Patrick Flaherty

24 papers A* 1A 3Journal 19Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
Maximum a Posteriori Inference for Factor Graphs via Benders' Decomposition.
SIAM J. Math. Data Sci.
Harsh Vardhan Dubey, Ji Ah Lee, Patrick Flaherty
2024 J jnl
Doubly Non-Central Beta Matrix Factorization for Stable Dimensionality Reduction of Bounded Support Matrix Data.
CoRR
Anjali Nagulpally, Patrick Flaherty, Aaron Schein
2024 J jnl
Maximum a Posteriori Inference for Factor Graphs via Benders' Decomposition.
CoRR
Harsh Vardhan Dubey, Ji Ah Lee, Patrick Flaherty
2023 J jnl
Identification of significant gene expression changes in multiple perturbation experiments using knockoffs.
Briefings Bioinform.
Tingting Zhao, Guangyu Zhu, Harsh Vardhan Dubey, Patrick Flaherty
2022 J jnl
Cost-aware Generalized α-investing for Multiple Hypothesis Testing.
CoRR
Thomas Cook, Harsh Vardhan Dubey, Ji Ah Lee, Guangyu Zhu, Tingting Zhao, Patrick Flaherty
2022 J jnl
Model-based identification of conditionally-essential genes from transposon-insertion sequencing data.
PLoS Comput. Biol.
Vishal Kumar Sarsani, Berent Aldikacti, Shai He, Rilee Zeinert, Peter Chien, Patrick Flaherty
2021 A conf
Cluster Trellis: Data Structures & Algorithms for Exact Inference in Hierarchical Clustering.
AISTATS
Sebastian Macaluso, Craig S. Greenberg, Nicholas Monath, Ji Ah Lee, Patrick Flaherty, Kyle Cranmer, Andrew McGregor, Andrew McCallum
2021 J jnl
Doubly Non-Central Beta Matrix Factorization for DNA Methylation Data.
CoRR
Aaron Schein, Anjali Nagulpally, Hanna M. Wallach, Patrick Flaherty
2021 A conf
Doubly non-central beta matrix factorization for DNA methylation data.
UAI
Aaron Schein, Anjali Nagulpally, Hanna M. Wallach, Patrick Flaherty
2021 J jnl
Exact and Approximate Hierarchical Clustering Using A.
CoRR
Craig S. Greenberg, Sebastian Macaluso, Nicholas Monath, Avinava Dubey, Patrick Flaherty, Manzil Zaheer, Amr Ahmed, Kyle Cranmer, Andrew McCallum
2021 A conf
Exact and approximate hierarchical clustering using A.
UAI
Craig S. Greenberg, Sebastian Macaluso, Nicholas Monath, Avinava Dubey, Patrick Flaherty, Manzil Zaheer, Amr Ahmed, Kyle Cranmer, Andrew McCallum
2020 J jnl
Compact Representation of Uncertainty in Hierarchical Clustering.
CoRR
Craig S. Greenberg, Sebastian Macaluso, Nicholas Monath, Ji Ah Lee, Patrick Flaherty, Kyle Cranmer, Andrew McGregor, Andrew McCallum
2020 J jnl
SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data.
BMC Bioinform.
Collin Giguere, Harsh Vardhan Dubey, Vishal Kumar Sarsani, Hachem Saddiki, Shai He, Patrick Flaherty
2019 J jnl
Maximum a-Posteriori Estimation for the Gaussian Mixture Model via Mixed Integer Nonlinear Programming.
CoRR
Patrick Flaherty, Pitchaya Wiratchotisatian, Ji Ah Lee, Andrew C. Trapp
2018 A* conf
Compact Representation of Uncertainty in Clustering.
NeurIPS
Craig S. Greenberg, Nicholas Monath, Ari Kobren, Patrick Flaherty, Andrew McGregor, Andrew McCallum
2018 J jnl
Recovering all generalized order-preserving submatrices: new exact formulations and algorithms.
Ann. Oper. Res.
Andrew C. Trapp, Chao Li, Patrick Flaherty
2017 J jnl
Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data.
BMC Bioinform.
Fan Zhang, Patrick Flaherty
2016 J jnl
GEMINI: a computationally-efficient search engine for large gene expression datasets.
BMC Bioinform.
Timothy DeFreitas, Hachem Saddiki, Patrick Flaherty
2015 J jnl
GLAD: a mixed-membership model for heterogeneous tumor subtype classification.
Bioinform.
Hachem Saddiki, Jon McAuliffe, Patrick Flaherty
2015 J jnl
RVD2: an ultra-sensitive variant detection model for low-depth heterogeneous next-generation sequencing data.
Bioinform.
Yuting He, Fan Zhang, Patrick Flaherty
2015 J jnl
Robust Optimization of Biological Protocols.
Technometrics
Patrick Flaherty, Ronald W. Davis
2008 J jnl
A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction.
PLoS Comput. Biol.
Patrick Flaherty, Mala L. Radhakrishnan, Tuan Dinh, Robert A. Rebres, Tamara I. Roach, Michael I. Jordan, Adam P. Arkin
2005 J jnl
A latent variable model for chemogenomic profiling.
Bioinform.
Patrick Flaherty, Guri Giaever, Jochen Kumm, Michael I. Jordan, Adam P. Arkin
2005 — conf
Robust design of biological experiments.
NIPS
Patrick Flaherty, Michael I. Jordan, Adam P. Arkin