STAIR

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2023

Integration of 168,000 samples reveals global patterns of the human gut microbiome
Integration of 168,000 samples reveals global patterns of the human gut microbiome
Richard J. Abdill, Samantha P. Graham, Vincent Rubinetti, Frank W. Albert, Casey S. Greene, Sean Davis, Ran Blekhman
Cold Spring Harbor Laboratory   ·   11 Oct 2023   ·   doi:10.1101/2023.10.11.560955
Latent Multimodal Functional Graphical Model Estimation
Latent Multimodal Functional Graphical Model Estimation
Katherine Tsai, Boxin Zhao, Sanmi Koyejo, Mladen Kolar
arXiv   ·   03 Oct 2023   ·   arXiv:2210.17237
Diagnosing failures of fairness transfer across distribution shift in real-world medical settings
Diagnosing failures of fairness transfer across distribution shift in real-world medical settings
Jessica Schrouff, Natalie Harris, Oluwasanmi Koyejo, Ibrahim Alabdulmohsin, Eva Schnider, ..., Vivek Natarajan, Alan Karthikesalingam, Katherine Heller, Silvia Chiappa, Alexander D'Amour
arXiv   ·   19 Jun 2023   ·   arXiv:2202.01034
Federated Auto-weighted Domain Adaptation
Federated Auto-weighted Domain Adaptation
Enyi Jiang, Yibo Jacky Zhang, Oluwasanmi Koyejo
arXiv   ·   01 Jun 2023   ·   arXiv:2302.05049
Are Emergent Abilities of Large Language Models a Mirage?
Are Emergent Abilities of Large Language Models a Mirage?
Rylan Schaeffer, Brando Miranda, Sanmi Koyejo
arXiv   ·   23 May 2023   ·   arXiv:2304.15004
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes
Ricardo Avila, Vincent Rubinetti, Xinghua Zhou, Dongbo Hu, Zhongchao Qian, Marco Alvarado Cano, Everaldo Rodolpho, Ginger Tsueng, Casey Greene, Chunlei Wu
Nucleic Acids Research   ·   18 Apr 2023   ·   doi:10.1093/nar/gkad289
Double Descent Demystified: Identifying, Interpreting & Ablating the Sources of a Deep Learning Puzzle
Double Descent Demystified: Identifying, Interpreting & Ablating the Sources of a Deep Learning Puzzle
Rylan Schaeffer, Mikail Khona, Zachary Robertson, Akhilan Boopathy, Kateryna Pistunova, Jason W. Rocks, Ila Rani Fiete, Oluwasanmi Koyejo
arXiv   ·   27 Mar 2023   ·   arXiv:2303.14151
One Policy is Enough: Parallel Exploration with a Single Policy is Near-Optimal for Reward-Free Reinforcement Learning
One Policy is Enough: Parallel Exploration with a Single Policy is Near-Optimal for Reward-Free Reinforcement Learning
Pedro Cisneros-Velarde, Boxiang Lyu, Sanmi Koyejo, Mladen Kolar
arXiv   ·   03 Mar 2023   ·   arXiv:2205.15891
Hetnet connectivity search provides rapid insights into how two biomedical entities are related
Hetnet connectivity search provides rapid insights into how two biomedical entities are related
Daniel S. Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J. Heil, ..., David N. Nicholson, Yun Hao, Blair D. Sullivan, Michael W. Nagle, Casey S. Greene
Cold Spring Harbor Laboratory   ·   07 Jan 2023   ·   doi:10.1101/2023.01.05.522941

