arXiv subjects

Mark Jones

Publications and source records attributed to Mark Jones.

At least 55 records · Page 3Linked to original sources

arXiv2020

Maximum parsimony distance on phylogenetictrees: a linear kernel and constant factor approximation algorithm

Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we address this shortcoming by showing that the problem is fixed parameter tractable. We do this by establishing a linear kernel i.e., that after applying certain reduction rules the resulting instance has size that is bounded by a linear function of the distance. As powerful corollaries to this result we prove that the problem permits a polynomial-time constant-factor approximation algorithm; that the treewidth of a natural auxiliary graph structure encountered in phylogenetics is bounded by a function of the distance; and that the distance is within a constant factor of the size of a maximum agreement forest of the two trees, a well studied object in phylogenetics.

cs.DS↗

arXiv2019

Combining Networks using Cherry Picking Sequences

Phylogenetic networks are important for the study of evolution. The number of methods to find such networks is increasing, but most such methods can only reconstruct small networks. To find bigger networks, one can attempt to combine small networks. In this paper, we study the {\sc Network Hybridization} problem, a problem of combining networks into another network with low complexity. We characterize this complexity via a restricted problem, {\sc Tree-child Network Hybridization}, and we present an FPT algorithm to efficiently solve this restricted problem.

cs.DM↗

arXiv2019

Modelling Airway Geometry as Stock Market Data using Bayesian Changepoint Detection

Numerous lung diseases, such as idiopathic pulmonary fibrosis (IPF), exhibit dilation of the airways. Accurate measurement of dilatation enables assessment of the progression of disease. Unfortunately the combination of image noise and airway bifurcations causes high variability in the profiles of cross-sectional areas, rendering the identification of affected regions very difficult. Here we introduce a noise-robust method for automatically detecting the location of progressive airway dilatation given two profiles of the same airway acquired at different time points. We propose a probabilistic model of abrupt relative variations between profiles and perform inference via Reversible Jump Markov Chain Monte Carlo sampling. We demonstrate the efficacy of the proposed method on two datasets; (i) images of healthy airways with simulated dilatation; (ii) pairs of real images of IPF-affected airways acquired at 1 year intervals. Our model is able to detect the starting location of airway dilatation with an accuracy of 2.5mm on simulated data. The experiments on the IPF dataset display reasonable agreement with radiologists. We can compute a relative change in airway volume that may be useful for quantifying IPF disease progression. The code is available at https://github.com/quan14/Modelling_Airway_Geometry_as_Stock_Market_Data

cs.LG↗

arXiv2019

Cutting an alignment with Ockham's razor

In this article, we investigate different parsimony-based approaches towards finding recombination breakpoints in a multiple sequence alignment. This recombination detection task is crucial in order to avoid errors in evolutionary analyses caused by mixing together portions of sequences which had a different evolution history. Following an overview of the field of recombination detection, we formulate four computational problems for this task with different objective functions. The four problems aim to minimize (1) the total homoplasy of all blocks (2) the maximum homoplasy per block (3) the total homoplasy ratio of all blocks and (4) the maximum homoplasy ratio per block. We describe algorithms for each of these problems, which are fixed-parameter tractable (FPT) when the characters are binary. We have implemented and tested the algorithms on simulated data, showing that minimizing the total homoplasy gives, in most cases, the most accurate results. Our implementation and experimental data have been made publicly available. Finally, we also consider the problem of combining blocks into non-contiguous blocks consisting of at most p contiguous parts. Fixing the homoplasy h of each block to 0, we show that this problem is NP-hard when p >= 3, but polynomial-time solvable for p = 2. Furthermore, the problem is FPT with parameter h for binary characters when p = 2. A number of interesting problems remain open.

q-bio.PE↗

arXiv2019

Polynomial-Time Algorithms for Phylogenetic Inference Problems involving duplication and reticulation

