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The \emph{central levels problem} asserts that the subgraph of the $(2m+1)$-dimensional hypercube induced by all bitstrings with at least $m+1-\ell$ many 1s and at most $m+\ell$ many 1s, i.e., the vertices in the middle $2\ell$ levels, has a Hamilton cycle for any $m\geq 1$ and $1\le \ell\le m+1$.\ud This problem was raised independently by Buck and Wiedemann, Savage, Gregor and {\v{S}}krekovski, and by Shen and Williams, and it is a common generalization of the well-known \emph{middle levels problem}, namely the case $\ell=1$, and classical binary Gray codes, namely the case $\ell=m+1$.\ud In this paper we present a general constructive solution of the central levels problem.\ud Our results also imply the existence of optimal cycles through any sequence of $\ell$ consecutive levels in the $n$-dimensional hypercube for any $n\ge 1$ and $1\le \ell \le n+1$.\ud Moreover, extending an earlier construction by Streib and Trotter, we construct a Hamilton cycle through the $n$-dimensional hypercube, $n\geq 2$, that contains the symmetric chain decomposition constructed by Greene and Kleitman in the 1970s, and we provide a loopless algorithm for computing the corresponding Gray code.

We consider the problem of finding an incremental solution to a cardinality-constrained maximization problem that not only captures the solution for a fixed cardinality, but also describes how to gradually grow the solution as the cardinality bound increases. The goal is to find an incremental solution that guarantees a good competitive ratio against the optimum solution for all cardinalities simultaneously. The central challenge is to characterize maximization problems where this is possible, and to determine the best-possible competitive ratio that can be attained. A lower bound of 2.18 and an upper bound of φ + 1 ≈ 2.618 are known on the competitive ratio for monotone and accountable objectives [Bernstein et al., Math. Prog., 2022], which capture a wide range of maximization problems. We introduce a continuization technique and identify an optimal incremental algorithm that provides strong evidence that φ + 1 is the best-possible competitive ratio. Using this continuization, we obtain an improved lower bound of 2.246 by studying a particular recurrence relation whose characteristic polynomial has complex roots exactly beyond the lower bound. Based on the optimal continuous algorithm combined with a scaling approach, we also provide a 1.772-competitive randomized algorithm. We complement this by a randomized lower bound of 1.447 via Yao’s principle., LIPIcs, Vol. 261, 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023), pages 47:1-47:17

This work describes the winning implementation of the CG:SHOP 2023 Challenge. The topic of the Challenge was the convex cover problem: given a polygon P (with holes), find a minimum-cardinality set of convex polygons whose union equals P. We use a three-step approach: (1) Create a suitable partition of P. (2) Compute a visibility graph of the pieces of the partition. (3) Solve a vertex clique cover problem on the visibility graph, from which we then derive the convex cover. This way we capture the geometric difficulty in the first step and the combinatorial difficulty in the third step., LIPIcs, Vol. 258, 39th International Symposium on Computational Geometry (SoCG 2023), pages 66:1-66:9

We focus on efficient computations of topological descriptors for voxel data. This type of data includes 2D greyscale images, 3D medical scans, but also higher-dimensional scalar fields arising from physical simulations. In recent years we have seen an increase in applications of topological methods for such data. However, computational issues remain an obstacle. We therefore propose a streaming scheme which simplifies large 3-dimensional voxel data - while provably retaining its persistent homology. We combine this scheme with an efficient boundary matrix reduction implementation, obtaining an end-to-end tool for persistent homology of large data. Computational experiments show its state-of-the-art performance. In particular, we are now able to robustly handle complex datasets with several billions voxels on a regular laptop. A software implementation called Cubicle is available as open-source: https://bitbucket.org/hubwag/cubicle., LIPIcs, Vol. 258, 39th International Symposium on Computational Geometry (SoCG 2023), pages 60:1-60:16

We consider finite algebraic structures and ask whether every solution of a given system of equations satisfies some other equation. This can be formulated as checking the validity of certain first order formulae called quasi-identities. Checking the validity of quasi-identities is closely linked to solving systems of equations. For systems of equations over finite algebras with finitely many fundamental operations, a complete P/NPC dichotomy is known, while the situation appears to be more complicated for single equations. The complexity of checking the validity of a quasi-identity lies between the complexity of term equivalence (checking whether two terms induce the same function) and the complexity of solving systems of polynomial equations. We prove that for each finite algebra with a Mal'cev term and finitely many fundamental operations, checking the validity of quasi-identities is coNP-complete if the algebra is not abelian, and in P when the algebra is abelian., LIPIcs, Vol. 254, 40th International Symposium on Theoretical Aspects of Computer Science (STACS 2023), pages 4:1-4:12

A subset of $[n] = \{1,2,\ldots,n\}$ is called stable if it forms an independent set in the cycle on the vertex set $[n]$. In 1978, Schrijver proved via a topological argument that for all integers $n$ and $k$ with $n \geq 2k$, the family of stable $k$-subsets of $[n]$ cannot be covered by $n-2k+1$ intersecting families. We study two total search problems whose totality relies on this result. In the first problem, denoted by $\mathsf{Schrijve}r(n,k,m)$, we are given an access to a coloring of the stable $k$-subsets of $[n]$ with $m = m(n,k)$ colors, where $m \leq n-2k+1$, and the goal is to find a pair of disjoint subsets that are assigned the same color. While for $m = n-2k+1$ the problem is known to be $\mathsf{PPA}$-complete, we prove that for $m < d \cdot \lfloor \frac{n}{2k+d-2} \rfloor$, with $d$ being any fixed constant, the problem admits an efficient algorithm. For $m = \lfloor n/2 \rfloor-2k+1$, we prove that the problem is efficiently reducible to the $\mathsf{Kneser}$ problem. Motivated by the relation between the problems, we investigate the family of unstable $k$-subsets of $[n]$, which might be of independent interest. In the second problem, called Unfair Independent Set in Cycle, we are given $\ell$ subsets $V_1, \ldots, V_\ell$ of $[n]$, where $\ell \leq n-2k+1$ and $|V_i| \geq 2$ for all $i \in [\ell]$, and the goal is to find a stable $k$-subset $S$ of $[n]$ satisfying the constraints $|S \cap V_i| \leq |V_i|/2$ for $i \in [\ell]$. We prove that the problem is $\mathsf{PPA}$-complete and that its restriction to instances with $n=3k$ is at least as hard as the Cycle plus Triangles problem, for which no efficient algorithm is known. On the contrary, we prove that there exists a constant $c$ for which the restriction of the problem to instances with $n \geq c \cdot k$ can be solved in polynomial time., 23 pages

