相关论文: DiscoVista: interpretable visualizations of gene t…

Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…

A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…

Diffusion models have demonstrated remarkable performance in generation tasks. Nevertheless, explaining the diffusion process remains challenging due to it being a sequence of denoising noisy images that are difficult for experts to…

Recent advances in image and video creation, especially AI-based image synthesis, have led to the production of numerous visual scenes that exhibit a high level of abstractness and diversity. Consequently, Visual Storytelling (VST), a task…

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…

The standard approach to estimate species trees is to align a selected set of genes, concatenate the alignments and then estimate a consensus tree. However, individual genes contain differing levels of evolutionary information, either…

Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…

Variable trees are a new method for the exploration of discrete multivariate data. They display nested subsets and corresponding frequencies and percentages. Manual calculation of these quantities can be laborious, especially when there are…

We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…

The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…

Design study is an established approach of conducting problem-driven visualization research. The academic visualizationcommunity has produced a large body of work for reporting on design studies, informed by a handful of theoretical…

Similarity analyses between multiple correlation or covariance tables constitute the cornerstone of network neuroscience. Here, we introduce covSTATIS, a versatile, linear, unsupervised multi-table method designed to identify structured…

We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct…

The differential diagnosis of neurodegenerative diseases, characterized by overlapping symptoms, may be challenging. Brain imaging coupled with artificial intelligence has been previously proposed for diagnostic support, but most of these…

Evolving trees arise in many real-life scenarios from computer file systems and dynamic call graphs, to fake news propagation and disease spread. Most layout algorithms for static trees do not work well in an evolving setting (e.g., they…

Many language generation models are now available for a wide range of generation tasks, including machine translation and summarization. Combining such diverse models may lead to further progress, but ensembling generation models is…

Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the…

Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…

This article presents the prediction difference analysis method for visualizing the response of a deep neural network to a specific input. When classifying images, the method highlights areas in a given input image that provide evidence for…

We introduce a hybrid metaphor for the visualization of the reconciliations of co-phylogenetic trees, that are mappings among the nodes of two trees. The typical application is the visualization of the co-evolution of hosts and parasites in…