2025 2024 2023 2022 2021 2020 2019 2018 2017 2016 and before
Selected highlights
Optimizing generative AI by backpropagating language model feedback. [PDF]
Mert Yuksekgonul, Fede Bianchi, Joseph Boen, Sheng Liu, Pan Lu, Zhi Huang, Carlos Guestrin, James Zou.
Nature (2025).
Spatial transcriptomic clocks reveal cell proximity effects in brain aging. [PDF]
Eric Sun, Olivia Zhou, Max Hauptschein, Nimrod Rappoport, Lucy Xu, Paloma Negredo, Ling Liu, Tom Rando, James Zou*, Anne Brunet*.
Nature (2024).
Simple and effective embedding model for single-cell biology built from ChatGPT. [PDF]
Yiqun Chen, James Zou.
Nature Biomedical Engineering (2024).
Generative AI for designing and validating easily synthesizable and structurally novel antibiotics. [PDF]
Kyle Swanson, Gary Liu, Denise Catacutan, Autumn Arnold, James Zou*, Jon Stokes*.
Nature Machine Intelligence (2024).
TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses. [PDF]
Eric Sun, Rong Ma, Paloma Negredo, Anne Brunet, James Zou.
Nature Methods (2024).
A visual–language foundation model for pathology image analysis using medical Twitter. [PDF]
Zhi Huang, Federico Bianchi, Mert Yuksekgonul, Tom Montine, James Zou.
Nature Medicine (2023). Cover article.
Blinded, randomized trial of sonographer versus AI cardiac function assessment. [PDF]
Bryan He, Alan Kwan, Jae Cho, Neal Yuan, C. Pollick, T. Shiota, J. Ebinger, N. Bello, J. Wei, K. Josan, G. Duffy, M. Jujjavarapu, R. Siegel, Susan Cheng*, James Zou*, David Ouyang*.
Nature (2023).
From patterns to patients: Advances in clinical machine learning for cancer diagnosis, prognosis, and treatment. [PDF]
Kyle Swanson, Eric Wu, Angela Zhang, Ash Alizadeh, James Zou.
Cell (2023).
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).
2025
An automated framework for assessing how well LLMs cite relevant medical references. [PDF]
Kevin Wu, Eric Wu, Kevin Wei, Angela Zhang, Allison Casasola, Teresa Nguyen, Sith Riantawan, Patricia Shi, Dan Ho, James Zou.
Nature Communications (2025).
Optimizing generative AI by backpropagating language model feedback. [PDF]
Mert Yuksekgonul, Fede Bianchi, Joseph Boen, Sheng Liu, Pan Lu, Zhi Huang, Carlos Guestrin, James Zou.
Nature (2025).
The rise of agentic AI teammates in medicine. [PDF]
James Zou, Eric Topol.
The Lancet (2025).
Efficient and Asymptotically Unbiased Constrained Decoding for Large Language Models.
Haotian Ye, Himanshu Jain, Chong You, Ananda Theertha Suresh, Haowei Lin, James Zou, Felix Yu.
AISTATS (2025).
Reducing Hallucinations in Large Vision-Language Models via Latent Space Steering. [PDF]
Sheng Liu, Haotian Ye, James Zou.
International Conference on Learning Representations (ICLR 2025). Spotlight
Mixture-of-Agents Enhances Large Language Model Capabilities. [PDF]
Junlin Wang, Jue Wang, Ben Athiwaratkun, Ce Zhang, James Zou.
International Conference on Learning Representations (ICLR 2025). Spotlight
Locality Alignment Improves Vision-Language Models. [PDF]
Ian Covert, Tony Sun, James Zou*, Tatsu Hashimoto*.
International Conference on Learning Representations (ICLR 2025).
Capturing the Temporal Dependence of Training Data Influence. [PDF]
Jiachen Wang, Dawn Song, James Zou, Prateek Mittal, Ruoxi Jia.
International Conference on Learning Representations (ICLR 2025). Oral
MedTrinity-25M: A Large-scale Multimodal Dataset with Multigranular Annotations for Medicine. [PDF]
Yunfei Xie, Ce Zhou, Lang Gao, Juncheng Wu, Xianhang Li, Hong-Yu Zhou, Sheng Liu, Lei Xing, James Zou, Cihang Xie, Yuyin Zhou.
