Meghana Kshirsagar

Sr. Applied Research Scientist

Papiers de Collaboration

Afficher par:

- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet Projet
- 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 Projet Projet
- 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 Projet
- 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 Projet Projet Projet
- 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 Projet Projet

- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet Projet
- 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 Projet Projet Projet
- 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 Projet Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet Projet
- 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 Projet Projet
- 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 Projet
- 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 Projet Projet
- 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 Projet Projet Projet

- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet
- 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 Projet Projet
- 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 Projet Projet
- 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 Projet
- 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 Projet Projet Projet
- 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 Projet
- 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 Projet Projet
- 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