Related papers: Multi-SpaM: a Maximum-Likelihood approach to Phylo…

We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…

Tree search has recently emerged as a powerful framework for aligning generative models with task-specific rewards at test time. Applying tree search to Masked Diffusion Language Models, however, introduces two key challenges: (i) parallel…

Probability estimation of tree topologies is one of the fundamental tasks in phylogenetic inference. The recently proposed subsplit Bayesian networks (SBNs) provide a powerful probabilistic graphical model for tree topology probability…

Tree-based models underpin many modern semantic search engines and recommender systems due to their sub-linear inference times. In industrial applications, these models operate at extreme scales, where every bit of performance is critical.…

Recently, considerable effort has been put into developing fast algorithms to reconstruct a rooted phylogenetic network that explains two rooted phylogenetic trees and has a minimum number of hybridization vertices. With the standard…

Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we…

In this paper we consider a transformer with an $n$-gram structure, such as the one underlying ChatGPT. The transformer provides next word probabilities, which can be used to generate word sequences. We consider methods for computing word…

When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic of a larger collection of sequences. For example, one may…

In this paper we introduce Latent Tree Language Model (LTLM), a novel approach to language modeling that encodes syntax and semantics of a given sentence as a tree of word roles. The learning phase iteratively updates the trees by moving…

We study the natural problem of Triplet Reconstruction (also Rooted Triplets Consistency or Triplet Clustering), originally motivated in computational biology and relational databases (Aho, Sagiv, Szymanski, and Ullman, 1981): given $n$…

Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a…

We propose an unsupervised method to obtain cross-lingual embeddings without any parallel data or pre-trained word embeddings. The proposed model, which we call multilingual neural language models, takes sentences of multiple languages as…

Counterfactual explanations are usually generated through heuristics that are sensitive to the search's initial conditions. The absence of guarantees of performance and robustness hinders trustworthiness. In this paper, we take a…

A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…

Here we present an investigation into using nested sampling algorithms in cosmological likelihood analysis. We present a new nested sampling algorithm, ESNested, that uses Evolution Strategies for sample proposals. This quickly finds the…

A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree…

We address the problem of clustering words (or constructing a thesaurus) based on co-occurrence data, and using the acquired word classes to improve the accuracy of syntactic disambiguation. We view this problem as that of estimating a…

Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…

This paper addresses the deduplication of multilingual textual data using advanced NLP tools. We compare a two-step method involving translation to English followed by embedding with mpnet, and a multilingual embedding model (distiluse).…