arXiv:2602. 13136v2 Announce Type: replace Abstract: Template-free retrosynthesis methods treat the task as black-box sequence generation, limiting learning efficiency, while semi-template approaches rely on rigid reaction libraries that constrain generalization.
By Chenguang Wang, Zihan Zhou, Lei Bai, Tianshu Yu
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
arXiv:2602. 03554v2 Announce Type: replace-cross Abstract: Recent progress has expanded the use of large language models (LLMs) in drug discovery, including synthesis planning.
By Bogdan Zagribelnyy, Ivan Ilin, Maksim Kuznetsov, Nikita Bondarev, Mathieu Reymond, Roman Schutski, Thomas MacDougall, Rim Shayakhmetov, Zulfat Miftakhutdinov, Mikolaj Mizera, Vladimir Aladinskiy, Alex Aliper, Alex Zhavoronkov
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: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
arXiv:2608. 11233v1 Announce Type: cross Abstract: A dense, pretrained language model can be retrofitted with recurrent depth and learn an iterative latent transition that persists after outcome-only annealing.
By Mark Shapiro
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
arXiv:2607. 10391v1 Announce Type: cross Abstract: Despite exposing rich intermediate representations, Vision Transformers (ViTs) are almost exclusively utilized as black-box feature extractors, where only the last layer is considered for downstream tasks.
By Francesco Di Salvo, Shyam Nandan Rai, Hamed Damirchi, Ignacio Meza De la Jara, Sebastian Doerrich, Marco Lents, Christian Ledig
arXiv:2608. 14076v1 Announce Type: cross Abstract: Transition-state (TS) structures define the energetic barriers and mechanistic pathways of elementary chemical reactions, yet their identification remains computationally demanding because conventional saddle-point searches require expensive quantum-mechanical calculations.
By Kaipeng Zeng, Wenxi Zhai, Shengrui Xu, Jie Zhao, Bowen Li, Shiyue Wang, Junchi Yan, Tong Zhu
arXiv:2607. 17671v1 Announce Type: new Abstract: Large-scale single-cell perturbation atlases make it possible to ask an inverse question: given an observed transcriptional response, which annotated targets and compounds in a fixed library are most consistent with that response?
By Kseniia Vaniushkina, Jeongmin Lim, Jinyong Park
arXiv:2501. 12434v3 Announce Type: replace-cross Abstract: Motivation: Retrosynthesis plays a crucial role in organic synthesis and drug discovery, focusing on identifying a set of reactants capable of synthesizing a target product molecule.
By Jiaxi Zhuang, Yu Zhang, Ying Qian, Aimin Zhou
arXiv:2603. 25062v2 Announce Type: replace Abstract: Autoregressive molecular models assign probability to molecular serializations even though chemical identity is invariant to serialization.
By Xinyu Wang, Fei Dou, Jinbo Bi, Minghu Song