Related papers: Combinatorial perspectives on Dollo-$k$ characters…
The selection problem, where one wishes to locate the $k^{th}$ smallest element in an unsorted array of size $n$, is one of the basic problems studied in computer science. The main focus of this work is designing algorithms for solving the…
Sequence labeling architectures use word embeddings for capturing similarity, but suffer when handling previously unseen or rare words. We investigate character-level extensions to such models and propose a novel architecture for combining…
We address phylogenetic reconstruction when the data is generated from a mixture distribution. Such topics have gained considerable attention in the biological community with the clear evidence of heterogeneity of mutation rates. In our…
The performance of a dynamic dictionary is measured mainly by its update time, lookup time, and space consumption. In terms of update time and lookup time there are known constructions that guarantee constant-time operations in the worst…
The ratio of two densities provides a direct characterization of their differences. We consider the two-sample comparison problem by estimating this ratio given i.i.d. observations from two distributions. To this end, we propose additive…
Tree trace reconstruction aims to learn the binary node labels of a tree, given independent samples of the tree passed through an appropriately defined deletion channel. In recent work, Davies, R\'acz, and Rashtchian used combinatorial…
Phylogenetic trees represent the evolutionary relationships between extant lineages, where extinct or non-sampled lineages are omitted. Extending the work of Stadler and collaborators, this paper focuses on the branch lengths in…
We introduce and study a new notion of patterns in Stirling and $k$-Stirling permutations, which we call block patterns. We prove a general result which allows us to compute generating functions for the occurrences of various block patterns…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
Understanding which phenotypic traits are consistently correlated throughout evolution is a highly pertinent problem in modern evolutionary biology. Here, we propose a multivariate phylogenetic latent liability model for assessing the…
In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…
Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical,…
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…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a genealogy--a rooted, binary, timed tree, with tips corresponding…
Understanding how stochastic and non-linear deterministic processes interact is a major challenge in population dynamics theory. After a short review, we introduce a stochastic individual-centered particle model to describe the evolution in…
One possible data encryption scheme is related to stream ciphers, which use a sufficiently long pseudo-random sequence. To increase the cryptographic strength of the cipher, linear shift algorithms (generated by linear recurrent sequences…
There is a long tradition of the axiomatic study of consensus methods in phylogenetics that satisfy certain desirable properties. One recently-introduced property is associative stability, which is desirable because it confers a…
We study the distribution and the popularity of some patterns in $k$-ary faro words, i.e. words over the alphabet $\{1, 2, \ldots, k\}$ obtained by interlacing the letters of two nondecreasing words of lengths differing by at most one. We…
This paper introduces a novel approach to contextual stochastic optimization, integrating operations research and machine learning to address decision-making under uncertainty. Traditional methods often fail to leverage contextual…