Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction

6 November 2018

Papers citing "Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction"

50 / 60 papers shown

Title
A Reproduction Study: The Kernel PCA Interpretation of Self-Attention Fails Under Scrutiny Karahan Sarıtaş Çağatay Yıldız 34 0 0 12 May 2025
HiPerRAG: High-Performance Retrieval Augmented Generation for Scientific Insights Ozan Gokdemir Carlo Siebenschuh Alexander Brace Azton Wells Brian Hsu ... A. Anandkumar Ian Foster R. Stevens V. Vishwanath A. Ramanathan VLM 37 0 0 07 May 2025
Enhancing Chemical Reaction and Retrosynthesis Prediction with Large Language Model and Dual-task Learning Xuan Lin Qingrui Liu Hongxin Xiang Daojian Zeng Xiangxiang Zeng 40 1 0 05 May 2025
Chemical knowledge-informed framework for privacy-aware retrosynthesis learning Guikun Chen Xu Zhang Yuqing Yang Wenguan Wang 47 0 0 26 Feb 2025
Enhancing Retrosynthesis with Conformer: A Template-Free Method Jiaxi Zhuang Qian Zhang Ying Qian 163 0 0 21 Jan 2025
Challenging reaction prediction models to generalize to novel chemistry John Bradshaw Anji Zhang Babak Mahjour David E. Graff Marwin H. S. Segler Connor W. Coley 40 1 0 11 Jan 2025
Smirk: An Atomically Complete Tokenizer for Molecular Foundation Models Alexius Wadell Anoushka Bhutani Venkatasubramanian Viswanathan 159 0 0 19 Sep 2024
Efficient Evolutionary Search Over Chemical Space with Large Language Models Haorui Wang Marta Skreta C. Ser Wenhao Gao Lingkai Kong ... Yanqiao Zhu Yuanqi Du Alán Aspuru-Guzik Kirill Neklyudov Chao Zhang 47 12 0 23 Jun 2024
RLSF: Reinforcement Learning via Symbolic Feedback Piyush Jha Prithwish Jana Arnav Arora Vijay Ganesh LRM 49 3 0 26 May 2024
Practical and efficient quantum circuit synthesis and transpiling with Reinforcement Learning David Kremer Victor Villar Hanhee Paik Ivan Duran Ismael Faro Juan Cruz-Benito 43 15 0 21 May 2024
Aligning Transformers with Continuous Feedback via Energy Rank Alignment Shriram Chennakesavalu Frank Hu Sebastian Ibarraran Grant M. Rotskoff 41 3 0 21 May 2024
Transformers for molecular property prediction: Lessons learned from the past five years Afnan Sultan Jochen Sieg M. Mathea Andrea Volkamer AI4CE 29 10 0 05 Apr 2024
GP-MoLFormer: A Foundation Model For Molecular Generation Jerret Ross Brian M. Belgodere Samuel C. Hoffman Vijil Chenthamarakshan Youssef Mroueh Payel Das Payel Das 38 5 0 04 Apr 2024
Setting the Record Straight on Transformer Oversmoothing G. Dovonon M. Bronstein Matt J. Kusner 28 5 0 09 Jan 2024
Holistic chemical evaluation reveals pitfalls in reaction prediction models Victor Sabanza Gil Andres M Bran Malte Franke Remi Schlama J. Luterbacher Philippe Schwaller ELM 33 1 0 14 Dec 2023
Transformer-Powered Surrogates Close the ICF Simulation-Experiment Gap with Extremely Limited Data M. Olson Shusen Liu Jayaraman J. Thiagarajan B. Kustowski Weng-Keen Wong Rushil Anirudh AI4CE 33 1 0 06 Dec 2023
Molecule-Edit Templates for Efficient and Accurate Retrosynthesis Prediction Mikolaj Sacha Michal Sadowski Piotr Kozakowski Ruard van Workum Stanislaw Jastrzebski 21 1 0 11 Oct 2023
Language models in molecular discovery Chaoqi Wang Yibo Jiang Chenghao Yang Han Liu Yuxin Chen 25 7 0 28 Sep 2023
Large-scale Pretraining Improves Sample Efficiency of Active Learning based Molecule Virtual Screening Zhonglin Cao Simone Sciabola Ye Wang 35 1 0 20 Sep 2023
SALSA VERDE: a machine learning attack on Learning With Errors with sparse small secrets Cathy Li Emily Wenger Zeyuan Allen-Zhu François Charton Kristin E. Lauter AAML 27 10 0 20 Jun 2023
Language models can generate molecules, materials, and protein binding sites directly in three dimensions as XYZ, CIF, and PDB files Daniel Flam-Shepherd Alán Aspuru-Guzik 27 52 0 09 May 2023
G-MATT: Single-step Retrosynthesis Prediction using Molecular Grammar Tree Transformer K. Zhang Vipul Mann V. Venkatasubramanian 27 7 0 04 May 2023
Bayesian Optimization of Catalysis With In-Context Learning Mayk Caldas Ramos Shane S. Michtavy Marc D. Porosoff Andrew D. White BDL 44 30 0 11 Apr 2023
Unifying Molecular and Textual Representations via Multi-task Language Modelling Dimitrios Christofidellis Giorgio Giannone Jannis Born Ole Winther Teodoro Laino Matteo Manica AI4CE 24 79 0 29 Jan 2023
RCsearcher: Reaction Center Identification in Retrosynthesis via Deep Q-Learning Zixun Lan Zuo Zeng Binjie Hong Zhenfu Liu Fei Ma 27 10 0 28 Jan 2023
