Preprint

Deepmechanics

Abhay Shinde, Aryan Amit Barsainyan, Jose Siguenza, Ankita Vaishnobi Bisoi, Rakshit Kr Singh, Bharath Ramsundar

arXiv preprint 2026 Link

Preprint

AgriVariant: Variant Effect Prediction using DeepChem-Variant for Precision Breeding in Rice

Ankita Vaishnobi Bisoi, Bharath Ramsundar

arXiv preprint 2026 Link

Preprint

A fully differentiable framework for training proxy Exchange Correlation Functionals for periodic systems

Rakshit Kumar Singh, Aryan Amit Barsainyan, Bharath Ramsundar

arXiv preprint 2026 Link

Preprint

Protect*: Steerable Retrosynthesis through Neuro-Symbolic State Encoding

Shreyas Vinaya Sathyanarayana, Shah Rahil Kirankumar, Sharanabasava D Hiremath, Bharath Ramsundar

arXiv preprint 2026 Link

Journal Publication

DeepRetro discovers retrosynthetic pathways through iterative large language model reasoning

Shreyas Vinaya Sathyanarayana, Sharanabasava D Hiremath, Shah Rahil Kirankumar, Rishikesh Panda, Rahul Jana, Riya Singh, Rida Irfan, Ashwin Murali, Bharath Ramsundar

Scientific Reports, Nature 2026 Link

Preprint

Evaluating Long-Range Temporal Structure in Foundation Model-Based Forecasts of Heartbeat Dynamics

Adrian Serapio, Bharath Ramsundar, Sandya Subramanian

bioRxiv 2026 Link

Preprint

ProteomeScan: A Toolkit For Target Validation By Proteome-Wide Docking And Analysis

Aryan Amit Barsainyan, Rishikesh Panda, Jose Siguenza, Daniele Merico, Bharath Ramsundar

bioRxiv 2026 Link

Journal Publication

ChemBERTa-3: an open source training framework for chemical foundation models

Riya Singh, Aryan Amit Barsainyan, Rida Irfan, Connor Joseph Amorin, Stewart He, Tony Davis, Arun Thiagarajan, Shiva Sankaran, Seyone Chithrananda, Walid Ahmad, Derek Jones, Kevin McLoughlin, Hyojin Kim, Anoushka Bhutani, Shreyas Vinaya Sathyanarayana, Venkat Viswanathan, Jonathan E Allen, Bharath Ramsundar

Digital Discovery, Royal Society of Chemistry 2026 Link

Preprint

Inferring Dynamic Hidden Graph Structure in Heterogeneous Correlated Time Series

Jeshwanth Mohan, Bharath Ramsundar, Sandya Subramanian

arXiv preprint 2025 Link

Preprint

Density-based Neural Temporal Point Processes for Heartbeat Dynamics

Sandya Subramanian, Bharath Ramsundar

arXiv preprint 2025 Link

Preprint

Foundation models for discovery and exploration in chemical space

Alexius Wadell, Anoushka Bhutani, Victor Azumah, Austin R Ellis-Mohr, Andrew J Stier, Kareem Hegazy, Alexander Brace, Hancheng Zhao, Celia Kelly, Anuj K Nayak, Yuhan Chen, Dimitrios Simatos, Hongyi Lin, Murali Emani, Venkatram Vishwanath, Kevin Gering, Melisa Alkan, Tom Gibbs, Jack Wells, Wesley W Qian, Richard C Gerkin, Benjamin Amorelli, Alexander B Wiltschko, Lav R Varshney, Bharath Ramsundar, Karthik Duraisamy, Michael W Mahoney, Arvind Ramanathan, Venkatasubramanian Viswanathan

arXiv preprint 2025 Link

Preprint

DeepChem Equivariant: SE (3)-Equivariant Support in an Open-Source Molecular Machine Learning Library

Jose Siguenza, Bharath Ramsundar

arXiv preprint 2025 Link

Preprint

DeepChem-DEL: An Open Source Framework for Reproducible DEL Modeling and Benchmarking

Aryan Amit Barsainyan, Riya Singh, Abhiraj Pravin Mengade, Rida Irfan, Bharath Ramsundar

ChemRxiv 2025 Link

Peer-reviewed Conference Publication

DeepChem-Variant: A Modular Open Source Framework for Genomic Variant Calling

Ankita Vaishnobi Bisoi, V Shreyas, Jose Siguenza, Bharath Ramsundar

Championing Open-source DEvelopment in ML Workshop @ ICML25 2025 Link

Patent

Detecting suitability of machine learning models for datasets.

