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Retrosynthesis poses a key challenge in biopharmaceuticals, aiding chemists in finding appropriate reactant molecules for given product molecules.
Computer-assisted design of complex organic syntheses: Pathways for molecular synthesis can be devised with a computer and equipment for graphical communication
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The logic of chemical synthesis
Elias James Corey · 1991
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Jascha Sohl-Dickstein, Eric Weiss, Niru Maheswaranathan, and Surya Ganguli · 2015
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What’s what: The (nearly) definitive guide to reaction role assignment
Nadine Schneider, Nikolaus Stiefl, and Gregory A Landrum · 2016
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Computer-assisted retrosynthesis based on molecular similarity
Connor W Coley, Luke Rogers, William H Green, and Klavs F Jensen · 2017
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Chemical reactions from us patents (1976-sep2016)
Daniel Lowe · 2017
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Attention is all you need
Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit, Llion Jones, Aidan N Gomez, Łukasz Kaiser, and Illia Polosukhin · 2017
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Why are sequence-to-sequence models so dull? understanding the low-diversity problem of chatbots
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Marwin HS Segler, Mike Preuss, and Mark P Waller · 2018
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Learning to make generalizable and diverse predictions for retrosynthesis
Benson Chen, Tianxiao Shen, Tommi S Jaakkola, and Regina Barzilay · 2019
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Molecular transformer: a model for uncertainty-calibrated chemical reaction prediction
Philippe Schwaller, Teodoro Laino, Théophile Gaudin, Peter Bolgar, Christopher A Hunter, Costas Bekas, and Alpha A Lee · 2019
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Generative modeling by estimating gradients of the data distribution
Yang Song and Stefano Ermon · 2019
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Predicting retrosynthetic reactions using self-corrected transformer neural networks
Shuangjia Zheng, Jiahua Rao, Zhongyue Zhang, Jun Xu, and Yuedong Yang · 2019
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Denoising diffusion probabilistic models
Jonathan Ho, Ajay Jain, and Pieter Abbeel · 2020
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Decoding and diversity in machine translation
Nicholas Roberts, Davis Liang, Graham Neubig, and Zachary C Lipton · 2020
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Predicting retrosynthetic pathways using transformer-based models and a hyper-graph exploration strategy
Philippe Schwaller, Riccardo Petraglia, Valerio Zullo, Vishnu H Nair, Rico Andreas Haeuselmann, Riccardo Pisoni, Costas Bekas, Anna Iuliano, and Teodoro Laino · 2020
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A graph to graphs framework for retrosynthesis prediction
Chence Shi, Minkai Xu, Hongyu Guo, Ming Zhang, and Jian Tang · 2020
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Learning graph models for template-free retrosynthesis
Vignesh Ram Somnath, Charlotte Bunne, Connor W Coley, Andreas Krause, and Regina Barzilay · 2020
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Geodiff: A geometric diffusion model for molecular conformation generation
Minkai Xu, Lantao Yu, Yang Song, Chence Shi, Stefano Ermon, and Jian Tang · 2021
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Diffdock: Diffusion steps, twists, and turns for molecular docking
Gabriele Corso, Hannes Stärk, Bowen Jing, Regina Barzilay, and Tommi S Jaakkola · 2022
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Modeling diverse chemical reactions for single-step retrosynthesis via discrete latent variables
Hua-Rui He, Jie Wang, Yunfei Liu, and Feng Wu · 2022
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Equivariant 3d-conditional diffusion models for molecular linker design
Ilia Igashov, Hannes Stärk, Clement Vignac, Victor Garcia Satorras, Pascal Frossard, Max Welling, Michael M Bronstein, and Bruno Correia · 2022
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Chemformer: a pre-trained transformer for computational chemistry
Ross Irwin, Spyridon Dimitriadis, Jiazhen He, and Esben Jannik Bjerrum · 2022
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State-of-the-art augmented nlp transformer models for direct and single-step retrosynthesis
Igor V Tetko, Pavel Karpov, Ruud Van Deursen, and Guillaume Godin · 2020
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Retroxpert: Decompose retrosynthesis prediction like a chemist
Chaochao Yan, Qianggang Ding, Peilin Zhao, Shuangjia Zheng, Jinyu Yang, Yang Yu, and Junzhou Huang · 2020
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Structured denoising diffusion models in discrete state-spaces
Jacob Austin, Daniel D Johnson, Jonathan Ho, Daniel Tarlow, and Rianne Van Den Berg · 2021
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Deep retrosynthetic reaction prediction using local reactivity and global attention
Shuan Chen and Yousung Jung · 2021
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Valid, plausible, and diverse retrosynthesis using tied two-way transformers with latent variables
Eunji Kim, Dongseon Lee, Youngchun Kwon, Min Sik Park, and Youn-Suk Choi · 2021
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Improved denoising diffusion probabilistic models
Alexander Quinn Nichol and Prafulla Dhariwal · 2021
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Molecule edit graph attention network: modeling chemical reactions as sequences of graph edits
Mikołaj Sacha, Mikołaj Błaz, Piotr Byrski, Paweł Dabrowski-Tumanski, Mikołaj Chrominski, Rafał Loska, Paweł Włodarczyk-Pruszynski, and Stanisław Jastrzebski · 2021
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Score-based generative modeling of graphs via the system of stochastic differential equations
Jaehyeong Jo, Seul Lee, and Sung Ju Hwang · 2022
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Permutation invariant graph-to-sequence model for template-free retrosynthesis and reaction prediction
Zhengkai Tu and Connor W Coley · 2022
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Digress: Discrete denoising diffusion for graph generation
Clement Vignac, Igor Krawczuk, Antoine Siraudin, Bohan Wang, Volkan Cevher, and Pascal Frossard · 2022
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Retroformer: Pushing the limits of end-to-end retrosynthesis transformer
Yue Wan, Chang-Yu Hsieh, Ben Liao, and Shengyu Zhang · 2022
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Retrocomposer: composing templates for template-based retrosynthesis prediction
Chaochao Yan, Peilin Zhao, Chan Lu, Yang Yu, and Junzhou Huang · 2022
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Root-aligned smiles: a tight representation for chemical reaction prediction
Zipeng Zhong, Jie Song, Zunlei Feng, Tiantao Liu, Lingxiang Jia, Shaolun Yao, Min Wu, Tingjun Hou, and Mingli Song · 2022
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Retrobridge: Modeling retrosynthesis with markov bridges
Ilia Igashov, Arne Schneuing, Marwin Segler, Michael Bronstein, and Bruno Correia · 2023
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Retrosynthesis prediction with local template retrieval
Shufang Xie, Rui Yan, Junliang Guo, Yingce Xia, Lijun Wu, and Tao Qin · 2023
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