Meghana Kshirsagar

Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm

Meghana Kshirsagar, Artur Meller, Ian R. Humphreys, Samuel Sledzieski, Yixi Xu, Rahul Dodhia, Eric Horvitz, Bonnie Berger, Gregory R. Bowman, Juan M. Lavista Ferres, David Baker, Minkyung Baek

Nature Communications | February 2025

Publication PDF Project

Enhanced Macular Telangiectasia Type 2 Detection: Leveraging Self-Supervised Learning and Ensemble Models

Shahrzad Gholami, Lea Scheppke, Meghana Kshirsagar, Yue Wu, Rahul Dodhia, Roberto Bonelli, Irene Leung, Ferenc B Sallo, Alyson Muldrew, Catherine Jamison, Tunde Peto, Juan M. Lavista Ferres, Bill Weeks, Martin Friedlander, Aaron Lee, Lowy Medical Research Institute

Ophthalmology Science | January 2025

Publication DOI Project

Democratizing Protein Language Models with Parameter-Efficient Fine-Tuning

Samuel Sledzieski, Meghana Kshirsagar, Minkyung Baek, Bonnie Berger, Rahul Dodhia, Juan M. Lavista Ferres

PNAS | June 2024

Publication DOI Project

Self-Supervised Learning for Improved Optical Coherence Tomography Detection of Macular Telangiectasia Type 2

Shahrzad Gholami, Lea Scheppke, Meghana Kshirsagar, Yue Wu, Rahul Dodhia, Roberto Bonelli, Irene Leung, Ferenc B. Sallo, Alyson Muldrew, Catherine Jamison, Tunde Peto, Juan M. Lavista Ferres, Bill Weeks, Martin Friedlander, Aaron Y. Lee

JAMA Ophthalmology | February 2024

Publication Project

Assessment of Differentially Private Synthetic Data for Utility and Fairness in End-to-End Machine Learning Pipelines for Tabular Data

Mayana Pereira, Meghana Kshirsagar, Sumit Mukherjee, Rahul Dodhia, Juan M. Lavista Ferres, Rafael de Sousa

PLOS ONE | February 2024

Publication DOI

Parameter-Efficient Fine-Tuning of Protein Language Models Improves Prediction of Protein-Protein Interactions

Samuel Sledzieski, Meghana Kshirsagar, Bonnie Berger, Rahul Dodhia, Juan M. Lavista Ferres

Machine Learning for Structural Biology Workshop, NeurIPS | December 2023

Publication Project

Predicting the Locations of Cryptic Pockets from Single Protein Structures Using the PocketMiner Graph Neural Network

Artur Meller, Michael Ward, Jonathan Borowsky, Jeffrey M. Lotthammer, Meghana Kshirsagar, Felipe Oviedo, Juan M. Lavista Ferres, Gregory R. Bowman

Nature Communications | February 2023

Publication DOI Project

Identifying long-term effects of SARS-CoV-2 and their association with social determinants of health in a cohort of over one million COVID-19 survivors

Sumit Mukherjee, Meghana Kshirsagar, Nicholas Becker, Yixi Xu, Bill Weeks, Shwetak Patel, Juan M. Lavista Ferres, Michael L. Jackson

BMC Public Health | December 2022

Publication PDF Project Project

The Risk of Hospitalization and Mortality After Breakthrough SARS-CoV-2 Infection by Vaccine Type: Observational Study of Medical Claims Data

Meghana Kshirsagar, Md Nasir, Sumit Mukherjee, Nicholas Becker, Rahul Dodhia, Bill Weeks, Juan M. Lavista Ferres, Barbra Richardson

JMIR Public Health Surveillance | November 2022

Publication PDF Project Project

BindVAE: Dirichlet Variational Autoencoders for De Novo Motif Discovery from Accessible Chromatin

Meghana Kshirsagar, Han Yuan, Juan M. Lavista Ferres, Christina Leslie

Genome Biology | August 2022

Publication PDF Github Project

Comparing Recurrent Convolutional Neural Networks for Large Scale Bird Species Classification

