Related papers: Reconstructing Biological and Digital Phylogenetic…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
$k$d-trees are widely used in parallel databases to support efficient neighborhood/similarity queries. Supporting parallel updates to $k$d-trees is therefore an important operation. In this paper, we present BDL-tree, a parallel,…
The supertree construction problem is about combining several phylogenetic trees with possibly conflicting information into a single tree that has all the leaves of the source trees as its leaves and the relationships between the leaves are…
An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…
A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
We consider the problem of structure recovery in a graphical model of a tree where some variables are latent. Specifically, we focus on the Gaussian case, which can be reformulated as a well-studied problem: recovering a semi-labeled tree…
Dynamic regression trees are an attractive option for automatic regression and classification with complicated response surfaces in on-line application settings. We create a sequential tree model whose state changes in time with the…
We study the problem of learning a latent tree graphical model where samples are available only from a subset of variables. We propose two consistent and computationally efficient algorithms for learning minimal latent trees, that is, trees…
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…
Rooted phylogenetic networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate…
We give the first {\sl reconstruction algorithm} for decision trees: given queries to a function $f$ that is $\mathrm{opt}$-close to a size-$s$ decision tree, our algorithm provides query access to a decision tree $T$ where: $\circ$ $T$ has…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Federated learning is a distributed machine learning approach to privacy preservation and two major technical challenges prevent a wider application of federated learning. One is that federated learning raises high demands on communication,…
Biological tree (BioTree) analysis is a foundational tool in biology, enabling the exploration of evolutionary and differentiation relationships among organisms, genes, and cells. Traditional tree construction methods, while instrumental in…
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…
This paper studies the performances of BERT combined with tree structure in short sentence ranking task. In retrieval-based question answering system, we retrieve the most similar question of the query question by ranking all the questions…
We propose a general framework for end-to-end learning of data structures. Our framework adapts to the underlying data distribution and provides fine-grained control over query and space complexity. Crucially, the data structure is learned…
Phylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is…