Given two rooted, ordered, and labeled trees $P$ and $T$ the tree inclusion problem is to determine if $P$ can be obtained from $T$ by deleting nodes in $T$. This problem has recently been recognized as an important query primitive in XML databases. Kilpeläinen and Mannila [\emph{SIAM J. Comput. 1995}] presented the first polynomial time algorithm using quadratic time and space. Since then several improved results have been obtained for special cases when $P$ and $T$ have a small number of leaves or small depth. However, in the worst case these algorithms still use quadratic time and space. Let $n_S$, $l_S$, and $d_S$ denote the number of nodes, the number of leaves, and the %maximum depth of a tree $S \in \{P, T\}$. In this paper we show that the tree inclusion problem can be solved in space $O(n_T)$ and time: O(\min(l_Pn_T, l_Pl_T\log \log n_T + n_T, \frac{n_Pn_T}{\log n_T} + n_{T}\log n_{T})). This improves or matches the best known time complexities while using only linear space instead of quadratic. This is particularly important in practical applications, such as XML databases, where the space is likely to be a bottleneck.
The tree inclusion problem is, given two node-labeled trees $P$ and $T$ (the ``pattern tree'' and the ``target tree''), to locate every minimal subtree in $T$ (if any) that can be obtained by applying a sequence of node insertion operations to $P$. Although the ordered tree inclusion problem is solvable in polynomial time, the unordered tree inclusion problem is NP-hard. The currently fastest algorithm for the latter is a classic algorithm by Kilpeläinen and Mannila from 1995 that runs in $O(2^{2d} mn)$ time, where $m$ and $n$ are the sizes of the pattern and target trees, respectively, and $d…
Suffix trees are a fundamental data structure in stringology, but their space usage, though linear, is an important problem for its applications. We design and implement a new compressed suffix tree targeted to highly repetitive texts, such as large genomic collections of the same species. Our suffix tree tree builds on Block Trees, a recent Lempel-Ziv-bounded data structure that captures the repetitiveness of its input. We use Block Trees to compress the topology of the suffix tree, and augment the Block Tree nodes with data that speeds up suffix tree navigation. Our compressed suffix tree is…
Computing optimal transport (OT) distances such as the earth mover's distance is a fundamental problem in machine learning, statistics, and computer vision. In this paper, we study the problem of approximating the general OT distance between two discrete distributions of size $n$. Given the cost matrix $C=AA^\top$ where $A \in \mathbb{R}^{n \times d}$, we proposed a faster Sinkhorn's Algorithm to approximate the OT distance when matrix $A$ has treewidth $τ$. To approximate the OT distance, our algorithm improves the state-of-the-art results [Dvurechensky, Gasnikov, and Kroshnin ICML 2018] from…
We design two incremental algorithms for computing an inclusion-minimal completion of an arbitrary graph into a cograph. The first one is able to do so while providing an additional property which is crucial in practice to obtain inclusion-minimal completions using as few edges as possible : it is able to compute a minimum-cardinality completion of the neighbourhood of the new vertex introduced at each incremental step. It runs in $O(n+m')$ time, where $m'$ is the number of edges in the completed graph. This matches the complexity of the algorithm in [Lokshtanov, Mancini and Papadopoulos 2010]…
Let $G = (V, E)$ be an undirected connected simple graph on $n$ vertices. A cut-equivalent tree of $G$ is an edge-weighted tree on the same vertex set $V$, such that for any pair of vertices $s, t\in V$, the minimum $(s, t)$-cut in the tree is also a minimum $(s, t)$-cut in $G$, and these two cuts have the same cut value. In a recent paper [Abboud, Krauthgamer and Trabelsi, 2021], the authors propose the first subcubic time algorithm for constructing a cut-equivalent tree. More specifically, their algorithm has $\widetilde{O}(n^{2.5})$ running time. In this paper, we improve the running time t…
Tree edit distance is a well-studied measure of dissimilarity between rooted trees with node labels. It can be computed in $O(n^3)$ time [Demaine, Mozes, Rossman, and Weimann, ICALP 2007], and fine-grained hardness results suggest that the weighted version of this problem cannot be solved in truly subcubic time unless the APSP conjecture is false [Bringmann, Gawrychowski, Mozes, and Weimann, SODA 2018]. We consider the unweighted version of tree edit distance, where every insertion, deletion, or relabeling operation has unit cost. Given a parameter $k$ as an upper bound on the distance, the pr…
The $k^2$-tree is a successful compact representation of binary relations that exhibit sparseness and/or clustering properties. It can be extended to $d$ dimensions, where it is called a $k^d$-tree. The representation boils down to a long bitvector. We show that interpreting the $k^d$-tree as a dynamic trie on the Morton codes of the points, instead of as a dynamic representation of the bitvector as done in previous work, yields operation times that are below the lower bound of dynamic bitvectors and offers improved time performance in practice.