International Conference on Learning Representations (ICLR 2025).
MMed-RAG: Versatile Multimodal RAG System for Medical Vision Language Models. [PDF]
Peng Xia, Kangyu Zhu, Haoran Li, Tianze Wang, Weijia Shi, Sheng Wang, Linjun Zhang, James Zou, Huaxiu Yao.
International Conference on Learning Representations (ICLR 2025).
GMValuator: Similarity-based Data Valuation for Generative Models. [PDF]
Jiaxi Yang, Wenlong Deng, Benlin Liu, Yangsibo Huang, James Zou, Xiaoxiao Li.
International Conference on Learning Representations (ICLR 2025).
ADMET-AI Enables Interpretable Predictions of Drug-Induced Cardiotoxicity. [PDF]
Souhrid Mukherjee, Kyle Swanson, Parker Walther, Rabindra V. Shivnaraine, Jeremy Leitz, Paul Pang, James Zou*, Joe Wu*.
Circulation (2025).
Characterizing mutation-treatment effects using clinico-genomics data of 78,287 patients with 20 types of cancers. [PDF]
Ruishan Liu, Shemra Rizzo, Lisa Wang, Nayan Chaudhary, Sophia Maund, Marius Garmhausen, Sarah McGough, Ryan Copping, James Zou.
Nature Communications (2025).
2024
Spatial transcriptomic clocks reveal cell proximity effects in brain aging. [PDF]
Eric Sun, Olivia Zhou, Max Hauptschein, Nimrod Rappoport, Lucy Xu, Paloma Negredo, Ling Liu, Tom Rando, James Zou*, Anne Brunet*.
Nature (2024).
FrugalGPT: How to Use Large Language Models While Reducing Cost and Improving Performance. [PDF]
Lingjiao Chen, Matei Zaharia, James Zou.
Transactions on Machine Learning Research (2024).
Simple and effective embedding model for single-cell biology built from ChatGPT. [PDF]
Yiqun Chen, James Zou.
Nature Biomedical Engineering (2024).
ChatGPT is transforming peer review — how can we use it responsibly? [PDF]
James Zou.
Nature (2024).
Are More LLM Calls All You Need? Towards the Scaling Properties of Compound AI Systems. [PDF]
Lingjiao Chen, Jared Quincy Davis, Boris Hanin, Peter Bailis, Ion Stoica, Matei Zaharia, James Zou.
NeurIPS (2024).
Stochastic Amortization: A Unified Approach to Accelerate Feature and Data Attribution. [PDF]
Ian Covert, Chanwoo Kim, Su-In Lee*, James Zou*, Tatsunori Hashimoto*.
NeurIPS (2024).
AvaTaR: Optimizing LLM Agents for Tool-Assisted Knowledge Retrieval. [PDF]
Shirley Wu, Shiyu ZHao, Qian Huang, Kexin Huang, Michihiro Yasunaga, Kaidi Cao, Vassilis Ioannidis, Karthik Subbian, Jure Leskovec, James Zou.
NeurIPS (2024).
GraphMETRO: Mitigating Complex Graph Distribution Shifts via Mixture of Aligned Experts. [PDF]
Shirley Wu, Kaidi Cao, Bruno Ribeiro, James Zou*, Jure Leskovec*.
NeurIPS (2024).
Accelerating Transformers with Spectrum-Preserving Token Merging. [PDF]
Hoai-Chau Tran, Duy M. H. Nguyen, Duy M. Nguyen, Trung-Tin Nguyen, Ngan Le, Pengtao Xie, Daniel Sonntag, James Zou, Binh T. Nguyen, Mathias Niepert.
NeurIPS (2024).
Enhancing Large Vision Language Models with Self-Training on Image Comprehension. [PDF]
Yihe Deng, Pan Lu, Fan Yin, Ziniu Hu, Sheng Shen, James Zou, Kai-Wei Chang, Wei Wan.
NeurIPS (2024).
TFG: Unified Training-Free Guidance for Diffusion Models. [PDF]
Haotian Ye, Haowei Lin, Jiaqi Han, Minkai Xu, Sheng Liu, Yitao Liang, Jianzhu Ma, James Zou, Stefano Ermon.