A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree based on a model with speciation and duplication where duplications are clustered in duplication episodes. The goal is to minimize the number of such episodes. The second variant, Parental Hybridization, aims at inferring a species \emph{network} based on a model with speciation and reticulation. The goal is to minimize the number of reticulation events. It is a variant of the well-studied Hybridization Number problem with a more generous view on which gene trees are consistent with a given species network. We show that these seemingly different problems are in fact closely related and can, surprisingly, both be solved in polynomial time, using a structure we call "beaded trees". However, we also show that methods based on these problems have to be used with care because the optimal species phylogenies always have a restricted form. To mitigate this problem, we introduce a new variant of Unrestricted Minimal Episodes Inference that minimizes the duplication episode depth. We prove that this new variant of the problem can also be solved in polynomial time

q-bio.PE↗

arXiv2019

Reconstructing Tree-Child Networks from Reticulate-Edge-Deleted Subnetworks

Network reconstruction lies at the heart of phylogenetic research. Two well studied classes of phylogenetic networks include tree-child networks and level-$k$ networks. In a tree-child network, every non-leaf node has a child that is a tree node or a leaf. In a level-$k$ network, the maximum number of reticulations contained in a biconnected component is $k$. Here, we show that level-$k$ tree-child networks are encoded by their reticulate-edge-deleted subnetworks, which are subnetworks obtained by deleting a single reticulation edge, if $k\geq 2$. Following this, we provide a polynomial-time algorithm for uniquely reconstructing such networks from their reticulate-edge-deleted subnetworks. Moreover, we show that this can even be done when considering subnetworks obtained by deleting one reticulation edge from each biconnected component with $k$ reticulations.

math.CO↗

arXiv2019

A Practical Fixed-Parameter Algorithm for Constructing Tree-Child Networks from Multiple Binary Trees

We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm uses the recently introduced framework of cherry picking sequences and runs in $O((8k)^k \mathrm{poly}(n, t))$ time, where $n$ is the number of leaves of every tree, $t$ is the number of trees, and $k$ is the reticulation number of the constructed network. Moreover, we provide an efficient parallel implementation of the algorithm and show that it can deal with up to $100$ input trees on a standard desktop computer, thereby providing a major improvement over previous phylogenetic network construction methods.

cs.DM↗

arXiv2019

Constructing a Consensus Phylogeny from a Leaf-Removal Distance

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 genes or species, and aims at finding a single tree that minimizes the leaf-removal distance to the input trees. This problem is a specific instance of the general consensus/supertree problem, widely used to combine or summarize discordant evolutionary trees. The problem we introduce is specifically tailored to address the case of discrepancies between the input trees due to the misplacement of individual taxa. Most supertree or consensus tree problems are computationally intractable, and we show that the problem we introduce is also NP-hard. We provide tractability results in form of a 2-approximation algorithm. We also introduce a variant that minimizes the maximum number $d$ of leaves that are removed from any input tree, and provide a parameterized algorithm for this problem with parameter $d$.

cs.DS↗

arXiv2019

A third strike against perfect phylogeny

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 parsimonious trees are preferable as a hypothesis of evolution. A classical result states that 2-state characters permit a perfect phylogeny precisely if each subset of 2 characters permits one. More recently, it was shown that for 3-state characters the same property holds but for size-3 subsets. A long-standing open problem asked whether such a constant exists for each number of states. More precisely, it has been conjectured that for any fixed integer $r$, there exists a constant $f(r)$ such that a set of $r$-state characters $C$ has a perfect phylogeny if and only if every subset of at most $f(r)$ characters has a perfect phylogeny. In this paper, we show that this conjecture is false. In particular, we show that for any constant $t$, there exists a set $C$ of $8$-state characters such that $C$ has no perfect phylogeny, but there exists a perfect phylogeny for every subset of $t$ characters. This negative result complements the two negative results ("strikes") of Bodlaender et al. We reflect on the consequences of this third strike, pointing out that while it does close off some routes for efficient algorithm development, many others remain open.

