arXiv subjects

Norbert Zeh

Publications and source records attributed to Norbert Zeh.

At least 19 recordsLinked to original sources

arXiv2026

Orienting Unrooted Binary Networks Faster: Focus on the Generator

The problem of orienting an unrooted network to obtain a specific class of rooted phylogenetic networks is known to be NP-hard in many cases. In this paper, we introduce two algorithmic frameworks that yield significantly improved fixed-parameter tractable (FPT) algorithms parameterized by the network level $\ell$. Our first main contribution shows that for several prominent network classes, the core algorithmic difficulty lies in finding a directed spanning tree on the network's undirected generator. By enumerating these spanning trees in $O(5.3334^\ell + \ell)$ time and orienting all remaining edges in polynomial time, we solve the orientation problem in $O(5.3334^\ell \cdot n)$ time for tree-based networks and in $O(5.3334^\ell \cdot n^2)$ time for orchards, where $n$ is the number of vertices of the graph. Extending this approach with further branching yields $O(10.6667^\ell \cdot n^2)$-time algorithms for tree-child and normal networks. Our second technique bypasses spanning trees by directly guessing the placement of reticulations on the generator. This framework provides $O(12.2071^\ell \cdot n^2)$-time algorithms for temporal, reticulation-visible, and tree-sibling networks. Finally, we demonstrate the versatility of the reticulation-guessing framework by showing that even computing an orientation with minimum scanwidth is single-exponential FPT with respect to the level. Together, these results significantly improve the best-known running times for phylogenetic network orientation.

cs.DS↗

arXiv2026

A Class of Unrooted Phylogenetic Networks Inspired by the Properties of Rooted Tree-Child Networks

A directed phylogenetic network is tree-child if every non-leaf vertex has a child that is not a reticulation. As a class of directed phylogenetic networks, tree-child networks are very useful from a computational perspective. For example, several computationally difficult problems in phylogenetics become tractable when restricted to tree-child networks. At the same time, the class itself is rich enough to contain quite complex networks. Furthermore, checking whether a directed network is tree-child can be done in polynomial time. In this paper, we seek a class of undirected phylogenetic networks that is rich and computationally useful in a similar way to the class tree-child directed networks. A natural class to consider for this role is the class of tree-child-orientable networks which contains all those undirected phylogenetic networks whose edges can be oriented to create a tree-child network. However, we show here that recognizing such networks is NP-hard, even for binary networks, and as such this class is inappropriate for this role. Towards finding a class of undirected networks that fills a similar role to directed tree-child networks, we propose new classes called $q$-cuttable networks, for any integer $q\geq 1$. We show that these classes have many of the desirable properties, similar to tree-child networks in the rooted case, including being recognizable in polynomial time, for all $q\geq 1$. Towards showing the computational usefulness of the class, we show that the NP-hard problem Tree Containment is polynomial-time solvable when restricted to $q$-cuttable networks with $q\geq 3$.

math.CO↗

arXiv2026

Limits of Kernelization and Parametrization for Phylogenetic Diversity with Dependencies

In the Maximize Phylogenetic Diversity problem, we are given a phylogenetic tree that represents the genetic proximity of species, and we are asked to select a subset of species of maximum phylogenetic diversity to be preserved through conservation efforts, subject to budgetary constraints that allow only k species to be saved. This neglects that it is futile to preserve a predatory species if we do not also preserve at least a subset of the prey it feeds on. Thus, in the Optimizing PD with Dependencies ($\epsilon$-PDD) problem, we are additionally given a food web that represents the predator-prey relationships between species. The goal is to save a set of k species of maximum phylogenetic diversity such that for every saved species, at least one of its prey is also saved. This problem is NP-hard even when the phylogenetic tree is a star. The $\alpha$-PDD problem alters PDD by requiring that at least some fraction $\alpha$ of the prey of every saved species are also saved. In this paper, we study the parameterized complexity of $\alpha$-PDD. We prove that the problem is W[1]-hard and in XP when parameterized by the solution size k, the diversity threshold D, or their complements. When parameterized by the vertex cover number of the food web, $\alpha$-PDD is fixed-parameter tractable (FPT). A key measure of the computational difficulty of a problem that is FPT is the size of the smallest kernel that can be obtained. We prove that, when parameterized by the distance to clique, 1-PDD admits a linear kernel. Our main contribution is to prove that $\alpha$-PDD does not admit a polynomial kernel when parameterized by the vertex cover number plus the diversity threshold D, even if the phylogenetic tree is a star. This implies the non-existence of a polynomial kernel for $\alpha$-PDD also when parameterized by a range of structural parameters of the food web, such as its dist[...]

cs.CC↗

arXiv2026

The First Known Problem That Is FPT with Respect to Node Scanwidth but Not Treewidth

