Publications (outdated). Please check my CV above / google scholar instead.
Journals and Proceedings
Under review:
"Becoming good at AI for good", Meghana Kshirsagar*, Caleb Robinson*, Siyu Yang* et al.
"Recurrent Convolutional Neural Networks for large scale Bird species classification", Gaurav Gupta, Meghana Kshirsagar, Ming Zhong, Shahrzad Gholami, Juan Lavista Ferres
"Identifying Human Interactors of SARS-CoV-2 Proteins and Drug Targets for COVID-19 using Network-Based Label Propagation",
Jeffrey N. Law, Kyle Akers, Nure Tasnina, Catherine M. Della Santina, Meghana Kshirsagar, Judith Klein-Seetharaman, Mark Crovella, Padmavathy Rajagopalan, Simon Kasif, T. M. Murali
Accepted
"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 and Judith Klein-Seetharaman
Pacific Symposium on Biocomputing 2021
[Paper]
[Code]
"A Network-Based Label Propagation Framework to Reposition Drugs for COVID-19", Jeffrey Law, Meghana Kshirsagar, Mark Crovella, Padmavathy Rajagopalan, Judith Klein-Seetharaman, Simon Kasif and T. M. Murali
Intelligent Systems for Molecular Biology 2020, COVID-19 special session
"BindSpace: decoding transcription factor binding signals by large-scale joint embedding", Han Yuan, Meghana Kshirsagar, Lee Zamparo, Yuheng Lu, and Christina Leslie
Nature Methods 2019
[Paper on biorxiv]
"Learning interpretable models of transcription factor binding from atac-seq data", Meghana Kshirsagar, Han Yuan, Lee Zamparo, and Christina Leslie. (In preparation).
"Learning task structure via sparsity grouped multitask
learning", Meghana Kshirsagar, Eunho Yang, and Aurelie C. Lozano
European Conference on Machine Learning (ECML 2017)
[Paper on Arxiv]
"Multitask matrix completion for learning protein interactions
across diseases", Meghana Kshirsagar, Keerthiram Murugesan, Jaime
Carbonell and Judith Klein-Seetharaman.
In Research in Computational and Molecular Biology (RECOMB 2016) [Paper] [Code]
Journal of Computational Biology, 2017 (extended version)
"Frame-Semantic Role Labeling with Heterogeneous Annotations",
Meghana Kshirsagar, Sam Thomson, Nathan Schneider, Jaime Carbonell, Noah
A. Smith and Chris Dyer, Assoc. for Computational Linguistics (ACL) 2015 [Paper] [Code] [Slides] (part of the SEMAFOR system)
"Techniques for transferring host-pathogen protein interactions
knowledge to new tasks", Meghana Kshirsagar, Sylvia Schleker, Jaime
Carbonell and Judith Klein-Seetharaman, Frontiers in Microbiology, 2015. [Paper] [Code]
"Comparing human–Salmonella with plant–Salmonella
protein–protein interaction predictions", Sylvia Schleker, Meghana
Kshirsagar and Judith Klein-Seetharaman, Frontiers in Microbiology, 2015. [Paper]
"Multi-task learning for Host-Pathogen protein interactions", Meghana Kshirsagar, Jaime Carbonell and Judith Klein-Seetharaman
In Intelligent Systems for Molecular Biology (ISMB) and
Bioinformatics 2013
[Paper] [Supplementary, Data, Code]
"Techniques to cope with missing data in host-pathogen protein
interaction prediction", Meghana Kshirsagar, Jaime Carbonell and Judith
Klein-Seetharaman
In European Conference for Computational Biology (ECCB) and
Bioinformatics 2012
[Paper] [Supplementary Info]
"Virus interactions with human signal transduction pathways",
Zhongming Zhao, Junfeng Xia, Oznur Tastan, Irtisha Singh, Meghana
Kshirsagar, Jaime Carbonell, Judith Klein-Seetharaman, I. J. Computational Biology and Drug Design 4(1): 83-105 (2011). [Paper]
"High Precision Web Extraction using Site Knowledge", Meghana
Kshirsagar, Rajeev Rastogi, Sandeepkumar Satpal, Srinivasan Sangamedu
and Venu Satuluri, Conference On Management of Data (COMAD) 2010 (Best Paper Award) [Paper]
"Keyword search on external memory data graphs", Bhavana Dalvi, Meghana Kshirsagar and S. Sudarshan, Very Large Databases (VLDB) 2008. [Paper]
Workshop papers, Posters
"Inferring transcription factor binding profiles jointly from SELEX and ATAC-seq", Meghana Kshirsagar, Han Yuan, Christina Leslie Cold Spring Harbor Labs (CSHL) workshop for Quantitative Biology, 2017.
"Iteratively Regrouped Lasso: learning group structure in genome
wide association studies in crops", Meghana Kshirsagar, Aurelie Lozano
and Eunho Yang, Workshop on Data Science for Food, Energy and Water, Knowledge Discovery and Data Mining (KDD) 2016
"Automated Sorghum Phenotyping and Trait Development Platform",
Mitch Tuiinstra, Cliff Weil, Addie Thompson, Chris Boomsma, Melba
Crawford, Ayman Habib, Edward Delp, Keith Cherkauer, Larry Biehl, Naoki
Abe, Meghana Kshirsagar, Aurelie Lozano, Karthikeyan Natesan, Peder
Olsen, Eunho Yang, Workshop on Data Science for Food, Energy and Water, Knowledge Discovery and Data Mining (KDD) 2016
"Leveraging Heterogeneous Data Sources for Relational Semantic Parsing", Meghana Kshirsagar, Nathan Schneider and Chris Dyer, Assoc. for Computational Linguistics (ACL) 2014 workshop on Semantic Parsing
"Multisource transfer learning for host-pathogen protein
interaction prediction in unlabeled tasks", Meghana Kshirsagar, Jaime
Carbonell and Judith Klein-Seetharaman, NIPS Workshop on Machine Learning for Computational Biology, 2013 [Paper] [Talk Slides]
"Confident prediction of Salmonella-human protein-protein
interactions" Schleker S., Nouretdinov I., Garcia-Garcia J., Oliva B.,
Meghana Kshirsagar, Klein-Seetharaman J. and Gammerman A, ECCB 2012.
"Transfer learning based methods towards the discovery of
host-pathogen protein-protein interactions", Meghana Kshirsagar, Jaime
Carbonell and Judith Klein-Seetharaman, ISMB 2012. [Poster]
Reviewing/ Program Committee
PLoS Comp Bio, NIPS 2016-18, ICLR 2017-18, ICML 2017-19, WWW 2017-18 Posters, Neural Computation, Biotechnology Journal, IJCAI 2016, BMC Genomics 2014, Workshop for ML in Comp Bio 2016
PC Co-chair/ Organizer: ICML Workshop for Comp Bio 2017, ICML Workshop for Comp Bio 2018
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