相关论文: On the group theoretical background of assigning s…

Markov models of character substitution on phylogenies form the foundation of phylogenetic inference frameworks. Early models made the simplifying assumption that the substitution process is homogeneous over time and across sites in the…

Crystal-structure match (CSM), the atom-to-atom correspondence between two crystalline phases, is used extensively to describe solid-solid phase transition (SSPT) mechanisms. However, existing computational methods cannot account for all…

By using a mixture model for the density distribution of the three pseudobond angles formed by $C_\alpha$ atoms of four consecutive residues, the local structural states are discretized as 17 conformational letters of a protein structural…

Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…

Somatic mutations in cancer can be viewed as a mixture distribution of several mutational signatures, which can be inferred using non-negative matrix factorization (NMF). Mutational signatures have previously been parametrized using either…

Choi et. al (2011) introduced a minimum spanning tree (MST)-based method called CLGrouping, for constructing tree-structured probabilistic graphical models, a statistical framework that is commonly used for inferring phylogenetic trees.…

The purpose of this article is to show how the isotropy subgroup of leaf permutations on binary trees can be used to systematically identify tree-informative invariants relevant to models of phylogenetic evolution. In the quartet case, we…

Evolutionary models measure the probability of amino acid substitutions occurring over different evolutionary distances. We examine various evolutionary models based on empirically derived amino acid substitution matrices. The models are…

Embeddings of graphs into distributions of trees that preserve distances in expectation are a cornerstone of many optimization algorithms. Unfortunately, online or dynamic algorithms which use these embeddings seem inherently randomized and…

A variety of selection-mutation models for DNA (or RNA) sequences, well known in molecular evolution, can be translated into a model of coupled Ising quantum chains. This correspondence is used to investigate the genetic variability and…

In phylogenetics it is of interest for rate matrix sets to satisfy closure under matrix multiplication as this makes finding the set of corresponding transition matrices possible without having to compute matrix exponentials. It is also…

Ontology matching (OM) plays an essential role in enabling semantic interoperability and integration across heterogeneous knowledge sources, particularly in the biomedical domain which contains numerous complex concepts related to diseases…

The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…

A schema is a naturally defined subset of the space of fixed-length binary strings. The Holland Schema Theorem gives a lower bound on the expected fraction of a population in a schema after one generation of a simple genetic algorithm. This…

OpenStreetMap (OSM) is one of the richest openly available sources of volunteered geographic information. Although OSM includes various geographical entities, their descriptions are highly heterogeneous, incomplete, and do not follow any…

Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…

We contribute to the efficient approximation of the Pareto-set for the classical $\mathcal{NP}$-hard multi-objective minimum spanning tree problem (moMST) adopting evolutionary computation. More precisely, by building upon preliminary work,…

Kernel matrices (e.g. Gram or similarity matrices) are essential for many state-of-the-art approaches to classification, clustering, and dimensionality reduction. For large datasets, the cost of forming and factoring such kernel matrices…

We study the problem of determining the minimal genus of a simple finite connected graph. We present an algorithm which, for an arbitrary graph $G$ with $n$ vertices and $m$ edges, determines the orientable genus of $G$ in…

Motivation: Word-based or `alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate. Most of these methods calculate pairwise distances for a set of input…