NeurIPS (2024).
ClashEval: Quantifying the tug-of-war between an LLM’s internal prior and external evidence. [PDF]
Kevin Wu, Eric Wu, James Zou.
NeurIPS Datasets and Benchmarks (2024).
UniTox: Leveraging LLMs to Curate a Unified Dataset of Drug-Induced Toxicity from FDA Labels. [PDF]
Jake Silberg, Kyle Swanson, Elana Simon, Angela Zhang, Zaniar Ghazizadeh, Scott Ogden, Hisham Hamadeh, James Zou.
NeurIPS Datasets and Benchmarks (2024).
CARES: A Comprehensive Benchmark of Trustworthiness in Medical Vision Language Models. [PDF]
Peng Xia, et al, James Zou, Huaxiu Yao.
NeurIPS Datasets and Benchmarks (2024).
STaRK: Benchmarking LLM Retrieval on Textual and Relational Knowledge Bases. [PDF]
Shirley Wu, Shiyu Zhao, Michihiro Yasunaga, Kexin Huang, Kaidi Cao, Qian Huang, Vassilis N. Ioannidis, Karthik Subbian, James Zou*, Jure Leskovec*.
NeurIPS Datasets and Benchmarks (2024).
Language models for biological research: a primer. [PDF]
Elana Simons, Kyle Swanson, James Zou.
Nature Methods (2024).
Discovery and generalization of tissue structures from spatial omics data. [PDF]
Zhenqin Wu, et al, James Zou*, Aaron Mayer*, Alex Trevino*.
Cell Reports Methods (2024).
ADMET-AI: a machine learning ADMET platform for evaluation of large-scale chemical libraries. [PDF]
Kyle Swanson, Parker Walther, Jeremy Leitz, Souhrid Mukherjee, Joe Wu, Rabin Shinaraine, James Zou.
Bioinformatics (2024).
A generalist vision-language foundation model for diverse biomedical tasks. [PDF]
Kai Zhang et al.
Nature Medicine (2024).
Can Large Language Models Provide Useful Feedback on Research Papers? A Large-Scale Empirical Analysis. [PDF]
Weixin Liang, Yuhui Zhang, Hancheng Cao, et al. James Zou.
NEJM AI (2024).
SPRITE: improving spatial gene expression imputation with gene and cell networks. [PDF]
Eric Sun, Rong Ma, James Zou.
Bioinformatics (ISMB 2024).
Regulating AI Adaptation: An Analysis of AI Medical Device Updates. [PDF]
Kevin Wu, Eric Wu, Kit Rodolfa, Dan Ho, James Zou.
Conference on Health, Inference and Learning (CHIL 2024).
Model ChangeLists: Characterizing Updates to ML Models. [PDF]
Sabri Eyuboglu, Karan Goel, Arjun Desai, Lingjiao Chen, Mathew Monfort, Chris Re, James Zou.
ACM FAccT (2024).
A pathologist–AI collaboration framework for enhancing diagnostic accuracies and efficiencies. [PDF]
Zhi Huang, et al, Tom Montine, James Zou.
Nature Biomedical Engineering (2024).
Systematic analysis of 32,111 AI model cards characterizes documentation practice in AI. [PDF]
Weixin Liang, Nazneen Rajani, Xinyu Yang, Ezi Ozoani, Eric Wu, Yiqun Chen, Daniel Smith, James Zou.
Nature Machine Intelligence (2024).
How is ChatGPT's behavior changing over time? [PDF]
Lingjiao Chen, Matei Zaharia, James Zou.
Harvard Data Science Review (2024).
Assessing the Impact of ChatGPT in AI Conference Peer Reviews. [PDF]
Weixin Liang, Zach Izzo, Yaohui Zhang, Haley Lepp, Hancheng Cao, Xuandong Zhao, Lingjiao Chen, Haotian Ye, Sheng Liu, Zhi Huang, Dan McFarland, James Zou.
ICML (2024).
