Related papers: DiscoVista: interpretable visualizations of gene t…
We introduce TableVista, a comprehensive benchmark for evaluating foundation models in multimodal table reasoning under visual and structural complexity. TableVista consists of 3,000 high-quality table reasoning problems, where each…
Recent advances in deep neuroevolution have demonstrated that evolutionary algorithms, such as evolution strategies (ES) and genetic algorithms (GA), can scale to train deep neural networks to solve difficult reinforcement learning (RL)…
Machine learning methods for estimating treatment effect heterogeneity promise greater flexibility than existing methods that test a few pre-specified hypotheses. However, one problem these methods can have is that it can be challenging to…
Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…
Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A…
Despite the explosive growth of the aging population worldwide, older adults have been largely overlooked by visualization research. This paper is a critical reflection on the underrepresentation of older adults in visualization research.…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
We recently presented DISentangled COunterfactual Visual interpretER (DISCOVER), a method toward systematic visual interpretability of image-based classification models and demonstrated its applicability to two biomedical domains. Here we…
For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species…
Learning informative representations of phylogenetic tree structures is essential for analyzing evolutionary relationships. Classical distance-based methods have been widely used to project phylogenetic trees into Euclidean space, but they…
Accurately inferring Gene Regulatory Networks (GRNs) is a critical and challenging task in biology. GRNs model the activatory and inhibitory interactions between genes and are inherently causal in nature. To accurately identify GRNs,…
In recent years, deep learning models have been extensively applied to biological data across various modalities. Discriminative deep learning models have excelled at classifying images into categories (e.g., healthy versus diseased,…
The assumption of positivity in causal inference (also known as common support and co-variate overlap) is necessary to obtain valid causal estimates. Therefore, confirming it holds in a given dataset is an important first step of any causal…
The inference of the evolutionary history of a collection of organisms is a problem of fundamental importance in evolutionary biology. The abundance of DNA sequence data arising from genome sequencing projects has led to significant…
This paper presents two approaches to quantifying and visualizing variation in datasets of trees. The first approach localizes subtrees in which significant population differences are found through hypothesis testing and sparse classifiers…
Phylogenetic tree inference using deep DNA sequencing is reshaping our understanding of rapidly evolving systems, such as the within-host battle between viruses and the immune system. Densely sampled phylogenetic trees can contain special…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…