Susan P. Holmes

Publication Activity (10 Years)

Years Active: 1997-2022
Publications (10 Years): 21

Top Topics

High Dimensional Datasets

Similarity Metric

Dimensionality Reduction

Top Venues

PLoS Comput. Biol.

Publications

Laura Symul, Susan P. Holmes
Labeling Self-Tracked Menstrual Health Records With Hidden Semi-Markov Models. IEEE J. Biomed. Health Informatics 26 (3) (2022)
Christof Seiler, Anne-Maud Ferreira, Lisa M. Kronstad, Laura J. Simpson, Mathieu Le Gars, Elena Vendrame, Catherine A. Blish, Susan P. Holmes
CytoGLMM: conditional differential analysis for flow and mass cytometry experiments. BMC Bioinform. 22 (1) (2021)
Nina Miolane, Nicolas Guigui, Hadi Zaatiti, Christian Shewmake, Hatem Hajri, Daniel Brooks, Alice Le Brigant, Johan Mathe, Benjamin Hou, Yann Thanwerdas, Stefan Heyder, Olivier Peltre, Niklas Koep, Yann Cabanes, Thomas Gerald, Paul Chauchat, Bernhard Kainz, Claire Donnat, Susan P. Holmes, Xavier Pennec
Introduction to Geometric Learning in Python with Geomstats. SciPy (2020)
Nina Miolane, Susan P. Holmes
Learning Weighted Submanifolds With Variational Autoencoders and Riemannian Variational Autoencoders. CVPR (2020)
Nina Miolane, Frédéric Poitevin, Yee-Ting Li, Susan P. Holmes
Estimation of Orientation and Camera Parameters from Cryo-Electron Microscopy Images with Variational Autoencoders and Generative Adversarial Networks. CVPR Workshops (2020)
Nina Miolane, Alice Le Brigant, Johan Mathe, Benjamin Hou, Nicolas Guigui, Yann Thanwerdas, Stefan Heyder, Olivier Peltre, Niklas Koep, Hadi Zaatiti, Hatem Hajri, Yann Cabanes, Thomas Gerald, Paul Chauchat, Christian Shewmake, Bernhard Kainz, Claire Donnat, Susan P. Holmes, Xavier Pennec
Geomstats: A Python Package for Riemannian Geometry in Machine Learning. CoRR (2020)
Lan H. Nguyen, Susan P. Holmes
Ten quick tips for effective dimensionality reduction. PLoS Comput. Biol. 15 (6) (2019)
Claire Donnat, Susan P. Holmes
Convex Hierarchical Clustering for Graph-Structured Data. CoRR (2019)
Claire Donnat, Susan P. Holmes
Convex Hierarchical Clustering for Graph-Structured Data. ACSSC (2019)
Nina Miolane, Susan P. Holmes
Learning Weighted Submanifolds with Variational Autoencoders and Riemannian Variational Autoencoders. CoRR (2019)
Nina Miolane, Frédéric Poitevin, Yee-Ting Li, Susan P. Holmes
Estimation of Orientation and Camera Parameters from Cryo-Electron Microscopy Images with Variational Autoencoders and Generative Adversarial Networks. CoRR (2019)
Nina Miolane, Susan P. Holmes, Xavier Pennec
Topologically Constrained Template Estimation via Morse-Smale Complexes Controls Its Statistical Consistency. SIAM J. Appl. Algebra Geom. 2 (2) (2018)
Claire Donnat, Susan P. Holmes
Tracking Network Dynamics: a review of distances and similarity metrics. CoRR (2018)
Christof Seiler, Tamar Green, David Hong, Lindsay Chromik, Lynne Huffman, Susan P. Holmes, Allan L. Reiss
Multi-Table Differential Correlation Analysis of Neuroanatomical and Cognitive Interactions in Turner Syndrome. Neuroinformatics 16 (1) (2018)
Julia Fukuyama, Laurie Rumker, Kris Sankaran, Pratheepa Jeganathan, Les Dethlefsen, David A. Relman, Susan P. Holmes
Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment. PLoS Comput. Biol. 13 (8) (2017)
Lan H. Nguyen, Susan P. Holmes
Bayesian Unidimensional Scaling for visualizing uncertainty in high dimensional datasets with latent ordering of observations. BMC Bioinform. 18 (S-10) (2017)
Nina Miolane, Susan P. Holmes, Xavier Pennec
