NeuralFDR: learning decision threshold from hypothesis features.
Martin Zhang, Fei Xia, David Tse, James Zou
Neural Information Processing Systems (NIPS 2017).

The effects of memory replay in reinforcement learning.
Ruishan Liu and James Zou
Submitted 2017. 

Why adaptively collected data has negative bias and how to correct for it. [arXiv] 
Xinkun Nie, Xiaoying Tian-Harris, Jonathan Taylor, James Zou
Submitted 2017. ICML Workshop on Picky Learners Best Paper Award.

Linear regression with shuffled labels. [arXiv] 
Abubakar Abid, Ada Poon, 
James Zou
Submitted 2017

Estimating the unseen from multiple populations. [arXiv] 
Aditi Rangunathan, Greg Valiant, James Zou
International Conference on Machine Learning (ICML 2017)

Learning latent space models with angular constraints. [arXiv] 
Pengtao Xie, Yuntian Deng, Yi Zhou, Abhimanu Kumar, Yaoliang Yu, James Zou, Eric Xing. 
International Conference on Machine Learning (ICML 2017)

How much does your data exploration overfit? Controlling bias via information usage. [arXiv] 
Daniel Russo, 
James Zou [alphabetical]. 
Submitted 2017 (subsumes the AISTATS'16 paper with new results and improved presentation)

Quantifying the accuracy of approximate diffusions and Markov chains. [arXiv]
Jonathan Huggins, 
James Zou.
AISTATS (2017).

Signal to noise in matching markets. [arXiv] 
Matt Weinberg, James Zou.
Submitted 2017.

Beyond bilingual: multi-sense word embedding using multi-lingual context. [arXiv] 
Shyam Upadhyay
, Kai-Wei Chang, Matt Taddy, Adam Kalai, James Zou.                                                     Representation Learning for NLP (Rep4NLP 2017). Best Paper Award.

Deep learning the regulatory potential of DNA sequences from massively parallel reporter assays.
Joe Paggi, Kevin Tian, Anshul Kundajie*, 
James Zou* [equal contribution]
In submission (2017).

DeepLofting: building 3D cardiovascular models with convolutional neural networks.

Gabriel Maher, Jameson Merkow, 
James Zou, Zhuowen Tu, David Kriegman, Alison Marsden.
In submission (2017).

Correcting for cell-type heterogeneity in DNA methylation: avoiding statistical flaws.
Elior Rahmani, Noah Zaitlen, Yael Baran, Celeste Eng, Donglei Hu, Joshua Galanter, Sam Oh, Esteban Burchard, Eleazar Eskin, 
James Zou, Eran Halperin. 
Nature Methods in press (2017). 

2016 and before

Computational biology

Quantifying the unobserved protein-coding variants in human populations provides a roadmap for large-scale sequencing projects. [PDF]
James Zou, Greg Valiant, Paul Valiant, Konrad Karczewski, Siu On Chan, Kaitlin Samocha, Monkol Lek, Exome Aggregation Consortium, Shamil Sunyaev, Mark Daly, Daniel MacArthur
Nature Communications (2016).

Analysis of protein-coding genetic variation in 60,706 humans. [arXiv]
Exome Aggregation Consortium.
Nature in press (2016).

Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies.
Elior Rahmani, Noah Zaitlen, Yael Baran, Celeste Eng, Donglei Hu, Joshua Galanter, Sam Oh, Esteban Burchard, Eleazar Eskin, 
James Zou, Eran Halperin.
Nature Methods in press (2016).

A genetic and socio-economic study of mate choice in Latinos reveals novel assortment patterns. [PDF] [Press] 
James Zou [corresponding author], Danny Park, Esteban Burchard, Dara Torgerson, Maria Pino-Yanes, Yun Song, Sriram Sankararaman, Eran Halperin, Noah Zaitlen 
Proceedings of the National Academy of Sciences 112(44):13621-6 (2015).

Inferring parental genomic ancestries using pooled semi-Markov processes. [PDF]
James Zou [corresponding author], Eran Halperin, Esteban Burchard, Sriram Sankararaman.
Bioinformatics 31(12):i190-6 (2015).

Correcting for sample heterogeneity in epigenome-wide association studies. [PDF]
James Zou.
Methods Mol Biol. (2015).

Undesired usage and the robust self-assembly of heterogeneous structures. [PDF]
Arvind Murugan, 
James Zou, Michael Brenner.
Nature Communications 11;6:6203 (2015).

Extended fertility and longevity: the genetic and epigenetic link. [PDF]
Kerem Wainer-Katsir, 
James Zou, Michal Linial.
Fertil Steril. 103(5):1117-24 (2015).

Epigenome-wide association studies without the need for cell-type composition. [PDF]
James Zou [corresponding author], Christoph Lippert, David Heckerman, Martin Aryee, Jennifer Listgarten.
Nature Methods 11(3):309-11 (2014).
Highlight talk at ISMB 2015. 
Highlight talk at RECOMB 2015. 
Platform presentation at the 2013 Wellcome Trust Epigenomics of Common Diseases conference. 
Platform presentation at the 2013 Machine Learning in Computational Biology meeting.

Genome-wide chromatin state transitions elicited by developmental and environmental cues. [PDF]
Jiang Zhu, Mazhar Adli, 
James Zou, et al.
Cell 152(3):642-54 (2013).

