Related papers: Optimality of the Neighbor Joining Algorithm and F…
Imaging interferometric data in radio astronomy requires the use of non-linear algorithms that rely on different assumptions on the source structure and may produce non-unique results. This is especially true for Very Long Baseline…
It is known that unsupervised nonlinear dimensionality reduction and clustering is sensitive to the selection of hyperparameters, particularly for deep learning based methods, which hinders its practical use. How to select a proper network…
A common assumption in multiple scientific applications is that the distribution of observed data can be modeled by a latent tree graphical model. An important example is phylogenetics, where the tree models the evolutionary lineages of a…
In this paper, we will analyze the behavior of the Neighbor Joining algorithm on five taxa and we will show that the partition of the sample (data) space for estimation of a tree topology with five taxa into subspaces, within each of which…
Multiple sequence alignment is increasingly important to bioinformatics, with several applications ranging from phylogenetic analyses to domain identification. There are several ways to perform multiple sequence alignment, an important way…
UPGMA is a heuristic method identifying the least squares equidistant phylogenetic tree given empirical distance data among $n$ taxa. We study this classic algorithm using the geometry of the space of all equidistant trees with $n$ leaves,…
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…
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…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
2-colored best match graphs (2-BMGs) form a subclass of sink-free bi-transitive graphs that appears in phylogenetic combinatorics. There, 2-BMGs describe evolutionarily most closely related genes between a pair of species. They are…
This paper presents the Min-Cut Bayesian Network Consensus (MCBNC) algorithm, a greedy method for structural consensus of Bayesian Networks (BNs), with applications in federated learning and model aggregation. MCBNC prunes weak edges from…
1. Inferring ecological interactions is hard because we often lack suitable parametric representations to portray them. Neural ordinary differential equations (NODEs) provide a way of estimating interactions nonparametrically from time…
Minimum Routing Cost Clustered Tree Problem (CluMRCT) is applied in various fields in both theory and application. Because the CluMRCT is NP-Hard, the approximate approaches are suitable to find the solution for this problem. Recently,…
The study of Markov processes and broadcasting on trees has deep connections to a variety of areas including statistical physics, graphical models, phylogenetic reconstruction, Markov Chain Monte Carlo, and community detection in random…
Point matching refers to the process of finding spatial transformation and correspondences between two sets of points. In this paper, we focus on the case that there is only partial overlap between two point sets. Following the approach of…
A merge tree is a fundamental topological structure used to capture the sub-level set (and similarly, super-level set) topology in scalar data analysis. The interleaving distance is a theoretically sound, stable metric for comparing merge…
Good representations for phylogenetic trees and networks are important for optimizing storage efficiency and implementation of scalable methods for the inference and analysis of evolutionary trees for genes, genomes and species. We…
We observe $n$ sequences at each of $m$ sites, and assume that they have evolved from an ancestral sequence that forms the root of a binary tree of known topology and branch lengths, but the sequence states at internal nodes are unknown.…
We present a constant-round algorithm in the massively parallel computation (MPC) model for evaluating a natural join where every input relation has two attributes. Our algorithm achieves a load of $\tilde{O}(m/p^{1/\rho})$ where $m$ is the…
Optimization tasks over relational data, such as clustering, often suffer from the prohibitive cost of join operations, which are necessary to access the full dataset. While geometric data structures like BBD trees yield fast approximation…