The Schrijver graph $S(n,k)$ is defined for integers $n$ and $k$ with $n \geq 2k$ as the graph whose vertices are all the $k$-subsets of $\{1,2,\ldots,n\}$ that do not include two consecutive elements modulo $n$, where two such sets are adjacent if they are disjoint. A result of Schrijver asserts that the chromatic number of $S(n,k)$ is $n-2k+2$ (Nieuw Arch. Wiskd., 1978). In the computational Schrijver problem, we are given an access to a coloring of the vertices of $S(n,k)$ with $n-2k+1$ colors, and the goal is to find a monochromatic edge. The Schrijver problem is known to be complete in the complexity class $\mathsf{PPA}$. We prove that it can be solved by a randomized algorithm with running time $n^{O(1)} \cdot k^{O(k)}$, hence it is fixed-parameter tractable with respect to the parameter $k$., 19 pages. arXiv admin note: substantial text overlap with arXiv:2204.06761

The Kneser graph $K(n,k)$ is defined for integers $n$ and $k$ with $n \geq 2k$ as the graph whose vertices are all the $k$-subsets of $\{1,2,\ldots,n\}$ where two such sets are adjacent if they are disjoint. A classical result of Lov\'asz asserts that the chromatic number of $K(n,k)$ is $n-2k+2$. In the computational Kneser problem, we are given an oracle access to a coloring of the vertices of $K(n,k)$ with $n-2k+1$ colors, and the goal is to find a monochromatic edge. We present a randomized algorithm for the Kneser problem with running time $n^{O(1)} \cdot k^{O(k)}$. This shows that the problem is fixed-parameter tractable with respect to the parameter $k$. The analysis involves structural results on intersecting families and on induced subgraphs of Kneser graphs. We also study the Agreeable-Set problem of assigning a small subset of a set of $m$ items to a group of $\ell$ agents, so that all agents value the subset at least as much as its complement. As an application of our algorithm for the Kneser problem, we obtain a randomized polynomial-time algorithm for the Agreeable-Set problem for instances that satisfy $\ell \geq m - O(\frac{\log m}{\log \log m})$. We further show that the Agreeable-Set problem is at least as hard as a variant of the Kneser problem with an extended access to the input coloring., Comment: 24 pages

Persistent homology is perhaps the most popular and useful tool offered by topological data analysis - with point-cloud data being the most common setup. Its older cousin, the Euler characteristic curve (ECC) is less expressive - but far easier to compute. It is particularly suitable for analyzing imaging data, and is commonly used in fields ranging from astrophysics to biomedical image analysis. These fields are embracing GPU computations to handle increasingly large datasets. We therefore propose an optimized GPU implementation of ECC computation for 2D and 3D grayscale images. The goal of this paper is twofold. First, we offer a practical tool, illustrating its performance with thorough experimentation - but also explain its inherent shortcomings. Second, this simple algorithm serves as a perfect backdrop for highlighting basic GPU programming techniques that make our implementation so efficient - and some common pitfalls we avoided. This is intended as a step towards a wider usage of GPU programming in computational geometry and topology software. We find this is particularly important as geometric and topological tools are used in conjunction with modern, GPU-accelerated machine learning frameworks., LIPIcs, Vol. 224, 38th International Symposium on Computational Geometry (SoCG 2022), pages 64:1-64:16

We continue the study initiated by Bonomo-Braberman and Gonzalez in 2020 on r-locally checkable problems. We propose a dynamic programming algorithm that takes as input a graph with an associated clique-width expression and solves a 1-locally checkable problem under certain restrictions. We show that it runs in polynomial time in graphs of bounded clique-width, when the number of colors of the locally checkable problem is fixed. Furthermore, we present a first extension of our framework to global properties by taking into account the sizes of the color classes, and consequently enlarge the set of problems solvable in polynomial time with our approach in graphs of bounded clique-width. As examples, we apply this setting to show that, when parameterized by clique-width, the [k]-Roman domination problem is FPT, and the k-community problem, Max PDS and other variants are XP., LIPIcs, Vol. 248, 33rd International Symposium on Algorithms and Computation (ISAAC 2022), pages 31:1-31:20

