Related papers: DiscoVista: interpretable visualizations of gene t…

Random forests are a machine learning method used to automatically classify datasets and consist of a multitude of decision trees. While these random forests often have higher performance and generalize better than a single decision tree,…

Recent research has increasingly focused on the reasoning capabilities of Large Language Models (LLMs) in multi-turn interactions, as these scenarios more closely mirror real-world problem-solving. However, analyzing the intricate reasoning…

Phylogenetic diversity indices such as the Fair Proportion (FP) index are frequently discussed as prioritization criteria in biodiversity conservation. They rank species according to their contribution to overall diversity by taking into…

Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…

One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy…

The log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple non-mixture models of sequence evolution. Here we prove that the log-det distance, coupled…

We propose and study a multi-scale approach to vector quantization. We develop an algorithm, dubbed reconstruction trees, inspired by decision trees. Here the objective is parsimonious reconstruction of unsupervised data, rather than…

The collection of large, complex datasets has become common across a wide variety of domains. Visual analytics tools increasingly play a key role in exploring and answering complex questions about these large datasets. However, many…

When communicating critical information to decision-makers, one of the major challenges in visualization is whether the communication is affected by different perceptual or cognitive abilities, one major influencing factor is age. We review…

Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…

Distance covariance is a widely used statistical methodology for testing the dependency between two groups of variables. Despite the appealing properties of consistency and superior testing power, the testing results of distance covariance…

Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…

While measurement advances now allow extensive surveys of gene activity (large numbers of genes across many samples), interpretation of these data is often confounded by noise -- expression counts can differ strongly across samples due to…

The advent of high-throughput sequencing technologies has lead to vast comparative genome sequences. The construction of gene-gene interaction networks or dependence graphs on the genome scale is vital for understanding the regulation of…

Neural networks are widely adopted to solve complex and challenging tasks. Especially in high-stakes decision-making, understanding their reasoning process is crucial, yet proves challenging for modern deep networks. Feature visualization…

Pharmaceutical research and development has accumulated vast and heterogeneous archives of data. Much of this knowledge stems from discontinued programs, and reusing these archives is invaluable for reverse translation. However, in…

Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…

A wide range of synthesized crystalline inorganic materials exhibit compositional disorder, where multiple atomic species partially occupy the same crystallographic site. As a result, the physical and chemical properties of such materials…

With an increasing outreach of digital platforms in our lives, researchers have taken a keen interest to study different facets of social interactions that seem to be evolving rapidly. Analysing the spread of information (aka diffusion) has…