2022

Hetnet connectivity search provides rapid insights into how biomedical entities are related
Hetnet connectivity search provides rapid insights into how biomedical entities are related
Daniel S Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J Heil, ..., David N Nicholson, Yun Hao, Blair D Sullivan, Michael W Nagle, Casey S Greene
GigaScience   ·   28 Dec 2022   ·   doi:10.1093/gigascience/giad047
Adapting to Latent Subgroup Shifts via Concepts and Proxies
Adapting to Latent Subgroup Shifts via Concepts and Proxies
Ibrahim Alabdulmohsin, Nicole Chiou, Alexander D'Amour, Arthur Gretton, Sanmi Koyejo, Matt J. Kusner, Stephen R. Pfohl, Olawale Salaudeen, Jessica Schrouff, Katherine Tsai
arXiv   ·   22 Dec 2022   ·   arXiv:2212.11254
Fair Wrapping for Black-box Predictions
Fair Wrapping for Black-box Predictions
Alexander Soen, Ibrahim Alabdulmohsin, Sanmi Koyejo, Yishay Mansour, Nyalleng Moorosi, Richard Nock, Ke Sun, Lexing Xie
arXiv   ·   03 Nov 2022   ·   arXiv:2201.12947
A Reduction to Binary Approach for Debiasing Multiclass Datasets
A Reduction to Binary Approach for Debiasing Multiclass Datasets
Ibrahim Alabdulmohsin, Jessica Schrouff, Oluwasanmi Koyejo
arXiv   ·   11 Oct 2022   ·   arXiv:2205.15860
Quadratic Metric Elicitation for Fairness and Beyond
Quadratic Metric Elicitation for Fairness and Beyond
Gaurush Hiranandani, Jatin Mathur, Harikrishna Narasimhan, Oluwasanmi Koyejo
arXiv   ·   23 Aug 2022   ·   arXiv:2011.01516
Adversarially Robust Models may not Transfer Better: Sufficient Conditions for Domain Transferability from the View of Regularization
Adversarially Robust Models may not Transfer Better: Sufficient Conditions for Domain Transferability from the View of Regularization
Xiaojun Xu, Jacky Yibo Zhang, Evelyn Ma, Danny Son, Oluwasanmi Koyejo, Bo Li
arXiv   ·   27 Jun 2022   ·   arXiv:2202.01832
MolEvolvR: A web-app for characterizing proteins using molecular evolution and phylogeny
MolEvolvR: A web-app for characterizing proteins using molecular evolution and phylogeny
Jacob D Krol, Joseph T Burke, Samuel Z Chen, Lo Sosinski, Faisal S Alquaddoomi, ..., Vince P Rubinetti, Shaddai Amolitos, Kellen M Reason, John B Johnston, Janani Ravi
Cold Spring Harbor Laboratory   ·   22 Feb 2022   ·   doi:10.1101/2022.02.18.461833

2021

A Nonconvex Framework for Structured Dynamic Covariance Recovery
A Nonconvex Framework for Structured Dynamic Covariance Recovery
Katherine Tsai, Mladen Kolar, Oluwasanmi Koyejo
arXiv   ·   20 Jul 2021   ·   arXiv:2011.05601
Uncovering the Connections Between Adversarial Transferability and Knowledge Transferability
Uncovering the Connections Between Adversarial Transferability and Knowledge Transferability
Kaizhao Liang, Jacky Y. Zhang, Boxin Wang, Zhuolin Yang, Oluwasanmi Koyejo, Bo Li
arXiv   ·   12 Jul 2021   ·   arXiv:2006.14512
Optimizing Black-box Metrics with Iterative Example Weighting
Optimizing Black-box Metrics with Iterative Example Weighting
Gaurush Hiranandani, Jatin Mathur, Harikrishna Narasimhan, Mahdi Milani Fard, Oluwasanmi Koyejo
arXiv   ·   25 Jun 2021   ·   arXiv:2102.09492
Advances and Open Problems in Federated Learning
Advances and Open Problems in Federated Learning
Peter Kairouz, H. Brendan McMahan, Brendan Avent, Aurélien Bellet, Mehdi Bennis, ..., Zheng Xu, Qiang Yang, Felix X. Yu, Han Yu, Sen Zhao
arXiv   ·   10 Mar 2021   ·   arXiv:1912.04977
Bayesian Coresets: Revisiting the Nonconvex Optimization Perspective
Bayesian Coresets: Revisiting the Nonconvex Optimization Perspective
Jacky Y. Zhang, Rajiv Khanna, Anastasios Kyrillidis, Oluwasanmi Koyejo
arXiv   ·   01 Mar 2021   ·   arXiv:2007.00715
EMIXER: End-to-end Multimodal X-ray Generation via Self-supervision
EMIXER: End-to-end Multimodal X-ray Generation via Self-supervision
Siddharth Biswal, Peiye Zhuang, Ayis Pyrros, Nasir Siddiqui, Sanmi Koyejo, Jimeng Sun
arXiv   ·   19 Jan 2021   ·   arXiv:2007.05597