How Well Can LLMs Negotiate? NegotiationArena Platform and Analysis. [PDF]
Federico Bianchi, Patrick John Chia, Mert Yuksekgonul, Jacopo Tagliabue, Dan Jurafsky, James Zou.
ICML (2024).
In-context Vectors: Making In Context Learning More Effective and Controllable Through Latent Space Steering. [PDF]
Sheng Liu, Haotian He, Lei Xing, James Zou.
ICML (2024).
Scaling Laws for the Value of Individual Data Points in Machine Learning.
Ian Covert, Wenlong Ji, Tatsunori Hashimoto, James Zou.
ICML (2024).
ArtWhisperer: A Dataset for Characterizing Human-AI Interactions in Artistic Creations. [PDF]
Kailas Vodrahalli, James Zou.
ICML (2024).
SleepFM: Multi-modal Representation Learning for Sleep across ECG, EEG and Respiratory Signals.
Rahul Thapa, Bryan He, Magnus Kjaer, Hyatt Moore, Gauri Ganjoo, Emmanuel Mignot, James Zou.
ICML (2024).
Learning and Forgetting Unsafe Examples in Large Language Models. [PDF]
Jiachen Zhao, Zhun Deng, David Madras, James Zou, Mengye Ren
ICML (2024).
Simple linear attention language models balance the recall-throughput tradeoff. [PDF]
Sabri Eyuboglu, Simran Arora, Michael Zhang, Aman Timalsina, Silas Alberti, James Zou, Atri Rudra, Christ Re.
ICML (2024).
Selecting Large Language Model to Fine-tune via Rectified Scaling Law. [PDF]
Haowei Lin, Baizhou Huang, Haotian Ye, Qinyu Chen, Zihao Wang, Sujian Li, Jianzhu Ma, Xiaojun Wan, James Zou, Yitao Liang.
ICML (2024).
Rethinking Data Shapley for Data Selection Tasks: Misleads and Merits.
Jiachen Wang, Tianji Yang, James Zou, Yongchan Kwon, Ruoxi Jia.
ICML (2024).
Prospector Heads: Generalized Feature Attribution for Large Models & Data. [PDF]
Gautam Machiraju, et al.
ICML (2024).
TrustLLM: Trustworthiness in Large Language Models. [PDF]
Yue Huang, et al.
ICML (2024).
Scaling adoption of medical AI—reimbursement from value-based care and fee-for-service perspectives. [PDF]
Michael Abramoff, Tinglong Dai, James Zou.
New England Journal of Medicine AI (2024).
Provable Membership Inference Privacy. [PDF]
Zach Izzo, Jinsung Yoon, Sercan Arik, James Zou.
Transactions on ML Research (2024).
New Evaluation Metrics Capture Quality Degradation due to LLM Watermarking. [PDF]
Karan Singh, James Zou.
Transactions on ML Research (2024).
Generative AI for designing and validating easily synthesizable and structurally novel antibiotics. [PDF]
Kyle Swanson, Gary Liu, Denise Catacutan, Autumn Arnold, James Zou*, Jon Stokes*.
Nature Machine Intelligence (2024).
Bridging the literacy gap for surgical consents: an AI-human expert collaborative approach. [PDF]
Rohaid Ali, Ian Connolly, Oliver Tang, et al, James Zou, Curtis Doberstein
npj Digital Medicine (2024).
Principled and interpretable alignability testing and integration of single-cell data. [PDF]
Rong Ma, Eric Sun, David Donoho, James Zou.
Proceedings of the National Academy of Sciences (2024).
Systematic analysis of off-label and off-guideline cancer therapy usage in a real-world cohort of 165,912 US patients. [PDF]
Ruishan Liu, Lisa Wang, Shemra Rizzo, Marius Garmhausen, Navdeep Pal, Sarah Waliany, Sarah McGough, Yvonne Lin, Zhi Huang, Joel Neal, Ryan Copping, James Zou.
Cell Reports Medicine (2024).
TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses. [PDF]
Eric Sun, Rong Ma, Paloma Negredo, Anne Brunet, James Zou.
Nature Methods (2024).
What Should Data Science Education Do With Large Language Models? [PDF]
Xinming Tu, James Zou, Weijie Su, Linjun Zhang.
Harvard Data Science Review (2024).
