Related papers: DiscoVista: interpretable visualizations of gene t…

Decision trees are flexible prediction models which are constructed to quantify outcome-covariate relationships and characterize relevant population subgroups. However, the standard graphical representation of fitted decision trees…

Principal Components Analysis (PCA) is a common way to study the sources of variation in a high-dimensional data set. Typically, the leading principal components are used to understand the variation in the data or to reduce the dimension of…

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…

Real-world observational datasets and machine learning have revolutionized data-driven decision-making, yet many models rely on empirical associations that may be misleading due to confounding and subgroup heterogeneity. Simpson's paradox…

Scientific expertise often requires recognizing subtle visual differences that remain challenging to articulate even for domain experts. We present a system that leverages generative models to automatically discover and visualize minimal…

From the intuitive notion of disentanglement, the image variations corresponding to different factors should be distinct from each other, and the disentangled representation should reflect those variations with separate dimensions. To…

We present VISTA (Visualization of Internal States and Their Associations), a novel pipeline for visually exploring and interpreting neural network representations. VISTA addresses the challenge of analyzing vast multidimensional spaces in…

The architecture of eukaryotic coding genes allows the production of several different protein isoforms by genes. Current gene phylogeny reconstruction methods make use of a single protein product per gene, ignoring information on…

In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…

Ensembles of decision trees perform well on many problems, but are not interpretable. In contrast to existing approaches in interpretability that focus on explaining relationships between features and predictions, we propose an alternative…

The Phylogenetic Genome Annotator (PGA) is a computer program that enables real-time comparison of 'gene trees' versus 'species trees' obtained from predicted open reading frames of whole genome data. The gene phylogenies are inferred for…

Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes. A variety of methods based on pairwise sequence comparisons…

Different sources of information might tell different stories about the evolutionary history of a given set of species. This leads to (rooted) phylogenetic trees that "disagree" on triples of species, which we call "conflict triples". An…

Understanding the population structure and patterns of gene flow within species is of fundamental importance to the study of evolution. In the fields of population and evolutionary genetics, measures of genetic differentiation are commonly…

Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the…

This paper describes techniques for growing classification and regression trees designed to induce visually interpretable trees. This is achieved by penalizing splits that extend the subset of features used in a particular branch of the…

It is becoming increasingly important for machine learning methods to make predictions that are interpretable as well as accurate. In many practical applications, it is of interest which features and feature interactions are relevant to the…

Species trees represent the historical divergences of populations or species, while gene trees trace the ancestry of individual gene copies sampled within those populations. In cases involving rapid speciation, gene trees with topologies…

Existing dynamic weighted graph visualization approaches rely on users' mental comparison to perceive temporal evolution of dynamic weighted graphs, hindering users from effectively analyzing changes across multiple timeslices. We propose…

Data visualisation is a key tool in data mining for understanding big datasets. Many visualisation methods have been proposed, including the well-regarded state-of-the-art method t-Distributed Stochastic Neighbour Embedding. However, the…