Structural parameters of graphs, such as treewidth, play a central role in the study of the parameterized complexity of graph problems. Motivated by the study of parametrized algorithms on phylogenetic networks, scanwidth was introduced recently as a new treewidth-like structural parameter for directed acyclic graphs (DAGs) that respects the edge directions in the DAG. The utility of this width measure has been demonstrated by results that show that a number of problems that are fixed-parameter tractable (FPT) with respect to both treewidth and scanwidth allow algorithms with a better dependence on scanwidth than on treewidth. More importantly, these scanwidth-based algorithms are often much simpler than their treewidth-based counterparts: the name ``scanwidth'' reflects that traversing a tree extension (the scanwidth-equivalent of a tree decomposition) of a DAG amounts to ``scanning'' the DAG according to a well-chosen topological ordering. While these results show that scanwidth is useful especially for solving problems on phylogenetic networks, all problems studied through the lens of scanwidth so far are either FPT with respect to both scanwidth and treewidth, or W[$\ell$]-hard, for some $\ell \ge 1$, with respect to both. In this paper, we show that scanwidth is not just a proxy for treewidth and provides information about the structure of the input graph not provided by treewidth, by proving a fairly stark complexity-theoretic separation between these two width measures. Specifically, we prove that Weighted Phylogenetic Diversity with Dependencies is FPT with respect to the scanwidth of the food web but W[$\ell$]-hard with respect to its treewidth, for all $\ell \ge 1$. To the best of our knowledge, no such separation between these two width measures has been shown for any problem before.

cs.CC↗

arXiv2025

When Many Trees Go to War: On Sets of Phylogenetic Trees With Almost No Common Structure

It is known that any two trees on the same $n$ leaves can be displayed by a network with $n-2$ reticulations, and there are two trees that cannot be displayed by a network with fewer reticulations. But how many reticulations are needed to display multiple trees? For any set of $t$ trees on $n$ leaves, there is a trivial network with $(t - 1)n$ reticulations that displays them. To do better, we have to exploit common structure of the trees to embed non-trivial subtrees of different trees into the same part of the network. In this paper, we show that for $t \in o(\sqrt{\lg n})$, there is a set of $t$ trees with virtually no common structure that could be exploited. More precisely, we show for any $t\in o(\sqrt{\lg n})$, there are $t$ trees such that any network displaying them has $(t-1)n - o(n)$ reticulations. For $t \in o(\lg n)$, we obtain a slightly weaker bound. We also prove that already for $t = c\lg n$, for any constant $c > 0$, there is a set of $t$ trees that cannot be displayed by a network with $o(n \lg n)$ reticulations, matching up to constant factors the known upper bound of $O(n \lg n)$ reticulations sufficient to display \emph{all} trees with $n$ leaves. These results are based on simple counting arguments and extend to unrooted networks and trees.

math.CO↗

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

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↗

arXiv2023

Another virtue of wavelet forests?

A wavelet forest for a text $T [1..n]$ over an alphabet $\sigma$ takes $n H_0 (T) + o (n \log \sigma)$ bits of space and supports access and rank on $T$ in $O (\log \sigma)$ time. K\"arkk\"ainen and Puglisi (2011) implicitly introduced wavelet forests and showed that when $T$ is the Burrows-Wheeler Transform (BWT) of a string $S$, then a wavelet forest for $T$ occupies space bounded in terms of higher-order empirical entropies of $S$ even when the forest is implemented with uncompressed bitvectors. In this paper we show experimentally that wavelet forests also have better access locality than wavelet trees and are thus interesting even when higher-order compression is not effective on $S$, or when $T$ is not a BWT at all.

cs.DS↗

arXiv2023

Sum-of-Local-Effects Data Structures for Separable Graphs

It is not difficult to think of applications that can be modelled as graph problems in which placing some facility or commodity at a vertex has some positive or negative effect on the values of all the vertices out to some distance, and we want to be able to calculate quickly the cumulative effect on any vertex's value at any time or the list of the most beneficial or most detrimential effects on a vertex. In this paper we show how, given an edge-weighted graph with constant-size separators, we can support the following operations on it in time polylogarithmic in the number of vertices and the number of facilities placed on the vertices, where distances between vertices are measured with respect to the edge weights: Add (v, f, w, d) places a facility of weight w and with effect radius d onto vertex v. Remove (v, f) removes a facility f previously placed on v using Add from v. Sum (v) or Sum (v, d) returns the total weight of all facilities affecting v or, with a distance parameter d, the total weight of all facilities whose effect region intersects the ``circle'' with radius d around v. Top (v, k) or Top (v, k, d) returns the k facilities of greatest weight that affect v or, with a distance parameter d, whose effect region intersects the ``circle'' with radius d around v. The weights of the facilities and the operation that Sum uses to ``sum'' them must form a semigroup. For Top queries, the weights must be drawn from a total order.