Template Shape Estimation: Correcting an Asymptotic Bias. SIAM J. Imaging Sci. 10 (2) (2017)
Benjamin J. Callahan, Diana Proctor, David A. Relman, Julia Fukuyama, Susan P. Holmes
Reproducible Research Workflow in R for the Analysis of Personalized Human Microbiome Data. PSB (2016)
Nina Miolane, Susan P. Holmes, Xavier Pennec
Template shape estimation: correcting an asymptotic bias. CoRR (2016)
Paul J. McMurdie, Susan P. Holmes
Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking. Bioinform. 31 (2) (2015)
Sergio Bacallado, Persi Diaconis, Susan P. Holmes
de Finetti Priors using Markov chain Monte Carlo computations. Stat. Comput. 25 (4) (2015)
Paul J. McMurdie, Susan P. Holmes
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible. PLoS Comput. Biol. 10 (4) (2014)
Christof Seiler, Simon Rubinstein-Salzedo, Susan P. Holmes
Positive Curvature and Hamiltonian Monte Carlo. NIPS (2014)
Christof Seiler, Xavier Pennec, Susan P. Holmes
Random Spatial Structure of Geometric Deformations and Bayesian Nonparametrics. GSI (2013)
Paul J. McMurdie, Susan P. Holmes
phyloseq: A Bioconductor Package for Handling and Analysis of High-Throughput Phylogenetic Sequence Data. Pacific Symposium on Biocomputing (2012)
Julia Fukuyama, Paul J. McMurdie, Les Dethlefsen, David A. Relman, Susan P. Holmes
Comparisons of Distance Methods for Combining Covariates and Abundances in Microbiome Studies. Pacific Symposium on Biocomputing (2012)
Michael J. Rosen, Benjamin J. Callahan, Daniel S. Fisher, Susan P. Holmes
Denoising PCR-amplified metagenome data. BMC Bioinform. 13 (2012)
Susan P. Holmes, Alexander V. Alekseyenko, Alden Timme, Tyrrell Nelson, Pankaj Jay Pasricha, Alfred Spormann
Visualization and Statistical Comparisons of Microbial Communities Using R Packages on Phylochip Data. Pacific Symposium on Biocomputing (2011)
Adam Guetz, Susan P. Holmes
Adaptive importance sampling for network growth models. Ann. Oper. Res. 189 (1) (2011)
Kathleen M. Doherty, Priyanka Nakka, Bracken M. King, Soo-Yon Rhee, Susan P. Holmes, Robert W. Shafer, Mala L. Radhakrishnan
A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes. BMC Bioinform. 12 (2011)
Elizabeth C. Reuman, Severine Margeridon-Thermet, Harrison B. Caudill, Tommy F. Liu, Katyna Borroto-Esoda, Evguenia S. Svarovskaia, Susan P. Holmes, Robert W. Shafer
A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads. Bioinform. 26 (23) (2010)
Persi Diaconis, Susan P. Holmes, Svante Janson
Threshold Graph Limits and Random Threshold Graphs. Internet Math. 5 (3) (2008)
Soo-Yon Rhee, Tommy F. Liu, Susan P. Holmes, Robert W. Shafer
HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation. PLoS Comput. Biol. 3 (5) (2007)
Persi Diaconis, Susan P. Holmes, Richard Montgomery
Dynamical Bias in the Coin Toss. SIAM Rev. 49 (2) (2007)
Serban Nacu, Rebecca Critchley-Thorne, Peter P. Lee, Susan P. Holmes
Gene expression network analysis and applications to immunology. Bioinform. 23 (7) (2007)
Ali E. Abbas, Susan P. Holmes
Bioinformatics and Management Science: Some Common Tools and Techniques. Oper. Res. 52 (2) (2004)
Louis J. Billera, Susan P. Holmes, Karen Vogtmann
Erratum to: "Geometry of the Space of Phylogenetic Trees": [Adv. in Appl. Math. 27 (2001) 733-767]. Adv. Appl. Math. 29 (1) (2002)
Louis J. Billera, Susan P. Holmes, Karen Vogtmann
Geometry of the Space of Phylogenetic Trees. Adv. Appl. Math. 27 (4) (2001)
Philippe Lagacherie, Susan P. Holmes
Addressing Geographical Data Errors in a Classification Tree for Soil Unit Prediction. Int. J. Geogr. Inf. Sci. 11 (2) (1997)