Protein structure generation via folding diffusion. [PDF]
Kevin Wu, Kevin Yang, Rianne van den Berg, Sarah Alamdari, James Zou, Alex Lu, Ava Amini.
Nature Communications (2024).
DataInf: Efficiently Estimating Data Influence in LoRA-tuned LLMs and Diffusion Models. [PDF]
Yongchan Kwon, Eric Wu, Kevin Wu, James Zou.
International Conference on Learning Representations (ICLR 2024).
Safety-Tuned LLaMAs: Lessons From Improving the Safety of Large Language Models that Follow Instructions. [PDF]
Fede Bianchi, Mirac Suzgun, Giuseppe Attanasio, Paul Rottger, Dan Jurafsy, Tatsu Hashimoto, James Zou.
International Conference on Learning Representations (ICLR 2024).
Navigating dataset documentations in AI: a large-scale analysis of dataset cards on Hugging Face. [PDF]
Xinyu Yang, Weixin Liang, James Zou.
International Conference on Learning Representations (ICLR 2024).
Zoology: Measuring and Improving Recall in Efficient Language Models. [PDF]
Simran Arora, Sabri Eyuboglu, Aman Timalsina, I. Johnson, M. Poli, James Zou, Atri Rudra, Chris Re
International Conference on Learning Representations (ICLR 2024).
Using ChatGPT to facilitate truly informed medical consent. [PDF]
Fatima Mirza, Oliver Tang, Ian Connolly, et al., James Zou, Rohaid Ali.
New England Journal of Medicine AI (2024).
The power of contrast for feature learning: a theoretical analysis. [PDF]
Wenlong Ji, Zhun Deng, Ryumei Nakada, James Zou, Linjun Zhang.
Journal of Machine Learning Research (2024).
VetLLM: large language model for predicting diagnosis from veterinary notes. [PDF]
Yixing Jiang, Jeremy Irvin, Andrew Ng, James Zou.
Proceedings of the Pacific Symposium on Biocomputing (PSB 2024).
PEPSI: polarity measurements from spatial proteomics imaging suggest immune cell engagement. [PDF]
Eric Wu, Michael Wu, Aaron Mayer, Alex Trevino, James Zou.
Proceedings of the Pacific Symposium on Biocomputing (PSB 2024).
2023
Characterizing the Clinical Adoption of Medical AI Devices through U.S. Insurance Claims. [PDF]
Kevin Wu, Eric Wu, et al, James Zou.
New England Journal of Medicine AI (2023).
TWIGMA: A dataset of AI-Generated Images with Metadata From Twitter. [PDF]
Yiqun Chen, James Zou.
NeurIPS Datasets and Benchmarks Track (2023).
Beyond Confidence: Reliable Models Should Also Consider Atypicality. [PDF]
Mert Yuksekgonul, Linjun Zhang, James Zou*, Carlos Guestrin*.
NeurIPS (2023).
OpenDataVal: a Unified Benchmark for Data Valuation. [PDF]
Kevin Jiang, Weixin Liang, James Zou, Yongchan Kwon.
NeurIPS Datasets and Benchmarks Track (2023).
Factorized Contrastive Learning: Going Beyond Multi-view Redundancy. [PDF]
Paul Liang, Zihao Deng, Martin Ma, James Zou, Louis-Philippe Morency, Ruslan Salakhutdinov.
NeurIPS (2023).
DataPerf: Benchmarks for Data-Centric AI Development. [PDF]
DataPerf team.
NeurIPS Datasets and Benchmarks Track (2023).
Improving genetic risk prediction across diverse population by disentangling ancestry representations. [PDF]
Prashnna Gyawali, Yann Le Guen, Xiaoxia Liu, Michael Belloy, Hua Tang, James Zou*, Zhihuai He*.
Communications Biology (2023).
A clinically applicable AI system for diagnosis of congenital heart diseases based on computed tomography images. [PDF]
Xiaowei Xu, Qianjun Jia, Haiyun Yuan, Hailong Qiu, Yuhao Dong, Wen Xie, Zeyang Yao, Jiawei Zhang, Zhiqaing Nie, Xiaomeng Li, Yiyu Shi, James Zou*, Meiping Huang*, Jian Zhuang*.
