Paper accepted at conference CP 2020 which will appear in Springer LNCS proceedings. This is an extended version of that paper which contains additional material. DOI will be added when known
The Exact Satisfiability problem, XSAT, is defined as the problem of finding a satisfying assignment to a formula in CNF such that there is exactly one literal in each clause assigned to be 1 and the other literals in the same clause are set to 0. If we restrict the length of each clause to be at most 3 literals, then it is known as the X3SAT problem. In this paper, we consider the problem of counting the number of satisfying assignments to the X3SAT problem, which is also known as #X3SAT.
The current state of the art exact algorithm to solve #X3SAT is given by Dahllöf, Jonsson and Beigel and runs in $O(1.1487^n)$, where $n$ is the number of variables in the formula. In this paper, we propose an exact algorithm for the #X3SAT problem that runs in $O(1.1120^n)$ with very few branching cases to consider, by using a result from Monien and Preis to give us a bisection width for graphs with at most degree 3.
Many modern sequence alignment tools implement fast string matching using the space efficient data structure called FM-index. The succinct nature of this data structure presents unique challenges for the algorithm designers. In this paper, we explore the opportunities for parallelization of the exact and inexact matches and present an efficient SIMD solution for the Occ portion of the algorithm. Our implementation computes all eight Occ values required for the inexact match algorithm step in a single pass. We showcase the algorithm performance in a multi-core genome aligner and discuss effects…
Counting the number of ones in a binary stream is a common operation in database, information-retrieval, cryptographic and machine-learning applications. Most processors have dedicated instructions to count the number of ones in a word (e.g., popcnt on x64 processors). Maybe surprisingly, we show that a vectorized approach using SIMD instructions can be twice as fast as using the dedicated instructions on recent Intel processors. The benefits can be even greater for applications such as similarity measures (e.g., the Jaccard index) that require additional Boolean operations. Our approach has b…
This short article presents a new implementation for decision trees. By introducing pre-sorted deques, the leaf-wise greedy tree growing strategy no longer needs to re-sort data at each node, and takes O(kn) time and O(1) extra memory locating the best split and branching. The consistent, superior performance - plus its simplicity and guarantee in producing the same classification results as the standard decision trees - makes the new implementation a drop-in replacement for depth-wise tree induction with strong performance.
Counting the independent sets of a graph is a classical #P-complete problem, even in the bipartite case. We give an exponential-time approximation scheme for this problem which is faster than the best known algorithm for the exact problem. The running time of our algorithm on general graphs with error tolerance $\varepsilon$ is at most $O(2^{0.2680n})$ times a polynomial in $1/\varepsilon$. On bipartite graphs, the exponential term in the running time is improved to $O(2^{0.2372n})$. Our methods combine techniques from exact exponential algorithms with techniques from approximate counting. Alo…
Matroids are a fundamental object of study in combinatorial optimization. Three closely related and important problems involving matroids are maximizing the size of the union of $k$ independent sets (that is, $k$-fold matroid union), computing $k$ disjoint bases (a.k.a. matroid base packing), and covering the elements by $k$ bases (a.k.a. matroid base covering). These problems generalize naturally to integral and real-valued capacities on the elements. This work develops faster exact and/or approximation problems for these and some other closely related problems such as optimal reinforcement a…
The measure and conquer approach has proven to be a powerful tool to analyse exact algorithms for combinatorial problems, like Dominating Set and Independent Set. In this paper, we propose to use measure and conquer also as a tool in the design of algorithms. In an iterative process, we can obtain a series of branch and reduce algorithms. A mathematical analysis of an algorithm in the series with measure and conquer results in a quasiconvex programming problem. The solution by computer to this problem not only gives a bound on the running time, but also can give a new reduction rule, thus givi…
We show how full-text search based on inverted indices can be accelerated by clustering the documents without losing results (SeCluD -- SEarch with CLUstered Documents). We develop a fast multilevel clustering algorithm that explicitly uses query cost for conjunctive queries as an objective function. Depending on the inputs we get up to four times faster than non-clustered search. The resulting clusters are also useful for data compression and for distributing the work over many machines.
We give an algorithm for counting self-avoiding walks or self-avoiding polygons that runs in time $\exp(C\sqrt{n\log n})$ on 2-dimensional lattices and time $\exp(C_dn^{(d-1)/d}\log n)$ on $d$-dimensional lattices for $d>2$.