2020

Local AdaAlter: Communication-Efficient Stochastic Gradient Descent with Adaptive Learning Rates
Local AdaAlter: Communication-Efficient Stochastic Gradient Descent with Adaptive Learning Rates
Cong Xie, Oluwasanmi Koyejo, Indranil Gupta, Haibin Lin
arXiv   ·   08 Dec 2020   ·   arXiv:1911.09030
CSER: Communication-efficient SGD with Error Reset
CSER: Communication-efficient SGD with Error Reset
Cong Xie, Shuai Zheng, Oluwasanmi Koyejo, Indranil Gupta, Mu Li, Haibin Lin
arXiv   ·   08 Dec 2020   ·   arXiv:2007.13221
Open collaborative writing with Manubot
Open collaborative writing with Manubot
Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
PLOS Computational Biology   ·   04 Dec 2020   ·   doi:10.1371/journal.pcbi.1007128
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Manubot
Manuscript Source
Website
open science collaboration
Fair Performance Metric Elicitation
Fair Performance Metric Elicitation
Gaurush Hiranandani, Harikrishna Narasimhan, Oluwasanmi Koyejo
arXiv   ·   04 Nov 2020   ·   arXiv:2006.12732
Fairness with Overlapping Groups
Fairness with Overlapping Groups
Forest Yang, Moustapha Cisse, Sanmi Koyejo
arXiv   ·   25 Jun 2020   ·   arXiv:2006.13485
Toward a Controllable Disentanglement Network
Toward a Controllable Disentanglement Network
Zengjie Song, Oluwasanmi Koyejo, Jiangshe Zhang
arXiv   ·   23 Jun 2020   ·   arXiv:2001.08572
Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene
Genome Biology   ·   11 May 2020   ·   doi:10.1186/s13059-020-02021-3
Learning Sparse Distributions using Iterative Hard Thresholding
Learning Sparse Distributions using Iterative Hard Thresholding
Jacky Y. Zhang, Rajiv Khanna, Anastasios Kyrillidis, Oluwasanmi Koyejo
arXiv   ·   03 Feb 2020   ·   arXiv:1910.13389
Constructing knowledge graphs and their biomedical applications
Constructing knowledge graphs and their biomedical applications
David N. Nicholson, Casey S. Greene
Computational and Structural Biotechnology Journal   ·   01 Jan 2020   ·   doi:10.1016/j.csbj.2020.05.017

2019

Consistent Classification with Generalized Metrics
Consistent Classification with Generalized Metrics
Xiaoyan Wang, Ran Li, Bowei Yan, Oluwasanmi Koyejo
arXiv   ·   27 Aug 2019   ·   arXiv:1908.09057
FMRI data augmentation via synthesis
FMRI data augmentation via synthesis
Peiye Zhuang, Alexander G. Schwing, Sanmi Koyejo
arXiv   ·   16 Jul 2019   ·   arXiv:1907.06134
Max-Sliced Wasserstein Distance and its use for GANs
Max-Sliced Wasserstein Distance and its use for GANs
Ishan Deshpande, Yuan-Ting Hu, Ruoyu Sun, Ayis Pyrros, Nasir Siddiqui, Sanmi Koyejo, Zhizhen Zhao, David Forsyth, Alexander Schwing
arXiv   ·   12 Apr 2019   ·   arXiv:1904.05877
Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality
Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality
Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene
Cold Spring Harbor Laboratory   ·   11 Mar 2019   ·   doi:10.1101/573782

2018

Sci-Hub provides access to nearly all scholarly literature
Sci-Hub provides access to nearly all scholarly literature
Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S Greene
eLife   ·   01 Mar 2018   ·   doi:10.7554/eLife.32822