Medical Image Analysis (2023).
A visual–language foundation model for pathology image analysis using medical Twitter. [PDF]
Zhi Huang, Federico Bianchi, Mert Yuksekgonul, Tom Montine, James Zou.
Nature Medicine (2023). Cover article.
Implications of predicting race variables from medical images. [PDF]
James Zou, Judy Gichoya, Daniel Ho, Ziad Obermeyer.
Science (2023).
A deep learning-based electrocardiogram risk score for long term cardiovascular death and disease. [PDF]
Weston Hughes, et al, David Ouyang*, Euan Ashley*, James Zou*, Marco Perez*.
npj Digital Medicine (2023).
Skin Tone Analysis for Representation in Educational Materials (STAR-ED) using machine learning. [PDF]
Girmaw Tadesse, Celia Cintas, Kush Varshney, et al., James Zou*, Roxana Daneshjou*.
npj Digital Medicine (2023).
GPT detectors are biased against non-native English writers. [PDF]
Weixin Liang, Mert Yuksekgonul, Yining Mao, Eric Wu, James Zou.
Patterns (2023).
Beyond Positive Scaling: How Negation Impacts Scaling Trends of Language Models. [PDF]
Yuhui Zhang, Michi Yasunaga, Zhengping Zhou, Z. HaoChen, James Zou, Percy Liang Serena Yeung.
ACL Findings (ACL 2023).
Machine learning modeling of RNA structures: methods, challenges and future perspectives. [PDF]
Kevin Wu, James Zou*, Howard Chang*.
Briefings in Bioinformatics (2023).
Deep learning-based electrocardiographic screening for chronic kidney disease. [PDF]
Lauri Holmstrom, Matthew Christensen, Neal Yuan, Weston Hughes, John Theurer, M. Jujjavarapu, P. Fatehi, A. Kwan, R. Sandhu, J. Ebinger, S. Cheng, James Zou, Sumeet Chugh, David Ouyang.
Communications Medicine (2023).
7-UP: generating in silico CODEX from a small set of immunofluorescence markers. [PDF]
Eric Wu, Alex Trevino, et al, Aaron Mayer, James Zou.
PNAS Nexus (2023).
Who counts as an inventor? Seniority and gender in 430,000 biomedical inventor–researcher teams. [PDF]
Anoop Manjunath, Nathan Kahrobai, Jaya Manjunath, Angelina Seffens, Arya Gowda, Rohaan Umbarkar, Esha Umbarkar, James Zou*, Ishan Kumar*.
Nature Biotechnology (2023).
Brain proteomic analysis implicates actin filament processes and injury response in resilience to Alzheimer’s disease. [PDF]
Zhi Huang, Gennifer Merrihew, Eric Larson, Jea Park, Deanna Plubell, Eddie Fox, Kathy Montine, Caitlin Latimer, C. Keene, James Zou*, Mike MacCoss*, Tom Montine*.
Nature Communications (2023).
Leveraging Physiology and Artificial Intelligence to Deliver Advancements in Health Care. [PDF]
Angela Zhang, Zhenqin Wu, Eric Wu, Matthew Wu, Michael Snyder, James Zou, Joe Wu.
Physiological Review (2023).
Data-OOB: Out-of-bag Estimate as a Simple and Efficient Data Value. [PDF]
Yongchan Kwon, James Zou.
International Conference on Machine Learning (ICML 2023).
Discover and Cure: Concept-aware Mitigation of Spurious Correlation. [PDF]
Shirley Wu, Mert Yuksekgonul, Linjun Zhang, James Zou.
International Conference on Machine Learning (ICML 2023).
On the nonlinear correlation of ML performance between data subpopulations. [PDF]
Weixin Liang, Yining Mao, Yongchan Kwon, Xinyu Yang, James Zou.
International Conference on Machine Learning (ICML 2023).
Data-Driven Subgroup Discovery for Linear Regression. [PDF]
Zach Izzo, Ruishan Liu, James Zou.
International Conference on Machine Learning (ICML 2023).
Collecting data when missingness is unknown: a method for improving model performance given under-reporting in patient populations.
