相关论文: Whole Genome Phylogenetic Tree Reconstruction Usin…

Multiple methods of finding the vertices belonging to a planted dense subgraph in a random dense $G(n, p)$ graph have been proposed, with an emphasis on planted cliques. Such methods can identify the planted subgraph in polynomial time, but…

An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…

The modular decomposition of a symmetric map $\delta\colon X\times X \to \Upsilon$ (or, equivalently, a set of symmetric binary relations, a 2-structure, or an edge-colored undirected graph) is a natural construction to capture key features…

We propose the fully explainable Decision Tree Graph Neural Network (DT+GNN) architecture. In contrast to existing black-box GNNs and post-hoc explanation methods, the reasoning of DT+GNN can be inspected at every step. To achieve this, we…

Modern generative models achieve excellent quality in a variety of tasks including image or text generation and chemical molecule modeling. However, existing methods often lack the essential ability to generate examples with requested…

We present an algebraic construction of trace-based De Bruijn tori over finite fields, focusing on the nonzero variant that omits the all-zero pattern. The construction arranges nonzero field elements on a toroidal grid using two…

The number of complete chloroplastic genomes increases day after day, making it possible to rethink plants phylogeny at the biomolecular era. Given a set of close plants sharing in the order of one hundred of core chloroplastic genes, this…

Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…

Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…

Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…

Colour patterning contributes to important plant traits that influence ecological interactions, horticultural breeding, and agricultural performance. High-throughput phenotyping of colour is valuable for understanding plant biology and…

Structural pruning enables model acceleration by removing structurally-grouped parameters from neural networks. However, the parameter-grouping patterns vary widely across different models, making architecture-specific pruners, which rely…

The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…

Gene regulation is a dynamic process that underlies all aspects of human development, disease response, and other key biological processes. The reconstruction of temporal gene regulatory networks has conventionally relied on regression…

Recent years have witnessed the breakthrough success of deep convolutional neural networks (DCNNs) in image classification and other vision applications. Although freeing users from the troublesome handcrafted feature extraction by…

Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a genealogy--a rooted, binary, timed tree, with tips corresponding…

One of the most basic facts related to the famous Ulam reconstruction conjecture is that the connectedness of a graph can be determined by the deck of its vertex-deleted subgraphs, which are considered up to isomorphism. We strengthen this…

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…

Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…

Inspired by the seminal result that a graph and an associated rotation system uniquely determine the topology of a closed manifold, we propose a combinatorial method for reconstruction of surfaces from points. Our method constructs a…