Related papers: Indirect Identification of Horizontal Gene Transfe…
Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree $T$ to vertices and edges of a species tree $S$. The relative timing of the last common…
Horizontal gene transfer events partition a gene tree $T$ and thus, its leaf set into subsets of genes whose evolutionary history is described by speciation and duplication events alone. Indirect phylogenetic methods can be used to infer…
Horizontal gene transfer is an important contributor to evolution. According to Walter M.\ Fitch, two genes are xenologs if they are separated by at least one HGT. More formally, the directed Fitch graph has a set of genes is its vertices,…
In this article we are describing a new algorithm for detecting and validating partial horizontal gene transfers (HGT). The presented algorithm is based on a sliding window procedure which analyzes fragments of the given multiple sequence…
Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying…
Two genes are xenologs in the sense of Fitch if they are separated by at least one horizontal gene transfer event. Horizonal gene transfer is asymmetric in the sense that the transferred copy is distinguished from the one that remains…
Lateral gene transfer (LGT) is a common mechanism of non-vertical evolution where genetic material is transferred between two more or less distantly related organisms. It is particularly common in bacteria where it contributes to adaptive…
Recent years have witnessed the emerging success of graph neural networks (GNNs) for modeling structured data. However, most GNNs are designed for homogeneous graphs, in which all nodes and edges belong to the same types, making them…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
Encoding a driving scene into vector representations has been an essential task for autonomous driving that can benefit downstream tasks e.g. trajectory prediction. The driving scene often involves heterogeneous elements such as the…
Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…
Multi-view learning has progressed rapidly in recent years. Although many previous studies assume that each instance appears in all views, it is common in real-world applications for instances to be missing from some views, resulting in…
In this paper we resolve the complexity of the isomorphism problem on all but finitely many of the graph classes characterized by two forbidden induced subgraphs. To this end we develop new techniques applicable for the structural and…
Graph neural networks have recently achieved remarkable success in representing graph-structured data, with rapid progress in both the node embedding and graph pooling methods. Yet, they mostly focus on capturing information from the nodes…
Inferring the graph structure from observed data is a key task in graph machine learning to capture the intrinsic relationship between data entities. While significant advancements have been made in learning the structure of homogeneous…
Scene graph generation (SGG) aims to detect objects and predict their pairwise relationships within an image. Current SGG methods typically utilize graph neural networks (GNNs) to acquire context information between objects/relationships.…
Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…
Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot…
A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the…
In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…