Connor W. Coley

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 91

Top Topics

Virtual Screening

Top Venues

J. Chem. Inf. Model.

Publications

Samuel Goldman, Jiayi Xin, Joules Provenzano, Connor W. Coley
MIST-CF: Chemical Formula Inference from Tandem Mass Spectra. J. Chem. Inf. Model. 64 (7) (2024)
Shitong Luo, Wenhao Gao, Zuofan Wu, Jian Peng, Connor W. Coley, Jianzhu Ma
Projecting Molecules into Synthesizable Chemical Spaces. CoRR (2024)
Wenhao Gao, Priyanka Raghavan, Ron Shprints, Connor W. Coley
Substrate Scope Contrastive Learning: Repurposing Human Bias to Learn Atomic Representations. CoRR (2024)
Yanqiao Zhu, Jeehyun Hwang, Keir Adams, Zhen Liu, Bozhao Nan, Brock Stenfors, Yuanqi Du, Jatin Chauhan, Olaf Wiest, Olexandr Isayev, Connor W. Coley, Yizhou Sun, Wei Wang
Learning Over Molecular Conformer Ensembles: Datasets and Benchmarks. ICLR (2024)
Chenqing Hua, Connor W. Coley, Guy Wolf, Doina Precup, Shuangjia Zheng
Effective Protein-Protein Interaction Exploration with PPIretrieval. CoRR (2024)
Babak A. Mahjour, Connor W. Coley
RDCanon: A Python Package for Canonicalizing the Order of Tokens in SMARTS Queries. J. Chem. Inf. Model. 64 (8) (2024)
Vincent Fan, Yujie Qian, Alex Wang, Amber Wang, Connor W. Coley, Regina Barzilay
OpenChemIE: An Information Extraction Toolkit For Chemistry Literature. CoRR (2024)
Kevin Yu, Jihye Roh, Ziang Li, Wenhao Gao, Runzhong Wang, Connor W. Coley
Double-Ended Synthesis Planning with Goal-Constrained Bidirectional Search. CoRR (2024)
Vincent Fan, Yujie Qian, Alex Wang, Amber Wang, Connor W. Coley, Regina Barzilay
OpenChemIE: An Information Extraction Toolkit for Chemistry Literature. J. Chem. Inf. Model. 64 (14) (2024)
Joonyoung F. Joung, Mun Hong Fong, Jihye Roh, Zhengkai Tu, John Bradshaw, Connor W. Coley
Beyond Major Product Prediction: Reproducing Reaction Mechanisms with Machine Learning Models Trained on a Large-Scale Mechanistic Dataset. CoRR (2024)
Jenna C. Fromer, Connor W. Coley
An algorithmic framework for synthetic cost-aware decision making in molecular design. Nat. Comput. Sci. 4 (6) (2024)
Yujie Qian, Jiang Guo, Zhengkai Tu, Connor W. Coley, Regina Barzilay
RxnScribe: A Sequence Generation Model for Reaction Diagram Parsing. CoRR (2023)
Yanqiao Zhu, Jeehyun Hwang, Keir Adams, Zhen Liu, Bozhao Nan, Brock Stenfors, Yuanqi Du, Jatin Chauhan, Olaf Wiest, Olexandr Isayev, Connor W. Coley, Yizhou Sun, Wei Wang
Learning Over Molecular Conformer Ensembles: Datasets and Benchmarks. CoRR (2023)
Yujie Qian, Jiang Guo, Zhengkai Tu, Connor W. Coley, Regina Barzilay
RxnScribe: A Sequence Generation Model for Reaction Diagram Parsing. J. Chem. Inf. Model. 63 (13) (2023)
Samuel Goldman, John Bradshaw, Jiayi Xin, Connor W. Coley
Prefix-Tree Decoding for Predicting Mass Spectra from Molecules. NeurIPS (2023)
Jenna C. Fromer, David E. Graff, Connor W. Coley
Pareto Optimization to Accelerate Multi-Objective Virtual Screening. CoRR (2023)
Xuan Zhang, Limei Wang, Jacob Helwig, Youzhi Luo, Cong Fu, Yaochen Xie, Meng Liu, Yuchao Lin, Zhao Xu, Keqiang Yan, Keir Adams, Maurice Weiler, Xiner Li, Tianfan Fu, Yucheng Wang, Haiyang Yu, Yuqing Xie, Xiang Fu, Alex Strasser, Shenglong Xu, Yi Liu, Yuanqi Du, Alexandra Saxton, Hongyi Ling, Hannah Lawrence, Hannes Stärk, Shurui Gui, Carl Edwards, Nicholas Gao, Adriana Ladera, Tailin Wu, Elyssa F. Hofgard, Aria Mansouri Tehrani, Rui Wang, Ameya Daigavane, Montgomery Bohde, Jerry Kurtin, Qian Huang, Tuong Phung, Minkai Xu, Chaitanya K. Joshi, Simon V. Mathis, Kamyar Azizzadenesheli, Ada Fang, Alán Aspuru-Guzik, Erik Bekkers, Michael M. Bronstein, Marinka Zitnik, Anima Anandkumar, Stefano Ermon, Pietro Liò, Rose Yu, Stephan Günnemann, Jure Leskovec, Heng Ji, Jimeng Sun, Regina Barzilay, Tommi S. Jaakkola, Connor W. Coley, Xiaoning Qian, Xiaofeng Qian, Tess E. Smidt, Shuiwang Ji
Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems. CoRR (2023)
Hanchen Wang, Tianfan Fu, Yuanqi Du, Wenhao Gao, Kexin Huang, Ziming Liu, Payal Chandak, Shengchao Liu, Peter Van Katwyk, Andreea Deac, Anima Anandkumar, Karianne Bergen, Carla P. Gomes, Shirley Ho, Pushmeet Kohli, Joan Lasenby, Jure Leskovec, Tie-Yan Liu, Arjun Manrai, Debora S. Marks, Bharath Ramsundar, Le Song, Jimeng Sun, Jian Tang, Petar Velickovic, Max Welling, Linfeng Zhang, Connor W. Coley, Yoshua Bengio, Marinka Zitnik
Scientific discovery in the age of artificial intelligence. Nat. 620 (7972) (2023)
Rocío Mercado, Steven M. Kearnes, Connor W. Coley
Data Sharing in Chemistry: Lessons Learned and a Case for Mandating Structured Reaction Data. J. Chem. Inf. Model. 63 (14) (2023)
Samuel Goldman, John Bradshaw, Jiayi Xin, Connor W. Coley
Prefix-tree Decoding for Predicting Mass Spectra from Molecules. CoRR (2023)
Yujie Qian, Zhening Li, Zhengkai Tu, Connor W. Coley, Regina Barzilay
Predictive Chemistry Augmented with Text Retrieval. CoRR (2023)
Yujie Qian, Jiang Guo, Zhengkai Tu, Zhening Li, Connor W. Coley, Regina Barzilay
MolScribe: Robust Molecular Structure Recognition with Image-to-Graph Generation. J. Chem. Inf. Model. 63 (7) (2023)
Nicholas David, Wenhao Sun, Connor W. Coley
The promise and pitfalls of AI for molecular and materials synthesis. Nat. Comput. Sci. 3 (5) (2023)
Jenna C. Fromer, Connor W. Coley
Computer-aided multi-objective optimization in small molecule discovery. Patterns 4 (2) (2023)
Yujie Qian, Zhening Li, Zhengkai Tu, Connor W. Coley, Regina Barzilay
Predictive Chemistry Augmented with Text Retrieval. EMNLP (2023)
Samuel Goldman, Jeremy Wohlwend, Martin Strazar, Guy Haroush, Ramnik J. Xavier, Connor W. Coley
Annotating metabolite mass spectra with domain-inspired chemical formula transformers. Nat. Mac. Intell. 5 (9) (2023)
Nathan C. Frey, Ryan Soklaski, Simon Axelrod, Siddharth Samsi, Rafael Gómez-Bombarelli, Connor W. Coley, Vijay Gadepally
Neural scaling of deep chemical models. Nat. Mac. Intell. 5 (11) (2023)
Keir Adams, Connor W. Coley
Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design. ICLR (2023)
Jiang Guo, A. Santiago Ibanez-Lopez, Hanyu Gao, Victor Quach, Connor W. Coley, Klavs F. Jensen, Regina Barzilay
Automated Chemical Reaction Extraction from Scientific Literature. J. Chem. Inf. Model. 62 (9) (2022)
David E. Graff, Matteo Aldeghi, Joseph A. Morrone, Kirk E. Jordan, Edward O. Pyzer-Knapp, Connor W. Coley
Self-focusing virtual screening with active design space pruning. CoRR (2022)
Jenna C. Fromer, Connor W. Coley
Computer-Aided Multi-Objective Optimization in Small Molecule Discovery. CoRR (2022)
Yujie Qian, Zhengkai Tu, Jiang Guo, Connor W. Coley, Regina Barzilay
Robust Molecular Image Recognition: A Graph Generation Approach. CoRR (2022)
Wenhao Gao, Tianfan Fu, Jimeng Sun, Connor W. Coley
Sample Efficiency Matters: A Benchmark for Practical Molecular Optimization. NeurIPS (2022)
Keir Adams, Connor W. Coley
Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design. CoRR (2022)
Wenhao Gao, Rocío Mercado, Connor W. Coley
Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Design. ICLR (2022)
Tianfan Fu, Wenhao Gao, Connor W. Coley, Jimeng Sun
Reinforced Genetic Algorithm for Structure-based Drug Design. NeurIPS (2022)
Samuel Goldman, Ria Das, Kevin K. Yang, Connor W. Coley
Machine learning modeling of family wide enzyme-substrate specificity screens. PLoS Comput. Biol. 18 (2) (2022)
Min Htoo Lin, Zhengkai Tu, Connor W. Coley
Improving the performance of models for one-step retrosynthesis through re-ranking. J. Cheminformatics 14 (1) (2022)
Zhengkai Tu, Connor W. Coley
Permutation Invariant Graph-to-Sequence Model for Template-Free Retrosynthesis and Reaction Prediction. J. Chem. Inf. Model. 62 (15) (2022)
Wenhao Gao, Tianfan Fu, Jimeng Sun, Connor W. Coley
Sample Efficiency Matters: A Benchmark for Practical Molecular Optimization. CoRR (2022)
David E. Graff, Matteo Aldeghi, Joseph A. Morrone, Kirk E. Jordan, Edward O. Pyzer-Knapp, Connor W. Coley
Self-Focusing Virtual Screening with Active Design Space Pruning. J. Chem. Inf. Model. 62 (16) (2022)
Divya Nori, Connor W. Coley, Rocío Mercado
De novo PROTAC design using graph-based deep generative models. CoRR (2022)
Matteo Aldeghi, Connor W. Coley
A graph representation of molecular ensembles for polymer property prediction. CoRR (2022)
Tianfan Fu, Wenhao Gao, Connor W. Coley, Jimeng Sun
Reinforced Genetic Algorithm for Structure-based Drug Design. CoRR (2022)
Matteo Aldeghi, David E. Graff, Nathan C. Frey, Joseph A. Morrone, Edward O. Pyzer-Knapp, Kirk E. Jordan, Connor W. Coley
Roughness of Molecular Property Landscapes and Its Impact on Modellability. J. Chem. Inf. Model. 62 (19) (2022)
David E. Graff, Connor W. Coley
pyscreener: A Python Wrapper for Computational Docking Software. J. Open Source Softw. 7 (71) (2022)
Katherine S. Lim, Andrew G. Reidenbach, Bruce K. Hua, Jeremy W. Mason, Christopher J. Gerry, Paul A. Clemons, Connor W. Coley
Machine Learning on DNA-Encoded Library Count Data Using an Uncertainty-Aware Probabilistic Loss Function. J. Chem. Inf. Model. 62 (10) (2022)
Tianfan Fu, Wenhao Gao, Cao Xiao, Jacob Yasonik, Connor W. Coley, Jimeng Sun
Differentiable Scaffolding Tree for Molecule Optimization. ICLR (2022)
Keir Adams, Lagnajit Pattanaik, Connor W. Coley
Learning 3D Representations of Molecular Chirality with Invariance to Bond Rotations. ICLR (2022)
Octavian-Eugen Ganea, Lagnajit Pattanaik, Connor W. Coley, Regina Barzilay, Klavs F. Jensen, William H. Green Jr., Tommi S. Jaakkola
GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles. CoRR (2021)
Nathan C. Frey, Siddharth Samsi, Bharath Ramsundar, Connor W. Coley, Vijay Gadepally
Bringing Atomistic Deep Learning to Prime Time. CoRR (2021)
Samuel Goldman, Ria Das, Kevin K. Yang, Connor W. Coley
Machine learning modeling of family wide enzyme-substrate specificity screens. CoRR (2021)
Zhengkai Tu, Connor W. Coley
Permutation invariant graph-to-sequence model for template-free retrosynthesis and reaction prediction. CoRR (2021)
Katherine S. Lim, Andrew G. Reidenbach, Bruce K. Hua, Jeremy W. Mason, Christopher J. Gerry, Paul A. Clemons, Connor W. Coley
Machine learning on DNA-encoded library count data using an uncertainty-aware probabilistic loss function. CoRR (2021)
Kexin Huang, Tianfan Fu, Wenhao Gao, Yue Zhao, Yusuf Roohani, Jure Leskovec, Connor W. Coley, Cao Xiao, Jimeng Sun, Marinka Zitnik