An intensive line of research on fixed parameter tractability of integer programming is focused on exploiting the relation between the sparsity of a constraint matrix A and the norm of the elements of its Graver basis. In particular, integer programming is fixed parameter tractable when parameterized by the primal tree-depth and the entry complexity of A, and when parameterized by the dual tree-depth and the entry complexity of A; both these parameterization imply that A is sparse, in particular, the number of its non-zero entries is linear in the number of columns or rows, respectively. We study preconditioners transforming a given matrix to an equivalent sparse matrix if it exists and provide structural results characterizing the existence of a sparse equivalent matrix in terms of the structural properties of the associated column matroid. In particular, our results imply that the 𝓁₁-norm of the Graver basis is bounded by a function of the maximum 𝓁₁-norm of a circuit of A. We use our results to design a parameterized algorithm that constructs a matrix equivalent to an input matrix A that has small primal/dual tree-depth and entry complexity if such an equivalent matrix exists. Our results yield parameterized algorithms for integer programming when parameterized by the 𝓁₁-norm of the Graver basis of the constraint matrix, when parameterized by the 𝓁₁-norm of the circuits of the constraint matrix, when parameterized by the smallest primal tree-depth and entry complexity of a matrix equivalent to the constraint matrix, and when parameterized by the smallest dual tree-depth and entry complexity of a matrix equivalent to the constraint matrix., LIPIcs, Vol. 229, 49th International Colloquium on Automata, Languages, and Programming (ICALP 2022), pages 29:1-29:20

Various forms of sorting problems have been studied over the years. Recently, two kinds of sorting puzzle apps are popularized. In these puzzles, we are given a set of bins filled with colored units, balls or water, and some empty bins. These puzzles allow us to move colored units from a bin to another when the colors involved match in some way or the target bin is empty. The goal of these puzzles is to sort all the color units in order. We investigate computational complexities of these puzzles. We first show that these two puzzles are essentially the same from the viewpoint of solvability. That is, an instance is sortable by ball-moves if and only if it is sortable by water-moves. We also show that every yes-instance has a solution of polynomial length, which implies that these puzzles belong to in NP. We then show that these puzzles are NP-complete. For some special cases, we give polynomial-time algorithms. We finally consider the number of empty bins sufficient for making all instances solvable and give non-trivial upper and lower bounds in terms of the number of filled bins and the capacity of bins., 17 pages, 10 figures

A Lyndon word is a word that is lexicographically smaller than all of its non-trivial rotations (e.g. ananas is a Lyndon word; banana is not a Lyndon word due to its smaller rotation abanan). The Lyndon forest (or equivalently Lyndon table) identifies maximal Lyndon factors of a word, and is of great combinatoric interest, e.g. when finding maximal repetitions in words. While optimal linear time algorithms for computing the Lyndon forest are known, none of them work in an online manner. We present algorithms that compute the Lyndon forest of a word in a reverse online manner, processing the input word from back to front. We assume a general ordered alphabet, i.e. the only elementary operations on symbols are comparisons of the form less-equal-greater. We start with a naive algorithm and show that, despite its quadratic worst-case behaviour, it already takes expected linear time on words drawn uniformly at random. We then introduce a much more sophisticated algorithm that takes linear time in the worst case. It borrows some ideas from the offline algorithm by Bille et al. (ICALP 2020), combined with new techniques that are necessary for the reverse online setting. While the back-to-front approach for this computation is rather natural (see Franek and Liut, PSC 2019), the steps required to achieve linear time are surprisingly intricate. We envision that our algorithm will be useful for the online computation of maximal repetitions in words., LIPIcs, Vol. 223, 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022), pages 13:1-13:23

You provide us with a matroid and an initial base. We say that a subset of the bases "belongs to us" if we can visit each one via a sequence of base exchanges starting from the initial base. It is well-known that "All your base are belong to us". We refine this classic result by showing that it can be done by a simple greedy algorithm. For example, the spanning trees of a graph can be generated by edge exchanges using the following greedy rule: Minimize the larger label of an edge that enters or exits the current spanning tree and which creates a spanning tree that is new (i.e., hasn't been visited already). Amazingly, this works for any graph, for any labeling of its edges, for any initial spanning tree, and regardless of how you choose the edge with the smaller label in each exchange. Furthermore, by maintaining a small amount of information, we can generate each successive spanning tree without storing the previous trees. In general, for any matroid, we can greedily compute a listing of all its bases matroid such that consecutive bases differ by a base exchange. Our base exchange Gray codes apply a prefix-exchange on a prefix-minor of the matroid, and we can generate these orders using "history-free" iterative algorithms. More specifically, we store O(m) bits of data, and use O(m) time per base assuming O(1) time independence and coindependence oracles. Our work generalizes and extends a number of previous results. For example, the bases of the uniform matroid are combinations, and they belong to us using homogeneous transpositions via an Eades-McKay style order. Similarly, the spanning trees of fan graphs belong to us via face pivot Gray codes, which extends recent results of Cameron, Grubb, and Sawada [Pivot Gray Codes for the Spanning Trees of a Graph ft. the Fan, COCOON 2021]., LIPIcs, Vol. 226, 11th International Conference on Fun with Algorithms (FUN 2022), pages 22:1-22:28

The number of ordered trees (also known as plane trees) with n nodes is the (n-1)st Catalan number C_{n-1}. An ordered tree can be stored directly using nodes and pointers, or represented indirectly by a Dyck word. This paper presents a loopless algorithm for generating ordered trees with n nodes using pointer-based representations. In other words, we spend 𝒪(C_{n-1})-time to generate all of the trees, and moreover, the delay between consecutive trees is worst-case 𝒪(1)-time. To achieve this run-time, each tree must differ from the previous by a constant amount. In other words, the algorithm must create a type of Gray code order. Our algorithm operates on the children of a node like a stack, by popping the first child off of one node’s stack and pushing the result onto another node’s stack. We refer to this pop-push operation as a pull, and consecutive trees in our order differ by one or two pulls. There is a simple two-case successor rule that determines the pulls to apply directly from the current tree. When converted to Dyck words, our rule corresponds to a left-shift, and these shift generate a cool-lex variant of lexicographic order. Our results represent the first pull Gray code for ordered trees, and the first fully published loopless algorithm for ordered trees using pointer representations. More importantly, our algorithm is incredibly simple: A full implementation in C, including initialization and output, uses only three loops and three if-else blocks. Our work also establishes a simultaneous Gray code for Dyck words, ordered trees, and also binary trees, using cool-lex order., LIPIcs, Vol. 248, 33rd International Symposium on Algorithms and Computation (ISAAC 2022), pages 53:1-53:16

