Positive linear programs (LP), also known as packing and covering linear programs, are an important class of problems that bridges computer science, operations research, and optimization. Despite the consistent efforts on this problem, all known nearly-linear-time algorithms require $\tilde{O}(\varepsilon^{-4})$ iterations to converge to $1\pm \varepsilon$ approximate solutions. This $\varepsilon^{-4}$ dependence has not been improved since 1993, and limits the performance of parallel implementations for such algorithms. Moreover, previous algorithms and their analyses rely on update steps and convergence arguments that are combinatorial in nature and do not seem to arise naturally from an optimization viewpoint.
In this paper, we leverage new insights from optimization theory to construct a novel algorithm that breaks the longstanding $\varepsilon^{-4}$ barrier. Our algorithm has a simple analysis and a clear motivation. Our work introduces a number of novel techniques, such as the combined application of gradient descent and mirror descent, and a truncated, smoothed version of the standard multiplicative weight update, which may be of independent interest.
In this paper, we give a faster width-dependent algorithm for mixed packing-covering LPs. Mixed packing-covering LPs are fundamental to combinatorial optimization in computer science and operations research. Our algorithm finds a $1+\eps$ approximate solution in time $O(Nw/ \eps)$, where $N$ is number of nonzero entries in the constraint matrix and $w$ is the maximum number of nonzeros in any constraint. This run-time is better than Nesterov's smoothing algorithm which requires $O(N\sqrt{n}w/ \eps)$ where $n$ is the dimension of the problem. Our work utilizes the framework of area convexity in…
Motivated by recent Linear Programming solvers, we design dynamic data structures for maintaining the inverse of an $n\times n$ real matrix under $\textit{low-rank}$ updates, with polynomially faster amortized running time. Our data structure is based on a recursive application of the Woodbury-Morrison identity for implementing $\textit{cascading}$ low-rank updates, combined with recent sketching technology. Our techniques and amortized analysis of multi-level partial updates, may be of broader interest to dynamic matrix problems. This data structure leads to the fastest known LP solver for ge…
Packing and covering linear programs belong to the narrow class of linear programs that are efficiently solvable in parallel and distributed models of computation, yet are a powerful modeling tool for a wide range of fundamental problems in theoretical computer science, operations research, and many other areas. Following recent progress in obtaining faster distributed and parallel algorithms for packing and covering linear programs, we present a simple algorithm whose iteration count matches the best known $\tilde{O}(\frac{1}{ε^2})$ for this class of problems. The algorithm is similar to the …
We show that the shadow vertex simplex algorithm can be used to solve linear programs in strongly polynomial time with respect to the number $n$ of variables, the number $m$ of constraints, and $1/δ$, where $δ$ is a parameter that measures the flatness of the vertices of the polyhedron. This extends our recent result that the shadow vertex algorithm finds paths of polynomial length (w.r.t. $n$, $m$, and $1/δ$) between two given vertices of a polyhedron. Our result also complements a recent result due to Eisenbrand and Vempala who have shown that a certain version of the random edge pivot rule …
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 problem of maximizing the multilinear extension of a submodular function subject a single matroid constraint or multiple packing constraints with a small number of adaptive rounds of evaluation queries. We obtain the first algorithms with low adaptivity for submodular maximization with a matroid constraint. Our algorithms achieve a $1-1/e-ε$ approximation for monotone functions and a $1/e-ε$ approximation for non-monotone functions, which nearly matches the best guarantees known in the fully adaptive setting. The number of rounds of adaptivity is $O(\log^2{n}/ε^3)$, which is an…
This paper studies the problem of finding an $(1+ε)$-approximate solution to positive semidefinite programs. These are semidefinite programs in which all matrices in the constraints and objective are positive semidefinite and all scalars are non-negative. We present a simpler \NC parallel algorithm that on input with $n$ constraint matrices, requires $O(\frac{1}{ε^3} log^3 n)$ iterations, each of which involves only simple matrix operations and computing the trace of the product of a matrix exponential and a positive semidefinite matrix. Further, given a positive SDP in a factorized form, the …
Linear programming (LP) is an extremely useful tool which has been successfully applied to solve various problems in a wide range of areas, including operations research, engineering, economics, or even more abstract mathematical areas such as combinatorics. It is also used in many machine learning applications, such as $\ell_1$-regularized SVMs, basis pursuit, nonnegative matrix factorization, etc. Interior Point Methods (IPMs) are one of the most popular methods to solve LPs both in theory and in practice. Their underlying complexity is dominated by the cost of solving a system of linear equ…
