Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network. - Wengong Jin; Connor W. Coley; Regina Barzilay; Tommi S. Jaakkola (NIPS, 2017)

Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction. - Connor W. Coley; Regina Barzilay; William H. Green Jr.; Tommi S. Jaakkola; Klavs F. Jensen (J. Chem. Inf. Model., 2017)

SCScore: Synthetic Complexity Learned from a Reaction Corpus. - Connor W. Coley; Luke Rogers; William H. Green Jr.; Klavs F. Jensen (J. Chem. Inf. Model., 2018)

Retrosynthesis Prediction with Conditional Graph Logic Network. - Hanjun Dai; Chengtao Li; Connor W. Coley; Bo Dai 001; Le Song (NeurIPS, 2019)

Learning retrosynthetic planning through self-play. - John S. Schreck; Connor W. Coley; Kyle J. M. Bishop (CoRR, 2019)

Are Learned Molecular Representations Ready For Prime Time? - 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; et al. (CoRR, 2019)

RDChiral: An RDKit Wrapper for Handling Stereochemistry in Retrosynthetic Template Extraction and Application. - Connor W. Coley; William H. Green Jr.; Klavs F. Jensen (J. Chem. Inf. Model., 2019)

Analyzing Learned Molecular Representations for Property Prediction. - 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; et al. (J. Chem. Inf. Model., 2019)

Correction to Analyzing Learned Molecular Representations for Property Prediction. - 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; et al. (J. Chem. Inf. Model., 2019)

Learning to Navigate The Synthetically Accessible Chemical Space Using Reinforcement Learning. - Sai Krishna Gottipati; Boris Sattarov; Sufeng Niu; Yashaswi Pathak; Haoran Wei; Shengchao Liu; Simon Blackburn; Karam M. J. Thomas; Connor W. Coley; Jian Tang 005; Sarath Chandar; Yoshua Bengio (ICML, 2020)

Autonomous discovery in the chemical sciences part I: Progress. - Connor W. Coley; Natalie S. Eyke; Klavs F. Jensen (CoRR, 2020)

Autonomous discovery in the chemical sciences part II: Outlook. - Connor W. Coley; Natalie S. Eyke; Klavs F. Jensen (CoRR, 2020)

Learning Graph Models for Template-Free Retrosynthesis. - Vignesh Ram Somnath; Charlotte Bunne; Connor W. Coley; Andreas Krause 001; Regina Barzilay (CoRR, 2020)

Message Passing Networks for Molecules with Tetrahedral Chirality. - Lagnajit Pattanaik; Octavian-Eugen Ganea; Ian Coley; Klavs F. Jensen; William H. Green Jr.; Connor W. Coley (CoRR, 2020)

Accelerating high-throughput virtual screening through molecular pool-based active learning. - David E. Graff; Eugene I. Shakhnovich; Connor W. Coley (CoRR, 2020)

Data Augmentation and Pretraining for Template-Based Retrosynthetic Prediction in Computer-Aided Synthesis Planning. - Michael E. Fortunato; Connor W. Coley; Brian C. Barnes; Klavs F. Jensen (J. Chem. Inf. Model., 2020)

The Synthesizability of Molecules Proposed by Generative Models. - Wenhao Gao 001; Connor W. Coley (J. Chem. Inf. Model., 2020)

Uncertainty Quantification Using Neural Networks for Molecular Property Prediction. - Lior Hirschfeld; Kyle Swanson; Kevin Yang; Regina Barzilay; Connor W. Coley (J. Chem. Inf. Model., 2020)

Non-Autoregressive Electron Redistribution Modeling for Reaction Prediction. - Hangrui Bi; Hengyi Wang; Chence Shi; Connor W. Coley; Jian Tang 005; Hongyu Guo (ICML, 2021)

GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles. - Octavian Ganea; Lagnajit Pattanaik; Connor W. Coley; Regina Barzilay; Klavs F. Jensen; William H. Green Jr.; Tommi S. Jaakkola (NeurIPS, 2021)

Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development. - Kexin Huang; Tianfan Fu; Wenhao Gao 001; Yue Zhao 016; Yusuf H. Roohani; Jure Leskovec; Connor W. Coley; Cao Xiao; Jimeng Sun 001; Marinka Zitnik (NeurIPS Datasets and Benchmarks, 2021)

Learning Graph Models for Retrosynthesis Prediction. - Vignesh Ram Somnath; Charlotte Bunne; Connor W. Coley; Andreas Krause 001; Regina Barzilay (NeurIPS, 2021)

Therapeutics Data Commons: Machine Learning Datasets and Tasks for Therapeutics. - Kexin Huang; Tianfan Fu; Wenhao Gao 001; Yue Zhao 016; Yusuf H. Roohani; Jure Leskovec; Connor W. Coley; Cao Xiao; Jimeng Sun 001; Marinka Zitnik (CoRR, 2021)