Fractal dimension is widely adopted in spatial databases and data mining, among others as a measure of dataset skewness. State-of-the-art algorithms for estimating the fractal dimension exhibit linear runtime complexity whether based on box-counting or approximation schemes. In this paper, we revisit a correlation fractal dimension estimation algorithm that redundantly rescans the dataset and, extending that work, we propose another linear, yet faster and as accurate method, which completes in a single pass.
In the $k$-cut problem, we are given an edge-weighted graph $G$ and an integer $k$, and have to remove a set of edges with minimum total weight so that $G$ has at least $k$ connected components. The current best algorithms are an $O(n^{(2-o(1))k})$ randomized algorithm due to Karger and Stein, and an $\smash{\tilde{O}}(n^{2k})$ deterministic algorithm due to Thorup. Moreover, several $2$-approximation algorithms are known for the problem (due to Saran and Vazirani, Naor and Rabani, and Ravi and Sinha). It has remained an open problem to (a) improve the runtime of exact algorithms, and (b) to g…
The Permutation Pattern Matching problem asks, given two permutations $σ$ on $n$ elements and $π$, whether $σ$ admits a subsequence with the same relative order as $π$ (or, in the counting version, how many such subsequences are there). This natural problem was shown by Bose, Buss and Lubiw [IPL 1998] to be NP-complete, and hence we should seek exact exponential time solutions. The asymptotically fastest such solution up to date, by Berendsohn, Kozma and Marx [IPEC 2019], works in $\mathcal{O}(1.6181^n)$ time. We design a simple and faster $\mathcal{O}(1.415^{n})$ time algorithm for both the d…
Given a directed graph $G=(V,A)$, the Directed Maximum Leaf Spanning Tree problem asks to compute a directed spanning tree (i.e., an out-branching) with as many leaves as possible. By designing a Branch-and-Reduced algorithm combined with the Measure & Conquer technique for running time analysis, we show that the problem can be solved in time $\Oh^*(1.9043^n)$ using polynomial space. Hitherto, there have been only few examples. Provided exponential space this run time upper bound can be lowered to $\Oh^*(1.8139^n)$.
We show that, for any n-vertex graph G and integer parameter k, there are at most 3^{4k-n}4^{n-3k} maximal independent sets I \subset G with |I| <= k, and that all such sets can be listed in time O(3^{4k-n} 4^{n-3k}). These bounds are tight when n/4 <= k <= n/3. As a consequence, we show how to compute the exact chromatic number of a graph in time O((4/3 + 3^{4/3}/4)^n) ~= 2.4150^n, improving a previous O((1+3^{1/3})^n) ~= 2.4422^n algorithm of Lawler (1976).
We deal with exact algorithms for Bandwidth, a long studied NP-hard problem. For a long time nothing better than the trivial O*(n!) exhaustive search was known. In 2000, Feige an Kilian came up with a O*(10^n)-time algorithm. Recently we presented algorithm that runs in O*(5^n) time and O*(2^n) space.. In this paper we present a major modification to our algorithm which makes it run in O(4.83^n) time with the cost of O*(4^n) space complexity. This modification allowed us to perform Measure & Conquer analysis for the time complexity which was not used for such types of problems before.
We present a polynomial-space algorithm that computes the number independent sets of any input graph in time $O(1.1387^n)$ for graphs with maximum degree 3 and in time $O(1.2355^n)$ for general graphs, where n is the number of vertices. Together with the inclusion-exclusion approach of Björklund, Husfeldt, and Koivisto [SIAM J. Comput. 2009], this leads to a faster polynomial-space algorithm for the graph coloring problem with running time $O(2.2355^n)$. As a byproduct, we also obtain an exponential-space $O(1.2330^n)$ time algorithm for counting independent sets. Our main algorithm counts ind…
A tournament is a directed graph T such that every pair of vertices are connected by an arc. A feedback vertex set is a set S of vertices in T such that T - S is acyclic. In this article we consider the Feedback Vertex Set problem in tournaments. Here input is a tournament T and integer k, and the task is to determine whether T has a feedback vertex set of size at most k. We give a new algorithm for Feedback Vertex Set in Tournaments. The running time of our algorithm is upper bounded by O(1.618^k + n^{O(1)}) and by O(1.46^n). Thus our algorithm simultaneously improves over the fastest known p…
Least squares approximation is a technique to find an approximate solution to a system of linear equations that has no exact solution. In a typical setting, one lets $n$ be the number of constraints and $d$ be the number of variables, with $n \gg d$. Then, existing exact methods find a solution vector in $O(nd^2)$ time. We present two randomized algorithms that provide very accurate relative-error approximations to the optimal value and the solution vector of a least squares approximation problem more rapidly than existing exact algorithms. Both of our algorithms preprocess the data with the R…
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.
