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PETRI: Learning Unified Cell Embeddings from Unpaired Modalities via Early-Fusion Joint Reconstruction

Conference paper
Ryan W Conrad, Ethan Weinberger, Saradha Venkatachalapathy, Yuwen Chen, Darshini Shah, Bay Johnson, Max R Salick, Vaishaali Natarajan, Emily Fox
To appear International Conference on Learning Representations (ICLR)
Publication year: 2026

PertSpectra: Interpretable Matrix Factorization for Predicting Functional Impact of Genetic Perturbation Experiments

Conference paper
Seowon Chang, Anna Shcherbina, Tal Ashuach, Shahin Mohammadi, Stephanie See, Ninad Ranadive, Emily Fox, Navpreet Ranu
Pacific Symposium on Biocomputing
Publication year: 2026

KinDEL: DNA-Encoded Library Dataset for Kinase Inhibitors

Conference paper
Benson Chen, Tomasz Danel, Gabriel H. S. Dreiman, Patrick J. McEnaney, Nikhil Jain, Kirill Novikov, Spurti Umesh Akki, Joshua L. Turnbull, Virja Atul Pandya, Boris P. Belotserkovskii, Jared Bryce Weaver, Ankita Biswas, Dat Nguyen, Kent Gorday, Mohammad Sultan, Nathaniel Stanley, Daniel M Whalen, Divya Kanichar, Christoph Klein, Emily Fox, R. Edward Watts
International Conference on Machine Learning (ICML)
Publication year: 2025

HDP-Flow: Generalizable Bayesian Nonparametric Model for Time Series State Discovery

Conference paper
Sana Tonekaboni, Tina Behrouzi, Addison Weatherhead, Emily Fox, David Blei, Anna Goldenberg
Proc. Conference on Uncertainty in Artificial Intelligence
Publication year: 2025

Learning Explainable Treatment Policies with Clinician-Informed Representations: A Practical Approach

Conference paper
Johannes O. Ferstad, Emily B. Fox, David Scheinker, Ramesh Johari
Machine Learning for Health (ML4H) Symposium
Publication year: 2024

Hybrid^2 Neural ODE Causal Modeling and an Application to Glycemic Response

Conference paper
Bob Junyi Zou, Matthew E. Levine, Dessi P. Zaharieva, Ramesh Johari, Emily B. Fox
International Conference on Machine Learning (ICML)
Publication year: 2024

Automated Statistical Model Discovery with Language Models

Conference paper
Michael Y. Li, Emily B. Fox, Noah D. Goodman
International Conference on Machine Learning (ICML)
Publication year: 2024

Sequence Modeling with Multiresolution Convolutional Memory

Conference paper
Jiaxin Shi, Ke Alex Wang, Emily B. Fox
International Conference on Machine Learning (ICML)
Publication year: 2023

Interpretable Mechanistic Representations for Meal-level Glycemic Control in the Wild

Conference paper
Ke Alexander Wang and Emily B. Fox
Machine Learning for Health (ML4H) Symposium
Publication year: 2023

Model-based metrics: Sample-efficient estimates of predictive model subpopulation performance

Conference paper
Andrew C. Miller, Leon A. Gatys, Joseph Futoma, Emily B. Fox
Proceedings of Machine Learning for Healthcare (MLHC)
Publication year: 2021

Learning Insulin-Glucose Dynamics in the Wild

Conference paper
Andrew Miller, Nicholas Foti, and Emily B. Fox
Proceedings of Machine Learning for Healthcare (MLHC)
Publication year: 2020

Adaptively Truncating Backpropagation Through Time to Control Gradient Bias

Conference paper
Christopher Aicher, Nicholas Foti, and Emily B. Fox
Proc. Conference on Uncertainty in Artificial Intelligence
Publication year: 2019

A Simple Adaptive Tracker with Reminiscences

Conference paper
Christopher Xie, Emily Fox, and Zaid Harchaoui
Proc. IEEE International Conference on Robotics and Automation
Publication year: 2019

oi-VAE: Output Interpretable VAEs for Nonlinear Group Factor Analysis

Conference paper
Samuel Ainsworth, Nicholas Foti, Adrian KC Lee, Emily B. Fox
International Conference on Machine Learning (ICML)
Publication year: 2018

Large-Scale Stochastic Sampling from the Probability Simplex

Conference paper
Jack Baker, Paul Fearnhead, Emily B. Fox, and Chris Nemeth
Advances in Neural Information Processing Systems 31 (NeurIPS 2018)
Publication year: 2018

Stochastic Gradient MCMC Methods for Hidden Markov Models

Conference paper
Yi-An Ma, Nicholas Foti, & Emily B. Fox
International Conference on Machine Learning (ICML)
Publication year: 2017

A Complete Recipe for Stochastic Gradient MCMC

Conference paper
Yi-An Ma, Tianqi Chen, & Emily B. Fox
Advances in Neural Information Processing Systems 28 (NIPS 2015)
Publication year: 2016

Streaming Variational Inference for Bayesian Nonparametric Mixture Models

Conference paper
Alex Tank, Nicholas Foti, & Emily B. Fox
International Conference on Artificial Intelligence and Statistics (AISTATS)
Publication year: 2015