BioNavi-NP: Biosynthesis Navigator for Natural Products. - Shuangjia Zheng; Tao Zeng; Chengtao Li; Binghong Chen; Connor W. Coley; Yuedong Yang; Ruibo Wu (CoRR, 2021)

Differentiable Scaffolding Tree for Molecular Optimization. - Tianfan Fu; Wenhao Gao 001; Cao Xiao; Jacob Yasonik; Connor W. Coley; Jimeng Sun 001 (CoRR, 2021)

Scalable Geometric Deep Learning on Molecular Graphs. - Nathan C. Frey; Siddharth Samsi; Joseph McDonald; Lin Li; Connor W. Coley; Vijay Gadepally (CoRR, 2021)

Bringing Atomistic Deep Learning to Prime Time. - Nathan C. Frey; Siddharth Samsi; Bharath Ramsundar; Connor W. Coley; Vijay Gadepally (CoRR, 2021)

Direct Optimization across Computer-Generated Reaction Networks Balances Materials Use and Feasibility of Synthesis Plans for Molecule Libraries. - Hanyu Gao; Jean Pauphilet; Thomas J. Struble; Connor W. Coley; Klavs F. Jensen (J. Chem. Inf. Model., 2021)

Correction to Automated Chemical Reaction Extraction from Scientific Literature. - Jiang Guo; A. Santiago Ibanez-Lopez; Hanyu Gao; Victor Quach; Connor W. Coley; Klavs F. Jensen; Regina Barzilay (J. Chem. Inf. Model., 2021)

EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates. - Esther Heid; Samuel Goldman; Karthik Sankaranarayanan; Connor W. Coley; Christoph Flamm; William H. Green Jr. (J. Chem. Inf. Model., 2021)

Learning 3D Representations of Molecular Chirality with Invariance to Bond Rotations. - Keir Adams; Lagnajit Pattanaik; Connor W. Coley (ICLR, 2022)

Differentiable Scaffolding Tree for Molecule Optimization. - Tianfan Fu; Wenhao Gao 001; Cao Xiao; Jacob Yasonik; Connor W. Coley; Jimeng Sun 001 (ICLR, 2022)

Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Design. - Wenhao Gao 001; Rocío Mercado; Connor W. Coley (ICLR, 2022)

Sample Efficiency Matters: A Benchmark for Practical Molecular Optimization. - Wenhao Gao 001; Tianfan Fu; Jimeng Sun 001; Connor W. Coley (NeurIPS, 2022)

Reinforced Genetic Algorithm for Structure-based Drug Design. - Tianfan Fu; Wenhao Gao 001; Connor W. Coley; Jimeng Sun 001 (NeurIPS, 2022)

A graph representation of molecular ensembles for polymer property prediction. - Matteo Aldeghi; Connor W. Coley (CoRR, 2022)

Robust Molecular Image Recognition: A Graph Generation Approach. - Yujie Qian; Zhengkai Tu; Jiang Guo; Connor W. Coley; Regina Barzilay (CoRR, 2022)

De novo PROTAC design using graph-based deep generative models. - Divya Nori; Connor W. Coley; Rocío Mercado (CoRR, 2022)

Improving the performance of models for one-step retrosynthesis through re-ranking. - Min Htoo Lin; Zhengkai Tu; Connor W. Coley (J. Cheminformatics, 2022)

Roughness of Molecular Property Landscapes and Its Impact on Modellability. - Matteo Aldeghi; David E. Graff; Nathan C. Frey; Joseph A. Morrone; Edward O. Pyzer-Knapp; Kirk E. Jordan; Connor W. Coley (J. Chem. Inf. Model., 2022)

Self-Focusing Virtual Screening with Active Design Space Pruning. - David E. Graff; Matteo Aldeghi; Joseph A. Morrone; Kirk E. Jordan; Edward O. Pyzer-Knapp; Connor W. Coley (J. Chem. Inf. Model., 2022)

Automated Chemical Reaction Extraction from Scientific Literature. - Jiang Guo; A. Santiago Ibanez-Lopez; Hanyu Gao; Victor Quach; Connor W. Coley; Klavs F. Jensen; Regina Barzilay (J. Chem. Inf. Model., 2022)

Machine Learning on DNA-Encoded Library Count Data Using an Uncertainty-Aware Probabilistic Loss Function. - Katherine S. Lim; Andrew G. Reidenbach; Bruce K. Hua; Jeremy W. Mason; Christopher J. Gerry; Paul A. Clemons; Connor W. Coley (J. Chem. Inf. Model., 2022)

