Related papers: Incomplete Directed Perfect Phylogeny in Linear Ti…
In computational phylogenetics, the problem of constructing a supertree of a given set of rooted input trees can be formalized in different ways, to cope with contradictory information in the input. We consider the Minimum Flip Supertree…
We study how to construct compressed datasets that suffice to recover optimal decisions in linear programs with an unknown cost vector $c$ lying in a prior set $\mathcal{C}$. Recent work by Bennouna et al. provides an exact geometric…
Recently, it has been proven that evolutionary algorithms produce good results for a wide range of combinatorial optimization problems. Some of the considered problems are tackled by evolutionary algorithms that use a representation which…
For a phylogenetic tree, the phylogenetic diversity of a set A of taxa is the total weight of edges on paths to A. Finding small sets of maximal diversity is crucial for conservation planning, as it indicates where limited resources can be…
Several algorithms build on the perfect phylogeny model to infer evolutionary trees. This problem is particularly hard when evolutionary trees are inferred from the fraction of genomes that have mutations in different positions, across…
This paper categorizes the parameterized complexity of the algorithmic problems Perfect Phylogeny and Triangulating Colored Graphs when parameterized by the number of genes and colors, respectively. We show that they are complete for the…
The perfect phylogeny problem is a classic problem in computational biology, where we seek an unrooted phylogeny that is compatible with a set of qualitative characters. Such a tree exists precisely when an intersection graph associated…
In this paper, a fully compressed pattern matching problem is studied. The compression is represented by straight-line programs (SLPs), i.e. a context-free grammars generating exactly one string; the term fully means that both the pattern…
We show fast deterministic algorithms for fundamental problems on forests in the challenging low-space regime of the well-known Massive Parallel Computation (MPC) model. A recent breakthrough result by Coy and Czumaj [STOC'22] shows that,…
The Exact Circular Pattern Matching (ECPM) problem consists of reporting every occurrence of a rotation of a pattern $P$ in a text $T$. In many real-world applications, specifically in computational biology, circular rotations are of…
We introduce an extension of Dual Dynamic Programming (DDP) to solve convex nonlinear dynamic programming equations. We call Inexact DDP (IDDP) this extension which applies to situations where some or all primal and dual subproblems to be…
Determinantal point processes (DPPs) offer an elegant tool for encoding probabilities over subsets of a ground set. Discrete DPPs are parametrized by a positive semidefinite matrix (called the DPP kernel), and estimating this kernel is key…
Integer Linear Programming with $n$ binary variables and $m$ many $0/1$-constraints can be solved in time $2^{\tilde O(m^2)} \text{poly}(n)$ and it is open whether the dependence on $m$ is optimal. Several seemingly unrelated problems,…
We introduce an extension of Dual Dynamic Programming (DDP) to solve linear dynamic programming equations. We call this extension IDDP-LP which applies to situations where some or all primal and dual subproblems to be solved along the…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $\Delta$, the {\em exact string matching} problem consists of finding all occurrences of…
We revisit classic string problems considered in the area of parameterized complexity, and study them through the lens of dynamic data structures. That is, instead of asking for a static algorithm that solves the given instance efficiently,…
Reconciliation methods aim at recovering macro evolutionary events and at localizing them in the species history, by observing discrepancies between gene family trees and species trees. In this article we introduce an Integer Linear…
The evolutionary processes of complex systems contain critical information regarding their functional characteristics. The generation time of edges provides insights into the historical evolution of various networked complex systems, such…
In this paper, we consider tree decompositions, branch decompositions, and clique decompositions. We improve the running time of dynamic programming algorithms on these graph decompositions for a large number of problems as a function of…