Stochastic Variational Inference for Hidden Markov Models

Conference paper
Nicholas Foti, Jason Xu, Dillon Laird, & Emily B. Fox
Advances in Neural Information Processing Systems 27 (NIPS 2014)
Publication year: 2015

Expectation-Maximization for Learning Determinantal Point Processes

Conference paper
Jennifer Gillenwater, Alex Kuleza, Emily B. Fox, & Ben Taskar
Advances in Neural Information Processing Systems 27 (NIPS 2014)
Publication year: 2015

Bayesian Structure Learning for Stationary Time Series

Conference paper
Alex Tank, Nicholas Foti, & Emily B. Fox
Conference on Uncertainty in Artificial Intelligence (UAI)
Publication year: 2015

Stochastic Gradient Hamiltonian Monte Carlo

Conference paper
Tianqi Chen, Emily B. Fox, & Carlos E. Guestrin
International Conference on Machine Learning (ICML)
Publication year: 2014

Learning the Parameters of Determinantal Point Process Kernels

Conference paper
Raja Hafiz Affandi, Emily B. Fox, Ryan P. Adams, & Ben Taskar
International Conference on Machine Learning (ICML)
Publication year: 2014

Approximate Inference in Continuous Determinant Point Processes

Conference paper
Raja H. Affandi, Emily B. Fox, & Ben Taskar
Advances in Neural Information Processing Systems 26 (NIPS 2013)
Publication year: 2014

Representing Documents Through Their Readers

Conference paper
Khalid El-Arini, Min Xu, Emily B. Fox, & Carlos E. Guestrin
Conference on Knowledge Discovery and Data Mining (KDD)
Publication year: 2013

Parsing Epileptic Events Using a Markov Switching Process Model for Correlated Time Series

Conference paper
Drausin Wulsin, Emily B. Fox, & Brian Litt
International Conference on Machine Learning (ICML)
Publication year: 2013

Nystrom Approximation for Large-Scale Determinantal Processes

Conference paper
Raja H. Affandi, Alex Kulesza, Emily B. Fox, & Ben Taskar
International Conference on Artificial Intelligence and Statistics (AISTATS)
Publication year: 2013

Multiresolution Gaussian Processes

Conference paper
Emily B. Fox and David B. Dunson
Advances in Neural Information Processing Systems 25 (NIPS 2012)
Publication year: 2013

Effective Split-Merge Monte Carlo Methods for Nonparametric Models of Sequence Data

Conference paper
Michael C. Hughes, Emily B. Fox, & Erik B. Sudderth
Advances in Neural Information Processing Systems 25 (NIPS 2012)
Publication year: 2013

Markov Determinantal Point Processes

Conference paper
Raja H. Affandi, Alex Kulesza, & Emily B. Fox
Conference on Uncertainty in Artificial Intelligence (UAI)
Publication year: 2012

Hierarchical Latent Dictionaries for Models of Brain Activation

Conference paper
Alona M. Fyshe, Emily B. Fox, David B. Dunson, & Tom M. Mitchell
International Conference on Artificial Intelligence and Statistics (AISTATS)
Publication year: 2012

Sharing Features among Dynamical Systems with Beta Processes

Conference paper
Emily B. Fox, Erik B. Sudderth, Michael I. Jordan, & Alan S. Willsky
Advances in Neural Information Processing Systems 22 (NIPS 2009)
Publication year: 2010

Nonparametric Bayesian Learning of Switching Linear Dynamical Systems

Conference paper
Emily B. Fox, Erik B. Sudderth, Michael I. Jordan, & Alan S. Willsky
Advances in Neural Information Processing Systems 21 (NIPS 2008)
Publication year: 2009

Nonparametric Bayesian Identification of Jump Systems with Sparse Dependencies

Conference paper
Emily B. Fox, Erik B. Sudderth, Michael I. Jordan, & Alan S. Willsky
IFAC Symposium on System Identification
Publication year: 2009

An HDP-HMM for Systems with State Persistence

Conference paper
Emily B. Fox, Erik B. Sudderth, Michael I. Jordan, & Alan S. Willsky
International Conference on Machine Learning (ICML)
Publication year: 2008

Tracking a Non-cooperative Maneuvering Target using Hierarchical Dirichlet Processes

Conference paper
E.B. Fox, E.B. Sudderth, D.S. Choi, A.S. Willsky
Adaptive Sensor Array Processing Conference
Publication year: 2007

Hierarchical Dirichlet Processes for Tracking Maneuvering Targets

Conference paper
Emily B. Fox, Erik B. Sudderth, & Alan S. Willsky
International Conference on Information Fusion (FUSION)
Publication year: 2007

Nonparametric Bayesian Methods for Large Scale Multi-Target Tracking

Conference paper
Emily B. Fox, David S. Choi, & Alan S. Willsky
Asilomar Conference On Signals, Systems, and Computers
Publication year: 2006

Detection and Localization of Material Releases with Sparse Sensor Configurations

Conference paper
Emily B. Fox, Jason L. Williams, John W. Fisher, & Alan S. Willsky
IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP)
Publication year: 2006