Front Matter, Table of Contents, Preface, Conference Organization, LIPIcs, Vol. 244, 30th Annual European Symposium on Algorithms (ESA 2022), pages 0:i-0:xxii

LIPIcs, Volume 244, ESA 2022, Complete Volume, LIPIcs, Vol. 244, 30th Annual European Symposium on Algorithms (ESA 2022), pages 1-1406

Combinatorial reconfiguration studies reachability and related questions over the solution space formed by feasible solutions of an instance of a combinatorial search problem. For example, as the solution space for the satisfiability problem, we may consider the subgraph of the hypercube induced by the satisfying truth assignments of a given CNF formula. Then, the reachability problem for satisfiability is the problem of asking whether two given satisfying truth assignments are contained in the same connected component of the solution space. The study of reconfiguration problems has motivation from a variety of fields such as puzzles, statistical physics, and industry. In this decade, reconfiguration problems have been studied intensively for many central combinatorial search problems, such as satisfiability, independent set and coloring, from the algorithmic viewpoints. Many reconfiguration problems are PSPACE-complete in general, although several efficiently solvable cases have been obtained. In this talk, I will give a broad introduction of combinatorial reconfiguration., LIPIcs, Vol. 223, 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022), pages 1:1-1:1

A Conflict-Free Open Neighborhood coloring, abbreviated CFON^* coloring, of a graph G = (V,E) using k colors is an assignment of colors from a set of k colors to a subset of vertices of V(G) such that every vertex sees some color exactly once in its open neighborhood. The minimum k for which G has a CFON^* coloring using k colors is called the CFON^* chromatic number of G, denoted by χ_{ON}^*(G). The analogous notion for closed neighborhood is called CFCN^* coloring and the analogous parameter is denoted by χ_{CN}^*(G). The problem of deciding whether a given graph admits a CFON^* (or CFCN^*) coloring that uses k colors is NP-complete. Below, we describe briefly the main results of this paper. - For k ≥ 3, we show that if G is a K_{1,k}-free graph then χ_{ON}^*(G) = O(k²log Δ), where Δ denotes the maximum degree of G. Dębski and Przybyło in [J. Graph Theory, 2021] had shown that if G is a line graph, then χ_{CN}^*(G) = O(log Δ). As an open question, they had asked if their result could be extended to claw-free (K_{1,3}-free) graphs, which are a superclass of line graphs. Since it is known that the CFCN^* chromatic number of a graph is at most twice its CFON^* chromatic number, our result positively answers the open question posed by Dębski and Przybyło. - We show that if the minimum degree of any vertex in G is Ω(Δ/{log^ε Δ}) for some ε ≥ 0, then χ_{ON}^*(G) = O(log^{1+ε}Δ). This is a generalization of the result given by Dębski and Przybyło in the same paper where they showed that if the minimum degree of any vertex in G is Ω(Δ), then χ_{ON}^*(G)= O(logΔ). - We give a polynomial time algorithm to compute χ_{ON}^*(G) for interval graphs G. This answers in positive the open question posed by Reddy [Theoretical Comp. Science, 2018] to determine whether the CFON^* chromatic number can be computed in polynomial time on interval graphs. - We explore biconvex graphs, a subclass of bipartite graphs and give a polynomial time algorithm to compute their CFON^* chromatic number. This is interesting as Abel et al. [SIDMA, 2018] had shown that it is NP-complete to decide whether a planar bipartite graph G has χ_{ON}^*(G) = k where k ∈ {1, 2, 3}., LIPIcs, Vol. 241, 47th International Symposium on Mathematical Foundations of Computer Science (MFCS 2022), pages 19:1-19:14

The Weisfeiler-Leman (WL) algorithm is a combinatorial procedure that computes colorings on graphs, which can often be used to detect their (non-)isomorphism. Particularly the 1- and 2-dimensional versions 1-WL and 2-WL have received much attention, due to their numerous links to other areas of computer science. Knowing the expressive power of a certain dimension of the algorithm usually amounts to understanding the computed colorings. An increase in the dimension leads to finer computed colorings and, thus, more graphs can be distinguished. For example, on the class of planar graphs, 3-WL solves the isomorphism problem. However, the expressive power of 2-WL on the class is poorly understood (and, in particular, it may even well be that it decides isomorphism). In this paper, we investigate the colorings computed by 2-WL on planar graphs. Towards this end, we analyze the graphs induced by edge color classes in the graph. Based on the obtained classification, we show that for every 3-connected planar graph, it holds that: a) after coloring all pairs with their 2-WL color, the graph has fixing number 1 with respect to 1-WL, or b) there is a 2-WL-definable matching that can be used to transform the graph into a smaller one, or c) 2-WL detects a connected subgraph that is essentially the graph of a Platonic or Archimedean solid, a prism, a cycle, or a bipartite graph K_{2,𝓁}. In particular, the graphs from case (a) are identified by 2-WL., LIPIcs, Vol. 229, 49th International Colloquium on Automata, Languages, and Programming (ICALP 2022), pages 81:1-81:20