The maximum-cut problem is one of the fundamental problems in combinatorial optimization. With the advent of quantum computers, both the maximum-cut and the equivalent quadratic unconstrained binary optimization problem have experienced much interest in recent years. This article aims to advance the state of the art in the exact solution of both problems -- by using mathematical programming techniques on digital computers. The main focus lies on sparse problem instances, although also dense ones can be solved. We enhance several algorithmic components such as reduction techniques and cutting-p…
Computing sets of high quality solutions has gained increasing interest in recent years. In this paper, we investigate how to obtain sets of optimal solutions for the classical knapsack problem. We present an algorithm to count exactly the number of optima to a zero-one knapsack problem instance. In addition, we show how to efficiently sample uniformly at random from the set of all global optima. In our experimental study, we investigate how the number of optima develops for classical random benchmark instances dependent on their generator parameters. We find that the number of global optima c…
In this work, we consider $d$-{\sc Hyperedge Estimation} and $d$-{\sc Hyperedge Sample} problem in a hypergraph $\mathcal{H}(U(\mathcal{H}),\mathcal{F}(\mathcal{H}))$ in the query complexity framework, where $U(\mathcal{H})$ denotes the set of vertices and $\mathcal{F}(\mathcal{H})$ denotes the set of hyperedges. The oracle access to the hypergraph is called {\sc Colorful Independence Oracle} ({\sc CID}), which takes $d$ (non-empty) pairwise disjoint subsets of vertices $A_1,\ldots,A_d \subseteq U(\mathcal{H})$ as input, and answers whether there exists a hyperedge in $\mathcal{H}$ having (exa…
We address the problem of computing the distribution of induced connected subgraphs, aka \emph{graphlets} or \emph{motifs}, in large graphs. The current state-of-the-art algorithms estimate the motif counts via uniform sampling, by leveraging the color coding technique by Alon, Yuster and Zwick. In this work we extend the applicability of this approach, by introducing a set of algorithmic optimizations and techniques that reduce the running time and space usage of color coding and improve the accuracy of the counts. To this end, we first show how to optimize color coding to efficiently build a…
In this paper, we show $O(1.415^n)$-time and $O(1.190^n)$-space exact algorithms for 0-1 integer programs where constraints are linear equalities and coefficients are arbitrary real numbers. Our algorithms are quadratically faster than exhaustive search and almost quadratically faster than an algorithm for an inequality version of the problem by Impagliazzo, Lovett, Paturi and Schneider (arXiv:1401.5512), which motivated our work. Rather than improving the time and space complexity, we advance to a simple direction as inclusion of many NP-hard problems in terms of exact exponential algorithms.…
Triangle counting is a fundamental building block in graph algorithms. In this paper, we propose a block-based triangle counting algorithm to reduce data movement during both sequential and parallel execution. Our block-based formulation makes the algorithm naturally suitable for heterogeneous architectures. The problem of partitioning the adjacency matrix of a graph is well-studied. Our task decomposition goes one step further: it partitions the set of triangles in the graph. By streaming these small tasks to compute resources, we can solve problems that do not fit on a device. We demonstrate…
We present an exact quantum algorithm for solving the Exact Satisfiability (XSAT) problem, which belongs to the important NP-complete complexity class. The algorithm is based on an intuitive approach that can be divided into two parts: First, the identification and efficient characterization of a restricted subspace that contains all the valid assignments of the XSAT; Second, a quantum search in such restricted subspace. The quantum algorithm can be used either to find a valid assignment (or to certify that no solution exists) or to count the total number of valid assignments. The query comple…
We consider the problem of estimating the partition function $Z(β)=\sum_x \exp(-β(H(x))$ of a Gibbs distribution with a Hamilton $H(\cdot)$, or more precisely the logarithm of the ratio $q=\ln Z(0)/Z(β)$. It has been recently shown how to approximate $q$ with high probability assuming the existence of an oracle that produces samples from the Gibbs distribution for a given parameter value in $[0,β]$. The current best known approach due to Huber [9] uses $O(q\ln n\cdot[\ln q + \ln \ln n+\varepsilon^{-2}])$ oracle calls on average where $\varepsilon$ is the desired accuracy of approximation and $…
We first show that the Traveling Salesman Problem in an n-vertex graph with average degree bounded by d can be solved in O*(2^{(1-\eps_d)n}) time and exponential space for a constant \eps_d depending only on d, where the O*-notation suppresses factors polynomial in the input size. Thus, we generalize the recent results of Bjorklund et al. [TALG 2012] on graphs of bounded degree. Then, we move to the problem of counting perfect matchings in a graph. We first present a simple algorithm for counting perfect matchings in an n-vertex graph in O*(2^{n/2}) time and polynomial space; our algorithm mat…
In this paper we study the problem of finding a maximum induced d-degenerate subgraph in a given n-vertex graph from the point of view of exact algorithms. We show that for any fixed d one can find a maximum induced d-degenerate subgraph in randomized (2-eps_d)^n n^O(1) time, for some constant eps_d>0 depending only on d. Moreover, our algorithm can be used to sample inclusion-wise maximal induced d-degenerate subgraphs in such a manner that every such subgraph is output with probability at least (2-eps_d)^-n; hence, we prove that their number is bounded by (2-eps_d)^n.
