Latent JEPA is a new framework that trains continuous latent thoughts to anticipate informative aspects of future solutions in chemical reasoning, without verbalizing every intermediate step. It combines autoregressive learning with joint-embedding prediction of one or more future views, using textual and molecular prediction objectives that link latent thoughts to subsequent reasoning and molecular outcomes. Experiments on ChemCoTBench demonstrate improvements in molecular optimization, editing, and reaction metrics, and representation analyses show that future prediction makes latent thoughts more informative about molecular outcomes and better aligned with chemical structure.
By Xinjian Zhao, Yaoyao Xu, Xuemin Chen, Xiaozhuang Song, Tianshu Yu
arXiv:2602. 07075v5 Announce Type: replace-cross Abstract: Current chemical large language models (LLMs) predominantly rely on explicit Chain-of-Thought (CoT) to solve complex reasoning problems.
By Xinwu Ye, Yicheng Mao, Yuxuan Liao, Jia Zhang, Yimeng Liu, Li Hao, Fang Wu, Zhiwei Li, Zehong Wang, Zhiyuan Liu, Zhenfei Yin, Li Yuan, Philip Torr, Huan Sun, xiangxiang Zeng, Mengdi Wang, Le Cong, Shenghua Gao, Xiangru Tang
The paper introduces a multitask large reasoning model for molecular science that incorporates chemical knowledge via a multispecialist architecture, chain-of-thought supervision, and molecule-informed reinforcement learning. It coordinates prediction and inference specialists across ten molecular tasks—including description, generation, nomenclature translation, property prediction, and reaction prediction—using task-conditioned routing. The model surpasses more than 20 general-purpose and molecular large language models, improving aggregate performance by 50.3% and outperforming leading multitask baselines on most tasks, while maintaining interpretable chemical inference and demonstrating a workflow for CNS candidate generation and retrosynthetic planning.
By Pengfei Liu, Shuang Ge, Xiaobo Wang, Xin Liu, Jun Tao, Yan Li, Chao Liu, Ling Chen, Zhixiang Ren
arXiv:2508. 10967v3 Announce Type: replace-cross Abstract: Retrosynthesis prediction aims to infer the reactant molecules based on a given product molecule, which is a fundamental task in chemical synthesis.
By Xinyi Li, Sai Wang, Yutian Lin, Yu Wu
Local chemical perception and property reasoning are both essential for understanding how molecular structure determines properties. Current LLM-based chemical reasoning methods either receive SMILES/molecular images together with descriptions of local motifs, or reason directly from molecular images.
arXiv:2607. 21941v1 Announce Type: new Abstract: Chemists and materials scientists increasingly use machine learning models, such as graph neural networks (GNNs), to predict properties of molecules and the outcomes of their reactions.
By Shiyi Liu, Jiaqing Chen, Nicholas Hadler, Rostyslav Hnatyshyn, Michael W. Mahoney, Talita Perciano, John F. Hartwig, Gunther H. Weber, Ross Maciejewski
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
arXiv:2505.16782v3 Announce Type: replace
Abstract: Large Language Models (LLMs) have shown impressive performance on complex tasks through Chain-of-Thought (CoT) reasoning. However, conventional CoT...
By Xinghao Chen, Anhao Zhao, Heming Xia, Xuan Lu, Hanlin Wang, Yanjun Chen, Wei Zhang, Jian Wang, Wenjie Li, Xiaoyu Shen
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
arXiv:2607. 12771v1 Announce Type: new Abstract: Reaction mechanisms consist of the step-by-step sequences of elementary reactions that explain chemical transformations.
By Xingyu Dang, Haocheng Tang, Junmei Wang, Yanjun Li
arXiv:2608. 05806v1 Announce Type: cross Abstract: While standard Next-Token Prediction (NTP) lays the foundation of language model pre- training, its teacher-forced training paradigm may not be optimal for long-horizon reasoning and planning.
By Chang Shi, Tim Pearce, Manan Tomar, Siddhartha Sen, John Langford
The paper introduces Prototype-Mediated Process Supervision (PMPS), a method that uses learnable reasoning prototypes to provide structural supervision for latent chain-of-thought embeddings, addressing representation collapse and uneven information distribution. PMPS aligns latent and explicit CoT embeddings in a shared prototype space via many-to-many soft assignment and employs a Progressive Sequential Alignment module to guide training from positional priors to adaptive matching. Experiments show PMPS reduces output token length to under 50% of explicit CoT on GSM8K-Aug and improves accuracy by 2.08% over SIM-CoT, even surpassing CoT-SFT on GPT-2 and achieving the highest accuracy among latent reasoning methods on larger models and harder tasks.
By Yiqi Li, Xu Chen, Chen Ju, Jiangchao Yao, Zhaoyang Li, Jinsong Lan, Xiaoyong Zhu, Bo Zheng, Yu Wang