Minimum weighted vertex cover is the NP-hard graph problem of choosing a subset of vertices incident to all edges such that the sum of the weights of the chosen vertices is minimum. Previous efforts for solving this in practice have typically been based on search-based iterative heuristics or exact algorithms that rely on reduction rules and branching techniques. Although exact methods have shown success in solving instances with up to millions of vertices efficiently, they are limited in practice due to the NP-hardness of the problem. We present a new hybrid method that combines elements from exact methods, iterative search, and graph neural networks (GNNs). More specifically, we first compute a greedy solution using reduction rules whenever possible. If no such rule applies, we consult a GNN model that selects a vertex that is likely to be in or out of the solution, potentially opening up for further reductions. Finally, we use an improved local search strategy to enhance the solution further. Extensive experiments on graphs of up to a billion edges show that the proposed GNN-based approach finds better solutions than existing heuristics. Compared to exact solvers, the method produced solutions that are, on average, 0.04% away from the optimum while taking less time than all state-of-the-art alternatives., LIPIcs, Vol. 233, 20th International Symposium on Experimental Algorithms (SEA 2022), pages 12:1-12:17

For an undirected graph G and distinct vertices s₁, t₁, … , s_k, t_k called terminals, the shortest k-disjoint paths problem asks for k pairwise vertex-disjoint paths P₁, … , P_k such that P_i connects s_i and t_i for i = 1, … , k and the sum of their lengths is minimized. This problem is a natural optimization version of the well-known k-disjoint paths problem, and its polynomial solvability is widely open. One of the best results on the shortest k-disjoint paths problem is due to Datta et al. [Datta et al., 2018], who present a polynomial-time algorithm for the case when G is planar and all the terminals are on one face. In this paper, we extend this result by giving a polynomial-time randomized algorithm for the case when all the terminals except one are on some face of G. In our algorithm, we combine the arguments of Datta et al. with some results on the shortest disjoint (A + B)-paths problem shown by Hirai and Namba [Hirai and Namba, 2018]. To this end, we present a non-trivial bijection between k disjoint paths and disjoint (A + B)-paths, which is a key technical contribution of this paper., LIPIcs, Vol. 248, 33rd International Symposium on Algorithms and Computation (ISAAC 2022), pages 47:1-47:15

Molecular phylogenetics is a fundamental branch of biology. It studies the evolutionary relationships among the individuals of a population through their biological sequences, and may provide insights about the origin and the evolution of viral diseases, or highlight complex evolutionary trajectories. In this paper we develop a method called phyBWT, describing how to use the extended Burrows-Wheeler Transform (eBWT) for a collection of DNA sequences to directly reconstruct phylogeny, bypassing the alignment against a reference genome or de novo assembly. Our phyBWT hinges on the combinatorial properties of the eBWT positional clustering framework. We employ eBWT to detect relevant blocks of the longest shared substrings of varying length (unlike the k-mer-based approaches that need to fix the length k a priori), and build a suitable decomposition leading to a phylogenetic tree, step by step. As a result, phyBWT is a new alignment-, assembly-, and reference-free method that builds a partition tree without relying on the pairwise comparison of sequences, thus avoiding to use a distance matrix to infer phylogeny. The preliminary experimental results on sequencing data show that our method can handle datasets of different types (short reads, contigs, or entire genomes), producing trees of quality comparable to that found in the benchmark phylogeny., LIPIcs, Vol. 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), pages 23:1-23:19

Let $\widetilde{\alpha}$ be a length-$L$ cyclic sequence of characters from a size-$K$ alphabet $\mathcal{A}$ such that the number of occurrences of any length-$m$ string on $\mathcal{A}$ as a substring of $\widetilde{\alpha}$ is $\lfloor L / K^m \rfloor$ or $\lceil L / K^m \rceil$. When $L = K^N$ for any positive integer $N$, $\widetilde{\alpha}$ is a de Bruijn sequence of order $N$, and when $L \neq K^N$, $\widetilde{\alpha}$ shares many properties with de Bruijn sequences. We describe an algorithm that outputs some $\widetilde{\alpha}$ for any combination of $K \geq 2$ and $L \geq 1$ in $O(L)$ time using $O(L \log K)$ space. This algorithm extends Lempel's recursive construction of a binary de Bruijn sequence. An implementation written in Python is available at https://github.com/nelloreward/pkl., Comment: 18 pages, 3 algorithms, 1 table; v2 refines language and fixes references

We develop new algorithmic methods with provable guarantees for feature selection in regard to categorical data clustering. While feature selection is one of the most common approaches to reduce dimensionality in practice, most of the known feature selection methods are heuristics. We study the following mathematical model. We assume that there are some inadvertent (or undesirable) features of the input data that unnecessarily increase the cost of clustering. Consequently, we want to select a subset of the original features from the data such that there is a small-cost clustering on the selected features. More precisely, for given integers l (the number of irrelevant features) and k (the number of clusters), budget B, and a set of n categorical data points (represented by m-dimensional vectors whose elements belong to a finite set of values Σ), we want to select m-l relevant features such that the cost of any optimal k-clustering on these features does not exceed B. Here the cost of a cluster is the sum of Hamming distances (l0-distances) between the selected features of the elements of the cluster and its center. The clustering cost is the total sum of the costs of the clusters. We use the framework of parameterized complexity to identify how the complexity of the problem depends on parameters k, B, and |Σ|. Our main result is an algorithm that solves the Feature Selection problem in time f(k,B,|Σ|)⋅m^{g(k,|Σ|)}⋅n² for some functions f and g. In other words, the problem is fixed-parameter tractable parameterized by B when |Σ| and k are constants. Our algorithm for Feature Selection is based on a solution to a more general problem, Constrained Clustering with Outliers. In this problem, we want to delete a certain number of outliers such that the remaining points could be clustered around centers satisfying specific constraints. One interesting fact about Constrained Clustering with Outliers is that besides Feature Selection, it encompasses many other fundamental problems regarding categorical data such as Robust Clustering, Binary and Boolean Low-rank Matrix Approximation with Outliers, and Binary Robust Projective Clustering. Thus as a byproduct of our theorem, we obtain algorithms for all these problems. We also complement our algorithmic findings with complexity lower bounds., LIPIcs, Vol. 202, 46th International Symposium on Mathematical Foundations of Computer Science (MFCS 2021), pages 14:1-14:14

