arXiv Machine Learning

My Chemical Harness: Evolutionary Molecular Design over Synthetic Pathways with Large Language Model Agents

arXiv:2606. 11256v1 Announce Type: cross Abstract: Designing molecules with target properties is most useful when candidate structures are accompanied by feasible synthetic routes.

arXiv AI

Jul 17

RetroAgent: Harnessing LLMs to Search Over Structured Memory for Agentic Retrosynthesis Planning

arXiv:2607. 14512v1 Announce Type: new Abstract: Multi-step retrosynthesis planning seeks to decompose a target molecule into commercially available building blocks through a sequence of feasible reactions.

By Yanqiao Zhu, Jingru Gan, Xiaoqi Sun, Fang Sun, Yidan Shi, Md Mofijul Islam, Chao Shang, Wenhao Gao, Connor W. Coley, Yizhou Sun, Wei Wang

llms agents benchmarks

arXiv AI

Aug 10

Strategy-first synthesis planning for complex natural products

arXiv:2608. 07454v1 Announce Type: cross Abstract: The total synthesis of a complex molecule is among the most demanding intellectual and experimental feats in chemistry: a chemist must plan many steps ahead for how to assemble simple building blocks into an intricate target, devise backup strategies, and anticipate procedural challenges.

By Daniel Armstrong, Xuan-Vu Nguyen, Octavian Susanu, Gabriel Gibberd, Th\'eo A. Neukomm, Tadd\"aus Strunden, Dan Forster, Morgane Delattre, Shawn Teh, Cl\'ement Rols, John Federice, Hayden Leatherwood, M. Lavelle Barnes, Maarten R. Dobbelaere, Peter Wipf, Jon T. Njardarson, Jieping Zhu, Philippe Schwaller

llms agents benchmarks

arXiv Machine Learning

Jul 22

Adopting Reinforcement Learning with Verifiable Rewards for Molecular Generation

arXiv:2607. 19044v1 Announce Type: new Abstract: Leveraging large language models (LLMs) for molecular generation has shown remarkable potential in chemical and drug design.

By Mingxuan Ouyang, Hao Lan, Wanyu Lin

llms reinforcement-learning fine-tuning benchmarks

arXiv AI

Jul 7

URSA: Chemistry-Aware Benchmark for Utilitarian Retrosynthesis Assessment

arXiv:2607. 04688v1 Announce Type: cross Abstract: Synthesis planning aiming to find pathways of reactions for a target molecule is one of the most important and challenging tasks in drug discovery.

By Bogdan Zagribelnyy, Ivan Ilin, Nikita Bondarev, Anton Morgunov, Arkadii Lin, Maksim Kuznetsov, Rim Shayakhmetov, Vladimir Aladinskiy, Alex Aliper, Alex Zhavoronkov

llms benchmarks

arXiv AI

Jun 9

RetroReasoner: A Reasoning LLM for Strategic Retrosynthesis Prediction

arXiv:2603. 12666v2 Announce Type: replace-cross Abstract: Retrosynthesis prediction aims to identify reactants that can synthesize a given product molecule.

By Hanbum Ko, Chanhui Lee, Ye Rin Kim, Rodrigo Hormazabal, Sehui Han, Sungbin Lim, Sungwoong Kim

llms reinforcement-learning fine-tuning

arXiv Machine Learning

Jun 8

Controllable Molecular Generative Foundation Models

arXiv:2605. 15354v2 Announce Type: replace Abstract: 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.

By Yihan Zhu, Yuhan Liu, Weijiang Li, Tengfei Luo, Meng Jiang

rag diffusion reinforcement-learning benchmarks

arXiv Machine Learning

Jun 16

Generative Molecular Design with Steerable and Granular Synthesizability Control

arXiv:2505. 08774v2 Announce Type: replace-cross Abstract: Designing molecules that are both property-optimal and readily synthesizable is a central challenge in drug discovery.

By Jeff Guo, V\'ictor Sabanza-Gil, Olha Semenenko, Oleksii Hrabovskyi, Mykola Protopopov, Anna Kapeliukha, Oleksandr Mosia, Sofiia Hatych, Diana Alieksieieva, Tom Nelis, Patrick Molliet, Helena Sol\'e-\`Avila, Valentas Olikauskas, Nina Aregger, Irina Morozova, Joseph Schmidt, Zlatko Jon\v{c}ev, Olga Tarkhanova, Petro Borysko, Jerome Waser, Bruno Correia, Jeremy Luterbacher, Philippe Schwaller

arXiv AI

Jun 3

From Answers to States: Verifiable Process-Level Evaluation of Chemical Reasoning in Large Language Models

arXiv:2606. 03660v1 Announce Type: new Abstract: Large language models are increasingly used as chemistry assistants, yet most chemistry benchmarks still score only final answers.

By Hongyu Guo, Hao Li, He Cao, Gongbo Zhang, Li Yuan

llms benchmarks safety

arXiv AI

Jun 2

Agents on a Tree: Pathwise Coordination for Multi-Objective Molecular Optimization

arXiv:2606. 00008v1 Announce Type: new Abstract: Multi-objective molecular optimization requires searching vast chemical spaces under conflicting objectives, where early design decisions strongly constrain downstream outcomes.

By Jia Zhang, Tengfei Ma, Tianle Li, Daojian Zeng, Xieping Gao, Xiangxiang Zeng

agents benchmarks

arXiv AI

1d ago

RetroMPA: A Molecular Property-Aware Auxiliary Framework for Enhancing Retrosynthesis Prediction

arXiv:2608. 16111v1 Announce Type: cross Abstract: Retrosynthesis is a cornerstone of drug discovery and organic synthesis.

By Mianzhi Liu, Fan Xiao, Zhiliang Yu, Huayang Huang, Yuke Li, Yi Yang, Wenbo Liu, Yu Wu

rag

arXiv AI

Jun 3

Rethinking Molecular Text Representations for LLMs: An Empirical Study

arXiv:2606. 03057v1 Announce Type: cross Abstract: Large language models (LLMs) are increasingly used for molecular tasks, but it remains unclear which molecular representation to use.

By Arun Raja, Garrett M. Morris, Kian Ming A. Chai

llms nlp benchmarks

arXiv Machine Learning

Jun 25

Uncertainty-aware reinforcement learning for chemical language models

arXiv:2606. 24990v1 Announce Type: new Abstract: Reinforcement Learning (RL) has become a powerful paradigm for de novo molecular design, enabling Chemical Language Models (CLMs) to navigate and explore the chemical space while optimizing specific desired properties.

By Borja Medina, Jon Paul Janet

llms reinforcement-learning

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