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This project aims to investigate a novel sequence generation method inspired by the AlphaGo paradigm, adapting it for use with large language models (LLMs). The proposed approach involves creating search trees of different possible…
Identification of tree species plays a key role in forestry related tasks like forest conservation, disease diagnosis and plant production. There had been a debate regarding the part of the tree to be used for differentiation, whether it…
Verilog's design cycle is inherently labor-intensive and necessitates extensive domain expertise. Although Large Language Models (LLMs) offer a promising pathway toward automation, their limited training data and intrinsic sequential…
Inferential summaries of tree estimates are useful in the setting of evolutionary biology, where phylogenetic trees have been built from DNA data since the 1960's. In bioinformatics, psychometrics and data mining, hierarchical clustering…
The phylogenetic tree space introduced by Billera, Holmes, and Vogtmann (BHV tree space) is a CAT(0) continuous space that represents trees with edge weights with an intrinsic geodesic distance measure. The geodesic distance measure unique…
We derive tractable criteria for the consistency of Bayesian tree reconstruction procedures, which constitute a central class of algorithms for inferring common ancestry among DNA sequence samples in phylogenetics. Our results encompass…
The bacterial microbiome is increasingly being recognised as a key factor in human health, driven in large part by datasets collected using 16S rRNA (ribosomal ribonucleic acid) gene sequencing, which enable cost-effective quantification of…
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…
In this work, we propose the novel Prototypical Graph Regression Self-explainable Trees (ProGReST) model, which combines prototype learning, soft decision trees, and Graph Neural Networks. In contrast to other works, our model can be used…
Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
We present VBPI-Mixtures, an algorithm designed to enhance the accuracy of phylogenetic posterior distributions, particularly for tree-topology and branch-length approximations. Despite the Variational Bayesian Phylogenetic Inference…
Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…
Deep generative models such as conditional variational autoencoders (CVAEs) have shown great promise for predicting trajectories of surrounding agents in autonomous vehicle planning. State-of-the-art models have achieved remarkable accuracy…
Traditionally, phylogeny and sequence alignment are estimated separately: first estimate a multiple sequence alignment and then infer a phylogeny based on the sequence alignment estimated in the previous step. However, uncertainty in the…
Background: The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly…
We have developed an alignment-free method that calculates phylogenetic distances using a maximum likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic…
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…
Trees are fundamental data structure for many areas of computer science and system engineering. In this report, we show how to ensure eventual consistency of optimistically replicated trees. In optimistic replication, the different replicas…
Most decision tree induction algorithms are based on a greedy top-down recursive partitioning strategy for tree growth. In this paper, we propose several methods for induction of decision trees and their ensembles based on evolutionary…