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In conservation biology, phylogenetic diversity (PD) provides a way to quantify the impact of the current rapid extinction of species on the evolutionary `Tree of Life'. This approach recognises that extinction not only removes species but…
The tree inclusion problem is, given two node-labeled trees $P$ and $T$ (the ``pattern tree'' and the ``target tree''), to locate every minimal subtree in $T$ (if any) that can be obtained by applying a sequence of node insertion operations…
The order preserving pattern matching (OPPM) problem is, given a pattern string $p$ and a text string $t$, find all substrings of $t$ which have the same relative orders as $p$. In this paper, we consider two variants of the OPPM problem…
We initiate the study of fine-grained completeness theorems for exact and approximate optimization in the polynomial-time regime. Inspired by the first completeness results for decision problems in P (Gao, Impagliazzo, Kolokolova, Williams,…
We identify a sufficient condition, treewidth-pliability, that gives a polynomial-time algorithm for an arbitrarily good approximation of the optimal value in a large class of Max-2-CSPs parameterised by the class of allowed constraint…
The well-studied Tai mapping between two rooted labeled trees $T_1(V_1, E_1)$ and $T_2(V_2, E_2)$ defines a one-to-one mapping between nodes in $T_1$ and $T_2$ that preserves ancestor relationship. For unordered trees the problem of finding…
The Matching Augmentation Problem (MAP) has recently received significant attention as an important step towards better approximation algorithms for finding cheap $2$-edge connected subgraphs. This has culminated in a…
Considering the worst-case scenario, junction tree algorithm remains the most general solution for exact MAP inference with polynomial run-time guarantees. Unfortunately, its main tractability assumption requires the treewidth of a…
I present a single algorithm which solves the clique problems, "What is the largest size clique?", "What are all the maximal cliques?" and the decision problem, "Does a clique of size k exist?" for any given graph in polynomial time. The…
We consider the problem of finding a subgraph of a given graph which maximizes a given function evaluated at its degree sequence. While the problem is intractable already for convex functions, we show that it can be solved in polynomial…
In this paper we consider $m$ ($m \geq 1$)conjunctions of Max-atoms that is atoms of the form $\max(z,y) + r \geq x$, where the offset $r$ is a real constant and $x,y,z$ are variables. We show that the Max-atom problem (MAP) belongs to…
In this paper, we consider different constrained partition problems for weighted trees and cactus graphs. We focus on the (l,u)-partition problem, which is the problem of partitioning a weighted graph into connected clusters such that each…
We revisit the Maximum Node-Disjoint Paths problem, the natural optimization version of Node-Disjoint Paths, where we are given a graph $G$, $k$ pairs of vertices $(s_i, t_i)$ and an integer $\ell$, and are asked whether there exist at…
Given a tree $T$ on $n$ vertices, and $k, b, s_1, \ldots, s_b \in N$, the Tree Partitioning problem asks if at most $k$ edges can be removed from $T$ so that the resulting components can be grouped into $b$ groups such that the number of…
Phylogenetic trees are leaf-labelled trees, where the leaves correspond to extant species (taxa), and the internal vertices represent ancestral species. The evolutionary history of a set of species can be explained by more than one…
The study of optimal decision trees has gained increasing attention in recent years; however, despite substantial progress, it still suffers from two major challenges: First, trees constructed by existing optimal decision tree (ODT)…
Many problems are NP-hard and, unless P = NP, do not admit polynomial-time exact algorithms. The fastest known exact algorithms exactly usually take time exponential in the input size. Much research effort has gone into obtaining faster…
We present a deterministic algorithm for solving a wide range of dynamic programming problems in trees in $O(\log D)$ rounds in the massively parallel computation model (MPC), with $O(n^\delta)$ words of local memory per machine, for any…
Semi-labeled trees are phylogenies whose internal nodes may be labeled by higher-order taxa. Thus, a leaf labeled Mus musculus could nest within a subtree whose root node is labeled Rodentia, which itself could nest within a subtree whose…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…