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The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…
Biologists who want to analyse their single-cell transcriptomics dataset must install and use specialist software via the command line. This is often impractical for non-bioinformaticians. Whilst the popular CELLxGENE software provides an…
We study the enumeration of spinal tree-child phylogenetic networks, a rigid family of tree-child networks in which all internal vertices lie on a single root--to--leaf path. We provide two complementary combinatorial frameworks. First, we…
Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm…
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…
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…
Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…
Typefaces are an essential resource employed by graphic designers. The increasing demand for innovative type design work increases the need for good technological means to assist the designer in the creation of a typeface. We present an…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
Measuring the complexity of tree structures can be beneficial in areas that use tree data structures for storage, communication, and processing purposes. This complexity can then be used to compress tree data structures to their…
Learning discriminative global features plays a vital role in semantic segmentation. And most of the existing methods adopt stacks of local convolutions or non-local blocks to capture long-range context. However, due to the absence of…
Many data sets, crucial for today's applications, consist essentially of enormous networks, containing millions or even billions of elements. Having the possibility of visualizing such networks is of paramount importance. We propose an…
Given a set of graphs from some unknown family, we want to generate new graphs from that family. Recent methods use diffusion on either graph embeddings or the discrete space of nodes and edges. However, simple changes to embeddings (say,…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
Networks and network-like structures are amongst the central building blocks of many technological and biological systems. Given a mathematical graph representation of a network, methods from graph theory enable a precise investigation of…
Recent progress in generative models has significantly advanced image editing capabilities, yet precise and intuitive user control remains difficult. Specifically, users often struggle to communicate both exact spatial layouts and specific…
We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high- throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the…
In this paper, we propose a novel fully automatic pipeline to generate text images that are legible and strongly aligned to the desired semantic concept taken from the users' inputs. In our method, users are able to put three inputs into…