Related papers: Incomplete Directed Perfect Phylogeny in Linear Ti…
Determinantal Point Processes (DPPs) are a widely used probabilistic model for negatively correlated sets. DPPs have been successfully employed in Machine Learning applications to select a diverse, yet representative subset of data. In…
In a graph, a perfect matching cut is an edge cut that is a perfect matching. Perfect Matching Cut (PMC) is the problem of deciding whether a given graph has a perfect matching cut, and is known to be NP-complete. We revisit the problem and…
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…
Dynamic high resolution data on human population distribution is of great importance for a wide spectrum of activities and real-life applications, but is too difficult and expensive to obtain directly. Therefore, generating fine-scaled…
Determinantal point processes (DPPs) are an important concept in random matrix theory and combinatorics. They have also recently attracted interest in the study of numerical methods for machine learning, as they offer an elegant "missing…
In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…
We give a simple characterization of the functions that can be computed deterministically by anonymous processes in dynamic networks, depending on the number of leaders in the network. In addition, we provide efficient distributed…
Physics-informed neural networks (PINNs) have shown promising potential for solving partial differential equations (PDEs) using deep learning. However, PINNs face training difficulties for evolutionary PDEs, particularly for dynamical…
Network Phylogenetic Diversity (Network-PD) is a measure for the diversity of a set of species based on a rooted phylogenetic network (with branch lengths and inheritance probabilities on the reticulation edges) describing the evolution of…
Motivation: Many inference tools use the Perfect Phylogeny Model (PPM) to learn trees from noisy variant allele frequency (VAF) data. Learning in this setting is hard, and existing tools use approximate or heuristic algorithms. An…
In this paper, we present a new exact algorithm for counting perfect matchings, which relies on neither inclusion-exclusion principle nor tree-decompositions. For any bipartite graph of $2n$ nodes and $\Delta n$ edges such that $\Delta \geq…
Perfect phylogenies are fundamental in the study of evolutionary trees because they capture the situation when each evolutionary trait emerges only once in history; if such events are believed to be rare, then by Occam's Razor such…
This paper studies the complicated interplay of the completion time (as a measure of throughput) and the decoding delay performance in instantly decodable network coded (IDNC) systems over wireless broadcast erasure channels with memory,…
In this paper, we initiate the study of the dynamic maintenance of $2$-edge-connectivity relationships in directed graphs. We present an algorithm that can update the $2$-edge-connected blocks of a directed graph with $n$ vertices through a…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
In the NP-hard Optimizing PD with Dependencies (PDD) problem, the input consists of a phylogenetic tree $T$ over a set of taxa $X$, a food-web that describes the prey-predator relationships in $X$, and integers $k$ and $D$. The task is to…
Sequence assembly from short reads is an important problem in biology. It is known that solving the sequence assembly problem exactly on a bi-directed de Bruijn graph or a string graph is intractable. However finding a Shortest Double…
Fully dynamic graph is a data structure that (1) supports edge insertions and deletions and (2) answers problem specific queries. The time complexity of (1) and (2) are referred to as the update time and the query time respectively. There…
We revisit once more the problem of designing an oracle for answering connectivity queries in undirected graphs in the presence of vertex failures. Specifically, given an undirected graph $G$ with $n$ vertices and $m$ edges and an integer…
In a directed graph $D$ on vertex set $v_1,\dots ,v_n$, a \emph{forward arc} is an arc $v_iv_j$ where $i<j$. A pair $v_i,v_j$ is \emph{forward connected} if there is a directed path from $v_i$ to $v_j$ consisting of forward arcs. In the…