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
Meghana Kshirsagar
Sr. Applied Research Scientist
Publications
Publications by Year
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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
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
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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
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
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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
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
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
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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
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
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
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
Publications by Research Area
-
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
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
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
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
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
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
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
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
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
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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
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
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
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
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
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
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
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
-
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
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
-
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
Publications by Type
-
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
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
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
-
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
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
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
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
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
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
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
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
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