cs.DS↗

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↗

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↗

arXiv2020

Enhancement of Short Text Clustering by Iterative Classification

Short text clustering is a challenging task due to the lack of signal contained in such short texts. In this work, we propose iterative classification as a method to b o ost the clustering quality (e.g., accuracy) of short texts. Given a clustering of short texts obtained using an arbitrary clustering algorithm, iterative classification applies outlier removal to obtain outlier-free clusters. Then it trains a classification algorithm using the non-outliers based on their cluster distributions. Using the trained classification model, iterative classification reclassifies the outliers to obtain a new set of clusters. By repeating this several times, we obtain a much improved clustering of texts. Our experimental results show that the proposed clustering enhancement method not only improves the clustering quality of different clustering methods (e.g., k-means, k-means--, and hierarchical clustering) but also outperforms the state-of-the-art short text clustering methods on several short text datasets by a statistically significant margin.

cs.IR↗

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↗

arXiv2018

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↗

arXiv2016

Hybridization Number on Three Rooted Binary Trees is EPT

Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum of all indegrees minus the number of nodes plus one. The Hybridization Number problem takes as input a collection of phylogenetic trees and asks to construct a phylogenetic network that contains an embedding of each of the input trees and has a smallest possible hybridization number. We present an algorithm for the Hybridization Number problem on three binary trees on $n$ leaves, which runs in time $O(c^k poly(n))$, with $k$ the hybridization number of an optimal network and $c$ a constant. For two trees, an algorithm with running time $O(3.18^k n)$ was proposed before whereas an algorithm with running time $O(c^k poly(n))$ had prior to this article remained elusive for more than two trees. The algorithm for two trees uses the close connection to acyclic agreement forests to achieve a linear exponent in the running time, while previous algorithms for more than two trees (explicitly or implicitly) relied on a brute force search through all possible underlying network topologies, leading to running times that are not $O(c^k poly(n))$ for any $c$. The connection to acyclic agreement forests is much weaker for more than two trees, so even given the right agreement forest, reconstructing the network poses major challenges. We prove novel structural results that allow us to reconstruct a network without having to guess the underlying topology. Our techniques generalize to more than three input trees with the exception of one key lemma that maps nodes in the network to tree nodes and, thus, minimizes the amount of guessing involved in constructing the network. The main open problem therefore is to establish a similar mapping for more than three trees.

cs.DS↗

arXiv2013

QuPARA: Query-Driven Large-Scale Portfolio Aggregate Risk Analysis on MapReduce

Stochastic simulation techniques are used for portfolio risk analysis. Risk portfolios may consist of thousands of reinsurance contracts covering millions of insured locations. To quantify risk each portfolio must be evaluated in up to a million simulation trials, each capturing a different possible sequence of catastrophic events over the course of a contractual year. In this paper, we explore the design of a flexible framework for portfolio risk analysis that facilitates answering a rich variety of catastrophic risk queries. Rather than aggregating simulation data in order to produce a small set of high-level risk metrics efficiently (as is often done in production risk management systems), the focus here is on allowing the user to pose queries on unaggregated or partially aggregated data. The goal is to provide a flexible framework that can be used by analysts to answer a wide variety of unanticipated but natural ad hoc queries. Such detailed queries can help actuaries or underwriters to better understand the multiple dimensions (e.g., spatial correlation, seasonality, peril features, construction features, and financial terms) that can impact portfolio risk. We implemented a prototype system, called QuPARA (Query-Driven Large-Scale Portfolio Aggregate Risk Analysis), using Hadoop, which is Apache's implementation of the MapReduce paradigm. This allows the user to take advantage of large parallel compute servers in order to answer ad hoc risk analysis queries efficiently even on very large data sets typically encountered in practice. We describe the design and implementation of QuPARA and present experimental results that demonstrate its feasibility. A full portfolio risk analysis run consisting of a 1,000,000 trial simulation, with 1,000 events per trial, and 3,200 risk transfer contracts can be completed on a 16-node Hadoop cluster in just over 20 minutes.

cs.DC↗

arXiv2013

Fixed-Parameter and Approximation Algorithms for Maximum Agreement Forests

We present new and improved fixed-parameter algorithms for computing maximum agreement forests (MAFs) of pairs of rooted binary phylogenetic trees. The size of such a forest for two trees corresponds to their subtree prune-and-regraft distance and, if the agreement forest is acyclic, to their hybridization number. These distance measures are essential tools for understanding reticulate evolution. Our algorithm for computing maximum acyclic agreement forests is the first depth-bounded search algorithm for this problem. Our algorithms substantially outperform the best previous algorithms for these problems.

q-bio.PE↗

arXiv2013

Fixed-Parameter and Approximation Algorithms for Maximum Agreement Forests of Multifurcating Trees

We present efficient algorithms for computing a maximum agreement forest (MAF) of a pair of multifurcating (nonbinary) rooted trees. Our algorithms match the running times of the currently best algorithms for the binary case. The size of an MAF corresponds to the subtree prune-and-regraft (SPR) distance of the two trees and is intimately connected to their hybridization number. These distance measures are essential tools for understanding reticulate evolution, such as lateral gene transfer, recombination, and hybridization. Multifurcating trees arise naturally as a result of statistical uncertainty in current tree construction methods.

cs.DS↗