2022   2021   2020   2019   2018   2017   2016 and before

​

Selected highlights

​

Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. [PDF] 

Zhenqin Wu, Alex Trevino, Eric Wu, Kyle Swanson, Honesty Kim, Blaize D’Angio, Ryan Preska, Greg Charville, Piero Dalerba, Ann Egloff, R. Uppaluri, U. Duvvuri, Aaron Mayer, James Zou. 

Nature Biomedical Engineering (2022).

​

Systematic pan-cancer analysis of mutation-treatment interactions using large real-world clinicogenomics data. [PDF] 

Ruishan Liu, Shemra Rizzo, Sarah Waliany, Marius Garmhausen, Navdeep Pal, Zhi Huang, Nayan Chaudhary, Lisa Wang, Chris Harbron, Joel Neal, Ryan Copping, James Zou. 

Nature Medicine (2022).

​

Evaluating eligibility criteria of oncology trials using real-world data and AI. [PDF] [news​] [news​] [news​]

Ruishan Liu, Shemra Rizzo, Sam Whipple, Navdeep Pal, Arturo Pineda, Michael Lu, Brandon Arnieri, Ying Lu, William Copra, Ryan Copping, James Zou. 

Nature (2021). Finalist for Global Pharma Award 2021; Top 10 Clinical Research Achievement

​

How medical AI devices are evaluated: limitations and recommendations from an analysis of FDA approvals. [PDF] [website] [news​]

Eric Wu, Kevin Wu, Roxana Daneshjou, David Ouyang, Daniel Ho, James Zou. 

Nature Medicine  (2021).

​

Video-based AI for beat-to-beat assessment of cardiac function. [PDF] 

David Ouyang, Bryan He, Amirata Ghorbani, N. Yuan, J. Ebinger, C. Langlotz, P. Heidenrich, R. Harrington, D. Liang, E. Ashley, James Zou. 

Nature (2020).

​

Integrating spatial gene expression and breast tumour morphology with deep learning. [PDF] 

Bryan He, Ludvig Bergenstrahle, Linnea Stenbeck, Abu Abid, Alma Andersson, Ake Borg, Jonas Maaskola, Joakim Lundeberg, James Zou.

Nature Biomedical Engineering (2020).

​

FrugalML: how to use ML prediction APIs more accurately and cheaply. [PDF] 

Lingjiao Chen, Matei Zaharia, James Zou. 

NeurIPS (2020). Selected for oral presentation (top 1% of submissions).

​

How much does your data exploration overfit? Controlling bias via information usage. [arXiv] 

Daniel Russo, James Zou. 

IEEE Transactions on Information Theory (2019). 

 

Large dataset enables prediction of repair after CRISPR-Cas9 editing in primary T cells. [arXiv] 

Ryan Leenay, Amirali Aghazadeh, Joseph Hiatt, David Tse, T. Roth, R. Apathy, E. Shifrut, J. Hulquist, N. Krogan, Z. Wu, G. Carolina, H. Canaj, M. Leonetti, Alex Marson, Andrew May, James Zou. 

Nature Biotechnology (2019).

 

AdaFDR: a Fast, Powerful and Covariate-Adaptive Approach for Multiple Hypothesis Testing.[arXiv] 

Martin Zhang, Fei Xia, James Zou. 

Nature Communications (2019). RECOMB Best Paper Award.

​

Data Shapley: Equitable Data Valuation for Machine Learning. [arXiv] 

Amirata Ghorbani, James Zou. 

ICML (2019). 

​

Design AI so that it's fair. [PDF] 

James Zou and Londa Schiebinger. 

Nature (2018).

​

Word embeddings quantify 100 years of gender and ethnic stereotypes. [PDF] 

Nikhil Garg, Londa Schiebinger, Dan Jurafsky, James Zou. 

Proceedings of the National Academy of Sciences (2018).

​

2022

​

Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. [PDF] 

Zhenqin Wu, Alex Trevino, Eric Wu, Kyle Swanson, Honesty Kim, Blaize D’Angio, Ryan Preska, Greg Charville, Piero Dalerba, Ann Egloff, R. Uppaluri, U. Duvvuri, Aaron Mayer, James Zou. 

Nature Biomedical Engineering (2022).

​

Mind the Gap: Understanding the Modality Gap in Multi-modal Contrastive Representation Learning. 