Permutation Invariant Graph-to-Sequence Model for Template-Free Retrosynthesis and Reaction Prediction. - Zhengkai Tu; Connor W. Coley (J. Chem. Inf. Model., 2022)

pyscreener: A Python Wrapper for Computational Docking Software. - David E. Graff; Connor W. Coley (J. Open Source Softw., 2022)

Machine learning modeling of family wide enzyme-substrate specificity screens. - Samuel Goldman; Ria Das; Kevin K. Yang; Connor W. Coley (PLoS Comput. Biol., 2022)

Predictive Chemistry Augmented with Text Retrieval. - Yujie Qian; Zhening Li; Zhengkai Tu; Connor W. Coley; Regina Barzilay (EMNLP, 2023)

Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design. - Keir Adams; Connor W. Coley (ICLR, 2023)

Prefix-Tree Decoding for Predicting Mass Spectra from Molecules. - Samuel Goldman; John Bradshaw; Jiayi Xin; Connor W. Coley (NeurIPS, 2023)

Pareto Optimization to Accelerate Multi-Objective Virtual Screening. - Jenna C. Fromer; David E. Graff; Connor W. Coley (CoRR, 2023)

Scientific discovery in the age of artificial intelligence. - Hanchen Wang 002; Tianfan Fu; Yuanqi Du; Wenhao Gao 001; Kexin Huang; Ziming Liu; Payal Chandak; Shengchao Liu; Peter Van Katwyk; Andreea Deac; Anima Anandkumar; Karianne Bergen; et al. (Nat., 2023)

The promise and pitfalls of AI for molecular and materials synthesis. - Nicholas David; Wenhao Sun; Connor W. Coley (Nat. Comput. Sci., 2023)

Computer-aided multi-objective optimization in small molecule discovery. - Jenna C. Fromer; Connor W. Coley (Patterns, 2023)

MolScribe: Robust Molecular Structure Recognition with Image-to-Graph Generation. - Yujie Qian; Jiang Guo; Zhengkai Tu; Zhening Li; Connor W. Coley; Regina Barzilay (J. Chem. Inf. Model., 2023)

Data Sharing in Chemistry: Lessons Learned and a Case for Mandating Structured Reaction Data. - Rocío Mercado; Steven M. Kearnes; Connor W. Coley (J. Chem. Inf. Model., 2023)

RxnScribe: A Sequence Generation Model for Reaction Diagram Parsing. - Yujie Qian; Jiang Guo; Zhengkai Tu; Connor W. Coley; Regina Barzilay (J. Chem. Inf. Model., 2023)

Annotating metabolite mass spectra with domain-inspired chemical formula transformers. - Samuel Goldman; Jeremy Wohlwend; Martin Strazar; Guy Haroush; Ramnik J. Xavier; Connor W. Coley (Nat. Mac. Intell., 2023)

Neural scaling of deep chemical models. - Nathan C. Frey; Ryan Soklaski; Simon Axelrod; Siddharth Samsi; Rafael Gómez-Bombarelli; Connor W. Coley; Vijay Gadepally (Nat. Mac. Intell., 2023)

Learning Over Molecular Conformer Ensembles: Datasets and Benchmarks. - Yanqiao Zhu 001; Jeehyun Hwang; Keir Adams; Zhen Liu; Bozhao Nan; Brock Stenfors; Yuanqi Du; Jatin Chauhan; Olaf Wiest; Olexandr Isayev; Connor W. Coley; Yizhou Sun; et al. (ICLR, 2024)

Projecting Molecules into Synthesizable Chemical Spaces. - Shitong Luo; Wenhao Gao 001; Zuofan Wu; Jian Peng 001; Connor W. Coley; Jianzhu Ma (ICML, 2024)

Double-Ended Synthesis Planning with Goal-Constrained Bidirectional Search. - Kevin Yu; Jihye Roh; Ziang Li; Wenhao Gao 001; Runzhong Wang; Connor W. Coley (NeurIPS, 2024)

Effective Protein-Protein Interaction Exploration with PPIretrieval. - Chenqing Hua; Connor W. Coley; Guy Wolf; Doina Precup; Shuangjia Zheng (CoRR, 2024)

Substrate Scope Contrastive Learning: Repurposing Human Bias to Learn Atomic Representations. - Wenhao Gao 001; Priyanka Raghavan; Ron Shprints; Connor W. Coley (CoRR, 2024)

Beyond Major Product Prediction: Reproducing Reaction Mechanisms with Machine Learning Models Trained on a Large-Scale Mechanistic Dataset. - Joonyoung F. Joung; Mun Hong Fong; Jihye Roh; Zhengkai Tu; John Bradshaw; Connor W. Coley (CoRR, 2024)

