Randomized and Approximation Algorithms for Blue-Red Matching

The Stackelberg Minimum Spanning Tree Game is a two-level combinatorial pricing problem played on a graph representing a network. Its edges are colored either red or blue, and the red edges have a given fixed cost, representing the competitor's prices. The first player chooses an assignment of prices to the blue edges, and the second player then buys the cheapest spanning tree, using any combination of red and blue edges. The goal of the first player is to maximize the total price of purchased blue edges. We study this problem in the cases of planar and bounded-treewidth graphs. We show that the problem is NP-hard on planar graphs but can be solved in polynomial time on graphs of bounded treewidth.

Enumeration of all maximal bicliques in bipartite graphs is a well-studied fundamental problem. However, a wide range of applications need less overlapping bicliques with specific size constraints instead of all the maximal bicliques. In this paper, we study a new biclique problem, called the top-k t-biclique coverage problem. A t-biclique is a biclique with a size constraint <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$t$</tex> for one vertex set and the problem aims to find <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$k$</tex> t-bicliques maximising the coverage on the other vertex set. The top-k t-biclique coverage problem has novel applications such as finding top-k courses while maximising student engagement. We prove that this problem is NP-hard. A straightforward way to address the problem first needs to enumerate and store all t-bicliques and then greedily select <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$k$</tex> promising t-bicliques, leading an approximate guarantee on the coverage. However, it takes exponential space, which is impractical. We then apply a fast approximation scheme to solve this problem, which shaves the exponential space consumption by progressively updating top-k results during the t-biclique enumeration. Observing that the fast approximation algorithm takes too much time on updating the results due to the coverage is computed from scratch for each update, an online index is devised to address the drawback. Due the hardness of the problem, even the fast approximation algorithm cannot scale to large dataset. To devise a scalable solution, we then propose a heuristic algorithm running in polynomial time. Thanks for four carefully designed heuristic rules, the heuristic algorithm can find large coverage top-k t-bicliques extremely fast for large datasets. Apart from that, the heuristic result with large coverage can effectively prune unpromising enumerations in the fast greedy algorithm, which improves the efficiency of the fast approximation algorithm without compromising the approximation ratio. Extensive experiments are conducted on real datasets to justify the effectiveness and efficiency of the proposed algorithms.

Resource assignment problems occur in a vast variety of applications, from scheduling problems over image recognition to communication networks. Often these problems can be modeled by a maximum weight matching problem in (bipartite) graphs or generalizations thereof, and efficient and practical algorithms are known for these problems. Although in some of the applications an assignment of the resources may be needed only once, in many of these applications, the assignment has to be computed more often for different scenarios. In that case it is often essential that the assignments can be computed very fast. Moreover, implementing different assignments in different scenarios may come with a certain cost for the reconfiguration of the system. In this paper, we consider the problem of determining optimal assignments sequentially over a given time horizon, where consecutive assignments are coupled by constraints that control the cost of reconfiguration. We develop fast approximation and online algorithms for this problem with provable approximation guarantees and competitive ratios. Moreover, we present an extensive computational study about the applicability of our model and our algorithms in the context of orthogonal frequency division multiple access (OFDMA) wireless networks, finding a significant performance improvement for the total bandwidth of the system using our algorithms. For this application (the downlink of an OFDMA wireless cell) , the run time of matching algorithms is extremely important, having an acceptable range of a few milliseconds only. For the considered realistic instances, our algorithms perform extremely well: the solution quality is, on average, within a factor of 0.8–0.9 of optimal off-line solutions, and the running times are at most 5 ms per phase even in the worst case. Thus, our algorithms are well suited to be applied in the context of OFDMA systems. Data, as supplemental material, are available at http://dx.doi.org/10.1287/mnsc.2015.2221 . This paper was accepted by Teck-Hua Ho, optimization.

Graph matching problem, also known as quadratic assignment problem (QAP) in a practical context, aims at finding the best correspondence between two given graphs. If two nodes are connected in one graph, it would be ideal if their corresponding images are connected in the other. The optimal solution should maximize the number of matches between the two graphs, while minimizing the weight of mismatches. Graph isomorphism is a particular case where an exact correspondence with no mismatches could be found. The quadratic assignment problem itself is hard to solve due to its high computational complexity. In this paper, the researcher analyzes two optimization approaches in detail: convex relaxation and the Fast Approximate QAP algorithm, both trying to solve the problem with lower computational effort. The performances of these two methods are further compared through numerical experiments. This paper focuses on pairs of equal-sized undirected graphs. ρ correlated graphs are constructed to simulate the noise in inexact graph matching problems. After comparing two existing methods, we propose an even faster optimization approach with comparable accuracy. This new approach provides a particular way to approximate an ideal initialization for the traditional Fast Approximate QAP algorithm. The significant reduction in the runtime makes obtaining good correspondence between large graphs feasible.