Vassilevska and Williams (STOC 2009) showed how to count simple paths on $k$ vertices and matchings on $k/2$ edges in an $n$-vertex graph in time $n^{k/2+O(1)}$. In the same year, two different algorithms with the same runtime were given by Koutis and Williams~(ICALP 2009), and Björklund \emph{et al.} (ESA 2009), via $n^{st/2+O(1)}$-time algorithms for counting $t$-tuples of pairwise disjoint sets drawn from a given family of $s$-sized subsets of an $n$-element universe. Shortly afterwards, Alon and Gutner (TALG 2010) showed that these problems have $Ω(n^{\lfloor st/2\rfloor})$ and $Ω(n^{\lflo…
We give an improved branch-and-bound solver for the multiterminal cut problem, based on the recent work of Henzinger et al.. We contribute new, highly effective data reduction rules to transform the graph into a smaller equivalent instance. In addition, we present a local search algorithm that can significantly improve a given solution to the multiterminal cut problem. Our exact algorithm is able to give exact solutions to more and harder problems compared to the state-of-the-art algorithm by Henzinger et al.; and give better solutions for more than two third of the problems that are too large…
The Exact Satisfiability problem asks if we can find a satisfying assignment to each clause such that exactly one literal in each clause is assigned $1$, while the rest are all assigned $0$. We can generalise this problem further by defining that a $C^j$ clause is solved iff exactly $j$ of the literals in the clause are $1$ and all others are $0$. We now introduce the family of Generalised Exact Satisfiability problems called G$i$XSAT as the problem to check whether a given instance consisting of $C^j$ clauses with $j \in \{0,1,\ldots,i\}$ for each clause has a satisfying assignment. In this p…
Given nonnegative integers $n$ and $d$, where $n \gg d$, what is the minimum number $r$ such that there exist linear forms $\ell_1, \ldots, \ell_r \in \mathbb{C}[x_1, \ldots, x_n]$ so that $\ell_1^d + \cdots + \ell_r^d$ is supported exactly on the set of all degree-$d$ multilinear monomials in $x_1, \ldots, x_n$? We show that this and related questions have surprising and intimate connections to the areas of parameterized and exact algorithms, generalizing several well-known methods and providing a concrete approach to obtain faster approximate counting and deterministic decision algorithms. T…
In breakthrough work, Tardos (Oper. Res. '86) gave a proximity based framework for solving linear programming (LP) in time depending only on the constraint matrix in the bit complexity model. In Tardos's framework, one reduces solving the LP $\min \langle c,{x}\rangle$, $Ax=b$, $x \geq 0$, $A \in \mathbb{Z}^{m \times n}$, to solving $O(nm)$ LPs in $A$ having small integer coefficient objectives and right-hand sides using any exact LP algorithm. This gives rise to an LP algorithm in time poly$(n,m\logΔ_A)$, where $Δ_A$ is the largest subdeterminant of $A$. A significant extension to the real mo…
We consider the Exact-Weight-H problem of finding a (not necessarily induced) subgraph H of weight 0 in an edge-weighted graph G. We show that for every H, the complexity of this problem is strongly related to that of the infamous k-Sum problem. In particular, we show that under the k-Sum Conjecture, we can achieve tight upper and lower bounds for the Exact-Weight-H problem for various subgraphs H such as matching, star, path, and cycle. One interesting consequence is that improving on the O(n^3) upper bound for Exact-Weight-4-Path or Exact-Weight-5-Path will imply improved algorithms for 3-Su…
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} of degre…
NICTA（澳大利亚国家信息与通信技术研究院）；Australian National University（澳大利亚国立大学）
Maximum A Posteriori inference in graphical models is often solved via message-passing algorithms, such as the junction-tree algorithm, or loopy belief-propagation. The exact solution to this problem is well known to be exponential in the size of the model's maximal cliques after it is triangulated, while approximate inference is typically exponential in the size of the model's factors. In this paper, we take advantage of the fact that many models have maximal cliques that are larger than their constituent factors, and also of the fact that many factors consist entirely of latent variables (i.…