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Therapeutics. CoRR (2021)
Jiang Guo, A. Santiago Ibanez-Lopez, Hanyu Gao, Victor Quach, Connor W. Coley, Klavs F. Jensen, Regina Barzilay
Correction to Automated Chemical Reaction Extraction from Scientific Literature. J. Chem. Inf. Model. 61 (8) (2021)
Tianfan Fu, Wenhao Gao, Cao Xiao, Jacob Yasonik, Connor W. Coley, Jimeng Sun
Differentiable Scaffolding Tree for Molecular Optimization. CoRR (2021)
Hangrui Bi, Hengyi Wang, Chence Shi, Connor W. Coley, Jian Tang, Hongyu Guo
Non-Autoregressive Electron Redistribution Modeling for Reaction Prediction. ICML (2021)
Octavian Ganea, Lagnajit Pattanaik, Connor W. Coley, Regina Barzilay, Klavs F. Jensen, William H. Green Jr., Tommi S. Jaakkola
GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles. NeurIPS (2021)
Wenhao Gao, Rocío Mercado, Connor W. Coley
Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Design. CoRR (2021)
Hangrui Bi, Hengyi Wang, Chence Shi, Connor W. Coley, Jian Tang, Hongyu Guo
Non-Autoregressive Electron Redistribution Modeling for Reaction Prediction. CoRR (2021)
Nathan C. Frey, Siddharth Samsi, Joseph McDonald, Lin Li, Connor W. Coley, Vijay Gadepally
Scalable Geometric Deep Learning on Molecular Graphs. CoRR (2021)
Esther Heid, Samuel Goldman, Karthik Sankaranarayanan, Connor W. Coley, Christoph Flamm, William H. Green Jr.
EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates. J. Chem. Inf. Model. 61 (10) (2021)
Keir Adams, Lagnajit Pattanaik, Connor W. Coley
Learning 3D Representations of Molecular Chirality with Invariance to Bond Rotations. CoRR (2021)
Shuangjia Zheng, Tao Zeng, Chengtao Li, Binghong Chen, Connor W. Coley, Yuedong Yang, Ruibo Wu
BioNavi-NP: Biosynthesis Navigator for Natural Products. CoRR (2021)
Vignesh Ram Somnath, Charlotte Bunne, Connor W. Coley, Andreas Krause, Regina Barzilay
Learning Graph Models for Retrosynthesis Prediction. NeurIPS (2021)
Hanyu Gao, Jean Pauphilet, Thomas J. Struble, Connor W. Coley, Klavs F. Jensen
Direct Optimization across Computer-Generated Reaction Networks Balances Materials Use and Feasibility of Synthesis Plans for Molecule Libraries. J. Chem. Inf. Model. 61 (1) (2021)
Kexin Huang, Tianfan Fu, Wenhao Gao, Yue Zhao, Yusuf Roohani, Jure Leskovec, Connor W. Coley, Cao Xiao, Jimeng Sun, Marinka Zitnik
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development. NeurIPS Datasets and Benchmarks (2021)
Lior Hirschfeld, Kyle Swanson, Kevin Yang, Regina Barzilay, Connor W. Coley
Uncertainty Quantification Using Neural Networks for Molecular Property Prediction. J. Chem. Inf. Model. 60 (8) (2020)
Sai Krishna Gottipati, Boris Sattarov, Sufeng Niu, Yashaswi Pathak, Haoran Wei, Shengchao Liu, Simon Blackburn, Karam M. J. Thomas, Connor W. Coley, Jian Tang, Sarath Chandar, Yoshua Bengio
Learning to Navigate The Synthetically Accessible Chemical Space Using Reinforcement Learning. ICML (2020)
Hanjun Dai, Chengtao Li, Connor W. Coley, Bo Dai, Le Song
Retrosynthesis Prediction with Conditional Graph Logic Network. CoRR (2020)
Vignesh Ram Somnath, Charlotte Bunne, Connor W. Coley, Andreas Krause, Regina Barzilay
Learning Graph Models for Template-Free Retrosynthesis. CoRR (2020)
Michael E. Fortunato, Connor W. Coley, Brian C. Barnes, Klavs F. Jensen
Data Augmentation and Pretraining for Template-Based Retrosynthetic Prediction in Computer-Aided Synthesis Planning. J. Chem. Inf. Model. 60 (7) (2020)