The Weighted ℱ-Vertex Deletion for a class ℱ of graphs asks, weighted graph G, for a minimum weight vertex set S such that G-S ∈ ℱ. The case when ℱ is minor-closed and excludes some graph as a minor has received particular attention but a constant-factor approximation remained elusive for Weighted ℱ-Vertex Deletion. Only three cases of minor-closed ℱ are known to admit constant-factor approximations, namely Vertex Cover, Feedback Vertex Set and Diamond Hitting Set. We study the problem for the class ℱ of θ_c-minor-free graphs, under the equivalent setting of the Weighted c-Bond Cover problem, and present a constant-factor approximation algorithm using the primal-dual method. For this, we leverage a structure theorem implicit in [Joret et al., SIDMA'14] which states the following: any graph G containing a θ_c-minor-model either contains a large two-terminal protrusion, or contains a constant-size θ_c-minor-model, or a collection of pairwise disjoint constant-sized connected sets that can be contracted simultaneously to yield a dense graph. In the first case, we tame the graph by replacing the protrusion with a special-purpose weighted gadget. For the second and third case, we provide a weighting scheme which guarantees a local approximation ratio. Besides making an important step in the quest of (dis)proving a constant-factor approximation for Weighted ℱ-Vertex Deletion, our result may be useful as a template for algorithms for other minor-closed families., LIPIcs, Vol. 207, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2021), pages 7:1-7:14

The Home Service Assignment, Routing, and Appointment scheduling (H-SARA) problem integrates the strategic fleet-sizing, tactical assignment, operational vehicle routing and scheduling problems at different decision levels, with a single period planning horizon and uncertainty (stochasticity) from the service duration, travel time, and customer cancellation rate. We propose a stochastic mixed-integer linear programming model for the H-SARA problem. Additionally, a reduced deterministic version is introduced which allows to solve small-scale instances to optimality with two acceleration approaches. For larger instances, we develop a tailored two-stage decision support system that provides high-quality and in-time solutions based on information revealed at different stages. Our solution method aims to reduce various costs under stochasticity, to create reasonable routes with balanced workload and team-based customer service zones, and to increase customer satisfaction by introducing a two-stage appointment notification system updated at different time stages before the actual service. Our two-stage heuristic is competitive to CPLEX’s exact solution methods in providing time and cost-effective decisions and can update previously-made decisions based on an increased level of information. Results show that our two-stage heuristic is able to tackle reasonable-size instances and provides good-quality solutions using less time compared to the deterministic and stochastic models on the same set of simulated instances., OASIcs, Vol. 96, 21st Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2021), pages 4:1-4:21

We investigate the relationship between various isomorphism invariants for finite groups. Specifically, we use the Weisfeiler-Leman dimension (WL) to characterize, compare and quantify the effectiveness and complexity of invariants for group isomorphism. It turns out that a surprising number of invariants and characteristic subgroups that are classic to group theory can be detected and identified by a low dimensional Weisfeiler-Leman algorithm. These include the center, the inner automorphism group, the commutator subgroup and the derived series, the abelian radical, the solvable radical, the Fitting group and π-radicals. A low dimensional WL-algorithm additionally determines the isomorphism type of the socle as well as the factors in the derives series and the upper and lower central series. We also analyze the behavior of the WL-algorithm for group extensions and prove that a low dimensional WL-algorithm determines the isomorphism types of the composition factors of a group. Finally we develop a new tool to define a canonical maximal central decomposition for groups. This allows us to show that the Weisfeiler-Leman dimension of a group is at most one larger than the dimensions of its direct indecomposable factors. In other words the Weisfeiler-Leman dimension increases by at most 1 when taking direct products., LIPIcs, Vol. 244, 30th Annual European Symposium on Algorithms (ESA 2022), pages 27:1-27:14

The coloring problem (i.e., computing the chromatic number of a graph) can be solved in O^*(2ⁿ) time, as shown by Björklund, Husfeldt and Koivisto in 2009. For k = 3,4, better algorithms are known for the k-coloring problem. 3-coloring can be solved in O(1.33ⁿ) time (Beigel and Eppstein, 2005) and 4-coloring can be solved in O(1.73ⁿ) time (Fomin, Gaspers and Saurabh, 2007). Surprisingly, for k > 4 no improvements over the general O^*(2ⁿ) are known. We show that both 5-coloring and 6-coloring can also be solved in O((2-ε) ⁿ) time for some ε > 0. As a crucial step, we obtain an exponential improvement for computing the chromatic number of a very large family of graphs. In particular, for any constants Δ,α > 0, the chromatic number of graphs with at least α⋅ n vertices of degree at most Δ can be computed in O((2-ε) ⁿ) time, for some ε = ε_{Δ,α} > 0. This statement generalizes previous results for bounded-degree graphs (Björklund, Husfeldt, Kaski, and Koivisto, 2010) and graphs with bounded average degree (Golovnev, Kulikov and Mihajlin, 2016). We generalize the aforementioned statement to List Coloring, for which no previous improvements are known even for the case of bounded-degree graphs., LIPIcs, Vol. 198, 48th International Colloquium on Automata, Languages, and Programming (ICALP 2021), pages 113:1-113:20