Gaurav Gupta, Meghana Kshirsagar, Ming Zhong, Shahrzad Gholami, Juan M. Lavista Ferres

Scientific Reports | August 2021

Publication PDF Project Project Project

An Analysis of the Deployment of Models Trained on Private Tabular Synthetic Data: Unexpected Surprises

Mayana Pereira, Meghana Kshirsagar, Sumit Mukherjee, Rahul Dodhia, Juan M. Lavista Ferres

June 2021

Preprint

Becoming Good at AI for Good

Meghana Kshirsagar, Siyu Yang, Caleb Robinson, Shahrzad Gholami, Ivan Klyuzhin, Sumit Mukherjee, Md Nasir, Anthony Ortiz, Felipe Oviedo, Darren Tanner, Anusua Trivedi, Yixi Xu, Ming Zhong, Bistra Dilkina, Rahul Dodhia, Juan M. Lavista Ferres

AAAI/ACM Conference on AI, Ethics, and Society (AIES'21) | April 2021

Publication

Protein sequence models for prediction and comparative analysis of the SARS-CoV-2 —human interactome

Meghana Kshirsagar, Nure Tasnina, Michael D. Ward, Jeffrey N. Law, T. M. Murali, Juan M. Lavista Ferres, Gregory R. Bowman , Judith Klein-Seetharaman

Pacific Symposium on Biocomputing | January 2021

Publication Project Project

Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm

Meghana Kshirsagar, Artur Meller, Ian R. Humphreys, Samuel Sledzieski, Yixi Xu, Rahul Dodhia, Eric Horvitz, Bonnie Berger, Gregory R. Bowman, Juan M. Lavista Ferres, David Baker, Minkyung Baek

Nature Communications | February 2025

Publication PDF Project

Enhanced Macular Telangiectasia Type 2 Detection: Leveraging Self-Supervised Learning and Ensemble Models

Shahrzad Gholami, Lea Scheppke, Meghana Kshirsagar, Yue Wu, Rahul Dodhia, Roberto Bonelli, Irene Leung, Ferenc B Sallo, Alyson Muldrew, Catherine Jamison, Tunde Peto, Juan M. Lavista Ferres, Bill Weeks, Martin Friedlander, Aaron Lee, Lowy Medical Research Institute

Ophthalmology Science | January 2025

Publication DOI Project

Democratizing Protein Language Models with Parameter-Efficient Fine-Tuning

Samuel Sledzieski, Meghana Kshirsagar, Minkyung Baek, Bonnie Berger, Rahul Dodhia, Juan M. Lavista Ferres

PNAS | June 2024

Publication DOI Project

Self-Supervised Learning for Improved Optical Coherence Tomography Detection of Macular Telangiectasia Type 2

Shahrzad Gholami, Lea Scheppke, Meghana Kshirsagar, Yue Wu, Rahul Dodhia, Roberto Bonelli, Irene Leung, Ferenc B. Sallo, Alyson Muldrew, Catherine Jamison, Tunde Peto, Juan M. Lavista Ferres, Bill Weeks, Martin Friedlander, Aaron Y. Lee

JAMA Ophthalmology | February 2024

Publication Project

Assessment of Differentially Private Synthetic Data for Utility and Fairness in End-to-End Machine Learning Pipelines for Tabular Data

Mayana Pereira, Meghana Kshirsagar, Sumit Mukherjee, Rahul Dodhia, Juan M. Lavista Ferres, Rafael de Sousa

PLOS ONE | February 2024

Publication DOI

Parameter-Efficient Fine-Tuning of Protein Language Models Improves Prediction of Protein-Protein Interactions

Samuel Sledzieski, Meghana Kshirsagar, Bonnie Berger, Rahul Dodhia, Juan M. Lavista Ferres

Machine Learning for Structural Biology Workshop, NeurIPS | December 2023

Publication Project

The Risk of Hospitalization and Mortality After Breakthrough SARS-CoV-2 Infection by Vaccine Type: Observational Study of Medical Claims Data