Weixin Liang, Yuhui Zhang, Yongchan Kwon, Serena Yeung, James Zou. 

NeurIPS (2022).

​

WeightedSHAP: analyzing and improving Shapley based feature attributions.

Yongchan Kwon and James Zou. 

NeurIPS (2022).

​

Uncalibrated Models Can Improve Human-AI Collaboration. 

Kailas Vodrahalli, Tobi Gerstenberg, James Zou. 

NeurIPS (2022).

​

Estimating and Explaining Model Performance When Both Covariates and Labels Shift. 

Lingjiao Chen, Matei Zaharia, James Zou. 

NeurIPS (2022).

​

mixReg: A Simple Way to Improve Generalization in Regression for Deep Neural Networks. 

Huaxiu Yao, Yiping Wang, Linjun Zhang, James Zou, Chelsea Finn. 

NeurIPS (2022).

​

SKINCON: A skin disease dataset densely annotated by domain experts for fine-grained debugging and analysis.

Roxana Daneshjou, Mert Yuksekgonul, Zhuo Ran Cai, Rob Novoa, James Zou. 

NeurIPS Datasets and Benchmarks Track (2022).

​

HAPI: A Large-scale Longitudinal Dataset of Commercial ML API Predictions.

Lingjiao Chen, Zhihua Jin, Sabri Eyuboglu, Christopher Re, Matei Zaharia, James Zou. 

NeurIPS Datasets and Benchmarks Track (2022).

​

SEAL: Interactive Tool for Systematic Error Analysis and Labeling.

Nazneen Rajani, Weixin Liang, Lingjiao Chen, Meg Mitchell, James Zou. 

EMNLP Demo Track (2022).

​

Systematic analysis of 50 years of Stanford University technology transfer and commercialization. [PDF]

Weixin Liang, Scott Elrod, Daniel McFarland, James Zou. 

Patterns (2022).

​

Artificial Intelligence, machine learning and the changing landscape of molecular biology. [PDF]

James Zou, Hongzhe Li, Sylvia Plevritis ​

Journal of Molecular Biology (2022).

​

Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data. [PDF]

Martin Zhang, et al. 

Nature Genetics (2022).

​

Advances, challenges and opportunities in creating data for trustworthy AI. [PDF]

Weixin Liang, Girmaw Tadesse, Daniel Ho, Fei-Fei Li, Matei Zaharia, Ce Zhang, James Zou. 

Nature Machine Intelligence (2022).

​

Disparities in dermatology AI performance on a diverse, curated clinical image set. [PDF] 

Roxana Daneshjou, Kailas Vodrahalli, et al., James Zou*, Andrew Chiou*. 

Science Advances (2022).     *co-corresponding authors

​

Systematic pan-cancer analysis of mutation-treatment interactions using large real-world clinicogenomics data. [PDF] [Stanford News]

Ruishan Liu, Shemra Rizzo, Sarah Waliany, Marius Garmhausen, Navdeep Pal, Zhi Huang, Nayan Chaudhary, Lisa Wang, Chris Harbron, Joel Neal, Ryan Copping, James Zou. 

Nature Medicine (2022).

​

Shifting machine learning for healthcare from development to deployment and from models to data. [PDF]

Angela Zhang, Lei Xing, James Zou, Joe Wu.

Nature Biomedical Engineering (2022).

​

Meaningfully debugging model mistakes using conceptual counterfactual explanations. [PDF]

Abu Abid, Mert Yuksekgonul, James Zou.

International Conference on Machine Learning (ICML 2022).

​

FrugalMCT: Efficient Online ML API Selection for Multi-Label Classification Tasks. [PDF]

Lingjiao Chen, Matei Zaharia, James Zou.

International Conference on Machine Learning (ICML 2022).

​

When and How Mixup Improves Calibration. [PDF]

Linjun Zhang, Zhun Deng, Kenji Kawaguchi, James Zou.

International Conference on Machine Learning (ICML 2022).

​

Improving Out-of-Distribution Robustness via Selective Augmentation. [PDF]

Huaxiu Yao, Yu Wang, Sai Li, Linjun Zhang, Weixin Liang, James Zou, Chelsea Finn. 

International Conference on Machine Learning (ICML 2022).