In 1982, Papadimitriou and Yannakakis introduced the Exact Matching (EM) problem where given an edge colored graph, with colors red and blue, and an integer k, the goal is to decide whether or not the graph contains a perfect matching with exactly k red edges. Although they conjectured it to be NP-complete, soon after it was shown to be solvable in randomized polynomial time in the seminal work of Mulmuley et al., placing it in the complexity class RP. Since then, all attempts at finding a deterministic algorithm for EM have failed, thus leaving it as one of the few natural combinatorial problems in RP but not known to be contained in P, and making it an interesting instance for testing the hypothesis RP = P. Progress has been lacking even on very restrictive classes of graphs despite the problem being quite well known as evidenced by the number of works citing it. In this paper we aim to gain more insight into EM by studying a new optimization problem we call Top-k Perfect Matching (TkPM) which we show to be polynomially equivalent to EM. By virtue of being an optimization problem, it is more natural to approximate TkPM so we provide approximation algorithms for it. Some of the approximation algorithms rely on a relaxation of EM on bipartite graphs where the output is required to be a perfect matching with a number of red edges differing from k by at most k/2, which is of independent interest and generalizes to the Exact Weight Perfect Matching (EWPM) problem. We also consider parameterized algorithms and show that TkPM can be solved in FPT time parameterized by k and the independence number of the graph. This result again relies on new tools developed for EM which are also of independent interest.

Emerging single-molecule sequencing technologies from Pacific Biosciences and Oxford Nanopore have revived interest in long-read mapping algorithms. Alignment-based seed-and-extend methods demonstrate good accuracy, but face limited scalability, while faster alignment-free methods typically trade decreased precision for efficiency. In this article, we combine a fast approximate read mapping algorithm based on minimizers with a novel MinHash identity estimation technique to achieve both scalability and precision. In contrast to prior methods, we develop a mathematical framework that defines the types of mapping targets we uncover, establish probabilistic estimates of p-value and sensitivity, and demonstrate tolerance for alignment error rates up to 20%. With this framework, our algorithm automatically adapts to different minimum length and identity requirements and provides both positional and identity estimates for each mapping reported. For mapping human PacBio reads to the hg38 reference, our method is 290 × faster than Burrows-Wheeler Aligner-MEM with a lower memory footprint and recall rate of 96%. We further demonstrate the scalability of our method by mapping noisy PacBio reads (each ≥5 kbp in length) to the complete NCBI RefSeq database containing 838 Gbp of sequence and >60,000 genomes.

Parameterized algorithms for load coloring problem

Fast Heuristics and Approximation Algorithms

We build on the classical greedy sequential set cover algorithm, in the spirit of the primal-dual schema, to obtain simple parallel approximation algorithms for the set cover problem and its generalizations. Our algorithms use randomization, and our randomized voting lemmas may be of independent interest. Fast parallel approximation algorithms were known before for set cover, though not for any of its generalizations. >

Label cost optimization proposes a new improvement in label cost function, improving existing moves of α-expansion algorithm and introducing some new moves for this algorithm. In order to study the performance comparison, different metrics of energy minimization has been considered. An appropriate comparison has been drawn among proposed technique i.e. fast approximation algorithm and previous well known techniques. The objective is to effectively optimize energies so that satisfactory image segmentation can be obtained (represented with different labels respective to different objects). New combinatorial optimization algorithm have been proposed which shows promising experimental results with the new moves, which we believe could be used in any context where α -expansions are currently employed.

Observational or nonrandomized studies of treatment effects are often constructed with the aid of polynomial-time algorithms that optimally form matched treatment-control pairs or matched sets. Because each observational comparison may potentially be affected by bias, investigators often reinforce a single comparison with an additional comparison that is unlikely to be affected by the same biases, for instance using multiple control groups or evidence factors or control + instrument designs. Use of two comparisons affected by different biases may detect bias if the two comparisons disagree, or may show that two comparisons with different weakness concur in their conclusions. Even this simplest addition—a second comparison—creates design problems without polynomial-time solutions. Faced with a problem that no polynomial-time algorithm can solve, a so-called approximation algorithm is a type of compromise: it provides a solution in polynomial time that is provably not much worse than the unattainable optimal solution. Building upon existing techniques for related problems in operations research, we develop an approximation algorithm for minimum distance matching with near-fine balance for three comparison groups. This algorithm is a practical approach to most observational designs that add a second comparison. The method is applied to an observational study of the effects of side airbags on injury severity in the U.S. Fatality Analysis Reporting System. For many car makes and models, side airbags were initially unavailable, then later available as optional equipment for an additional fee, then still later provided as standard equipment. Within sets matched for make and model of car, for safety belt use, for direction of impact, and other covariates, we compare crashes in these three periods, where each comparison has different limitations. The method is implemented in the R package approxmatch, whose example reproduces some of the calculations. Supplementary materials for this article are available online.

