Related papers: Reconstructing a phylogenetic level-1 network from…
Rooted phylogenetic networks allow biologists to represent evolutionary relationships between present-day species by revealing ancestral speciation and hybridization events. A convenient and well-studied class of such networks are…
We study a Faulty Congested Clique model, in which an adversary may fail nodes in the network throughout the computation. We show that any task of $O(n\log{n})$-bit input per node can be solved in roughly $n$ rounds, where $n$ is the size…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
A probabilistic reconstruction of genealogies in a polyploid population (from 2x to 4x) is investigated, by considering genetic data analyzed as the probability of allele presence in a given genotype. Based on the likelihood of all possible…
Let M be a random (alpha n) x n matrix of rank r<<n, and assume that a uniformly random subset E of its entries is observed. We describe an efficient algorithm that reconstructs M from |E| = O(rn) observed entries with relative root mean…
We study recovering a 1D order from a noisy, locally sampled pairwise comparison matrix under a tight query budget. We recast the task as reconstructing a sparse, noisy line graph and present, to our knowledge, the first method that…
Phylogenetic reconciliation seeks to explain host-symbiont co-evolution by mapping parasite trees onto host trees through events such as cospeciation, duplication, host switching, and loss. Finding an optimal reconciliation that ensures…
Network topology plays a key role in many phenomena, from the spreading of diseases to that of financial crises. Whenever the whole structure of a network is unknown, one must resort to reconstruction methods that identify the least biased…
It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r).poly(m) whether there exists a phylogenetic network that…
Recent work has highlighted deep connections between sequence-length requirements for high-probability phylogeny reconstruction and the related problem of the estimation of ancestral sequences. In [Daskalakis et al.'09], building on the…
Phylogenetic networks are used to represent evolutionary scenarios in biology and linguistics. To find the most probable scenario, it may be necessary to compare candidate networks, to distinguish different networks, and to see when one…
The mathematical analysis of random phylogenetic networks via analytic and algorithmic methods has received increasing attention in the past years. In the present work we introduce branching process methods to their study. This approach…
We study tensor networks as a model of arithmetic computation for evaluating multilinear maps. These capture any algorithm based on low border rank tensor decompositions, such as $O(n^{\omega+\epsilon})$ time matrix multiplication, and in…
Genome-scale gene networks contain regulatory genes called hubs that have many interaction partners. These genes usually play an essential role in gene regulation and cellular processes. Despite recent advancements in high-throughput…
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…
We present the first parameterized analysis of a standard (1+1) Evolutionary Algorithm on a distribution of vertex cover problems. We show that if the planted cover is at most logarithmic, restarting the (1+1) EA every $O(n \log n)$ steps…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
In this paper we study detection and reconstruction of planted structures in Erd\H{o}s-R\'enyi random graphs. Motivated by a problem of communication security, we focus on planted structures that consist in a tree graph. For planted line…
Motivation: Word-based or `alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate. Most of these methods calculate pairwise distances for a set of input…
Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…