Sindhu Ghanta, Bharath Ramsundar, Drew Roselli, Nisha Talagala, Vinay Sridhar, Swaminathan Sundararaman, Lior Amar, Lior Khermosh, Sriram Subramanian

U.S. Patent 2025 Link

Preprint

DeepRetro: Retrosynthetic Pathway Discovery using Iterative LLM Reasoning.

Shreyas Vinaya Sathyanarayana, Rahil Shah, Sharanabasava D Hiremath, Rishikesh Panda, Rahul Jana, Riya Singh, Rida Irfan, Ashwin Murali, Bharath Ramsundar

arXiv preprint 2025 Link

Patent

Ai-based drug side effect prediction.

Bharath Ramsundar, Sandya Subramanian

U.S. Patent 2025 Link

Patent

Systems and methods for spatial graph convolutions with applications to drug discovery and molecular simulation.

Evan Nathaniel Feinberg, Vijay Satyanand Pande, Bharath Ramsundar

U.S. Patent 2025 Link

Preprint

Open-Source Protein Language Models for Function Prediction and Protein Design.

Shivasankaran Vanaja Pandi, Bharath Ramsundar

arXiv preprint 2024 Link

Preprint

Open-source Polymer Generative Pipeline.

Debasish Mohanty, V Shreyas, Akshaya Palai, Bharath Ramsundar

arXiv preprint 2024 Link

Preprint

Open source Differentiable ODE Solving Infrastructure.

Rakshit Kr Singh, Aaron Rock Menezes, Rida Irfan, Bharath Ramsundar

arXiv preprint 2024 Link

Preprint

A Modular Open Source Framework for Genomic Variant Calling.

Ankita Vaishnobi Bisoi, Shreyas V, Jose Siguenza, Bharath Ramsundar

arXiv preprint 2024 Link

Preprint

Open Source Infrastructure for Automatic Cell Segmentation.

Aaron Rock Menezes, Bharath Ramsundar

arXiv preprint 2024 Link

Preprint

Self-supervised Pretraining for Partial Differential Equations

Varun Madhavan, Amal S Sebastian, Bharath Ramsundar, Venkatasubramanian Viswanathan

arXiv preprint 2024 Link

Peer-Reviewed Conference Publications

Open-Source Molecular Processing Pipeline for Generating Molecules

V Shreyas, Jose Siguenza, Karan Bania, Bharath Ramsundar

arXiv preprint 2024 Link

Peer-Reviewed Conference Publications

Machine Learning-Driven Predictions for Janus Kinase 3 Protein Drug Effectiveness

Awani Gadre, Sindhu Ghanta, Bharath Ramsundar

IEEE First International Conference on Artificial Intelligence for Medicine, Health and Care 2024 Link

Peer-Reviewed Conference Publications

Open Source Fermionic Neural Networks with Ionic Charge Initialization

Shai Pranesh, Shang Zhu, Venkat Viswanathan, Bharath Ramsundar

arXiv preprint 2024 Link

Journal Publication

Differentiable Modeling and Optimization of Battery Electrolyte Mixtures Using Geometric Deep Learning.

Shang Zhu, Bharath Ramsundar, Emil Annevelink, Hongyi Lin, Adarsh Dave, Pin-Wen Guan, Kevin Gering, Venkatasubramanian Viswanathan

Nature Communications 2023 Link

Journal Publication

Scientific discovery in the age of artificial intelligence.

