arXiv subjects

Mark Jones

Publications and source records attributed to Mark Jones.

At least 37 records · Page 2Linked to original sources

arXiv2025

Reconstructing semi-directed level-1 networks using few quarnets

Semi-directed networks are partially directed graphs that model evolution where the directed edges represent reticulate evolutionary events. We present an algorithm that reconstructs binary $n$-leaf semi-directed level-1 networks in $O( n^2)$ time from its quarnets (4-leaf subnetworks). Our method assumes we have direct access to all quarnets, yet uses only an asymptotically optimal number of $O(n \log n)$ quarnets. When the network is assumed to contain no triangles, our method instead relies only on four-cycle quarnets and the splits of the other quarnets. A variant of our algorithm works with quartets rather than quarnets and we show that it reconstructs most of a semi-directed level-1 network from an asymptotically optimal $O(n \log n)$ of the quartets it displays. Additionally, we provide an $O(n^3)$ time algorithm that reconstructs the tree-of-blobs of any binary $n$-leaf semi-directed network with unbounded level from $O(n^3)$ splits of its quarnets.

q-bio.PE↗

arXiv2024

A Wild Sheep Chase Through an Orchard

Orchards are a biologically relevant class of phylogenetic networks as they can describe treelike evolutionary histories augmented with horizontal transfer events. Moreover, the class has attractive mathematical characterizations that can be exploited algorithmically. On the other hand, undirected orchard networks have hardly been studied yet. Here, we prove that deciding whether an undirected, binary phylogenetic network is an orchard -- or equivalently, whether it has an orientation that makes it a rooted orchard -- is NP-hard. For this, we introduce a new characterization of undirected orchards which could be useful for proving positive results.

q-bio.PE↗

arXiv2024

A Simple 4-Approximation Algorithm for Maximum Agreement Forests on Multiple Unrooted Binary Trees

We present a simple 4-approximation algorithm for computing a maximum agreement forest of multiple unrooted binary trees. This algorithm applies LP rounding to an extension of a recent ILP formulation of the maximum agreement forest problem on two trees by Van Wersch al. We achieve the same approximation ratio as the algorithm of Chen et al. but our algorithm is extremely simple. We also prove that no algorithm based on the ILP formulation by Van Wersch et al. can achieve an approximation ratio of $4 - \varepsilon$, for any $\varepsilon > 0$, even on two trees. To this end, we prove that the integrality gap of the ILP approaches 4 as the size of the two input trees grows.

cs.DS↗

arXiv2024

Maximizing Phylogenetic Diversity under Time Pressure: Planning with Extinctions Ahead

Phylogenetic Diversity (PD) is a measure of the overall biodiversity of a set of present-day species (taxa) within a phylogenetic tree. In Maximize Phylogenetic Diversity (MPD) one is asked to find a set of taxa (of bounded size/cost) for which this measure is maximized. MPD is a relevant problem in conservation planning, where there are not enough resources to preserve all taxa and minimizing the overall loss of biodiversity is critical. We consider an extension of this problem, motivated by real-world concerns, in which each taxon not only requires a certain amount of time to save, but also has an extinction time after which it can no longer be saved. In addition there may be multiple teams available to work on preservation efforts in parallel; we consider two variants of the problem based on whether teams are allowed to collaborate on the same taxa. These problems have much in common with machine scheduling problems, (with taxa corresponding to tasks and teams corresponding to machines), but with the objective function (the phylogenetic diversity) inspired by biological considerations. Our extensions are, in contrast to the original MPD, NP-hard, even in very restricted cases. We provide several algorithms and hardness-results and thereby show that the problems are fixed-parameter tractable (FPT) when parameterized the target phylogenetic diversity, and that the problem where teams are allowed to collaborate is FPT when parameterized the acceptable loss of diversity.

cs.CC↗

arXiv2023

Dataset for Investigating Anomalies in Compute Clusters

The dataset was collected for 332 compute nodes throughout May 19 - 23, 2023. May 19 - 22 characterizes normal compute cluster behavior, while May 23 includes an anomalous event. The dataset includes eight CPU, 11 disk, 47 memory, and 22 Slurm metrics. It represents five distinct hardware configurations and contains over one million records, totaling more than 180GB of raw data.