Syntax-Guided Procedural Synthesis of Molecules. - Michael Sun; Alston Lo; Wenhao Gao 001; Minghao Guo; Veronika Thost; Jie Chen 007; Connor W. Coley; Wojciech Matusik (CoRR, 2024)

Generative Artificial Intelligence for Navigating Synthesizable Chemical Space. - Wenhao Gao 001; Shitong Luo; Connor W. Coley (CoRR, 2024)

Batched Bayesian optimization with correlated candidate uncertainties. - Jenna C. Fromer; Runzhong Wang; Mrunali Manjrekar; Austin Tripp; José Miguel Hernández-Lobato; Connor W. Coley (CoRR, 2024)

OpenChemIE: An Information Extraction Toolkit for Chemistry Literature. - Vincent Fan; Yujie Qian; Alex Wang; Amber Wang; Connor W. Coley; Regina Barzilay (J. Chem. Inf. Model., 2024)

MIST-CF: Chemical Formula Inference from Tandem Mass Spectra. - Samuel Goldman; Jiayi Xin; Joules Provenzano; Connor W. Coley (J. Chem. Inf. Model., 2024)

RDCanon: A Python Package for Canonicalizing the Order of Tokens in SMARTS Queries. - Babak A. Mahjour; Connor W. Coley (J. Chem. Inf. Model., 2024)

An algorithmic framework for synthetic cost-aware decision making in molecular design. - Jenna C. Fromer; Connor W. Coley (Nat. Comput. Sci., 2024)

ShEPhERD: Diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design. - Keir Adams; Kento Abeywardane; Jenna C. Fromer; Connor W. Coley (ICLR, 2025)

Procedural Synthesis of Synthesizable Molecules. - Michael Sun; Alston Lo; Minghao Guo; Jie Chen 007; Connor W. Coley; Wojciech Matusik (ICLR, 2025)

Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems. - Xuan Zhang; Limei Wang; Jacob Helwig; Youzhi Luo; Cong Fu 003; Yaochen Xie; Meng Liu 015; Yuchao Lin; Zhao Xu 005; Keqiang Yan; Keir Adams; Maurice Weiler; et al. (Found. Trends Mach. Learn., 2025)

Optimal Compound Downselection To Promote Diversity and Parallel Chemistry. - Jenna C. Fromer; Alexandra D. Volkova; Connor W. Coley (J. Chem. Inf. Model., 2025)

Batched Bayesian Optimization by Maximizing the Probability of Including the Optimum. - Jenna C. Fromer; Runzhong Wang; Mrunali Manjrekar; Austin Tripp; José Miguel Hernández-Lobato; Connor W. Coley (J. Chem. Inf. Model., 2025)

ASKCOS: an open source software suite for synthesis planning. - Zhengkai Tu; Sourabh J. Choure; Mun Hong Fong; Jihye Roh; Itai Levin; Kevin Yu; Joonyoung F. Joung; Nathan Morgan; Shih-Cheng Li; Xiaoqi Sun; Huiqian Lin; Mark Murnin; et al. (CoRR, 2025)

Challenging reaction prediction models to generalize to novel chemistry. - John Bradshaw; Anji Zhang; Babak A. Mahjour; David E. Graff; Marwin H. S. Segler; Connor W. Coley (CoRR, 2025)

DiffMS: Diffusion Generation of Molecules Conditioned on Mass Spectra. - Montgomery Bohde; Mrunali Manjrekar; Runzhong Wang; Shuiwang Ji; Connor W. Coley (CoRR, 2025)

Electron flow matching for generative reaction mechanism prediction obeying conservation laws. - Joonyoung F. Joung; Mun Hong Fong; Nicholas Casetti; Jordan P. Liles; Ne S. Dassanayake; Connor W. Coley (CoRR, 2025)

The impact of conformer quality on learned representations of molecular conformer ensembles. - Keir Adams; Connor W. Coley (CoRR, 2025)

Neural Graph Matching Improves Retrieval Augmented Generation in Molecular Machine Learning. - Runzhong Wang; Rui-Xi Wang; Mrunali Manjrekar; Connor W. Coley (CoRR, 2025)

Optimization of Robotic Liquid Handling as a Capacitated Vehicle Routing Problem. - Guangqi Wu; Runzhong Wang; Connor W. Coley (CoRR, 2025)

Anticipating the Selectivity of Cyclization Reaction Pathways with Neural Network Potentials. - Nicholas Casetti; Dylan Anstine; Olexandr Isayev; Connor W. Coley (CoRR, 2025)

Electron flow matching for generative reaction mechanism prediction. - Joonyoung F. Joung; Mun Hong Fong; Nicholas Casetti; Jordan P. Liles; Ne S. Dassanayake; Connor W. Coley (Nat., 2025)