Jian Peng

Assistant Professor
Department of Computer Science
University of Illinois at Urbana-Champaign

Office: 2118 Siebel Center, 201 N Goodwin Ave Urbana, IL, 61801
Email: jianpeng(AT)illinois.edu

Recent news

-Our paper "Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks" describing a CASP-winning algorithm for protein contact prediction is accepted in Cell Systems. Congrats to Yang, Perry and Qing!
-Our paper on network-based drug target prediction appears in Nature Communications. Congrats to Yunan!
-Our recent reinforcement learning work "Stein Variational Policy Gradient" appears in UAI 2017
-Our work "Learning to Play in a Day: Faster Deep Reinforcement Learning by Optimality Tightening" appears in ICLR 2017
-Our work on Parkinson's disease gene network was featured as the cover article of the February 2017 issue of Cell Systems.
-Our team iFold_1 was ranked 1st in contact prediction in the worldwide protein structure prediction (CASP12, 2016) competition. Congrats to Yang and Qing!
-Our paper on large-scale biological network integration was published in Cell Systems (2016)

Selected recent awards

Microsoft Azure Research Award (2017-2018)
AWS Cloud Credits for Research (2017-2018)
NSF CAREER Award (2017-2022)
PhRMA Foundation Award in Informatics (2017-2018)
NCSA Faculty Fellowship (2016-2017)
Sloan Research Fellowship (2016-2018)

Publications

Research

Jian's current research spans many areas in bioinformatics and machine learning. His lab develops computational techniques for processing, integrating and analyzing massive datasets in genomics, systems biology and molecular biology. Recently, Jian has started to work on novel integrative and network-based approaches for understanding molecular mechanisms of human diseases and accelerating drug development. Jian and his students are also interested in machine learning, include deep reinforcement learning, efficient sampling algorithms, variational inference, deep generative models, and structural learning algorithms for high-dimensional graphical models.

Algorithms developed by Jian and his co-workers were successful in several scientific challenges, including the Critical Assessment of protein Structure Prediction (CASP) in 2010 and 2016, the Pharmacogenomics challenge in the Critical Assessment of Genome Interpretation (CAGI) in 2011, the Shared Task Challenge in Crowdsourcing at Scale in 2013, the Prostate Cancer DREAM Challenge in 2015, the ALS Stratification Prize4Life Challenge in 2015.

Short Bio

Jian Peng is an assistant professor in the Department of Computer Science at the University of Illinois at Urbana-Champaign. Before joining CS@Illinois in 2015, Jian was a postdoc in the Berger Lab at MIT, and a visiting scientist in the Lindquist Lab at the Whitehead Institute for Biomedical Research. He was a graduate student in the Xu Lab from 2007 and obtained his Ph.D. in Computer Science from Toyota Technological Institute at Chicago in 2013. He received his B.S. in Computer Science from Wuhan University, China. Jian worked on HIV protein analysis with Drs. David Heckerman and Jonathan Carlson in the eScience group at Microsoft Research in 2010.

Jian is on the program committee of several machine learning and bioinformatics conferences, including ISMB, RECOMB, AISTATS, ACM-BCB, AAAI and GLBIO. He is a reviewer for many scientific journals, including PNAS, PLOS Computational Biology, Bioinformatics, IEEE/ACM Transactions on Computational Biology and Bioinformatics and Molecular Cellular Proteomics.

Jian was a Microsoft Research PhD Fellow (2010-2012). He received a Young Investigator Award in the Conference on Retroviruses and Opportunistic Infections in 2011. Recently, he received a 2016 Sloan Research Fellowship, a 2017 PhRMA Foundation Award in Informatics and a 2016-2017 NCSA Fellowship. His research is also supported by NVIDIA, Intel, AWS, Microsoft Azure, and Jump Trading.

Teaching

Fall 2015: CS598 Machine Learning in Computational Biology
Spring 2016: CS466 Introduction to Bioinformatics