​

Do Humans Trust Advice More if it Comes from AI? An Analysis of Human-AI Interactions. [PDF]

Kailas Vodrahalli, Roxana Daneshjou, Tobi Gerstenberg, James Zou.

AI, Ethics and Society Conference (AIES 2022).

​

Clustering Plotted Data by Image Segmentation. [PDF]

Tarek Naous, Srinjay Sarkar, Abubakar Abid, James Zou.

Conference on Computer Vision and Pattern Recognition (CVPR Demo 2022).

​

A Unified f-divergence Framework Generalizing VAE and GAN. [PDF]

Jaime Roquero, James Zou.

International Symposium on Information Theory (ISIT 2022).

​

The Genetic Etiology of Periodic Leg Movement in Sleep. [PDF]

Jacob Edelson, et al., James Zou, Emmanuel Mignot. 

Sleep (2022).

​

Dynamical Systems Model of RNA Velocity Improves Inference of Single-cell Trajectory, Pseudo-time and Gene Regulation. [PDF]

Ruishan Liu, Angela Pisco, Emelie Braun, Sten Linnarsson, James Zou.  

Journal of Molecular Biology (2022).

​

Machine Learning Prediction of Clinical Trial Operational Efficiency. [PDF]

Kevin Wu, Eric Wu, M. DAndrea, N. Chitale, M. Lim, M. Dabrowski, K. Kantor, H. Rangi, R. Liu, M. Garmhausen, N. Pal, C. Harbron, S. Rizzo, R. Copping, James Zou.  

Journal of the American Association of Pharmaceutical Scientists (2022).

​

Assessment of COVID-19 data reporting in 100+ websites and apps in India. [PDF]

Varun Vasudevan, Abeynaya Gnanasekaran, B. Bansal, C. Lahariya, G. Parameswaran, James Zou.  

PLoS Global Health (2022).

​

Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers. [PDF]

Minjie Zhang, Irena Hwang, Kongpan Li, J. Bai, J. Chen, Tsachy Weisman, James Zou, Zhipeng Lu 

Genome Research (2022).

​

AI-enabled in silico immunohistochemical characterization for Alzheimer’s disease. [PDF]

Bryan He, Syed Bukhari, Edward Fox, Abu Abid, Jeanne Shen, Claudia Kawas, Maria Corrada, Tom Montine, James Zou.  

Cell Reports Methods (2022).

​

DynaMorph: self-supervised learning of morphodynamic states of live cells. [PDF]

Michael Wu, B. Chhun, G. Popova, S. Guo, C. Kim, L. Yeh, T. Nowakowski*, James Zou*, S. Mehta*.   

Molecular Biology of the Cell (2022).          *co-corresponding authors

​

How did the model change? Efficiently assessing machine learning API shifts. [PDF]

Lingjiao Chen, Matei Zaharia, James Zou.  

International Conference on Learning Representations (ICLR 2022).

​

MetaShift: a dataset of datasets for evaluating contextual distribution shifts and training conflicts. [PDF]

Weixin Liang, James Zou.  

International Conference on Learning Representations (ICLR 2022). 

​

Domino: discovering systematic errors with cross-modal embeddings. [PDF]

S. Eyuboglu, M. Varma, K. Saab, J. Delbrouck, C. Lee-Messer, J. Dunnmon, James Zou, S. C. Re.  

International Conference on Learning Representations (ICLR 2022). Oral 

​

Beta Shapley: a Unified and Noise-reduced Data Valuation Framework for Machine Learning. [PDF]

Yongchan Kwon, James Zou.  

International Conference on AI and Statistics (AISTATS 2022). Oral (top 3% of submissions)

​

MLDemon: Deployment Monitoring for Machine Learning Systems. [PDF]

Tony Ginart, Martin Zhang, James Zou.  

International Conference on AI and Statistics (AISTATS 2022). 

​

How to Learn when Data Gradually Reacts to Your Model. [PDF]

Zach Izzo, James Zou, Lexing Ying.  

International Conference on AI and Statistics (AISTATS 2022).

​

Diversifying history: A large-scale analysis of changes in researcher demographics and scholarly agendas. [PDF]

Stephen Risi, Mathias Nielsen, Emma Kerr, Emer Brady, Lanu Kim, Dan McFarland, Dan Jurafsky, James Zou, Londa Schiebinger.  

PLOS One (2022). 

