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