In a (k,2)-Constraint Satisfaction Problem we are given a set of arbitrary constraints on pairs of k-ary variables, and are asked to find an assignment of values to these variables such that all constraints are satisfied. The (k,2)-CSP problem generalizes problems like k-coloring and k-list-coloring. In the Unique (k,2)-CSP problem, we add the assumption that the input set of constraints has at most one satisfying assignment. Beigel and Eppstein gave an algorithm for (k,2)-CSP running in time O((0.4518k)^n) for k > 3 and O (1.356ⁿ) for k = 3, where n is the number of variables. Feder and Motwani improved upon the Beigel-Eppstein algorithm for k ≥ 11. Hertli, Hurbain, Millius, Moser, Scheder and Szedl{á}k improved these bounds for Unique (k,2)-CSP for every k ≥ 5. We improve the result of Hertli et al. and obtain better bounds for Unique (k,2)-CSP for k ≥ 5. In particular, we improve the running time of Unique (5,2)-CSP from O (2.254ⁿ) to O (2.232^n) and Unique (6,2)-CSP from O (2.652^n) to O (2.641^n). Recently, Li and Scheder also published an improvement over the algorithm of Hertli et al. in the same regime as ours. Their improvement does not include quantitative bounds, we compare the works in the paper., LIPIcs, Vol. 244, 30th Annual European Symposium on Algorithms (ESA 2022), pages 92:1-92:13

Motivated by indoor localization by tripwire lasers, we study the problem of cutting a polygon into small-size pieces, using the chords of the polygon. Several versions are considered, depending on the definition of the "size" of a piece. In particular, we consider the area, the diameter, and the radius of the largest inscribed circle as a measure of the size of a piece. We also consider different objectives, either minimizing the maximum size of a piece for a given number of chords, or minimizing the number of chords that achieve a given size threshold for the pieces. We give hardness results for polygons with holes and approximation algorithms for multiple variants of the problem., This paper will appear in ESA2020, Track A proceedings

The Colour Refinement procedure and its generalisation to higher dimensions, the Weisfeiler-Leman algorithm, are central subroutines in approaches to the graph isomorphism problem. In an iterative fashion, Colour Refinement computes a colouring of the vertices of its input graph. A trivial upper bound on the iteration number of Colour Refinement on graphs of order n is n-1. We show that this bound is tight. More precisely, we prove via explicit constructions that there are infinitely many graphs G on which Colour Refinement takes |G|-1 iterations to stabilise. Modifying the infinite families that we present, we show that for every natural number n >= 10, there are graphs on n vertices on which Colour Refinement requires at least n-2 iterations to reach stabilisation., 22 pages, 3 figures, full version of a paper accepted at ICALP 2020

Given a string $s$ of length $n$ over a general alphabet and an integer $k$, the problem is to decide whether $s$ is a concatenation of $k$ nonempty palindromes. Two previously known solutions for this problem work in time $O(kn)$ and $O(n\log n)$ respectively. Here we settle the complexity of this problem in the word-RAM model, presenting an $O(n)$-time online deciding algorithm. The algorithm simultaneously finds the minimum odd number of factors and the minimum even number of factors in a factorization of a string into nonempty palindromes. We also demonstrate how to get an explicit factorization of $s$ into $k$ palindromes with an $O(n)$-time offline postprocessing., accepted to MFCS 2020

We study the fair allocation of undesirable indivisible items, or chores. While the case of desirable indivisible items (or goods) is extensively studied, with many results known for different notions of fairness, less is known about the fair division of chores. We study the envy-free division of chores, and make three contributions. First, we show that determining the existence of an envy-free allocation is NP-complete, even in the simple case when agents have binary additive valuations. Second, we provide a polynomial-time algorithm for computing an allocation that satisfies envy-freeness up to one chore (EF1), correcting an existing proof in the literature. A straightforward modification of our algorithm can be used to compute an EF1 allocation for doubly monotone instances (wherein each agent can partition the set of items into objective goods and objective chores). Our third result applies to a mixed resources model consisting of indivisible items and a divisible, undesirable heterogeneous resource (i.e., a bad cake). We show that there always exists an allocation that satisfies envy-freeness for mixed resources (EFM) in this setting, complementing a recent result of Bei et al. (Art. Int. 2021) for indivisible goods and divisible cake., Comment: v2 to v3 incorporates changes suggested by reviewers. Accepted at APPROX 2021

A long line of research on fixed parameter tractability of integer programming culminated with showing that integer programs with n variables and a constraint matrix with tree-depth d and largest entry Δ are solvable in time g(d,Δ) poly(n) for some function g, i.e., fixed parameter tractable when parameterized by tree-depth d and Δ. However, the tree-depth of a constraint matrix depends on the positions of its non-zero entries and thus does not reflect its geometric structure. In particular, tree-depth of a constraint matrix is not preserved by row operations, i.e., a given integer program can be equivalent to another with a smaller dual tree-depth. We prove that the branch-depth of the matroid defined by the columns of the constraint matrix is equal to the minimum tree-depth of a row-equivalent matrix. We also design a fixed parameter algorithm parameterized by an integer d and the entry complexity of an input matrix that either outputs a matrix with the smallest dual tree-depth that is row-equivalent to the input matrix or outputs that there is no matrix with dual tree-depth at most d that is row-equivalent to the input matrix. Finally, we use these results to obtain a fixed parameter algorithm for integer programming parameterized by the branch-depth of the input constraint matrix and the entry complexity. The parameterization by branch-depth cannot be replaced by the more permissive notion of branch-width.

Recently, a few papers considering the polynomial equation satisfiability problem and the circuit satisfiability problem over finite supernilpotent algebras from so called congruence modular varieties were published. All the algorithms considered in these papers are quite similar and rely on checking a not too big set of potential solutions. Two of these algorithms achieving the lowest time complexity up to now, were presented in [Aichinger, 2019] (algorithm working for finite supernilpotent algebras) and in [Földvári, 2018] (algorithm working in the group case). In this paper we show a deterministic algorithm of the same type solving the considered problems for finite supernilpotent algebras which has lower computational complexity than the algorithm presented in [Aichinger, 2019] and in most cases even lower than the group case algorithm from [Földvári, 2018]. We also present a linear time Monte Carlo algorithm solving the same problem. This, together with the algorithm for nilpotent but not supernilpotent algebras presented in [Paweł M. Idziak et al., 2020], is the very first attempt to solving the circuit satisfiability problem using probabilistic algorithms.