cs.DM↗

arXiv2018

Treewidth of display graphs: bounds, brambles and applications

Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a function of many common dissimilarity measures between phylogenetic trees and this has been leveraged in fixed parameter tractability results. Here we further elucidate the properties of display graphs and their interaction with treewidth. We show that it is NP-hard to recognize display graphs, but that display graphs of bounded treewidth can be recognized in linear time. Next we show that if a phylogenetic network displays (i.e. topologically embeds) a phylogenetic tree, the treewidth of their display graph is bounded by a function of the treewidth of the original network (and also by various other parameters). In fact, using a bramble argument we show that this treewidth bound is sharp up to an additive term of 1. We leverage this bound to give an FPT algorithm, parameterized by treewidth, for determining whether a network displays a tree, which is an intensively-studied problem in the field. We conclude with a discussion on the future use of display graphs and treewidth in phylogenetics.

cs.DS↗

arXiv2018

Not all phylogenetic networks are leaf-reconstructible

Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks with at least five leaves can be uniquely reconstructed from their subnetworks obtained by deleting a single leaf and suppressing degree-2 vertices. Here, we show that this conjecture is false, by presenting a counter example for each possible number of leaves that is at least~4. Moreover, we show that the conjecture is still false when restricted to binary networks.

math.CO↗

arXiv2017

Exploring the tiers of rooted phylogenetic network space using tail moves

Popular methods for exploring the space of rooted phylogenetic trees use rearrangement moves such as rNNI (rooted Nearest Neighbour Interchange) and rSPR (rooted Subtree Prune and Regraft). Recently, these moves were generalized to rooted phylogenetic networks, which are a more suitable representation of reticulate evolutionary histories, and it was shown that any two rooted phylogenetic networks of the same complexity are connected by a sequence of either rSPR or rNNI moves. Here, we show that this is possible using only tail moves, which are a restricted version of rSPR moves on networks that are more closely related to rSPR moves on trees. The connectedness still holds even when we restrict to distance-1 tail moves (a localized version of tail-moves). Moreover, we give bounds on the number of (distance-1) tail moves necessary to turn one network into another, which in turn yield new bounds for rSPR, rNNI and SPR (i.e. the equivalent of rSPR on unrooted networks). The upper bounds are constructive, meaning that we can actually find a sequence with at most this length for any pair of networks. Finally, we show that finding a shortest sequence of tail or rSPR moves is NP-hard.

math.CO↗

arXiv2016

Parameterized Complexity of the $k$-Arc Chinese Postman Problem

In the Mixed Chinese Postman Problem (MCPP), given an edge-weighted mixed graph $G$ ($G$ may have both edges and arcs), our aim is to find a minimum weight closed walk traversing each edge and arc at least once. The MCPP parameterized by the number of edges was known to be fixed-parameter tractable using a simple argument. Solving an open question of van Bevern et al., we prove that the MCPP parameterized by the number of arcs is also fixed-parameter tractable. Our proof is more involved and, in particular, uses a well-known result of Marx, O'Sullivan and Razgon (2013) on the treewidth of torso graphs with respect to small separators. We obtain a small cut analog of this result, and use it to construct a tree decomposition which, despite not having bounded width, has other properties allowing us to design a fixed-parameter algorithm.

cs.DS↗

arXiv2016

Chinese Postman Problem on Edge-Colored Multigraphs

It is well-known that the Chinese postman problem on undirected and directed graphs is polynomial-time solvable. We extend this result to edge-colored multigraphs. Our result is in sharp contrast to the Chinese postman problem on mixed graphs, i.e., graphs with directed and undirected edges, for which the problem is NP-hard.

cs.DS↗

arXiv2016

Acyclicity in Edge-Colored Graphs

A walk $W$ in edge-colored graphs is called properly colored (PC) if every pair of consecutive edges in $W$ is of different color. We introduce and study five types of PC acyclicity in edge-colored graphs such that graphs of PC acyclicity of type $i$ is a proper superset of graphs of acyclicity of type $i+1$, $i=1,2,3,4.$ The first three types are equivalent to the absence of PC cycles, PC trails, and PC walks, respectively. While graphs of types 1, 2 and 3 can be recognized in polynomial time, the problem of recognizing graphs of type 4 is, somewhat surprisingly, NP-hard even for 2-edge-colored graphs (i.e., when only two colors are used). The same problem with respect to type 5 is polynomial-time solvable for all edge-colored graphs. Using the five types, we investigate the border between intractability and tractability for the problems of finding the maximum number of internally vertex disjoint PC paths between two vertices and the minimum number of vertices to meet all PC paths between two vertices.