​

CloudPred: Predicting Patient Phenotypes From Single-cell RNA-seq. [PDF]

Bryan He, Matthew Thomson, Meena Subramaniam, Richard Perez, Jimmie Ye, James Zou. 

Pacific Symposium on Biocomputating (2022).

​

Predicting Visuo-Motor Diseases From Eye Tracking Data. [PDF]

Kailas Vodrahalli, Maciej Filipkowski, Tiffany Chen, James Zou*, Joyce Liao* 

Pacific Symposium on Biocomputating (2022).    *Corresponding author

​

Prostate cancer therapy personalization via multi-modal deep learning on randomized phase III clinical trials. [PDF]

Esteva et al.  

npj Digital Medicine (2022). 

 

Artificial Intelligence for Retrosynthesis Prediction. [PDF]

Jiang et al.  

Engineering (2022). 

2021

​

Beyond Importance Scores: Interpreting Tabular ML by Visualizing Feature Semantics. [PDF]

Amirata Ghorbani, Dina Berenbaum, Maor Ivgi, Yuval Dafna, James Zou. 

MDPI Information (2021).

​

Super-resolved spatial transcriptomics by deep data fusion. [PDF] 

L. Bergenstrahle, B. He, J. Bergenstrahle, X. Abalo, R. Mirzazadeh, K. Thrane, A. Ji, A. Andersson, L. Larsson, N. Stakenborg, G. Boeckxstaens, P. Khavari, J. Zou, J. Lundeberg, J. Maaskola 

Nature Biotechnology (2021).

​

Quantification of Gender Bias and Sentiment Toward Political Leaders Over 20 Years of Kenyan News Using Natural Language Processing. [PDF]

Emma Pair, Nikitha Vicas, Ann Weber, V. Meausoone, James Zou, Amos Njuguna, Gary Darmstadt 

Frontiers in Psychology (2021).

​

Adversarial Training Helps Transfer Learning via Better Representations. [PDF]

Zhun Deng, Linjun Zhang, Kailas Vodrahalli, Kenji Kawaguchi, James Zou. 

NeurIPS (2021).

​

Deep learning evaluation of biomarkers from echocardiogram videos. [PDF] [podcast​]

Weston Hughes, N. Yuan, B. Hu, J. Ouyang, J. Ebinger, P. Botting, J. Lee, J. Theurer, J. Tooley, K. Nieman, M. Lungren, D. Liang, I. Schnittger, J. Chen, E. Ashley, S. Cheng, David Ouyang, James Zou. 

Lancet EbioMedicine (2021).

​

Lack of Transparency and Potential Bias in Artificial Intelligence Data Sets and Algorithms. [PDF] [news​]

Roxana Daneshjou, Mary Smith, Mary Sun, Veronica Rotemberg, James Zou. 

JAMA Dermatology (2021).

​

Patient Experience Surveys Reveal Gender‑Biased Descriptions of Their Care Providers. [PDF]

Dylan Haynes, Anu Pampari, C. Topham, K. Schwarzenberger, M. Heath, James Zou*, Teri Greiling*. 

Journal of Medical Systems (2021).    *Corresponding author

​

Disparity in the quality of COVID-19 data reporting across India. [PDF] [news​]

Varun Vasudevan, Abeynaya Gnanasekaran, Varsha Sankar, Siddarth Vasudevan, James Zou. 

BMC Public Health (2021).

​

Comprehensive analysis of 2.4 million patent-to-research citations maps the biomedical innovation and translation landscape. [PDF] [news​]

Anoop Manjunath, Hongyu Li, Shuchen Song, Zhixing Zhang, Shu Liu, Nathan Kahrobai, Arya Gowda, Angelina Seffens, James Zou*, Ishan Kumar. 

Nature Biotechnology (2021).    *Corresponding author

​

Large language models associate Muslims with violence. [PDF] [news​]

Abubakar Abid, Maheen Farooqi, James Zou. 

Nature Machine Intelligence (2021).   

​

How to learn when data reacts to your model: performative gradient descent. [PDF]

Zach Izzo, Lexing Ying, James Zou. 

ICML (2021).

​

Improving generalization in meta-learning via task augmentation. [PDF]

Huaxiu Yao, Longkai Huang, Linjun Zhang, Ying Wei, Li Tian, James Zou. Junzhou Huang, Z. Li. 

ICML (2021).

