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

-Congratulations to Abhinav and Anusri for winning the Siebel Scholarships!
-Our papers, including "emrQA: A Large Corpus for Question Answering on Electronic Medical Records" and others, are accepted by EMNLP 2018. Congrats to Anusri and all!
-Our paper entitled "Typing tumors using pathways selected by somatic evolution" is accepted by Nature Communications. Congrats to Sheng!
-Our paper on deep learning for protein structure search is accepted by ECCB 2018.
-Our paper on meta exploration algorithm is accepted by ICML 2018.
-Our generalizable single-cell mapping algorithm is accepted by Cell Systems.
-Our papers on graphical model inference and energy-efficient neural networks are accepted by IJCAI 2018.
-Our Cell Systems paper on Parkinson's disease gene network received the 2018 inaugural Bishop Dr. Karl Golser Award. Congratulations to Vik!
-We presented two recent deep RL papers, Genetic policy optimization and Action-dependent Stein control variate in the NIPS 2017 Deep Reinforcement Learning Symposium! They are also accepted by ICLR 2018.
-Our papers on mega-scale single-cell visualization and deciphering signaling specificity got accepted by RECOMB 2018.
-Our new off-policy learning algorithm got the third place in the 2017 NIPS Criteo Ad Placement Challenge
-Our paper "Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks" describing a CASP-winning algorithm for protein contact prediction is accepted by 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

Tencent AI Lab Rhino-Bird Gift Fund (2018-2019)
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)


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, Yumanity Therpeutics and Jump Trading.


Fall 2015: CS598 Machine Learning in Computational Biology
Spring 2016: CS466 Introduction to Bioinformatics
Fall 2016: CS361 Probability and Statistics for Computer Scientists
Spring 2018: CS466 Introduction to Bioinformatics
Fall 2018: CS598 Machine Learning in Computational Biology