Quadratic assignment problems arise in a wide variety of domains, spanning operations research, graph theory, computer vision, and neuroscience, to name a few. The graph matching problem is a special case of the quadratic assignment problem, and graph matching is increasingly important as graph-valued data is becoming more prominent. With the aim of efficiently and accurately matching the large graphs common in big data, we present our graph matching algorithm, the Fast Approximate Quadratic assignment algorithm. We empirically demonstrate that our algorithm is faster and achieves a lower objective value on over 80% of the QAPLIB benchmark library, compared with the previous state-of-the-art. Applying our algorithm to our motivating example, matching C. elegans connectomes (brain-graphs), we find that it efficiently achieves performance.

근사문자열매칭 문제는 다양한 분야에서 연구되어 왔다. 최근에는 차세대염기서열분석의 비용과 시간을 줄이기 위해 빠른 근사문자열매칭 알고리즘들이 이용되고 있다. 근사문자열매칭은 문자열들의 오차를 측정하기 위해 편집거리와 같은 거리함수를 이용한다. 알파벳 <TEX>${\Sigma}$</TEX>에 대한 길이가 각각 m, n인 두 문자열 X와 Y의 편집거리는 X를 Y로 변환하기 위해 필요한 최소 편집연산의 수로 정의된다. 두 문자열의 편집거리는 잘 알려진 동적프로그래밍을 이용하여 O(mn) 시간과 공간에 계산할 수 있으며, 4-러시안 알고리즘을 이용해서도 계산할 수 있다. 4-러시안 알고리즘은 블록 크기를 t라 할 때, 전처리 단계에서 <TEX>$O((3{\mid}{\Sigma}{\mid})^{2t}t^2)$</TEX> 시간과 <TEX>$O((3{\mid}{\Sigma}{\mid})^{2t}t)$</TEX> 공간이 필요하며, 계산 단계에서 O(mn/t) 시간과 O(mn) 공간을 이용하여 편집거리를 계산하는 알고리즘이다. 본 논문에서는 4-러시안 알고리즘의 계산 단계를 병렬화하고 실험을 통해 CPU 기반의 순차적 알고리즘과 CUDA로 구현한 GPU 기반의 병렬 알고리즘의 수행시간을 비교한다. 본 논문에서 제시하는 4-러시안 알고리즘의 계산단계는 m/t개의 쓰레드를 사용하여 O(m+n) 시간에 편집거리를 계산한다. GPU 기반의 알고리즘이 CPU 기반의 알고리즘 보다 t = 1일 때 약 10배 빠르고, t = 2일 때 약 3배 빠른 결과를 보였다. Approximate string matching problems have been studied in diverse fields. Recently, fast approximate string matching algorithms are being used to reduce the time and costs for the next generation sequencing. To measure the amounts of errors between two strings, we use a distance function such as the edit distance. Given two strings X(|X| = m) and Y(|Y| = n) over an alphabet <TEX>${\Sigma}$</TEX>, the edit distance between X and Y is the minimum number of edit operations to convert X into Y. The edit distance between X and Y can be computed using the well-known dynamic programming technique in O(mn) time and space. The edit distance also can be computed using the Four-Russians' algorithm whose preprocessing step runs in <TEX>$O((3{\mid}{\Sigma}{\mid})^{2t}t^2)$</TEX> time and <TEX>$O((3{\mid}{\Sigma}{\mid})^{2t}t)$</TEX> space and the computation step runs in O(mn/t) time and O(mn) space where t represents the size of the block. In this paper, we present a parallelized version of the computation step of the Four-Russians' algorithm. Our algorithm computes the edit distance between X and Y in O(m+n) time using m/t threads. Then we implemented both the sequential version and our parallelized version of the Four-Russians' algorithm using CUDA to compare the execution times. When t = 1 and t = 2, our algorithm runs about 10 times and 3 times faster than the sequential algorithm, respectively.

Motivated by the real time applications of adaptive signal processing algorithms a new Approximate RLS algorithm is developed. It is shown that the computational complexity of this algorithm is comparable to that of the LMS algorithm. Convergence analysis for this algorithm is presented showing the unconditional convergence of the algorithm in the mean and the mean square sense for stationary data. It is shown that the rate of convergence of this algorithm is n/sup -1/. The convergence characteristics of this algorithm shows that the algorithm is much faster than the LMS algorithm but somewhat slower than the RLS algorithm. Modifications to this algorithm are suggested for use in nonstationary data environment. Simulation results for this algorithm are compared with those for the LMS and the RLS algorithms. >

In this paper we propose a novel approach to identify anomalies in DNS traffic. The traffic time-points data is transformed to a string, which is used by new fast approximate string matching algorithm to detect anomalies. Our approach is generic in its nature and allows fast adaptation to different types of traffic. We evaluate the approach on a large public dataset of DNS traffic based on 10 days, discovering more than order of magnitude DNS attacks in comparison to auto-regression as a baseline. Moreover, the additional comparison has been made including other common regressors such as Linear Regression, Lasso, Random Forest and KNN, all of them showing the superiority of our approach.