Patrick Flaherty

Publication Activity (10 Years)

Years Active: 2005-2023
Publications (10 Years): 15

Top Topics

Gene Expression Datasets

Hierarchical Clustering Algorithm

Hypothesis Test

Exact And Approximate

Top Venues

Publications

Tingting Zhao, Guangyu Zhu, Harsh Vardhan Dubey, Patrick Flaherty
Identification of significant gene expression changes in multiple perturbation experiments using knockoffs. Briefings Bioinform. 24 (2) (2023)
Vishal Kumar Sarsani, Berent Aldikacti, Shai He, Rilee Zeinert, Peter Chien, Patrick Flaherty
Model-based identification of conditionally-essential genes from transposon-insertion sequencing data. PLoS Comput. Biol. 18 (3) (2022)
Thomas Cook, Harsh Vardhan Dubey, Ji Ah Lee, Guangyu Zhu, Tingting Zhao, Patrick Flaherty
Cost-aware Generalized α-investing for Multiple Hypothesis Testing. CoRR (2022)
Sebastian Macaluso, Craig S. Greenberg, Nicholas Monath, Ji Ah Lee, Patrick Flaherty, Kyle Cranmer, Andrew McGregor, Andrew McCallum
Cluster Trellis: Data Structures & Algorithms for Exact Inference in Hierarchical Clustering. AISTATS (2021)
Aaron Schein, Anjali Nagulpally, Hanna M. Wallach, Patrick Flaherty
Doubly Non-Central Beta Matrix Factorization for DNA Methylation Data. CoRR (2021)
Aaron Schein, Anjali Nagulpally, Hanna M. Wallach, Patrick Flaherty
Doubly non-central beta matrix factorization for DNA methylation data. UAI (2021)
Craig S. Greenberg, Sebastian Macaluso, Nicholas Monath, Avinava Dubey, Patrick Flaherty, Manzil Zaheer, Amr Ahmed, Kyle Cranmer, Andrew McCallum
Exact and approximate hierarchical clustering using A. UAI (2021)
Craig S. Greenberg, Sebastian Macaluso, Nicholas Monath, Avinava Dubey, Patrick Flaherty, Manzil Zaheer, Amr Ahmed, Kyle Cranmer, Andrew McCallum
Exact and Approximate Hierarchical Clustering Using A. CoRR (2021)
Craig S. Greenberg, Sebastian Macaluso, Nicholas Monath, Ji Ah Lee, Patrick Flaherty, Kyle Cranmer, Andrew McGregor, Andrew McCallum
Compact Representation of Uncertainty in Hierarchical Clustering. CoRR (2020)
Collin Giguere, Harsh Vardhan Dubey, Vishal Kumar Sarsani, Hachem Saddiki, Shai He, Patrick Flaherty
SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data. BMC Bioinform. 21 (1) (2020)
Patrick Flaherty, Pitchaya Wiratchotisatian, Ji Ah Lee, Andrew C. Trapp
Maximum a-Posteriori Estimation for the Gaussian Mixture Model via Mixed Integer Nonlinear Programming. CoRR (2019)
Craig S. Greenberg, Nicholas Monath, Ari Kobren, Patrick Flaherty, Andrew McGregor, Andrew McCallum
Compact Representation of Uncertainty in Clustering. NeurIPS (2018)
Andrew C. Trapp, Chao Li, Patrick Flaherty
Recovering all generalized order-preserving submatrices: new exact formulations and algorithms. Ann. Oper. Res. 263 (1-2) (2018)
Fan Zhang, Patrick Flaherty
Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data. BMC Bioinform. 18 (1) (2017)
Timothy DeFreitas, Hachem Saddiki, Patrick Flaherty
GEMINI: a computationally-efficient search engine for large gene expression datasets. BMC Bioinform. 17 (2016)
Hachem Saddiki, Jon McAuliffe, Patrick Flaherty
GLAD: a mixed-membership model for heterogeneous tumor subtype classification. Bioinform. 31 (2) (2015)
Yuting He, Fan Zhang, Patrick Flaherty
RVD2: an ultra-sensitive variant detection model for low-depth heterogeneous next-generation sequencing data. Bioinform. 31 (17) (2015)
Patrick Flaherty, Ronald W. Davis
Robust Optimization of Biological Protocols. Technometrics 57 (2) (2015)
Patrick Flaherty, Mala L. Radhakrishnan, Tuan Dinh, Robert A. Rebres, Tamara I. Roach, Michael I. Jordan, Adam P. Arkin
A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction. PLoS Comput. Biol. 4 (9) (2008)
Patrick Flaherty, Guri Giaever, Jochen Kumm, Michael I. Jordan, Adam P. Arkin
A latent variable model for chemogenomic profiling. Bioinform. 21 (15) (2005)
Patrick Flaherty, Michael I. Jordan, Adam P. Arkin
Robust design of biological experiments. NIPS (2005)