We present the first $m\,\text{polylog}(n)$ work, $\text{polylog}(n)$ time algorithm in the PRAM model that computes $(1+ε)$-approximate single-source shortest paths on weighted, undirected graphs. This improves upon the breakthrough result of Cohen~[JACM'00] that achieves $O(m^{1+ε_0})$ work and $\text{polylog}(n)$ time. While most previous approaches, including Cohen's, leveraged the power of hopsets, our algorithm builds upon the recent developments in \emph{continuous optimization}, studying the shortest path problem from the lens of the closely-related \emph{minimum transshipment} problem…
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…
In this paper we give a f-approximation algorithm for the minimum unweighted Vertex Cover problem with Hard Capacity constraints (VCHC) on f-hypergraphs. This problem generalizes standard vertex cover for which the best known approximation ratio is also f and cannot be improved assuming the unique game conjecture. Our result is therefore essentially the best possible. This improves over the previous 2.155 (for f=2) and 2f-approximation algorithms by Cheung, Goemans and Wong (CGW). At the heart of our approach is to apply iterative rounding to the problem with ideas coming from several previous…
We propose an exact algorithm for solving the longest simple path problem between two given vertices in undirected weighted graphs. By using graph partitioning and dynamic programming, we obtain an algorithm that is significantly faster than other state-of-the-art methods. This enables us to solve instances that were previously unsolved and solve hard instances significantly faster. Lastly, we present a scalable parallelization which yields the first efficient parallel algorithm for the problem.
SCAN (Structural Clustering Algorithm for Networks) is a well-studied, widely used graph clustering algorithm. For large graphs, however, sequential SCAN variants are prohibitively slow, and parallel SCAN variants do not effectively share work among queries with different SCAN parameter settings. Since users of SCAN often explore many parameter settings to find good clusterings, it is worthwhile to precompute an index that speeds up queries. This paper presents a practical and provably efficient parallel index-based SCAN algorithm based on GS*-Index, a recent sequential algorithm. Our parallel…
We revisit the minimum dominating set problem on graphs with arboricity bounded by $α$. Bansal and Umboh [BU17] gave an $O(α)$-approximation LP rounding algorithm, which also translates into a near-linear time algorithm using general-purpose approximation results for explicit mixed packing and covering or pure covering LPs [KY14, You14, AZO19, Qua10]. Moreover, [BU17] showed that it is NP-hard to achieve an asymptotic improvement for the approximation factor. On the other hand, the previous two non-LP-based algorithms, by Lenzen and Wattenhofer [LW10], and Jones et al. [JLR+13], achieve an app…
The k-center problem is one of several classic NP-hard clustering questions. For contemporary massive data sets, RAM-based algorithms become impractical. And although there exist good sequential algorithms for k-center, they are not easily parallelizable. In this paper, we design and implement parallel approximation algorithms for this problem. We observe that Gonzalez's greedy algorithm can be efficiently parallelized in several MapReduce rounds; in practice, we find that two rounds are sufficient, leading to a 4-approximation. We contrast this with an existing parallel algorithm for k-center…
Decompressing a file made by the gzip program at an arbitrary location is in principle impossible, due to the nature of the DEFLATE compression algorithm. Consequently, no existing program can take advantage of parallelism to rapidly decompress large gzip-compressed files. This is an unsatisfactory bottleneck, especially for the analysis of large sequencing data experiments. Here we propose a parallel algorithm and an implementation, pugz, that performs fast and exact decompression of any text file. We show that pugz is an order of magnitude faster than gunzip, and 5x faster than a highly-opti…
In this paper we introduce RADULS2, the fastest parallel sorter based on radix algorithm. It is optimized to process huge amounts of data making use of modern multicore CPUs. The main novelties include: extremely optimized algorithm for handling tiny arrays (up to about a hundred of records) that could appear even billions times as subproblems to handle and improved processing of larger subarrays with better use of non-temporal memory stores.
Enumerating simple cycles has important applications in computational biology, network science, and financial crime analysis. In this work, we focus on parallelising the state-of-the-art simple cycle enumeration algorithms by Johnson and Read-Tarjan along with their applications to temporal graphs. To our knowledge, we are the first ones to parallelise these two algorithms in a fine-grained manner. We are also the first to demonstrate experimentally a linear performance scaling. Such a scaling is made possible by our decomposition of long sequential searches into fine-grained tasks, which are …
We present a parallel approximation algorithm for a class of mixed packing and covering semidefinite programs which generalize on the class of positive semidefinite programs as considered by Jain and Yao [2011]. As a corollary we get a faster approximation algorithm for positive semidefinite programs with better dependence of the parallel running time on the approximation factor, as compared to that of Jain and Yao [2011]. Our algorithm and analysis is on similar lines as that of Young [2001] who considered analogous linear programs.
