Related papers: SICLE: A high-throughput tool for extracting evolu…

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…

Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…

The discovery of nucleic acids and the structure of DNA have brought considerable advances in the understanding of life. The development of next-generation sequencing technologies has led to a large-scale generation of data, for which…

Circular RNAs (circRNAs) are important components of the non-coding RNA regulatory network. Previous circRNA identification primarily relies on high-throughput RNA sequencing (RNA-seq) data combined with alignment-based algorithms that…

Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…

Relation extraction (RE) is an important information extraction task which provides essential information to many NLP applications such as knowledge base population and question answering. In this paper, we present a novel generative model…

This paper presents a novel clustering algorithm from the SPINEX (Similarity-based Predictions with Explainable Neighbors Exploration) algorithmic family. The newly proposed clustering variant leverages the concept of similarity and…

Unsupervised cell type identification is crucial for uncovering and characterizing heterogeneous populations in single cell omics studies. Although a range of clustering methods have been developed, most focus exclusively on intrinsic…

Phylogenetics is a fundamental component of evolutionary analysis frameworks in biology and linguistics. Recently, the advent of large-scale genomics and the SARS-CoV-2 pandemic has highlighted the necessity for phylogenetic software to…

Recent advances in computational methods for designing biological sequences have sparked the development of metrics to evaluate these methods performance in terms of the fidelity of the designed sequences to a target distribution and their…

Recent advancements in deep learning-based interactive segmentation methods have significantly improved pathology image segmentation. Most existing approaches utilize user-provided positive and negative clicks to guide the segmentation…

Sequential interaction networks (SIN) have been commonly adopted in many applications such as recommendation systems, search engines and social networks to describe the mutual influence between users and items/products. Efforts on…

Rooted acyclic graphs appear naturally when the phylogenetic relationship of a set $X$ of taxa involves not only speciations but also recombination, horizontal transfer, or hybridization, that cannot be captured by trees. A variety of…

PhyloFrame is a Python library for phylogenetic computation targeting the gap between specialist, compiler-optimized operations and flexible, script-based workflows -- with emphasis on fast, memory-efficient operations for very large tree…

Efficient code retrieval is critical for developer productivity, yet existing benchmarks largely focus on Python and rarely stress-test robustness beyond superficial lexical cues. To address the gap, we introduce an automated pipeline for…

Biclustering has gained interest in gene expression data analysis due to its ability to identify groups of samples that exhibit similar behaviour in specific subsets of genes (or vice versa), in contrast to traditional clustering methods…

A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…

In this work, we present a Web-based annotation tool `Relation Triplets Extractor' \footnote{https://abera87.github.io/annotate/} (RTE) for annotating relation triplets from the text. Relation extraction is an important task for extracting…

Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…

The goal of this paper is to study the similarity between sequences using a distance between the \emph{context} trees associated to the sequences. These trees are defined in the framework of \emph{Sparse Probabilistic Suffix Trees} (SPST),…