The Gomory-Hu tree or cut tree (Gomory and Hu, 1961) is a classic data structure for reporting $(s,t)$ mincuts (and by duality, the values of $(s,t)$ maxflows) for all pairs of vertices $s$ and $t$ in an undirected graph. Gomory and Hu showed that it can be computed using $n-1$ exact maxflow computations. Surprisingly, this remains the best algorithm for Gomory-Hu trees more than 50 years later, *even for approximate mincuts*. In this paper, we break this longstanding barrier and give an algorithm for computing a $(1+ε)$-approximate Gomory-Hu tree using $\text{polylog}(n)$ maxflow computations…
Semidefinite programming is a fundamental tool in optimization and theoretical computer science. It has been extensively used as a black-box for solving many problems, such as embedding, complexity, learning, and discrepancy. One natural setting of semidefinite programming is the small treewidth setting. The best previous SDP solver under small treewidth setting is due to Zhang-Lavaei '18, which takes $n^{1.5} τ^{6.5}$ time. In this work, we show how to solve a semidefinite programming with $n \times n$ variables, $m$ constraints and $τ$ treewidth in $n τ^{2ω+0.5}$ time, where $ω< 2.373$ denot…
We revisit the \textsc{$k$-Secluded Tree} problem. Given a vertex-weighted undirected graph $G$, its objective is to find a maximum-weight induced subtree $T$ whose open neighborhood has size at most $k$. We present a fixed-parameter tractable algorithm that solves the problem in time $2^{\mathcal{O}(k \log k)}\cdot n^{\mathcal{O}(1)}$, improving on a double-exponential running time from earlier work by Golovach, Heggernes, Lima, and Montealegre. Starting from a single vertex, our algorithm grows a $k$-secluded tree by branching on vertices in the open neighborhood of the current tree $T$. To …
Discrete-time Markov Chains (MCs) and Markov Decision Processes (MDPs) are two standard formalisms in system analysis. Their main associated quantitative objectives are hitting probabilities, discounted sum, and mean payoff. Although there are many techniques for computing these objectives in general MCs/MDPs, they have not been thoroughly studied in terms of parameterized algorithms, particularly when treewidth is used as the parameter. This is in sharp contrast to qualitative objectives for MCs, MDPs and graph games, for which treewidth-based algorithms yield significant complexity improveme…
We devise new cut sparsifiers that are related to the classical sparsification of Nagamochi and Ibaraki [Algorithmica, 1992], which is an algorithm that, given an unweighted graph $G$ on $n$ nodes and a parameter $k$, computes a subgraph with $O(nk)$ edges that preserves all cuts of value up to $k$. We put forward the notion of a friendly cut sparsifier, which is a minor of $G$ that preserves all friendly cuts of value up to $k$, where a cut in $G$ is called friendly if every node has more edges connecting it to its own side of the cut than to the other side. We present an algorithm that, give…
In the k-Path problem, the input is a directed graph $G$ and an integer $k\geq 1$, and the goal is to decide whether there is a simple directed path in $G$ with exactly $k$ vertices. We give a deterministic algorithm for k-Path with time complexity $O^*(2.554^k)$. This improves the previously best deterministic algorithm for this problem of Zehavi [ESA 2015] whose time complexity is $O^*(2.597^k)$. The technique used by our algorithm can also be used to obtain faster deterministic algorithms for k-Tree, r-Dimensional k-Matching, Graph Motif, and Partial Cover.