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 Marks, Bharath Ramsundar, Le Song, Jimeng Sun, Jian Tang, Petar Veličković, Max Welling, Linfeng Zhang, Connor W. Coley, Yoshua Bengio & Marinka Zitnik

Nature 2023 Link

Peer-Reviewed Conference Publications

Building AI Models of Patient-specific Drug Side Effect Predictions

Bharath Ramsundar, Sandya Subramanian

IEEE EMBS International Conference on Data Science and Engineering in Health Care and Biology 2023 Link

Peer-Reviewed Conference Publications

Open Source Infrastructure for Differentiable Density Functional Theory

Advika Vidhyadhiraja, Arun Pa Thiagarajan, Shang Zhu, Venkat Viswanathan, Bharath Ramsundar

arXiv preprint 2023 Link

Peer-Reviewed Conference Publications

Score Based Models for Molecule Generation

Dwaraknath Gnaneshwar, Bharath Ramsundar, Dhairya Gandhi, Rachel Kurchin, Venkatasubramanian Viswanathan

arXiv preprint 2023 Link

Journal Publication

AutoMat: Automated materials discovery for electrochemical systems.

Emil Annevelink, Rachel Kurchin, Eric Muckley, Lance Kavalsky, Vinay I. Hegde, Valentin Sulzer, Shang Zhu, Jiankun Pu, David Farina, Matthew Johnson, Dhairya Gandhi, Adarsh Dave, Hongyi Lin, Alan Edelman, Bharath Ramsundar, James Saal, Christopher Rackauckas, Viral Shah, Bryce Meredig & Venkatasubramanian Viswanathan

MRS Bulletin 2022 Link

Preprint

ChemBERTa-2: Towards Chemical Foundation Models

Walid Ahmad, Elana Simon, Seyone Chithrananda, Gabriel Grand, Bharath Ramsundar

arXiv preprint 2022 Link

Peer-Reviewed Conference Publications

FastFlows: Flow-based Models for Molecular Graph Generation

Nathan C. Frey, Vijay Gadepally, Bharath Ramsundar

arXiv preprint 2022 Link

Peer-Reviewed Conference Publications

ChemBERTa-2: Towards Chemical Foundation Models

Walid Ahmad, Elana Simon, Seyone Chithrananda, Gabriel Grand, Bharath Ramsundar

arXiv preprint 2022 Link

Preprint

Differentiable Physics: A Position Piece

Bharath Ramsundar, Dilip Krishnamurthy, Venkatasubramanian Viswanathan

arXiv preprint 2021 Link

Peer-Reviewed Conference Publications

Bringing Atomistic Deep Learning to Prime Time

Nathan C. Frey, Siddharth Samsi, Bharath Ramsundar, Connor W. Coley, Vijay Gadepally

arXiv preprint 2021 Link

Journal Publication

AMPL: A Data-Driven Modeling Pipeline for Drug Discovery.

Amanda J. Minnich, Kevin McLoughlin, Margaret Tse, Jason Deng, Andrew Weber, Neha Murad, Benjamin D. Madej, Bharath Ramsundar, Tom Rush, Stacie Calà-Thomson, Jim Brase, and Jonathan E. Allen.

Journal of chemical information and modeling 2020 Link

Preprint

SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics.

An Evolving Review of Diagnostics and Therapeutics: Halie M. Rando, Casey S. Greene, Michael P. Robson, Simina M. Boca, Nils Wellhausen, Ronan Lordan, Christian Brueffer, Sandipan Ray, Lucy D'Agostino McGowan, Anthony Gitter, Anna Ada Dattoli, Ryan Velazquez, John P. Barton, Jeffrey M. Field, Bharath Ramsundar, Adam L. MacLean, Alexandra J. Lee, Immunology Institute of the Icahn School of Medicine, Fengling Hu, Nafisa M. Jadavji, Elizabeth Sell, Vincent Rubinetti, Jinhui Wang, Diane N. Rafizadeh, Ashwin N. Skelly, Marouen Ben Guebila, Likhitha Kolla, David Manheim, Soumita Ghosh, James Brian Byrd, YoSon Park, Vikas Bansal, Stephen Capone, John J. Dziak, Yuchen Sun, Yanjun Qi, Lamonica Shinholster, Temitayo Lukan, Sergey Knyazev, Dimitri Perrin, Serghei Mangul, Shikta Das, Gregory L Szeto, Tiago Lubiana, David Mai, COVID-19 Review Consortium, Rishi Raj Goel, Joel D Boerckel, Amruta Naik, Yusha Sun

Manubot 2020 Link

Peer-Reviewed Conference Publications

ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction

Seyone Chithrananda, Gabriel Grand, Bharath Ramsundar

arXiv preprint 2020 Link

Peer-Reviewed Conference Publications

Flow Based Models for Active Molecular Graph Generation

Nathan C. Frey, Bharath Ramsundar

Machine Learning for Molecules Workshop, Neurips 2020 Link

Journal Publication

A guide to deep learning in healthcare.