​

Neural group testing to accelerate deep learning. [PDF]

Weixin Liang, James Zou. 

International Symposium on Information Theory (ISIT 2021).

​

Mixed dimension embedding with application to memory-efficient recommendation systems. [PDF]

Tony Ginart, Maxim Naumov, Dheevatsa Mudigere, Jiyan Yang, James Zou. 

International Symposium on Information Theory (ISIT 2021).

​

Who's responsible? Jointly quantifying the contribution of the learning algorithm and data. [PDF]

Gal Yona, Amirata Ghorbani, James Zou. 

AI, Ethics and Society Conference (2021).

​

Ensuring that biomedical AI benefits diverse populations. [PDF]

James Zou and Londa Schiebinger 

Lancet EBioMedicine (2021).

​

Evaluating eligibility criteria of oncology trials using real-world data and AI. [PDF] [news​] [news​] [news​]

Ruishan Liu, Shemra Rizzo, Sam Whipple, Navdeep Pal, Arturo Pineda, Michael Lu, Brandon Arnieri, Ying Lu, William Copra, Ryan Copping, James Zou. 

Nature (2021). Finalist for Global Pharma Award 2021

​

How medical AI devices are evaluated: limitations and recommendations from an analysis of FDA approvals. [PDF] [website] [news​]

Eric Wu, Kevin Wu, Roxana Daneshjou, David Ouyang, Daniel Ho, James Zou. 

Nature Medicine  (2021).

​

Mouse aging cell atlas analysis reveals global and cell type-specific aging signatures [PDF] [news​]

Martin Zhang, Angela Pisco, Spyros Darmanis, James Zou. 

eLife (2021).

​

BABEL enables cross-modality translation between multi-omic profiles at single-cell resolution. [PDF] 

Kevin Wu, Katie Yost, Howard Chang*, James Zou*. 

Proceedings of the National Academy of Sciences  (2021).

​

How to evaluate deep learning for cancer diagnostics: factors and recommendations. [PDF] 

Roxana Daneshjou, Bryan He, David Ouyang, James Zou. 

BBA Reviews on Cancer (2021).

​

Competing AI: how does competition feedback affect machine learning. [PDF] [news​]

Tony Ginart, Eva Zhang, Yongchan Kwon, James Zou. 

International Conference on AI and Statistics (AISTATS 2021).

​

Efficient computation and analysis of distributional Shapley values. [PDF] 

Yongchan Kwon, Manny Rivas, James Zou. 

International Conference on AI and Statistics (AISTATS 2021).

​

Approximate data deletion from machine learning models. [PDF] [news​​] 

Zach Izzo, Mary Smart, Kamalika Chaudhuri, James Zou. 

International Conference on AI and Statistics (AISTATS 2021).

​

Improving adversarial robustness via unlabeled out-of-domain data. [PDF] 

Linjun Zhang, Zhun Deng, Amirata Ghorbani, James Zou. 

International Conference on AI and Statistics (AISTATS 2021). Oral (top 3% of submissions).

​

How does mixup help with robustness and generalization? [PDF] 

Linjun Zhang, Zhun Deng, Kenji Kawaguchi, Amirata Ghorbani, James Zou. 

International Conference on Learning Representations (ICLR 2021). Spotlight 

​

TrueImage: A Machine Learning Algorithm to Improve the Quality of Telehealth Photos. [PDF] [news​​]

Kailas Vodrahalli, Roxana Daneshjou, Roberto Novoa, Albert Chiou, Justin Ko, James Zou. 

Pacific Symposium on Biocomputing (PSB 2021).

​

Data valuation for medical imaging using Shapley value and application to a large-scale chest X-ray dataset. [PDF] 

Siyi Tang, Amirata Ghorbani, R. Yamashita, S. Rehman, Jared Dunnmon, James Zou, Daniel Rubin 

Scientific Reports (2021).

​

2020

​

Variation in COVID-19 Data Reporting Across India: 6 Months into the Pandemic. [PDF] 

Varun Vasudevan, Abeynaya Gnanasekaran, Varsha Sankar, Siddarth Vasudevan, James Zou. 

Journal of the Indian Institute of Science (2020).  

​

FrugalML: how to use ML prediction APIs more accurately and cheaply. [PDF] 

Lingjiao Chen, Matei Zaharia, James Zou. 