Locus-specific chromatin inactivation at endogenous enhancers with programmable TALE-LSD1 fusions. [PDF]
Eric Mendenhall, Kaylyn Williamson, Deepak Reyon, 
James Zou, et al.
Nature Biotechnology 31(12):1133-6 (2013).

Getting the biggest birch for the bang: restoring and expanding upland birchwoods in the Scottish Highlands by managing red deer. [PDF]
Andrew Tanentzap, 
James Zou, David Coomes.
Ecology and Evolution 3(7):1890-901 (2013).

Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells. [PDF]
Hongfang Wang, 
James Zou [co-first author, corresponding author], et al.
Proceedings of the National Academy of Sciences 108(36):14908-13 (2011).

Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth. [PDF]
Bo Zhao, 
James Zou [co-first author], et al.
Proceedings of the National Academy of Sciences 108(36):14902-7 (2011).

Canonical NF-kappaB activation is essential for Epstein-Barr virus latent membrane protein 1 TES2/CTAR2 gene regulation. [PDF]
Ben Gewurz, Jessica Mar, Megha Padi, Bo Zhao, Nicholas Shinners, Kaoru Takasaki, Edward Bedoya, 
James Zou, et al.
Journal of Virology 85(13):6764-73 (2011).

Epstein-Barr virus nuclear antigens 3C and 3A maintain lymphoblastoid cell growth by repressing p16INK4A and p14ARF expression. [PDF]
Seiji Maruo, Bo Zhao, Eric Johannsen, Elliott Kieff, 
James Zou, Kenzo Takada.
Proceedings of the National Academy of Sciences 108(5):1919-24 (2011).

Religion and HIV in Tanzania: influence of religious beliefs on HIV stigma, disclosure, and treatment attitudes.[PDF]
James Zou [corresponding author], Yvonne Yamanaka, et al.
BMC Public Health 9:75 (2009).

Machine learning and AI

Man is to Computer Programmer as Woman is to Homemaker? Debiasing Word Embeddings. [arXiv] [TechReview] [Vice] [NPR]
Tolga Bolukbasi, Kai-Wei Chang, 
James Zou, Venkatesh Saligrama, Adam Kalai.
Neural Information Processing Systems (NIPS 2016).

Rich component analysis. [arXiv]
Rong Ge, 
James Zou [alphabetical].
International Conference on Machine Learning (ICML 2016).

Controlling bias in adaptive data analysis using information theory. [arXiv]
Daniel Russo, 
James Zou [alphabetical].
AISTATS (2016) (full oral; top 7% of submissions).
Information Theory and Applications (ITA) invited talk.

Clustering with a reject option: interactive clustering as Bayesian prior elicitation. 
Akash Srivastava, James Zou, Ryan Adams, Charles Sutton.
ArXiv (2016).

Intersecting faces: non-negative matrix factorization with new guarantees. [PDF]
Rong Ge, 
James Zou [alphabetical].
International Conference on Machine Learning (ICML 2015).

Crowdsourcing feature discovery via adaptively chosen comparisons. [PDF]
James Zou, Kamalika Chaudhuri, Adam Kalai.
HCOMP (2015); CrowdML workshop (ICML 2015); Feature extraction workshop (NIPS 2015)
Invited to Journal of Machine Learning Research (JMLR) special issue (2015).

Incentive compatible experimental design. [PDF]
Panos Toulis, David Parkes, Elery Pfeffer, 
James Zou.
ACM Conference on Economics and Computation (EC 2015).

Approval voting behavior in Doodle. [PDF]
James Zou, Reshef Meir, David Parkes.
ACM Conference CSCW
(2015). Honorable mention for best paper (top 5% of submissions).

Coordination through contingent payment mechanisms. 
Hongyao Ma, Reshef Meir, David C. Parkes, James Zou.
Conference on Auctions, Market Mechanisms and Their Applications (2015). INFORMS (2015)

Contrastive learning using spectral methods. [PDF]
James Zou, Daniel Hsu, David Parkes, Ryan Adams.
Neural Information Processing Systems (NIPS 2013).

Priors for diversity in generative latent variable models. [PDF]
James Zou, Ryan Adams.
Neural Information Processing Systems
(NIPS 2012).

A slime mold solver for linear programming problems. [PDF]
Anders Johannson, 
James Zou [alphabetical].
Lecture Notes in Computer Science 7318 (2012).

Get another worker? Active crowdlearning with sequential arrivals.  
James Zou, David Parkes.
Proceedings of Workshop on Machine Learning in Human Computation and Crowdsourcing (ICML 2012).

Threats and trade-Offs in resource critical crowdsourcing tasks over networks. [arXiv]
Swaprava Nath, Pankaj Dayama, Dinesh Garg, Y. Narahari, 
James Zou.
Proceedings 8th Workshop on Internet and Network Economics (WINE 2012).

Tolerable manipulability in dynamic assignment without money. [PDF]
James Zou, Sujit Gujar, David Parkes.
Proceedings 24th AAAI Conference on Artificial Intelligence (AAAI 2010).

Dynamic House Allocation. 
Sujit Gujar, 
James Zou, David Parkes.
Proceedings 5th Multidisciplinary Workshop on Advances in Preference Handling (MPREF 2010).

Systems and methods for quantifiable signaling in multi-user environments.
James Zou, David Parkes.
U.S. Provisional Application No.: 61/837,843 .

James Zou Stanford