Andre Esteva, Alexandre Robicquet, Bharath Ramsundar, Volodymyr Kuleshov, Mark DePristo, Katherine Chou, Claire Cui, Greg Corrado, Sebastian Thrun & Jeff Dean

Nature medicine 2019 Link

Preprint

Secure Computation in Decentralized Data Markets

Fattaneh Bayatbabolghani, Bharath Ramsundar

arXiv preprint 2019 Link

Journal Publication

MoleculeNet: a benchmark for molecular machine learning

Zhenqin Wu, Bharath Ramsundar, Evan N. Feinberg, Joseph Gomes, Caleb Geniesse c, Aneesh S. Pappu b, Karl Leswing and Vijay Pande

Chemical science 2018 Link

Journal Publication

PotentialNet for molecular property prediction.

Evan N. Feinberg, Debnil Sur, Zhenqin Wu, Brooke E. Husic, Huanghao Mai, Yang Li, Saisai Sun, Jianyi Yang, Bharath Ramsundar, Vijay S. Pande

ACS central science 2018 Link

Journal Publication

Solving the RNA design problem with reinforcement learning

Peter Eastman, Jade Shi, Bharath Ramsundar, Vijay S. Pande

PLoS computational biology 2018 Link

Preprint

Tokenized Data Markets

Bharath Ramsundar, Roger Chen, Alok Vasudev, Rob Robbins, Artur Gorokh

arXiv preprint 2018 Link

Journal Publication

Low Data Drug Discovery with One-Shot Learning

Han Altae-Tran, Bharath Ramsundar, Aneesh S. Pappu, Vijay Pande

ACS central science 2017 Link

Journal Publication

Retrosynthetic Reaction Prediction Using Neural Sequence-to-Sequence Models.

Bowen Liu, Bharath Ramsundar, Prasad Kawthekar, Jade Shi, Joseph Gomes, Quang Luu Nguyen, Stephen Ho, Jack Sloane, Paul Wender, Vijay Pande

ACS central science 2017 Link

Journal Publication

Is Multitask Deep Learning Practical for Pharma?

Bharath Ramsundar, Bowen Liu, Zhenqin Wu, Andreas Verras, Matthew Tudor, Robert P. Sheridan, Vijay Pande

Journal of chemical information and modeling 2017 Link

Journal Publication

Computational modeling of β-secretase 1 (BACE-1) inhibitors using ligand based approaches

Govindan Subramanian, Bharath Ramsundar, Vijay Pande, Rajiah Aldrin Denny

Journal of chemical information and modeling 2016 Link

Preprint

Learning Protein Dynamics with Metastable Switching Systems

Bharath Ramsundar, Vijay S. Pande

arXiv preprint 2016 Link

Preprint

Massively Multitask Networks for Drug Discovery

Bharath Ramsundar, Steven Kearnes, Patrick Riley, Dale Webster, David Konerding, Vijay Pande

arXiv preprint 2015 Link

Peer-Reviewed Conference Publications

Understanding Protein Dynamics with L1-Regularized Reversible Hidden Markov Models

Robert McGibbon, Bharath Ramsundar, Mohammad Sultan, Gert Kiss, Vijay Pande

Proceedings of the 31st International Conference on Machine Learning, PMLR 2014 Link

Peer-Reviewed Conference Publications

NVMKV: A Scalable and Lightweight Flash Aware Key-Value Store

Leonardo Mármol, Swaminathan Sundararaman, Nisha Talagala, Raju Rangaswami Bharath Ramsundar

6th USENIX Workshop on Hot Topics in Storage and File Systems (HotStorage 14) 2014 Link

Peer-Reviewed Conference Publications

The extended parameter filter

Yusuf Bugra Erol, Lei Li, Bharath Ramsundar, Russell Stuart

International Conference on Machine Learning 2013 Link

Peer-Reviewed Conference Publications

Dynamic scaled sampling for deterministic constraints

Lei Li, Bharath Ramsundar, Stuart Russell

Artificial Intelligence and Statistics. 2013 Link