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Motivation: Inferring the structure of gene regulatory networks from high--throughput datasets remains an important and unsolved problem. Current methods are hampered by problems such as noise, low sample size, and incomplete…
The \emph{Steiner tree} problem is one of the fundamental and classical problems in combinatorial optimization. In this paper, we study this problem in the $\mathcal{CONGESTED}$ $\mathcal{CLIQUE}$ model of distributed computing and present…
We give an $m^{1+o(1)}\beta^{o(1)}$-time algorithm for generating a uniformly random spanning tree in an undirected, weighted graph with max-to-min weight ratio $\beta$. We also give an $m^{1+o(1)}\epsilon^{-o(1)}$-time algorithm for…
We give the first O(m polylog(n)) time algorithms for approximating maximum flows in undirected graphs and constructing polylog(n) -quality cut-approximating hierarchical tree decompositions. Our algorithm invokes existing algorithms for…
Let $G$ be an $n$-node simple directed planar graph with nonnegative edge weights. We study the fundamental problems of computing (1) a global cut of $G$ with minimum weight and (2) a~cycle of $G$ with minimum weight. The best previously…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all…
We present the first sublinear-in-$n$ round algorithm for sampling an approximately uniform spanning tree of an $n$-vertex graph in the CongestedClique model of distributed computing. In particular, our algorithm requires…
Phylogenetic networks are useful in representing the evolutionary history of taxa. In certain scenarios, one requires a way to compare different networks. In practice, this can be rather difficult, except within specific classes of…
In this paper, we study the problem of constructing a network by observing ordered connectivity constraints, which we define herein. These ordered constraints are made to capture realistic properties of real-world problems that are not…
Let G be a directed graph with n vertices and non-negative weights in its directed edges, embedded on a surface of genus g, and let f be an arbitrary face of G. We describe a randomized algorithm to preprocess the graph in O(gn log n) time…
Phylogenetic networks are notoriously difficult to reconstruct. Here we suggest that it can be useful to view unknown genetic distance along edges in phylogenetic networks as analogous to unknown resistance in electric circuits. This…
Quartet Reconstruction, the task of recovering a phylogenetic tree from smaller trees on four species called \textit{quartets}, is a well-studied problem in theoretical computer science with far-reaching connections to statistics, graph…
Phylogenetic networks are rooted directed acyclic graphs that represent evolutionary relationships between species whose past includes reticulation events such as hybridisation and horizontal gene transfer. To search the space of…
Finding dense subgraphs is a fundamental algorithmic tool in data mining, community detection, and clustering. In this problem, one aims to find an induced subgraph whose edge-to-vertex ratio is maximized. We study the directed case of this…
We present near-optimal algorithms for detecting small vertex cuts in the CONGEST model of distributed computing. Despite extensive research in this area, our understanding of the vertex connectivity of a graph is still incomplete,…
A distributed network is modeled by a graph having $n$ nodes (processors) and diameter $D$. We study the time complexity of approximating {\em weighted} (undirected) shortest paths on distributed networks with a $O(\log n)$ {\em bandwidth…
We show the existence of an exact mimicking network of $k^{O(\log k)}$ edges for minimum multicuts over a set of terminals in an undirected graph, where $k$ is the total capacity of the terminals, as well as a method for computing a…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
The maximum/minimum bisection problems are, given an edge-weighted graph, to find a bipartition of the vertex set into two sets whose sizes differ by at most one, such that the total weight of edges between the two sets is…