In this paper we demonstrate the methodology for parallelizing the computation of large one-dimensional discrete fast Fourier transforms (DFFTs) on multi-core Intel Xeon processors. DFFTs based on the recursive Cooley-Tukey method have to control cache utilization, memory bandwidth and vector hardware usage, and at the same time scale across multiple threads or compute nodes. Our method builds on single-threaded Intel Math Kernel Library (MKL) implementation of DFFT, and uses the Intel Cilk Plus framework for thread parallelism. We demonstrate the ability of Intel Cilk Plus to handle parallel …
The maximal clique enumeration (MCE) problem has numerous applications in biology, chemistry, sociology, and graph modeling. Though this problem is well studied, most current research focuses on finding solutions in large sparse graphs or very dense graphs, while sacrificing efficiency on the most difficult medium-density benchmark instances that are representative of data sets often encountered in practice. We show that techniques that have been successfully applied to the maximum clique problem give significant speed gains over the state-of-the-art MCE algorithms on these instances. Specific…
We present new parallel sorting networks for $17$ to $20$ inputs. For $17, 19,$ and $20$ inputs these new networks are faster (i.e., they require less computation steps) than the previously known best networks. Therefore, we improve upon the known upper bounds for minimal depth sorting networks on $17, 19,$ and $20$ channels. The networks were obtained using a combination of hand-crafted first layers and a SAT encoding of sorting networks.
In this paper we present a deterministic $O(\log\log n)$-round algorithm for the 2-ruling set problem in the Massively Parallel Computation model with $\tilde{O}(n)$ memory; this algorithm also runs in $O(\log\log n)$ rounds in the Congested Clique model. This is exponentially faster than the fastest known deterministic 2-ruling set algorithm for these models, which is simply the $O(\log Δ)$-round deterministic Maximal Independent Set algorithm due to Czumaj, Davies, and Parter (SPAA 2020). Our result is obtained by derandomizing the 2-ruling set algorithm of Kothapalli and Pemmaraju (FSTTCS 2…
Hypergraph partitioning is an important preprocessing step for optimizing data placement and minimizing communication volumes in high-performance computing applications. To cope with ever growing problem sizes, it has become increasingly important to develop fast parallel partitioning algorithms whose solution quality is competitive with existing sequential algorithms. To this end, we present Mt-KaHyPar, the first shared-memory multilevel hypergraph partitioner with parallel implementations of many techniques used by the sequential, high-quality partitioning systems: a parallel coarsening algo…
The maximum labelled clique problem is a variant of the maximum clique problem where edges in the graph are given labels, and we are not allowed to use more than a certain number of distinct labels in a solution. We introduce a new branch-and-bound algorithm for the problem, and explain how it may be parallelised. We evaluate an implementation on a set of benchmark instances, and show that it is consistently faster than previously published results, sometimes by four or five orders of magnitude.
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…
We use exponential start time clustering to design faster and more work-efficient parallel graph algorithms involving distances. Previous algorithms usually rely on graph decomposition routines with strict restrictions on the diameters of the decomposed pieces. We weaken these bounds in favor of stronger local probabilistic guarantees. This allows more direct analyses of the overall process, giving: * Linear work parallel algorithms that construct spanners with $O(k)$ stretch and size $O(n^{1+1/k})$ in unweighted graphs, and size $O(n^{1+1/k} \log k)$ in weighted graphs. * Hopsets that lead to…
Priority queues with parallel access are an attractive data structure for applications like prioritized online scheduling, discrete event simulation, or branch-and-bound. However, a classical priority queue constitutes a severe bottleneck in this context, leading to very small throughput. Hence, there has been significant interest in concurrent priority queues with a somewhat relaxed semantics where deleted elements only need to be close to the minimum. In this paper we present a very simple approach based on multiple sequential priority queues. It turns out to outperform previous more complic…
The secondary structure that maximizes the number of non-crossing matchings between complimentary bases of an RNA sequence of length n can be computed in O(n^3) time using Nussinov's dynamic programming algorithm. The Four-Russians method is a technique that will reduce the running time for certain dynamic programming algorithms by a multiplicative factor after a preprocessing step where solutions to all smaller subproblems of a fixed size are exhaustively enumerated and solved. Frid and Gusfield designed an O(\frac{n^3}{\log n}) algorithm for RNA folding using the Four-Russians technique. In …