Kevin Wu, Dominik Dahlem, Christopher Hane, Eran Halperin, James Zou.
Conference on Health, Inference and Learning (CHIL 2023).
Understanding and Predicting the Effect of Environmental Factors on People with Type 2 Diabetes.
Kailas Vodrahalli, Gregory Lyng, Brian Hill, Kimmo Karkkainen, Jeffrey Hertzberg, James Zou*, Eran Halperin*.
Conference on Health, Inference and Learning (CHIL 2023).
Easily accessible text-to-image generation amplifies demographic stereotypes at large scale. [PDF]
Federico Bianchi, Pratyusha Kalluri, Esin Durmus, Faisal Ladhak, Myra Cheng, Debora Nozza, Tatsunori Hashimoto, Dan Jurafsky*, James Zou*, Aylin Caliskan*.
ACM Conference on Fairness, Accountability and Transparency (2023).
Blinded, randomized trial of sonographer versus AI cardiac function assessment. [PDF]
Bryan He, Alan Kwan, Jae Cho, Neal Yuan, C. Pollick, T. Shiota, J. Ebinger, N. Bello, J. Wei, K. Josan, G. Duffy, M. Jujjavarapu, R. Siegel, Susan Cheng*, James Zou*, David Ouyang*.
Nature (2023).
From patterns to patients: Advances in clinical machine learning for cancer diagnosis, prognosis, and treatment. [PDF]
Kyle Swanson, Eric Wu, Angela Zhang, Ash Alizadeh, James Zou.
Cell (2023).
AI-enabled assessment of cardiac function and video quality in emergency department point-of-care echocardiograms. [PDF]
Bryan He, Dev Dash, Youyou Duanmu, Ting Xu Tan, David Ouyang, James Zou.
Journal of Emergency Medicine (2023).
Development and clinical evaluation of an AI support tool for improving telemedicine photo quality. [PDF]
Kailas Vodrahalli, Justin Ko, Albert Chiou, Rob Novoa, Abu Abid, Michelle Phung, Kiana Yekrang, Paige Petrone, James Zou*, Roxana Daneshjou*.
JAMA Dermatology (2023).
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput. [PDF]
Jim Eberwine, Junhyong Kim, R. Anafi, S. Brem, M. Bucan, S. Fisher, M. Grady, A. Herr, D. Issadore, H. Jeong, H. Kim, D. Lee, S. Rubakhin, J. Sul, J. Sweedler, J. Wolf, K. Zaret, James Zou.
Nature Methods (2023).
A spectral method for assessing and combining multiple data visualizations. [PDF]
Rong Ma, Eric Sun, James Zou.
Nature Communications (2023). 2023 JSM Outstanding Paper Award
Video-Based Deep Learning for Automated Assessment of Left Ventricular Ejection Fraction in Pediatric Patients. [PDF]
Charitha Reddy, Leo Lopez, David Ouyang*, James Zou*, Bryan He*
Journal of the American Society of Echocardiography (2023).
Post-hoc Concept Bottleneck Models. [PDF]
Mert Yuksekgonul, Maggie Wang, James Zou.
International Conference on Learning Representations (ICLR 2023). Spotlight
When and why Vision-Language Models behave like Bags-of-Words, and what to do about it? [PDF]
Mert Yuksekgonul, Federico Bianchi, Pratyusha Kalluri, Dan Jurafsky, James Zou.
International Conference on Learning Representations (ICLR 2023). Oral/top 5% of accepted papers
FIFA: Making Fairness More Generalizable in Classifiers Trained on Imbalanced Data. [PDF]
Zhun Deng, Jiayao Zhang, Linjun Zhang, Ting Ye, Yates Coley, Weijie J Su, James Zou.
International Conference on Learning Representations (ICLR 2023).
FaiREE: fair classification with finite-sample and distribution-free guarantee. [PDF]
Puheng Li, James Zou, Linjun Zhang.
International Conference on Learning Representations (ICLR 2023).
DrML: Diagnosing and Rectifying Vision Models using Language. [PDF]
Yuhui Zhang, Jeff HaoChen, Shih-Cheng Huang, Kuan-Chieh Wang, James Zou, Serena Yeung.
International Conference on Learning Representations (ICLR 2023).
