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Pathogen genome data offers valuable structure for spatial models, but its utility is limited by incomplete sequencing coverage. We propose a probabilistic framework for inferring genetic distances between unsequenced cases and known…
We present new and improved fixed-parameter algorithms for computing maximum agreement forests (MAFs) of pairs of rooted binary phylogenetic trees. The size of such a forest for two trees corresponds to their subtree prune-and-regraft…
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…
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 $n$…
The goal of this paper is to study the similarity between sequences using a distance between the \emph{context} trees associated to the sequences. These trees are defined in the framework of \emph{Sparse Probabilistic Suffix Trees} (SPST),…
Phylogenetic stochastic mapping is a method for reconstructing the history of trait changes on a phylogenetic tree relating species/organisms carrying the trait. State-of-the-art methods assume that the trait evolves according to a…
In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitch's maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular,…
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…
Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…
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…
Reconstructing ancestral gene orders in a given phylogeny is a classical problem in comparative genomics. Most existing methods compare conserved features in extant genomes in the phylogeny to define potential ancestral gene adjacencies,…
Bayesian Markov chain Monte Carlo explores tree space slowly, in part because it frequently returns to the same tree topology. An alternative strategy would be to explore tree space systematically, and never return to the same topology. In…
We study the problem of learning hypergraphs with shortest-path queries (SP-queries), and present the first provably optimal online algorithm for a broad and natural class of hypertrees that we call orderly hypertrees. Our online algorithm…
The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…
In phylogenetics, distances are often used to measure the incongruence between a pair of phylogenetic trees that are reconstructed by different methods or using different regions of genome. Motivated by the maximum parsimony principle in…
In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to…
For pattern recognition like image recognition, it has become clear that each machine-learning dictionary data actually became data in probability space belonging to Euclidean space. However, the distances in the Euclidean space and the…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
We give a greedy learning algorithm for reconstructing an evolutionary tree based on a certain harmonic average on triplets of terminal taxa. After the pairwise distances between terminal taxa are estimated from sequence data, the algorithm…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…