training data and screening library. In de novo peptide-MHC binder design, MoLRSI developed workflows that jointly consider target binding and specificity, producing eight experimentally validated hits against MART-1 and SARS-CoV-1 pMHCs with preferential binding over tested off-targets while Claude Science completely failed. These findings demonstrate how experience-guided workflow optimization can address competing discovery objectives while improving the search strategies used in subsequent campaigns.

Explore related subjects

cs.AI

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Yikun Zhang, Xiwei Cheng, Mingze Yuan, Yu Zhang, Brian Shim, Aarti Krishnan, Daniel Rosen, Kunyang Sun, Yingze Wang, Zhenfeng Deng, Botao Yu, Bingxu Liu, David Liu, Tianyu Liu, Yuanqi Du, Nir Hacohen, James J. Collins, Wengong Jin. 2026-10-29. MoLRSI: A Recursive Self-Improving AI agent for Molecular Discovery. https://arxiv.org/abs/2610.39714

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Invert4TVG: A Temporal Video Grounding Framework with Inversion Tasks Preserving Action Understanding Ability

Temporal Video Grounding (TVG) aims to localize video segments corresponding to a given textual query, which often describes human actions. However, we observe that current methods, usually optimizing for high temporal Intersection-over-Union (IoU), frequently struggle to accurately recognize or understand the underlying actions in both the video and query, thus reducing the effectiveness of these methods. To address this, we propose a novel TVG framework that integrates inversion-based TVG as auxiliary objectives to maintain the model's action understanding ability. We introduce three kinds of inversion TVG tasks derived from the original TVG annotations: (1) Verb Completion, predicting masked verbs (actions) in queries given video segments; (2) Action Recognition, identifying query-described actions; and (3) Video Description, generating descriptions containing query-relevant actions given video segments. These inversion tasks are entirely derived from the original TVG tasks and are probabilistically integrated with them within a reinforcement learning framework. By leveraging carefully designed reward functions, the model preserves its ability to understand actions, thereby improving the accuracy of temporal grounding. Experiments show our method outperforms state-of-the-art approaches, achieving a 7.1\% improvement in R1@0.7 on Charades-STA for a 3B model.

cs.AI↗

arXiv2026

Pharos-ESG: A Framework for Multimodal Parsing, Contextual Narration, and Hierarchical Labeling of ESG Report

Environmental, Social, and Governance (ESG) principles are reshaping the foundations of global financial governance, transforming capital allocation architectures, regulatory frameworks, and systemic risk coordination mechanisms. However, as the core medium for assessing corporate ESG performance, the ESG reports present significant challenges for large-scale understanding, due to chaotic reading order from slide-like irregular layouts and implicit hierarchies arising from lengthy, weakly structured content. To address these challenges, we propose Pharos-ESG, a unified framework that transforms ESG reports into structured representations through multimodal parsing, contextual narration, and hierarchical labeling. It integrates a reading-order modeling module based on layout flow, hierarchy-aware segmentation guided by table-of-contents anchors, and a multi-modal aggregation pipeline that contextually transforms visual elements into coherent natural language. The framework further enriches its outputs with ESG, GRI, and sentiment labels, yielding annotations aligned with the analytical demands of financial research. Extensive experiments on annotated benchmarks demonstrate that Pharos-ESG consistently outperforms both dedicated document parsing systems and general-purpose multimodal models. In addition, we release Aurora-ESG, the first large-scale public dataset of ESG reports, spanning Mainland China, Hong Kong, and U.S. markets, featuring unified structured representations of multi-modal content, enriched with fine-grained layout and semantic annotations to better support ESG integration in financial governance and decision-making.

cs.AI↗

arXiv2026

PRISM: Pushing the Frontier of Deep Think via Process Reward Model-Guided Inference

DEEPTHINK methods improve reasoning by generating, refining, and aggregating populations of candidate solutions, which enables strong performance on complex mathematical and scientific tasks. However, existing frameworks can still suffer from unreliable correctness signals during inference, which creates a population- enhancement bottleneck where deeper deliberation amplifies errors, suppresses correct minority solutions, and yields weak returns to additional compute. In this paper, we introduce a functional decomposition of DEEPTHINK systems and propose PRISM, a Process Reward Model (PRM)-guided inference algorithm that uses step-level verification to guide resampling, proposal acceptance, and solution aggregation. During refinement, PRISM uses PRM scores to guide population resampling and stochastic local refinement, which concentrates computation on higher-quality reasoning while preserving diversity. When paired with PRM- score-vote, a PRM-guided aggregation method, PRISM is competitive with or outperforms existing DEEPTHINK methods, reaching 90.0%, 75.4%, and 71.4% with gpt-oss-20b on AIME25, HMMT25, and GPQA Diamond, respectively, while exceeding gpt-oss-120b. Additionally, our analysis shows that PRISM produces consistent net-directional correction during refinement and maintains competitive accuracy when the initial population contains few correct candidates.

cs.AI↗