Meghana Kshirsagar, Md Nasir, Sumit Mukherjee, Nicholas Becker, Rahul Dodhia, Bill Weeks, Juan M. Lavista Ferres, Barbra Richardson

JMIR Public Health Surveillance | November 2022

Publication PDF Project Project

Comparing Recurrent Convolutional Neural Networks for Large Scale Bird Species Classification

Gaurav Gupta, Meghana Kshirsagar, Ming Zhong, Shahrzad Gholami, Juan M. Lavista Ferres

Scientific Reports | August 2021

Publication PDF Project Project Project

An Analysis of the Deployment of Models Trained on Private Tabular Synthetic Data: Unexpected Surprises

Mayana Pereira, Meghana Kshirsagar, Sumit Mukherjee, Rahul Dodhia, Juan M. Lavista Ferres

June 2021

Preprint

Becoming Good at AI for Good

Meghana Kshirsagar, Siyu Yang, Caleb Robinson, Shahrzad Gholami, Ivan Klyuzhin, Sumit Mukherjee, Md Nasir, Anthony Ortiz, Felipe Oviedo, Darren Tanner, Anusua Trivedi, Yixi Xu, Ming Zhong, Bistra Dilkina, Rahul Dodhia, Juan M. Lavista Ferres

AAAI/ACM Conference on AI, Ethics, and Society (AIES'21) | April 2021

Publication

Protein sequence models for prediction and comparative analysis of the SARS-CoV-2 —human interactome

Meghana Kshirsagar, Nure Tasnina, Michael D. Ward, Jeffrey N. Law, T. M. Murali, Juan M. Lavista Ferres, Gregory R. Bowman , Judith Klein-Seetharaman

Pacific Symposium on Biocomputing | January 2021

Publication Project Project

Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm

Meghana Kshirsagar, Artur Meller, Ian R. Humphreys, Samuel Sledzieski, Yixi Xu, Rahul Dodhia, Eric Horvitz, Bonnie Berger, Gregory R. Bowman, Juan M. Lavista Ferres, David Baker, Minkyung Baek

Nature Communications | February 2025

Publication PDF Project

Enhanced Macular Telangiectasia Type 2 Detection: Leveraging Self-Supervised Learning and Ensemble Models

Shahrzad Gholami, Lea Scheppke, Meghana Kshirsagar, Yue Wu, Rahul Dodhia, Roberto Bonelli, Irene Leung, Ferenc B Sallo, Alyson Muldrew, Catherine Jamison, Tunde Peto, Juan M. Lavista Ferres, Bill Weeks, Martin Friedlander, Aaron Lee, Lowy Medical Research Institute

Ophthalmology Science | January 2025

Publication DOI Project

Democratizing Protein Language Models with Parameter-Efficient Fine-Tuning

Samuel Sledzieski, Meghana Kshirsagar, Minkyung Baek, Bonnie Berger, Rahul Dodhia, Juan M. Lavista Ferres

PNAS | June 2024

Publication DOI Project

Self-Supervised Learning for Improved Optical Coherence Tomography Detection of Macular Telangiectasia Type 2

Shahrzad Gholami, Lea Scheppke, Meghana Kshirsagar, Yue Wu, Rahul Dodhia, Roberto Bonelli, Irene Leung, Ferenc B. Sallo, Alyson Muldrew, Catherine Jamison, Tunde Peto, Juan M. Lavista Ferres, Bill Weeks, Martin Friedlander, Aaron Y. Lee

JAMA Ophthalmology | February 2024

Publication Project

Parameter-Efficient Fine-Tuning of Protein Language Models Improves Prediction of Protein-Protein Interactions

Samuel Sledzieski, Meghana Kshirsagar, Bonnie Berger, Rahul Dodhia, Juan M. Lavista Ferres

Machine Learning for Structural Biology Workshop, NeurIPS | December 2023

Publication Project

Predicting the Locations of Cryptic Pockets from Single Protein Structures Using the PocketMiner Graph Neural Network