Wenhao Gao, Connor W. Coley
The Synthesizability of Molecules Proposed by Generative Models. CoRR (2020)
Connor W. Coley, Natalie S. Eyke, Klavs F. Jensen
Autonomous discovery in the chemical sciences part I: Progress. CoRR (2020)
David E. Graff, Eugene I. Shakhnovich, Connor W. Coley
Accelerating high-throughput virtual screening through molecular pool-based active learning. CoRR (2020)
Sai Krishna Gottipati, Boris Sattarov, Sufeng Niu, Yashaswi Pathak, Haoran Wei, Shengchao Liu, Karam M. J. Thomas, Simon Blackburn, Connor W. Coley, Jian Tang, Sarath Chandar, Yoshua Bengio
Learning To Navigate The Synthetically Accessible Chemical Space Using Reinforcement Learning. CoRR (2020)
Connor W. Coley, Natalie S. Eyke, Klavs F. Jensen
Autonomous discovery in the chemical sciences part II: Outlook. CoRR (2020)
Lagnajit Pattanaik, Octavian-Eugen Ganea, Ian Coley, Klavs F. Jensen, William H. Green Jr., Connor W. Coley
Message Passing Networks for Molecules with Tetrahedral Chirality. CoRR (2020)
Lior Hirschfeld, Kyle Swanson, Kevin Yang, Regina Barzilay, Connor W. Coley
Uncertainty Quantification Using Neural Networks for Molecular Property Prediction. CoRR (2020)
Wenhao Gao, Connor W. Coley
The Synthesizability of Molecules Proposed by Generative Models. J. Chem. Inf. Model. 60 (12) (2020)
Hanjun Dai, Chengtao Li, Connor W. Coley, Bo Dai, Le Song
Retrosynthesis Prediction with Conditional Graph Logic Network. NeurIPS (2019)
John S. Schreck, Connor W. Coley, Kyle J. M. Bishop
Learning retrosynthetic planning through self-play. CoRR (2019)
Connor W. Coley, William H. Green Jr., Klavs F. Jensen
RDChiral: An RDKit Wrapper for Handling Stereochemistry in Retrosynthetic Template Extraction and Application. J. Chem. Inf. Model. 59 (6) (2019)
Kevin Yang, Kyle Swanson, Wengong Jin, Connor W. Coley, Philipp Eiden, Hua Gao, Angel Guzman-Perez, Timothy Hopper, Brian Kelley, Miriam Mathea, Andrew Palmer, Volker Settels, Tommi S. Jaakkola, Klavs F. Jensen, Regina Barzilay
Correction to Analyzing Learned Molecular Representations for Property Prediction. J. Chem. Inf. Model. 59 (12) (2019)
Kevin Yang, Kyle Swanson, Wengong Jin, Connor W. Coley, Philipp Eiden, Hua Gao, Angel Guzman-Perez, Timothy Hopper, Brian Kelley, Miriam Mathea, Andrew Palmer, Volker Settels, Tommi S. Jaakkola, Klavs F. Jensen, Regina Barzilay
Are Learned Molecular Representations Ready For Prime Time? CoRR (2019)
Kevin Yang, Kyle Swanson, Wengong Jin, Connor W. Coley, Philipp Eiden, Hua Gao, Angel Guzman-Perez, Timothy Hopper, Brian Kelley, Miriam Mathea, Andrew Palmer, Volker Settels, Tommi S. Jaakkola, Klavs F. Jensen, Regina Barzilay
Analyzing Learned Molecular Representations for Property Prediction. J. Chem. Inf. Model. 59 (8) (2019)
Connor W. Coley, Luke Rogers, William H. Green Jr., Klavs F. Jensen
SCScore: Synthetic Complexity Learned from a Reaction Corpus. J. Chem. Inf. Model. 58 (2) (2018)
Wengong Jin, Connor W. Coley, Regina Barzilay, Tommi S. Jaakkola
Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network. CoRR (2017)
Connor W. Coley, Regina Barzilay, William H. Green Jr., Tommi S. Jaakkola, Klavs F. Jensen
Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction. J. Chem. Inf. Model. 57 (8) (2017)
Wengong Jin, Connor W. Coley, Regina Barzilay, Tommi S. Jaakkola
Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network. NIPS (2017)