Interpretable and explainable machine learning: A methods‐centric overview with concrete examples

R Marcinkevičs, JE Vogt - Wiley Interdisciplinary Reviews: Data …, 2023‏ - Wiley Online Library
Interpretability and explainability are crucial for machine learning (ML) and statistical
applications in medicine, economics, law, and natural sciences and form an essential …

Interpretability and explainability: A machine learning zoo mini-tour

R Marcinkevičs, JE Vogt - arxiv preprint arxiv:2012.01805, 2020‏ - arxiv.org
In this review, we examine the problem of designing interpretable and explainable machine
learning models. Interpretability and explainability lie at the core of many machine learning …

Beyond normal: On the evaluation of mutual information estimators

P Czyż, F Grabowski, J Vogt… - Advances in Neural …, 2023‏ - proceedings.neurips.cc
Mutual information is a general statistical dependency measure which has found
applications in representation learning, causality, domain generalization and computational …

Compositional data analysis of the microbiome: fundamentals, tools, and challenges

MCB Tsilimigras, AA Fodor - Annals of epidemiology, 2016‏ - Elsevier
Purpose Human microbiome studies are within the realm of compositional data with the
absolute abundances of microbes not recoverable from sequence data alone. In …

Using control genes to correct for unwanted variation in microarray data

JA Gagnon-Bartsch, TP Speed - Biostatistics, 2012‏ - academic.oup.com
Microarray expression studies suffer from the problem of batch effects and other unwanted
variation. Many methods have been proposed to adjust microarray data to mitigate the …

Sparse Bayesian infinite factor models

A Bhattacharya, DB Dunson - Biometrika, 2011‏ - academic.oup.com
We focus on sparse modelling of high-dimensional covariance matrices using Bayesian
latent factor models. We propose a multiplicative gamma process shrinkage prior on the …

High-dimensional sparse factor modeling: applications in gene expression genomics

CM Carvalho, J Chang, JE Lucas… - Journal of the …, 2008‏ - Taylor & Francis
We describe studies in molecular profiling and biological pathway analysis that use sparse
latent factor and regression models for microarray gene expression data. We discuss breast …

Gene expression signatures diagnose influenza and other symptomatic respiratory viral infections in humans

AK Zaas, M Chen, J Varkey, T Veldman, AO Hero… - Cell host & …, 2009‏ - cell.com
Acute respiratory infections (ARIs) are a common reason for seeking medical attention, and
the threat of pandemic influenza will likely add to these numbers. Using human viral …

Bayesian exploratory factor analysis

G Conti, S Frühwirth-Schnatter, JJ Heckman… - Journal of …, 2014‏ - Elsevier
This paper develops and applies a Bayesian approach to Exploratory Factor Analysis that
improves on ad hoc classical approaches. Our framework relies on dedicated factor models …

A host transcriptional signature for presymptomatic detection of infection in humans exposed to influenza H1N1 or H3N2

CW Woods, MT McClain, M Chen, AK Zaas… - PloS one, 2013‏ - journals.plos.org
There is great potential for host-based gene expression analysis to impact the early
diagnosis of infectious diseases. In particular, the influenza pandemic of 2009 highlighted …