Artur Meller, Michael Ward, Jonathan Borowsky, Jeffrey M. Lotthammer, Meghana Kshirsagar, Felipe Oviedo, Juan M. Lavista Ferres, Gregory R. Bowman

Nature Communications | February 2023

Publication DOI Project

Identifying long-term effects of SARS-CoV-2 and their association with social determinants of health in a cohort of over one million COVID-19 survivors

Sumit Mukherjee, Meghana Kshirsagar, Nicholas Becker, Yixi Xu, Bill Weeks, Shwetak Patel, Juan M. Lavista Ferres, Michael L. Jackson

BMC Public Health | December 2022

Publication PDF Project Project

The Risk of Hospitalization and Mortality After Breakthrough SARS-CoV-2 Infection by Vaccine Type: Observational Study of Medical Claims Data

Meghana Kshirsagar, Md Nasir, Sumit Mukherjee, Nicholas Becker, Rahul Dodhia, Bill Weeks, Juan M. Lavista Ferres, Barbra Richardson

JMIR Public Health Surveillance | November 2022

Publication PDF Project Project

BindVAE: Dirichlet Variational Autoencoders for De Novo Motif Discovery from Accessible Chromatin

Meghana Kshirsagar, Han Yuan, Juan M. Lavista Ferres, Christina Leslie

Genome Biology | August 2022

Publication PDF Github Project

Protein sequence models for prediction and comparative analysis of the SARS-CoV-2 —human interactome

Meghana Kshirsagar, Nure Tasnina, Michael D. Ward, Jeffrey N. Law, T. M. Murali, Juan M. Lavista Ferres, Gregory R. Bowman , Judith Klein-Seetharaman

Pacific Symposium on Biocomputing | January 2021

Publication Project Project

Assessment of Differentially Private Synthetic Data for Utility and Fairness in End-to-End Machine Learning Pipelines for Tabular Data

Mayana Pereira, Meghana Kshirsagar, Sumit Mukherjee, Rahul Dodhia, Juan M. Lavista Ferres, Rafael de Sousa

PLOS ONE | February 2024

Publication DOI

An Analysis of the Deployment of Models Trained on Private Tabular Synthetic Data: Unexpected Surprises

Mayana Pereira, Meghana Kshirsagar, Sumit Mukherjee, Rahul Dodhia, Juan M. Lavista Ferres

June 2021

Preprint

Comparing Recurrent Convolutional Neural Networks for Large Scale Bird Species Classification

Gaurav Gupta, Meghana Kshirsagar, Ming Zhong, Shahrzad Gholami, Juan M. Lavista Ferres

Scientific Reports | August 2021

Publication PDF Project Project Project

Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm

Meghana Kshirsagar, Artur Meller, Ian R. Humphreys, Samuel Sledzieski, Yixi Xu, Rahul Dodhia, Eric Horvitz, Bonnie Berger, Gregory R. Bowman, Juan M. Lavista Ferres, David Baker, Minkyung Baek

Nature Communications | February 2025

Publication PDF Project

Enhanced Macular Telangiectasia Type 2 Detection: Leveraging Self-Supervised Learning and Ensemble Models

Shahrzad Gholami, Lea Scheppke, Meghana Kshirsagar, Yue Wu, Rahul Dodhia, Roberto Bonelli, Irene Leung, Ferenc B Sallo, Alyson Muldrew, Catherine Jamison, Tunde Peto, Juan M. Lavista Ferres, Bill Weeks, Martin Friedlander, Aaron Lee, Lowy Medical Research Institute

Ophthalmology Science | January 2025

Publication DOI Project

Democratizing Protein Language Models with Parameter-Efficient Fine-Tuning

Samuel Sledzieski, Meghana Kshirsagar, Minkyung Baek, Bonnie Berger, Rahul Dodhia, Juan M. Lavista Ferres

PNAS | June 2024

Publication DOI Project

Self-Supervised Learning for Improved Optical Coherence Tomography Detection of Macular Telangiectasia Type 2