cs.DM↗

arXiv2016

Cryptographic Enforcement of Information Flow Policies without Public Information via Tree Partitions

We may enforce an information flow policy by encrypting a protected resource and ensuring that only users authorized by the policy are able to decrypt the resource. In most schemes in the literature that use symmetric cryptographic primitives, each user is assigned a single secret and derives decryption keys using this secret and publicly available information. Recent work has challenged this approach by developing schemes, based on a chain partition of the information flow policy, that do not require public information for key derivation, the trade-off being that a user may need to be assigned more than one secret. In general, many different chain partitions exist for the same policy and, until now, it was not known how to compute an appropriate one. In this paper, we introduce the notion of a tree partition, of which chain partitions are a special case. We show how a tree partition may be used to define a cryptographic enforcement scheme and prove that such schemes can be instantiated in such a way as to preserve the strongest security properties known for cryptographic enforcement schemes. We establish a number of results linking the amount of secret material that needs to be distributed to users with a weighted acyclic graph derived from the tree partition. These results enable us to develop efficient algorithms for deriving tree and chain partitions that minimize the amount of secret material that needs to be distributed.

cs.CR↗

arXiv2015

Linear-Vertex Kernel for the Problem of Packing $r$-Stars into a Graph without Long Induced Paths

Let integers $r\ge 2$ and $d\ge 3$ be fixed. Let ${\cal G}_d$ be the set of graphs with no induced path on $d$ vertices. We study the problem of packing $k$ vertex-disjoint copies of $K_{1,r}$ ($k\ge 2$) into a graph $G$ from parameterized preprocessing, i.e., kernelization, point of view. We show that every graph $G\in {\cal G}_d$ can be reduced, in polynomial time, to a graph $G'\in {\cal G}_d$ with $O(k)$ vertices such that $G$ has at least $k$ vertex-disjoint copies of $K_{1,r}$ if and only if $G'$ has. Such a result is known for arbitrary graphs $G$ when $r=2$ and we conjecture that it holds for every $r\ge 2$.

cs.DS↗

arXiv2015

On the Workflow Satisfiability Problem with Class-Independent Constraints

A workflow specification defines sets of steps and users. An authorization policy determines for each user a subset of steps the user is allowed to perform. Other security requirements, such as separation-of-duty, impose constraints on which subsets of users may perform certain subsets of steps. The \emph{workflow satisfiability problem} (WSP) is the problem of determining whether there exists an assignment of users to workflow steps that satisfies all such authorizations and constraints. An algorithm for solving WSP is important, both as a static analysis tool for workflow specifications, and for the construction of run-time reference monitors for workflow management systems. Given the computational difficulty of WSP, it is important, particularly for the second application, that such algorithms are as efficient as possible. We introduce class-independent constraints, enabling us to model scenarios where the set of users is partitioned into groups, and the identities of the user groups are irrelevant to the satisfaction of the constraint. We prove that solving WSP is fixed-parameter tractable (FPT) for this class of constraints and develop an FPT algorithm that is useful in practice. We compare the performance of the FPT algorithm with that of SAT4J (a pseudo-Boolean SAT solver) in computational experiments, which show that our algorithm significantly outperforms SAT4J for many instances of WSP. User-independent constraints, a large class of constraints including many practical ones, are a special case of class-independent constraints for which WSP was proved to be FPT (Cohen {\em et al.}, J. Artif. Intel. Res. 2014). Thus our results considerably extend our knowledge of the fixed-parameter tractability of WSP.

cs.CR↗