NeurIPS (2020). Selected for oral presentation (top 1% of submissions).

​

Neuron Shapley: discoverying the responsible neurons. [PDF] 

Amirata Ghorbani, James Zou. 

NeurIPS (2020). 

​

MOPO: model based offline policy optimization. [PDF] 

T. Yu, G. Thomas, L. Yu, S. Ermon, J. Zou, S. Levine, C. Finn, T. Ma. 

NeurIPS (2020). 

​

ALICE: active learning with contrastive natural language explanations. [PDF] 

Weixin Liang, James Zou*, Zhou Yu*.

Empirical Methods in Natural Language Processing (EMNLP 2020).

​

Deep learning for biomedical videos: perspective and recommendations. [PDF] 

David Ouyang, Zhenqin Wu, Bryan He, James Zou. 

Artificial Inteliigence in Medicine (2020).

 

Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries. [PDF] 

Jie Zhou, Shantao Li, Kevin Leung, Brian O'Donovan, James Zou, Joe Derisi, Jim Wells. 

PNAS (2020).

​

A single-cell transcriptomic atlas characterizes aging tissues in the mouse. [PDF] 

The Tabula Muris Consortium. 

Nature (2020).

​

Integrating spatial gene expression and breast tumour morphology with deep learning. [PDF] 

Bryan He, Ludvig Bergenstrahle, Linnea Stenbeck, Abu Abid, Alma Andersson, Ake Borg, Jonas Maaskola, Joakim Lundeberg, James Zou.

Nature Biomedical Engineering (2020).

​

RNA-GPS predicts SARS-CoV-2 RNA residency to host mitochondria and nucleolus. [PDF] 

Kevin Wu, Furqan Fazal, Kevin Parker, James Zou*, Howard Chang*.

Cell Systems (2020).

​

Deep learning models to detect hidden clinical correlates. [PDF] 

David Ouyang, James Zou.

The Lancet Digital Health (2020).

​

Association of rapid eye movement sleep with mortality in middled-aged and older adults. [PDF] 

E. Leary, K. Watson, S. Ancoli-Israel, S. Redline, K. Yaffe, L. Ravelo, P. Peppard, J. Zou, S. Goodman, E. Mignot, K. Stone.

JAMA Neurology (2020).

​

Clinical genetics lacks standard definitions and protocols for the collection and use of diversity measures. [PDF] 

ClinGen Ancestry and Diversity Working Group.

American Journal of Human Genetics (2020).

​

A distributional framework for data valuation. [PDF] 

Amirata Ghorbani, Michael Kim, James Zou.

International Conference on Machine Learning (ICML 2020).

​

Predicting target genes of non-coding regulatory variants with ICE. [PDF] 

Michael Wu, Nilah Ioannidis, James Zou.

Bioinformatics (2020).

​

Beyond user self-reported Likert scale ratings: a comparison model for automatic dialog evaluation. [PDF] 

Weixin Liang, James Zou, Zhou Yu.

Annual Conference of the Association of Computational Linguistics (ACL 2020).

​

PB-Net: automatic peak integration by sequential deep learning for multiple reaction monitoring. [PDF] 

Zhenqin Wu, Daniel Serie, Gege Xu, James Zou.

Journal of Proteomics (2020).

​

RNA-GPS predicts RNA subcellular localization and highlights the role of splicing. [PDF] 

Kevin Wu, Kevin Parker, Furqan Fazal, Howard Chang, James Zou.

RNA (2020).

​

Video-based AI for beat-to-beat assessment of cardiac function. [PDF] 

David Ouyang, Bryan He, Amirata Ghorbani, N. Yuan, J. Ebinger, C. Langlotz, P. Heidenrich, R. Harrington, D. Liang, E. Ashley, James Zou. 

Nature (2020).

​

A benchmark of algorithms for the analysis of pooled CRISPR screens. [PDF] 
Sunil Bodapati, Tim Daley, Xueqiu Lin, James Zou*, Lei Qi*. 
Genome Biology (2020).

​

An online platform for interactive feedback in biomedical machine learning. [PDF] 

Abubakar Abid, Ali Abdalla, Ali Abid, Dawood Khan, Abdulrahman Alfozan, James Zou. 

Nature Machine Intelligence (2020).

 

Learning transport cost from subset correspondence. [PDF] 

Ruishan Liu, Akshay Balsubramani, James Zou. 

