Related papers: Alignment- and reference-free phylogenomics with c…

Deep learning-based networks are among the most prominent methods to learn linear patterns and extract this type of information from diverse imagery conditions. Here, we propose a deep learning approach based on graphs to detect plantation…

We introduce the notion of delineation. A graph class $\mathcal C$ is said delineated if for every hereditary closure $\mathcal D$ of a subclass of $\mathcal C$, it holds that $\mathcal D$ has bounded twin-width if and only if $\mathcal D$…

This paper is focused in designing an efficient on-line algorithm to reconstruct a DNA sequence and search the genes in it, we assume that the segment have no mutation or reading error, the algorithm is based on de Bruijn Graph for…

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…

Given a multi-hypergraph $G$ that is edge-colored into color classes $E_1, \ldots, E_n$, a full rainbow matching is a matching of $G$ that contains exactly one edge from each color class $E_i$. One way to guarantee the existence of a full…

The inability to resolve deep node relationships of highly divergent/rapidly evolving protein families is a major factor that stymies evolutionary studies. In this manuscript, we propose a Multiple Sequence Alignment (MSA) independent…

We develop a general framework for distribution-free predictive inference in regression, using conformal inference. The proposed methodology allows for the construction of a prediction band for the response variable using any estimator of…

A technique named Feature Learning from Image Markers (FLIM) was recently proposed to estimate convolutional filters, with no backpropagation, from strokes drawn by a user on very few images (e.g., 1-3) per class, and demonstrated for…

Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent--due to events such as incomplete lineage sorting or horizontal gene transfer--it can be misleading to…

We consider a family of problems that are concerned about making predictions for the majority of unlabeled, graph-structured data samples based on a small proportion of labeled samples. Relational information among the data samples, often…

We propose the first deep learning approach for exemplar-based local colorization. Given a reference color image, our convolutional neural network directly maps a grayscale image to an output colorized image. Rather than using hand-crafted…

Phylogenetic trees are important tools in the study of evolutionary relationships between species. Measures such as the index of Sackin, Colless, and Total Cophenetic have been extensively used to quantify tree balance, one key property of…

Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…

We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…

The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be a tree, or a network if it includes reticulations, representing events such as hybridization or admixture.…

We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct…

We propose a novel graph-regularized neural network (GRNN) algorithm for tree species classification. The proposed algorithm encompasses superpixel-based segmentation for graph construction, a pixel-wise neural network classifier, and the…

We propose a method for obtaining parsimonious decompositions of networks into higher order interactions which can take the form of arbitrary motifs.The method is based on a class of analytically solvable generative models, where vertices…

Guiding pretrained flow-based generative models for conditional generation or to produce samples with desired target properties enables solving diverse tasks without retraining on paired data. We present ESS-Flow, a gradient-free method…

In this paper we look at the problem of adjacency labeling of graphs. Given a family of undirected graphs the problem is to determine an encoding-decoding scheme for each member of the family such that we can decode the adjacency…