cs.DC↗

arXiv2023

Orienting undirected phylogenetic networks

This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of the root and reticulation vertices, can be oriented as a directed nonbinary phylogenetic network. Moreover, we characterize when this is possible and show that, in such instances, the resulting directed nonbinary phylogenetic network is unique. In addition, without being given the location of the root and the reticulation vertices, we describe an algorithm for deciding whether an undirected binary phylogenetic network $N$ can be oriented as a directed binary phylogenetic network of a certain class. The algorithm is fixed-parameter tractable (FPT) when the parameter is the level of $N$ and is applicable to classes of directed phylogenetic networks that satisfy certain conditions. As an example, we show that the well-studied class of binary tree-child networks satisfies these conditions.

cs.DS↗

arXiv2023

Embedding phylogenetic trees in networks of low treewidth

Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called \textsc{Tree Containment}, arises when validating networks constructed by phylogenetic inference methods.We present the first algorithm for (rooted) \textsc{Tree Containment} using the treewidth $t$ of the input network $N$ as parameter, showing that the problem can be solved in $2^{O(t^2)}\cdot|N|$ time and space.

q-bio.PE↗

arXiv2023

PyPWA: A Software Toolkit for Parameter Optimization and Amplitude Analysis

PyPWA is a toolkit designed to optimize parametric models describing data and generate simulated distributions according to a model. Its software has been written within the python ecosystem with the goal of performing Amplitude or Partial Wave Analysis (PWA) in nuclear and particle physics experiments. We briefly describe the general features of amplitude analysis and the PyPWA software design and usage. We provide benchmarks of the scaling and an example of its application.

physics.data-an↗

arXiv2023

Making a Network Orchard by Adding Leaves

Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the network class ideal for capturing evolutionary histories that involve horizontal gene transfers. Here, we study the minimum number of additional leaves needed to make a network orchard. We demonstrate that computing this proximity measure for a given network is NP-hard and describe a tight upper bound. We also give an equivalent measure based on vertex labellings to construct a mixed integer linear programming formulation. Our experimental results, which include both real-world and synthetic data, illustrate the effectiveness of our implementation.

math.CO↗

arXiv2022

A Near-Linear Kernel for Two-Parsimony Distance

The maximum parsimony distance $d_{\textrm{MP}}(T_1,T_2)$ and the bounded-state maximum parsimony distance $d_{\textrm{MP}}^t(T_1,T_2)$ measure the difference between two phylogenetic trees $T_1,T_2$ in terms of the maximum difference between their parsimony scores for any character (with $t$ a bound on the number of states in the character, in the case of $d_{\textrm{MP}}^t(T_1,T_2)$). While computing $d_{\textrm{MP}}(T_1, T_2)$ was previously shown to be fixed-parameter tractable with a linear kernel, no such result was known for $d_{\textrm{MP}}^t(T_1,T_2)$. In this paper, we prove that computing $d_{\textrm{MP}}^t(T_1, T_2)$ is fixed-parameter tractable for all~$t$. Specifically, we prove that this problem has a kernel of size $O(k \lg k)$, where $k = d_{\textrm{MP}}^t(T_1, T_2)$. As the primary analysis tool, we introduce the concept of leg-disjoint incompatible quartets, which may be of independent interest.

cs.DS↗

arXiv2022

Performance of photosensors in a high-rate environment for gas Cherenkov detectors

The solenoidal large intensity device (SoLID) at Jefferson Lab will push the boundaries of luminosity for a large-acceptance detector, which necessitates the use of a light-gas threshold Cherenkov counter for online event selection. Due to the high luminosity, the single-photon background rate in this counter can exceed 160 kHz/cm$^2$ at the photosensors. Therefore, it is essential to validate the high-rate limits of the planned photosensors and readout electronics in order to mitigate the risk of failure. We report on the design and an early set of studies carried out using a small telescopic Cherenkov device in a high-rate environment up to 60 kHz/cm$^2$, in Hall C at Jefferson Lab. Commercially available multi-anode photomultipliers (MaPMT) and low-cost large-area picosecond photodetectors (LAPPD) were tested using the JLab FADC250 modules for readout. The test beam results show that the MaPMT array and the internal stripline LAPPD can detect and identify single-electron and pair-production events in high-rate environments. Due to its higher quantum efficiency, the MaPMT array provided a better separation between the single-electron and the pair-production events compared to the internal stripline LAPPD. A GEANT4 simulation confirms the experimental performance of our telescopic device.

physics.ins-det↗

arXiv2022

Consistency of orthology and paralogy constraints in the presence of gene transfers

Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot be explained via a gene tree that both contains the depicted orthologs/paralogs, and that is consistent with a species tree $S$. This idea of detecting errors through inconsistency with a species tree has mostly been studied in the presence of speciation and duplication events only. In this work, we ask: could the given set of relations be consistent if we allow lateral gene transfers in the evolutionary model? We formalize this question and provide a variety of algorithmic results regarding the underlying problems. Namely, we show that deciding if a relation graph $R$ is consistent with a given species network $N$ is NP-hard, and that it is W[1]-hard under the parameter "minimum number of transfers". However, we present an FPT algorithm based on the degree of the $DS$-tree associated with $R$. We also study analogous problems in the case that the transfer highways on a species tree are unknown.

cs.DS↗

arXiv2021

Orchard Networks are Trees with Additional Horizontal Arcs

Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits, without any biological justification. Here, we show that orchard networks can be interpreted as trees with additional \emph{horizontal} arcs. Therefore, they are closely related to tree-based networks, where the difference is that in tree-based networks the additional arcs do not need to be horizontal. Then, we use this new characterization to show that the space of orchard networks is connected under the rNNI rearrangement move, with a diameter of at most $4kn+n\lceil \log_2(n) \rceil +2k+6n-8$.

math.CO↗

arXiv2021

Level-$2$ networks from shortest and longest distances

Recently it was shown that a certain class of phylogenetic networks, called level-$2$ networks, cannot be reconstructed from their associated distance matrices. In this paper, we show that they can be reconstructed from their induced shortest and longest distance matrices. That is, if two level-$2$ networks induce the same shortest and longest distance matrices, then they must be isomorphic. We further show that level-$2$ networks are reconstructible from their shortest distance matrices if and only if they do not contain a subgraph from a family of graphs. A generator of a network is the graph obtained by deleting all pendant subtrees and suppressing degree-$2$ vertices. We also show that networks with a leaf on every generator side is reconstructible from their induced shortest distance matrix, regardless of level.

math.CO↗

arXiv2021

Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes

Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees. These networks are able to incorporate reticulate evolutionary events such as hybridization, introgression, and lateral gene transfer. Recently, network-based Markov models of DNA sequence evolution have been introduced along with model-based methods for reconstructing phylogenetic networks. For these methods to be consistent, the network parameter needs to be identifiable from data generated under the model. Here, we show that the semi-directed network parameter of a triangle-free, level-1 network model with any fixed number of reticulation vertices is generically identifiable under the Jukes-Cantor, Kimura 2-parameter, or Kimura 3-parameter constraints.

q-bio.PE↗

arXiv2021

Challenges for the interaction region design of the Future Circular Collider FCC-ee

The FCC-ee is a proposed future high-energy, high-intensity and high-precision lepton collider. Here, we present the latest development for the FCC-ee interaction regions, which shall ensure optimum conditions for the particle physics experiments. We discuss measures of background reduction and a revised interaction region layout including a low impedance compact beam chamber design. We also discuss the possible impact of the radiation generated in the interaction region including beamstrahlung.

physics.acc-ph↗

arXiv2020

New FPT algorithms for finding the temporal hybridization number for sets of phylogenetic trees

We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of $m$ binary trees with $n$ leaves each with a running time of $O(5^k\cdot n\cdot m)$, where $k$ is the minimum temporal hybridization number. We also present the concept of temporal distance, which is a measure for how close a tree-child network is to being temporal. Then we introduce an algorithm for computing a tree-child network with temporal distance at most $d$ and at most $k$ reticulations in $O((8k)^d5^ k\cdot n\cdot m)$ time. Lastly, we introduce a $O(6^kk!\cdot k\cdot n^2)$ time algorithm for computing a minimum temporal hybridization network for a set of two nonbinary trees. We also provide an implementation of all algorithms and an experimental analysis on their performance.

cs.DS↗

arXiv2020

A Unifying Characterization of Tree-based Networks and Orchard Networks using Cherry Covers

Phylogenetic networks are used to study evolutionary relationships between species in biology. Such networks are often categorized into classes by their topological features, which stem from both biological and computational motivations. We study two network classes in this paper: tree-based networks and orchard networks. Tree-based networks are those that can be obtained by inserting edges between the edges of an underlying tree. Orchard networks are a recently introduced generalization of the class of tree-child networks. Structural characterizations have already been discovered for tree-based networks; this is not the case for orchard networks. In this paper, we introduce cherry covers---a unifying characterization of both network classes---in which we decompose the edges of the networks into so-called cherry shapes and reticulated cherry shapes. We show that cherry covers can be used to characterize the class of tree-based networks as well as the class of orchard networks. Moreover, we also generalize these results to non-binary networks.

math.CO↗