International Conference on Learning Representations (ICLR 2020). 

Deep learning interpretation of echocardiograms. [PDF] 
Amirata Ghorbani, David Ouyang, Abubakar Abid, Bryan He, Jonathan Chen, Robert Harrington, David Liang, Euan Ashley, James Zou. 
Nature Digital Medicine (2020). 

LitGen: genetic literature recommendation guided by human explanations.  
Allen Nie, et al., James Zou. 
Pacific Symposium on Biocomputing (PSB 2020). 

 

2019

 

Sex and gender analysis improves science and engineering. [PDF]

Cara Tannenbaum*, Robert Ellis*, Friederike Eyssel*, James Zou*, Londa Schiebinger. 

Nature (2019).   *co-first authors

Making AI forget you: data deletion in machine learning. [arXiv] 
Tony Ginart, Melody Guan, Greg Valiant, James Zou. 
NeurIPS (2019). Selected for spotlight talk (top 3% of submissions).

Toward automatic concept based explanations. [PDF]
Amirata Ghorbani, James Wexler, James Zou, Been Kim. 
NeurIPS (2019). 

How much does your data exploration overfit? Controlling bias via information usage. [arXiv] 
Daniel Russo, James Zou. 
IEEE Transactions on Information Theory (2019). 

Large dataset enables prediction of repair after CRISPR-Cas9 editing in primary T cells. [arXiv] 
Ryan Leenay, Amirali Aghazadeh, Joseph Hiatt, David Tse, Theo Roth, Ryan Apathy, Eric Shifrut, Judd Hulquist, N. Krogan, Z. Wu, G. Carolina, H. Canaj, M. Leonetti, Alex Marson, Andrew May, James Zou. 
Nature Biotechnology (2019).

AdaFDR: a Fast, Powerful and Covariate-Adaptive Approach for Multiple Hypothesis Testing. [arXiv] 
Martin Zhang, Fei Xia, James Zou. 
Nature Communications (2019). Preliminary version won the RECOMB Best Paper Award.

VetTag: improving automated veterinary diagnosis coding via large-scale language modeling. [arXiv] 
Yuhui Zhang, Allen Nie, Ashley Zehnder, Rodney Page, James Zou. 
Nature Digital Medicine (2019). 

​

Data Shapley: Equitable Data Valuation for Machine Learning. [arXiv] 
Amirata Ghorbani, James Zou. 
ICML (2019). 

​

Concrete Autoencoders for Differentiable Feature Selection and Reconstruction. [arXiv] 
Abubakar Abid, Muhammad Balin, James Zou. 
ICML (2019). 

​

Adaptive Monte Carlo Multiple Testing via Multi-Armed Bandits. [arXiv] 
Martin Zhang, James Zou, David Tse. 
ICML (2019). 

​

Discovering Conditionally Salient Features with Statistical Guarantees. 
Jaime Roquero, James Zou. 
ICML (2019). 

​

Contrastive multivariate singular spectrum analysis. [arXiv] 
Abdi-Hakin Dirie, Abubakar Abid, James Zou. 
IEEE Allerton (2019). Preliminary version selected for spotlight at NIPS'18 Spatio-temporal Workshop.

​

A Knowledge Graph-based Approach for Exploring the U.S. Opioid Epidemic. 
Maulik Kamdar, Tymor Hamansy, Shea Zhao, Ayin Vala, Tome Eftimov, James Zou, Suzanne Tamang. 
ICLR AI for Social Good (2019). Best Poster Award.

​

Modeling spatial correlation of transcripts with application to pancreas development. [PDF] 
Ruishan Liu, Marco Mignardi, Robert Jones, Martin Enge, Seung Kim, Steve Quake, James Zou. 
Scientific Reports (2019).

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Analyzing Polarization in Social Media: Method and Application to Tweets on 21 Mass Shootings. 
Dora Demszky, Nikhil Garg, Rob Voigt, James Zou, Jesse Shapiro, Matthew Gentzkow, Dan Jurafsky
NAACL (2019). Washington Post coverage. 

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Interpretation of neural network is fragile. [arXiv] 
Amirata Ghorbani, Abubakar Abid, James Zou. 
AAAI (2019). Selected for oral presentation.