Influence maximization (IM) is the problem of finding a seed vertex set that maximizes the expected number of vertices influenced under a given diffusion model. Due to the NP-Hardness of finding an optimal seed set, approximation algorithms are frequently used for IM. In this work, we describe a fast, error-adaptive approach that leverages Count-Distinct sketches and hash-based fused sampling. To estimate the number of influenced vertices throughout a diffusion, we use per-vertex Flajolet-Martin sketches where each sketch corresponds to a sampled subgraph. To efficiently simulate the diffusion…
Since its introduction Boson Sampling has been the subject of intense study in the world of quantum computing. The task is to sample independently from the set of all $n \times n$ submatrices built from possibly repeated rows of a larger $m \times n$ complex matrix according to a probability distribution related to the permanents of the submatrices. Experimental systems exploiting quantum photonic effects can in principle perform the task at great speed. In the framework of classical computing, Aaronson and Arkhipov (2011) showed that exact Boson Sampling problem cannot be solved in polynomial…
Graphs are used to model interactions in a variety of contexts, and there is a growing need to quickly assess the structure of such graphs. Some of the most useful graph metrics are based on triangles, such as those measuring social cohesion. Algorithms to compute them can be extremely expensive, even for moderately-sized graphs with only millions of edges. Previous work has considered node and edge sampling; in contrast, we consider wedge sampling, which provides faster and more accurate approximations than competing techniques. Additionally, wedge sampling enables estimation local clustering…
Clique counting is a fundamental task in network analysis, and even the simplest setting of $3$-cliques (triangles) has been the center of much recent research. Getting the count of $k$-cliques for larger $k$ is algorithmically challenging, due to the exponential blowup in the search space of large cliques. But a number of recent applications (especially for community detection or clustering) use larger clique counts. Moreover, one often desires \textit{local} counts, the number of $k$-cliques per vertex/edge. Our main result is Pivoter, an algorithm that exactly counts the number of $k$-cliqu…
We give a simple polynomial-time algorithm to exactly count the number of Euler Tours (ETs) of any Eulerian generalized series-parallel graph, and show how to adapt this algorithm to exactly sample a random ET of the given generalized series-parallel graph. Note that the class of generalized seriesparallel graphs includes all outerplanar graphs. We can perform the counting in time $O(mΔ^3)$, where $Δ$ is the maximum degree of the graph with $m$ edges. We use $O(mΔ^2 \log Δ)$ bits to store intermediate values during our computations. To date, these are the first known polynomial-time algorithms…
A major obstacle to implementing Shor's quantum number-factoring algorithm is the large size of modular-exponentiation circuits. We reduce this bottleneck by customizing reversible circuits for modular multiplication to individual runs of Shor's algorithm. Our circuit-synthesis procedure exploits spectral properties of multiplication operators and constructs optimized circuits from the traces of the execution of an appropriate GCD algorithm. Empirically, gate counts are reduced by 4-5 times, and circuit latency is reduced by larger factors.
We show a method resulting in the improvement of several polynomial-space, exponential-time algorithms. An instance of the problem Max (r,2)-CSP, or simply Max 2-CSP, is parametrized by the domain size r (often 2), the number of variables n (vertices in the constraint graph G), and the number of constraints m (edges in G). When G is cubic, and omitting sub-exponential terms here for clarity, we give an algorithm running in time r^((1/5)n) = r^((2/15)m); the previous best was r^((1/4)n) = r^((1/6)m). By known results, this improvement for the cubic case results in an algorithm running in time r…
Many clustering problems enjoy solutions by semidefinite programming. Theoretical results in this vein frequently consider data with a planted clustering and a notion of signal strength such that the semidefinite program exactly recovers the planted clustering when the signal strength is sufficiently large. In practice, semidefinite programs are notoriously slow, and so speedups are welcome. In this paper, we show how to sketch a popular semidefinite relaxation of a graph clustering problem known as minimum bisection, and our analysis supports a meta-claim that the clustering task is less comp…
