Research


My heart is motivated by the promise of precision medicine and my mind is captivated by the puzzles of statistical machine learning. You can find a list of my publications according to Google Scholar, Semantic Scholar, DBLP, or curated on my page here:

Papers in Review

Pre-prints available on request.
2018
Hybrid Subspace Learning for High-Dimensional Genomic Data
Micol Marchetti-Bowick, Benjamin J. Lengerich, Ankur Parikh, Eric P. Xing
2018
Precision Lasso: Accounting for Correlations and Linear Dependencies in High-Dimensional Genomic Data
Haohan Wang, Benjamin J. Lengerich, Bryon Aragam, Eric P. Xing

Publications

2018
Retrofitting Distributional Embeddings to Knowledge Graphs with Functional Relations
Benjamin J. Lengerich, Andrew L. Maas, Christopher Potts
ArXiv COLING
2018
Personalized Regression Enables Sample-Specific Pan-Cancer Analysis
Benjamin J. Lengerich, Bryon Aragam, Eric P. Xing
BioRXiv Bioinformatics ISMB Presentation Slides
2018
Opportunities And Obstacles For Deep Learning In Biology And Medicine
Author order was determined by a randomized algorithm.
Travers Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way, Enrico Ferrero, Paul-Michael Agapow, Wei Xie, Gail L. Rosen, Benjamin J. Lengerich, Johnny Israeli, Jack Lanchantin, Stephen Woloszynek, Anne E. Carpenter, Avanti Shrikumar, Jinbo Xu, Evan M. Cofer, David J. Harris, Dave DeCaprio, Yanjun Qi, Anshul Kundaje, Yifan Peng, Laura K. Wiley, Marwin H.S. Segler, Anthony Gitter, Casey S. Greene

BioRXiv RSIF
2014
Experimental and Computational Mutagenesis To Investigate the Positioning of a General Base within an Enzyme Active Site
Jason P. Schwans, Philip Hanoian, Benjamin J. Lengerich, Fanny Sunden, Ana Gonzalez, Yingssu Tsai, Sharon Hammes-Schiffer, and Daniel Herschlag
Biochemistry

Workshop and Poster Presentations

2018
Contextual Explanation Networks Enable Integrated Analysis Of Imaging And Genomic Data
Benjamin J. Lengerich, Maruan Al-Shedivat, Avinava Dubey, Amir Alavi, Jennifer Williams, Eric P. Xing
ISMB Machine Learning in Computational and Systems Biology
2017
Towards Visual Explanations for Convolutional Neural Networks via Input Resampling
Benjamin J. Lengerich*, Sandeep Konam*, Eric P. Xing, Stephanie Rosenthal, Manuela Veloso
ArXiv ICML Workshop on Visualization for Deep Learning
2016
GenAMap on the Web: Intuitive and Scalable Machine Learning for Structured Association Mapping.
Benjamin J. Lengerich*, Haohan Wang*, Min Kyung Lee, Eric P. Xing
ASHG