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Improving knockoff stability: simultaneous multiple knockoffs and entropy maximization. [arXiv] 
Jaime Gimenez, James Zou. 
AISTATS (2019).

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Knockoffs for the mass: new feature importance statistics with false discovery guarantees. [arXiv] 
Jaime Gimenez, Amirata Ghorbani, James Zou. 
AISTATS (2019).

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Feedback GAN for DNA optimizes protein functions. [PDF] 
Anvita Gupta, James Zou. 
Nature Machine Intelligence (2019).

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Multiaccuracy: black-box post-processing for fairness in classification. [PDF] 
Michael Kim, Amirata Ghorbani, James Zou. 
ACM/AAAI Conference of AI Ethics and Society (2019). 

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Contingent Payment Mechanisms for Resource Utilization.
Hongyao Ma, Reshef Meir, David Parkes, James Zou. 
18th International Conference on Autonomous Agents and Multiagent Systems (AAMAS) (2019).            Finalist for Best Paper Award.

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A large CRISPR-induced bystander mutation causes immune dysregulation. [PDF]
Dimitre Simeonov et al. 
Communications Biology (2019). 

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2018

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DeepTag: inferring diagnoses from veterinary clinical notes. [PDF] [press] 
Allen Nie, Ashley Zehnder, Rodney Page, Y. Zhang, A. Pineda, M. Rivas, C. Bustamante, James Zou. 
Nature Digital Medicine (2018).

A primer on deep learning in genomics. [PDF]  
James Zou, Mikael Huss, Abubakar Abid, Pejman Mohammadi, Ali Torkamani, Amalio Telenti. 
Nature Genetics (2018).

Design AI so that it's fair. [PDF] 
James Zou and Londa Schiebinger. 
Nature (2018).

Autowarp: learning a warping distance from unlabeled time series using sequence autoencoders. [PDF] 
Abubakar Abid, James Zou. 
NIPS (2018).

Stochastic EM for shuffled linear regression. [arXiv] 
Abubakar Abid, James Zou. 
IEEE Allerton (2018).

Minimizing close-k aggregate loss improves classification. [arXiv] 
Bryan He, James Zou. 
Under submission (2018).

Exploring patterns enriched in a dataset with contrastive principal component analysis. [PDF] 
Abubakar Abid, Vivek Bagaria, Martin Zhang, James Zou. 
Nature Communications (2018). ICML CompBio Workshop Top Paper Award Winner.

Word embeddings quantify 100 years of gender and ethnic stereotypes. [PDF] 
Nikhil Garg, Londa Schiebinger, Dan Jurafsky, James Zou. 
Proceedings of the National Academy of Sciences (2018).

CoVeR: learning covariate-specific vector representations with tensor decompositions. [arXiv] 
Kevin Tian, Teng Zhang, James Zou. 
International Conference of Machine Learning (ICML 2018).

Predicting target genes of non-coding regulatory variants with ICE.
Michael Wu, Nilah Ioannidis and James Zou. 
Under submission (2018).

The clinical imperative for inclusivity: race, ethnicity and ancestry in genomics. 
Alice Popejoy et al. 
Human Mutation (2018). 

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Why adaptively collected data has negative bias and how to correct for it. [arXiv] 
Xinkun Nie, Xiaoying Tian-Harris, Jonathan Taylor, James Zou. 
AISTATS 2018. ICML Workshop on Picky Learners Best Paper Award.

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Embedding for missingness: deep learning with incomplete data.
Amirata Ghorbani, James Zou. 
IEEE Allerton (2018).

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The effects of memory replay in reinforcement learning. [arXiv] 
Ruishan Liu and James Zou. Best Poster Award at BayLearn.
IEEE Allerton (2018). 

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The proteome of malaria plastid organelle, a key anti-parasitic target. [arXiv] 
Michael J Boucher, Sreejoyee Ghosh, Lichao Zhang, Avantika Lal, Se Won Jang, An Ju, Shuying Zhang, Xinzi Wang, Stuart A Ralph, James Zou, Joshua E Elias, Ellen Yeh. 
PLoS Biology (2018). 

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2017

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Mutation-convolution-max layers enhance deep learning of DNA motifs. 
Abubakar Abid, Amirata Ghorbani, James Zou. 
NIPS Machine Learning for CompBio Workshop (NIPS MLCB 2017). Spotlight paper 

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

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

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

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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). 

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

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 (2017).

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