We extend Babai's quasipolynomial-time graph isomorphism test (STOC 2016) and develop a quasipolynomial-time algorithm for the multiple-coset isomorphism problem. The algorithm for the multiple-coset isomorphism problem allows to exploit graph decompositions of the given input graphs within Babai's group-theoretic framework. We use it to develop a graph isomorphism test that runs in time $n^{\operatorname{polylog}(k)}$ where $n$ is the number of vertices and $k$ is the minimum treewidth of the given graphs and $\operatorname{polylog}(k)$ is some polynomial in $\operatorname{log}(k)$. Our result generalizes Babai's quasipolynomial-time graph isomorphism test., 52 pages, 1 figure

In the Zeckendorf representation an integer is expressed as a sum of Fibonacci numbers in which no two are consecutive. We show O(n log n) algorithm for multiplication of two n-digit numbers in Zeckendorf representation. For this purpose we investigate a relationship between the numeral system using Zeckendorf representations and the golden ratio numeral system. We also show O(n) algorithms for converting numbers between these systems.

A marked free monoid morphism is a morphism for which the image of each generator starts with a different letter, and immersions are the analogous maps in free groups. We show that the (simultaneous) PCP is decidable for immersions of free groups, and provide an algorithm to compute bases for the sets, called equalisers, on which the immersions take the same values. We also answer a question of Stallings about the rank of the equaliser. Analogous results are proven for marked morphisms of free monoids., 16 pages, final version incorporating referees comments

LIPIcs, Volume 173, ESA 2020, Complete Volume

We consider the isomorphism problem for hypergraphs taking as input two hypergraphs over the same set of vertices $V$ and a permutation group $\Gamma$ over domain $V$, and asking whether there is a permutation $\gamma \in \Gamma$ that proves the two hypergraphs to be isomorphic. We show that for input groups, all of whose composition factors are isomorphic to a subgroup of the symmetric group on $d$ points, this problem can be solved in time $(n+m)^{O((\log d)^{c})}$ for some absolute constant $c$ where $n$ denotes the number of vertices and $m$ the number of hyperedges. In particular, this gives the currently fastest isomorphism test for hypergraphs in general. The previous best algorithm for this problem due to Schweitzer and Wiebking (STOC 2019) runs in time $n^{O(d)}m^{O(1)}$. As an application of this result, we obtain, for example, an algorithm testing isomorphism of graphs excluding $K_{3,h}$ ($h \geq 3$) as a minor in time $n^{O((\log h)^{c})}$. In particular, this gives an isomorphism test for graphs of Euler genus at most $g$ running in time $n^{O((\log g)^{c})}$., Comment: 50 pages, 5 figures, full version of a paper accepted at ICALP 2020; second version improves the presentation of the results

Front Matter, Table of Contents, Preface, Conference Organization

Iterative augmentation has recently emerged as an overarching method for solving Integer Programs (IP) in variable dimension, in stark contrast with the volume and flatness techniques of IP in fixed dimension. Here we consider 4-block n-fold integer programs, which are the most general class considered so far. A 4-block n-fold IP has a constraint matrix which consists of n copies of small matrices A, B, and D, and one copy of C, in a specific block structure. Iterative augmentation methods rely on the so-called Graver basis of the constraint matrix, which constitutes a set of fundamental augmenting steps. All existing algorithms rely on bounding the 𝓁₁- or 𝓁_∞-norm of elements of the Graver basis. Hemmecke et al. [Math. Prog. 2014] showed that 4-block n-fold IP has Graver elements of 𝓁_∞-norm at most 𝒪_FPT(n^{2^{s_D}}), leading to an algorithm with a similar runtime; here, s_D is the number of rows of matrix D and 𝒪_FPT hides a multiplicative factor that is only dependent on the small matrices A,B,C,D, However, it remained open whether their bounds are tight, in particular, whether they could be improved to 𝒪_FPT(1), perhaps at least in some restricted cases. We prove that the 𝓁_∞-norm of the Graver elements of 4-block n-fold IP is upper bounded by 𝒪_FPT(n^{s_D}), improving significantly over the previous bound 𝒪_FPT(n^{2^{s_D}}). We also provide a matching lower bound of Ω(n^{s_D}) which even holds for arbitrary non-zero lattice elements, ruling out augmenting algorithm relying on even more restricted notions of augmentation than the Graver basis. We then consider a special case of 4-block n-fold in which C is a zero matrix, called 3-block n-fold IP. We show that while the 𝓁_∞-norm of its Graver elements is Ω(n^{s_D}), there exists a different decomposition into lattice elements whose 𝓁_∞-norm is bounded by 𝒪_FPT(1), which allows us to provide improved upper bounds on the 𝓁_∞-norm of Graver elements for 3-block n-fold IP. The key difference between the respective decompositions is that a Graver basis guarantees a sign-compatible decomposition; this property is critical in applications because it guarantees each step of the decomposition to be feasible. Consequently, our improved upper bounds let us establish faster algorithms for 3-block n-fold IP and 4-block IP, and our lower bounds strongly hint at parameterized hardness of 4-block and even 3-block n-fold IP. Furthermore, we show that 3-block n-fold IP is without loss of generality in the sense that 4-block n-fold IP can be solved in FPT oracle time by taking an algorithm for 3-block n-fold IP as an oracle.