Freeze then Train: Towards Provable Representation Learning under Spurious Correlations and Feature Noise. [PDF]
Haotian Ye, James Zou*, Linjun Zhang*.
International Conference on AI and Statistics (AISTATS 2023).
Understanding Multimodal Contrastive Learning and Incorporating Unpaired Data. [PDF]
Ryumei Nakada, Halil Gulluk, Zhun Deng, Wenlong Ji, James Zou*, Linjun Zhang*.
International Conference on AI and Statistics (AISTATS 2023).
Analyses of canine cancer mutations and treatment outcomes using real-world clinico-genomics data of 2119 dogs. [PDF]
Kevin Wu, Lucas Rodrigues, Gerald Post, Garrett Harvey, Michelle White, Aubrey Miller, Lindsay Lambert, Ben Lewis, Christina Lopes, James Zou.
npj Precision Oncology (2023).
Dynamic visualization of high dimensional data. [PDF]
Eric Sun, Rong Ma, James Zou.
Nature Computational Science (2023).
2022
Competition over data: how does data purchase affect users? [PDF]
Yongchan Kwon, Tony Ginart, James Zou.
Transactions of Machine Learning Research (2022).
Predicting Immune Escape with Pretrained Protein Language Model Embeddings. [PDF]
Kyle Swanson, Howard Chang, James Zou.
Machine Learning in Computational Biology (PMLR) (2022).
Ensembling improves stability and power of feature selection for deep learning models. [PDF]
Prashnna Gyawali, Xiaoxia Liu, James Zou*, Zihuai He*.
Machine Learning in Computational Biology (PMLR) (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. [PDF]
Weixin Liang, Yuhui Zhang, Yongchan Kwon, Serena Yeung, James Zou.
NeurIPS (2022).
WeightedSHAP: analyzing and improving Shapley-based feature attributions. [PDF]
Yongchan Kwon and James Zou.
NeurIPS (2022).
Uncalibrated Models Can Improve Human-AI Collaboration. [PDF]
Kailas Vodrahalli, Tobi Gerstenberg, James Zou.
NeurIPS (2022).
Estimating and Explaining Model Performance When Both Covariates and Labels Shift. [PDF]
Lingjiao Chen, Matei Zaharia, James Zou.
NeurIPS (2022).
mixReg: A Simple Way to Improve Generalization in Regression for Deep Neural Networks. [PDF]
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. [PDF]
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. [PDF]
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. [PDF]
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).
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.
Interpretation of neural network is fragile. [arXiv]
Amirata Ghorbani, Abubakar Abid, James Zou.
AAAI (2019). Selected for oral presentation.
Improving knockoff stability: simultaneous multiple knockoffs and entropy maximization. [arXiv]
Jaime Gimenez, James Zou.
AISTATS (2019).
Knockoffs for the mass: new feature importance statistics with false discovery guarantees. [arXiv]
Jaime Gimenez, Amirata Ghorbani, James Zou.
AISTATS (2019).
Feedback GAN for DNA optimizes protein functions. [PDF]
Anvita Gupta, James Zou.
Nature Machine Intelligence (2019).
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).
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.
A large CRISPR-induced bystander mutation causes immune dysregulation. [PDF]
Dimitre Simeonov et al.
Communications Biology (2019).
2018
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).
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.
Embedding for missingness: deep learning with incomplete data.
Amirata Ghorbani, James Zou.
IEEE Allerton (2018).
The effects of memory replay in reinforcement learning. [arXiv]
Ruishan Liu and James Zou. Best Poster Award at BayLearn.
IEEE Allerton (2018).
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).
2017
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
NeuralFDR: learning decision threshold from hypothesis features.
Martin Zhang, Fei Xia, James Zou, David Tse.
Neural Information Processing Systems (NIPS 2017).
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).
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).
2016 and earlier
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 (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 (2016).
A genetic and socio-economic study of mate choice in Latinos reveals novel assortment patterns. [PDF] [Press]
James Zou, 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, 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, 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, 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.
International Conference on Machine Learning (ICML 2016).
Controlling bias in adaptive data analysis using information theory. [arXiv]
Daniel Russo, James Zou.
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.
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.
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).