Shahrzad Gholami, Lea Scheppke, Meghana Kshirsagar, Yue Wu, Rahul Dodhia, Roberto Bonelli, Irene Leung, Ferenc B. Sallo, Alyson Muldrew, Catherine Jamison, Tunde Peto, Juan M. Lavista Ferres, Bill Weeks, Martin Friedlander, Aaron Y. Lee

JAMA Ophthalmology | February 2024

Publication Project

Assessment of Differentially Private Synthetic Data for Utility and Fairness in End-to-End Machine Learning Pipelines for Tabular Data

Mayana Pereira, Meghana Kshirsagar, Sumit Mukherjee, Rahul Dodhia, Juan M. Lavista Ferres, Rafael de Sousa

PLOS ONE | February 2024

Publication DOI

Predicting the Locations of Cryptic Pockets from Single Protein Structures Using the PocketMiner Graph Neural Network

Artur Meller, Michael Ward, Jonathan Borowsky, Jeffrey M. Lotthammer, Meghana Kshirsagar, Felipe Oviedo, Juan M. Lavista Ferres, Gregory R. Bowman

Nature Communications | February 2023

Publication DOI Project

Identifying long-term effects of SARS-CoV-2 and their association with social determinants of health in a cohort of over one million COVID-19 survivors

Sumit Mukherjee, Meghana Kshirsagar, Nicholas Becker, Yixi Xu, Bill Weeks, Shwetak Patel, Juan M. Lavista Ferres, Michael L. Jackson

BMC Public Health | December 2022

Publication PDF Project Project

The Risk of Hospitalization and Mortality After Breakthrough SARS-CoV-2 Infection by Vaccine Type: Observational Study of Medical Claims Data

Meghana Kshirsagar, Md Nasir, Sumit Mukherjee, Nicholas Becker, Rahul Dodhia, Bill Weeks, Juan M. Lavista Ferres, Barbra Richardson

JMIR Public Health Surveillance | November 2022

Publication PDF Project Project

BindVAE: Dirichlet Variational Autoencoders for De Novo Motif Discovery from Accessible Chromatin

Meghana Kshirsagar, Han Yuan, Juan M. Lavista Ferres, Christina Leslie

Genome Biology | August 2022

Publication PDF Github Project

Comparing Recurrent Convolutional Neural Networks for Large Scale Bird Species Classification

Gaurav Gupta, Meghana Kshirsagar, Ming Zhong, Shahrzad Gholami, Juan M. Lavista Ferres

Scientific Reports | August 2021

Publication PDF Project Project Project

Parameter-Efficient Fine-Tuning of Protein Language Models Improves Prediction of Protein-Protein Interactions

Samuel Sledzieski, Meghana Kshirsagar, Bonnie Berger, Rahul Dodhia, Juan M. Lavista Ferres

Machine Learning for Structural Biology Workshop, NeurIPS | December 2023

Publication Project

Becoming Good at AI for Good

Meghana Kshirsagar, Siyu Yang, Caleb Robinson, Shahrzad Gholami, Ivan Klyuzhin, Sumit Mukherjee, Md Nasir, Anthony Ortiz, Felipe Oviedo, Darren Tanner, Anusua Trivedi, Yixi Xu, Ming Zhong, Bistra Dilkina, Rahul Dodhia, Juan M. Lavista Ferres

AAAI/ACM Conference on AI, Ethics, and Society (AIES'21) | April 2021

Publication

Protein sequence models for prediction and comparative analysis of the SARS-CoV-2 —human interactome

Meghana Kshirsagar, Nure Tasnina, Michael D. Ward, Jeffrey N. Law, T. M. Murali, Juan M. Lavista Ferres, Gregory R. Bowman , Judith Klein-Seetharaman

Pacific Symposium on Biocomputing | January 2021

Publication Project Project

An Analysis of the Deployment of Models Trained on Private Tabular Synthetic Data: Unexpected Surprises

Mayana Pereira, Meghana Kshirsagar, Sumit Mukherjee, Rahul Dodhia, Juan M. Lavista Ferres

June 2021

Preprint