Related papers: Multi-SpaM: a Maximum-Likelihood approach to Phylo…
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…
One of the main aims of phylogenetics is the reconstruction of the correct evolutionary tree when data concerning the underlying species set are given. These data typically come in the form of DNA, RNA or protein alignments, which consist…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…
We show that the problem of constructing tree-structured descriptions of data layouts that are optimal with respect to space or other criteria from given sequences of displacements, can be solved in polynomial time. The problem is relevant…
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…
Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…
Phylogenetic trees and networks are graphs used to model evolutionary relationships, with trees representing strictly branching histories and networks allowing for events in which lineages merge, called reticulation events. While the…
A consensus tree is a phylogenetic tree that synthesizes a given collection of phylogenetic trees, all of which share the same leaf labels but may have different topologies, typically obtained through bootstrapping. Our research focuses on…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
Suffix tree (and the closely related suffix array) are fundamental structures capturing all substrings of a given text essentially by storing all its suffixes in the lexicographical order. In some applications, we work with a subset of $b$…
Tree matching techniques have been investigated in many fields, including web data mining and extraction, as a key component to analyze the content of web documents, existing tree matching approaches, like Tree-Edit Distance (TED) or…
The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…
Efficient methods for storing and querying are critical for scaling high-order n-gram language models to large corpora. We propose a language model based on compressed suffix trees, a representation that is highly compact and can be easily…
Sparse approximations using highly over-complete dictionaries is a state-of-the-art tool for many imaging applications including denoising, super-resolution, compressive sensing, light-field analysis, and object recognition. Unfortunately,…
Generating diverse responses from large language models (LLMs) is crucial for applications such as planning/search and synthetic data generation, where diversity provides distinct answers across generations. Prior approaches rely on…
Data augmentation methods for neural machine translation are particularly useful when limited amount of training data is available, which is often the case when dealing with low-resource languages. We introduce a novel augmentation method,…
We probe the layers in multilingual BERT (mBERT) for phylogenetic and geographic language signals across 100 languages and compute language distances based on the mBERT representations. We 1) employ the language distances to infer and…
We present TreeClone, a latent feature allocation model to reconstruct tumor subclones subject to phylogenetic evolution that mimics tumor evolution. Similar to most current methods, we consider data from next-generation sequencing of tumor…
Complex systems of polynomial equations have to be set up and solved algebraically in order to obtain analytic solutions for maximum likelihood on phylogenetic trees. This has restricted the types of systems previously resolved to the…