We consider the Modular Subset Sum problem: given a multiset $X$ of integers from $\mathbb{Z}_m$ and a target integer $t$, decide if there exists a subset of $X$ with a sum equal to $t \pmod{m}$. Recent independent works by Cardinal and Iacono (SOSA'21), and Axiotis et al. (SOSA'21) provided simple and near-linear algorithms for this problem. Cardinal and Iacono gave a randomized algorithm that runs in $O(m \log m)$ time, while Axiotis et al. gave a deterministic algorithm that runs in $O(m \text{ polylog } m)$ time. Both results work by reduction to a text problem, which is solved using a dyn…
In the Set Cover problem, the input is a ground set of $n$ elements and a collection of $m$ sets, and the goal is to find the smallest sub-collection of sets whose union is the entire ground set. The fastest algorithm known runs in time $O(mn2^n)$ [Fomin et al., WG 2004], and the Set Cover Conjecture (SeCoCo) [Cygan et al., TALG 2016] asserts that for every fixed $\varepsilon>0$, no algorithm can solve Set Cover in time $2^{(1-\varepsilon)n}poly(m)$, even if set sizes are bounded by $Δ=Δ(\varepsilon)$. We show strong connections between this problem and kTree, a special case of Subgraph Isomor…
A recent breakthrough by Ambainis, Balodis, Iraids, Kokainis, Prūsis and Vihrovs (SODA'19) showed how to construct faster quantum algorithms for the Traveling Salesman Problem and a few other NP-hard problems by combining in a novel way quantum search with classical dynamic programming. In this paper, we show how to apply this approach to the minimum Steiner tree problem, a well-known NP-hard problem, and construct the first quantum algorithm that solves this problem faster than the best known classical algorithms. More precisely, the complexity of our quantum algorithm is $\mathcal{O}(1.812^k…
Current network applications, such as utility networks (gas, water, electricity, and 4G/5G), the Internet of Things (IoT), social networks, and supply chains, are all based on binary state networks. Reliability is one of the most commonly used tools for evaluating network performance, and the minimal path (MP) is a basic algorithm for calculating reliability. However, almost all existing algorithms assume that all undirected arcs are homogeneous; that is, the probability of an arc from nodes a to b is equal to that from nodes b to a. Therefore, based on MPs, the binary-addition-tree algorithm …
Faster Algorithms for Finding and Counting Subgraphs
In this paper we study a natural generalization of both { \sc $k$ -Path} and { \sc $k$ -Tree} problems, namely, the { \sc Subgraph Isomorphism} problem. In the { \sc Subgraph Isomorphism} problem we are given two graphs $F$ and $G$ on $k$ and $n$ vertices respectively as an input, and the question is whether there exists a subgraph of $G$ isomorphic to $F$ . We show that if the treewidth of $F$ is at most $t$ , then there is a randomized algorithm for the { \sc Subgraph Isomorphism} problem running in time $\cO^*(2^k n^{2t})$ . To do so, we associate a new multivariate {Homomorphism polynomial…
Many modern programming languages are shifting toward a functional style for collection interfaces such as sets, maps, and sequences. Functional interfaces offer many advantages, including being safe for parallelism and providing simple and lightweight snapshots. However, existing high-performance functional interfaces such as PAM, which are based on balanced purely-functional trees, incur large space overheads for large-scale data analysis due to storing every element in a separate node in a tree. This paper presents PaC-trees, a purely-functional data structure supporting functional interfac…
BFS versus DFS for fixed-level targets in ordered trees
Dartmouth college（达特茅斯学院）；Faculty of Mathematics and Informatics, Sofia University（索非亚大学数学与信息学院）；Department of Mathematics and Computer Science, Davidson College（戴维森学院数学与计算机科学系）