Recent advances in artificial intelligence for retrosynthesis Zipeng Zhong Mingli Song Zunlei Feng Tiantao Liu Lingxiang Jia Shaolun Yao Tingjun Hou Mingli Song 31 5 0 14 Jan 2023
BARTSmiles: Generative Masked Language Models for Molecular Representations Gayane Chilingaryan Hovhannes Tamoyan Ani Tevosyan N. Babayan L. Khondkaryan Karen Hambardzumyan Zaven Navoyan Hrant Khachatrian Armen Aghajanyan SSL 35 25 0 29 Nov 2022
Extreme Acceleration of Graph Neural Network-based Prediction Models for Quantum Chemistry Hatem Helal J. Firoz Jenna A. Bilbrey M. M. Krell Tom Murray Ang Li S. Xantheas Sutanay Choudhury GNN 46 5 0 25 Nov 2022
MOFormer: Self-Supervised Transformer model for Metal-Organic Framework Property Prediction Zhonglin Cao Rishikesh Magar Yuyang Wang A. Farimani AI4CE 23 88 0 25 Oct 2022
ChemAlgebra: Algebraic Reasoning on Chemical Reactions Andrea Valenti D. Bacciu Antonio Vergari OOD LRM 35 0 0 05 Oct 2022
polyBERT: A chemical language model to enable fully machine-driven ultrafast polymer informatics Christopher Kuenneth R. Ramprasad 34 101 0 29 Sep 2022
Accurate, reliable and interpretable solubility prediction of druglike molecules with attention pooling and Bayesian learning Seongok Ryu Sumin Lee 19 5 0 29 Sep 2022
TransPolymer: a Transformer-based language model for polymer property predictions Changwen Xu Yuyang Wang A. Farimani 27 86 0 03 Sep 2022
Graph neural networks for materials science and chemistry Patrick Reiser Marlen Neubert André Eberhard Luca Torresi Chen Zhou ... Houssam Metni Clint van Hoesel Henrik Schopmans T. Sommer Pascal Friederich GNN AI4CE 50 373 0 05 Aug 2022
Learning from flowsheets: A generative transformer model for autocompletion of flowsheets Gabriel Vogel Lukas Schulze Balhorn Artur M. Schweidtmann AI4CE 40 33 0 01 Aug 2022
SELFIES and the future of molecular string representations Mario Krenn Qianxiang Ai Senja Barthel Nessa Carson Angelo Frei ... Andrew Wang Andrew D. White Adamo Young Rose Yu A. Aspuru‐Guzik 35 149 0 31 Mar 2022
Root-aligned SMILES: A Tight Representation for Chemical Reaction Prediction Zipeng Zhong Mingli Song Zunlei Feng Tiantao Liu Lingxiang Jia Shaolun Yao Min-Ying Wu Tingjun Hou Mingli Song 29 53 0 22 Mar 2022
Bayesian Sequential Stacking Algorithm for Concurrently Designing Molecules and Synthetic Reaction Networks Qi Zhang Chang Liu Stephen Wu Ryo Yoshida BDL 32 3 0 01 Mar 2022
Rxn Hypergraph: a Hypergraph Attention Model for Chemical Reaction Representation Mohammadamin Tavakoli Alexander Shmakov Francesco Ceccarelli Pierre Baldi GNN 39 8 0 02 Jan 2022
Permutation invariant graph-to-sequence model for template-free retrosynthesis and reaction prediction Zhengkai Tu Connor W. Coley 30 90 0 19 Oct 2021
Relative Molecule Self-Attention Transformer Lukasz Maziarka Dawid Majchrowski Tomasz Danel Piotr Gaiñski Jacek Tabor Igor T. Podolak Pawel M. Morkisz Stanislaw Jastrzebski MedIm 40 34 0 12 Oct 2021
Geometric Deep Learning on Molecular Representations Kenneth Atz F. Grisoni G. Schneider AI4CE 34 287 0 26 Jul 2021
Large-Scale Chemical Language Representations Capture Molecular Structure and Properties Jerret Ross Brian M. Belgodere Vijil Chenthamarakshan Inkit Padhi Youssef Mroueh Payel Das AI4CE 27 272 0 17 Jun 2021
Dual-view Molecule Pre-training Jinhua Zhu Yingce Xia Tao Qin Wen-gang Zhou Houqiang Li Tie-Yan Liu AI4CE 27 51 0 17 Jun 2021
A Survey of Transformers Tianyang Lin Yuxin Wang Xiangyang Liu Xipeng Qiu ViT 53 1,088 0 08 Jun 2021
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development Kexin Huang Tianfan Fu Wenhao Gao Yue Zhao Yusuf Roohani J. Leskovec Connor W. Coley Cao Xiao Jimeng Sun Marinka Zitnik OOD LM&MA 33 263 0 18 Feb 2021
Barking up the right tree: an approach to search over molecule synthesis DAGs John Bradshaw Brooks Paige Matt J. Kusner Marwin H. S. Segler José Miguel Hernández-Lobato 51 56 0 21 Dec 2020
RetroXpert: Decompose Retrosynthesis Prediction like a Chemist Chao-chao Yan Qianggang Ding P. Zhao Shuangjia Zheng Jinyu Yang Yang Yu Junzhou Huang 25 107 0 04 Nov 2020
Scientific intuition inspired by machine learning generated hypotheses Pascal Friederich Mario Krenn Isaac Tamblyn Alán Aspuru-Guzik AI4CE 24 34 0 27 Oct 2020
ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction Seyone Chithrananda Gabriel Grand Bharath Ramsundar AI4CE 37 389 0 19 Oct 2020