Patrick Flaherty

According to our database, Patrick Flaherty authored at least 21 papers between 2005 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Maximum a Posteriori Inference for Factor Graphs via Benders' Decomposition.

Harsh Vardhan Dubey, Ji Ah Lee, Patrick Flaherty

CoRR, 2024

Doubly Non-Central Beta Matrix Factorization for Stable Dimensionality Reduction of Bounded Support Matrix Data.

Anjali Nagulpally, Patrick Flaherty, Aaron Schein

CoRR, 2024

2023

Identification of significant gene expression changes in multiple perturbation experiments using knockoffs.

Tingting Zhao, Guangyu Zhu, Harsh Vardhan Dubey, Patrick Flaherty

Briefings Bioinform., March, 2023

2022

Model-based identification of conditionally-essential genes from transposon-insertion sequencing data.

Vishal Kumar Sarsani, Berent Aldikacti, Shai He, Rilee Zeinert, Peter Chien, Patrick Flaherty

PLoS Comput. Biol., 2022

Cost-aware Generalized α-investing for Multiple Hypothesis Testing.

Thomas Cook, Harsh Vardhan Dubey, Ji Ah Lee, Guangyu Zhu, Tingting Zhao, Patrick Flaherty

CoRR, 2022

2021

Doubly non-central beta matrix factorization for DNA methylation data.

Aaron Schein, Anjali Nagulpally, Hanna M. Wallach, Patrick Flaherty

Proceedings of the Thirty-Seventh Conference on Uncertainty in Artificial Intelligence, 2021

Exact and approximate hierarchical clustering using A.

Craig S. Greenberg, Sebastian Macaluso, Nicholas Monath, Avinava Dubey, Patrick Flaherty, Manzil Zaheer, Amr Ahmed, Kyle Cranmer, Andrew McCallum

Proceedings of the Thirty-Seventh Conference on Uncertainty in Artificial Intelligence, 2021

Cluster Trellis: Data Structures & Algorithms for Exact Inference in Hierarchical Clustering.

Sebastian Macaluso, Craig S. Greenberg, Nicholas Monath, Ji Ah Lee, Patrick Flaherty, Kyle Cranmer, Andrew McGregor, Andrew McCallum

Proceedings of the 24th International Conference on Artificial Intelligence and Statistics, 2021

2020

Compact Representation of Uncertainty in Hierarchical Clustering.

Craig S. Greenberg, Sebastian Macaluso, Nicholas Monath, Ji Ah Lee, Patrick Flaherty, Kyle Cranmer, Andrew McGregor, Andrew McCallum

CoRR, 2020

SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data.

Collin Giguere, Harsh Vardhan Dubey, Vishal Kumar Sarsani, Hachem Saddiki, Shai He, Patrick Flaherty

BMC Bioinform., 2020

2019

Maximum a-Posteriori Estimation for the Gaussian Mixture Model via Mixed Integer Nonlinear Programming.

Patrick Flaherty, Pitchaya Wiratchotisatian, Ji Ah Lee, Andrew C. Trapp

CoRR, 2019

2018

Recovering all generalized order-preserving submatrices: new exact formulations and algorithms.

Andrew C. Trapp, Chao Li, Patrick Flaherty

Ann. Oper. Res., 2018

Compact Representation of Uncertainty in Clustering.

Craig S. Greenberg, Nicholas Monath, Ari Kobren, Patrick Flaherty, Andrew McGregor, Andrew McCallum

Proceedings of the Advances in Neural Information Processing Systems 31: Annual Conference on Neural Information Processing Systems 2018, 2018

2017

Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data.

Fan Zhang, Patrick Flaherty

BMC Bioinform., 2017

2016

GEMINI: a computationally-efficient search engine for large gene expression datasets.

Timothy DeFreitas, Hachem Saddiki, Patrick Flaherty

BMC Bioinform., 2016

2015

Robust Optimization of Biological Protocols.

Patrick Flaherty, Ronald W. Davis

Technometrics, 2015

GLAD: a mixed-membership model for heterogeneous tumor subtype classification.

Hachem Saddiki, Jon McAuliffe, Patrick Flaherty

Bioinform., 2015

RVD2: an ultra-sensitive variant detection model for low-depth heterogeneous next-generation sequencing data.

Yuting He, Fan Zhang, Patrick Flaherty

Bioinform., 2015

2008

A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction.

Patrick Flaherty, Mala L. Radhakrishnan, Tuan Dinh, Robert A. Rebres, Tamara I. Roach, Michael I. Jordan, Adam P. Arkin

PLoS Comput. Biol., 2008

2005

A latent variable model for chemogenomic profiling.

Patrick Flaherty, Guri Giaever, Jochen Kumm, Michael I. Jordan, Adam P. Arkin

Bioinform., 2005

Robust design of biological experiments.

Patrick Flaherty, Michael I. Jordan, Adam P. Arkin

Proceedings of the Advances in Neural Information Processing Systems 18 [Neural Information Processing Systems, 2005