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Fusion Moves for Markov Random Field Optimization

IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2010年第8期32卷 1392-1405页

作者： Lempitsky, Victor Rother, Carsten Roth, Stefan Blake, Andrew Microsoft Res Cambridge CB3 0FB England Tech Univ Darmstadt GRIS D-64283 Darmstadt Germany

The efficient application of graph cuts to Markov Random Fields (MRFs) with multiple discrete or continuous labels remains an open question. In this paper, we demonstrate one possible way of achieving this by using graph cuts to combine pairs of suboptimal labelings or solutions. We call this combination process the fusion move. By employing recently developed graph-cut-based algorithms (so-called QPBO-graph cut), the fusion move can efficiently combine two proposal labelings in a theoretically sound way, which is in practice often globally optimal. We demonstrate that fusion moves generalize many previous graph-cut approaches, which allows them to be used as building blocks within a broader variety of optimization schemes than were considered before. In particular, we propose new optimization schemes for computer vision MRFs with applications to image restoration, stereo, and optical flow, among others. Within these schemes the fusion moves are used 1) for the parallelization of MRF optimization into several threads, 2) for fast MRF optimization by combining cheap-to-compute solutions, and 3) for the optimization of highly nonconvex continuous-labeled MRFs with 2D labels. Our final example is a nonvision MRF concerned with cartographic label placement, where fusion moves can be used to improve the performance of a standard inference method (loopy belief propagation).

关键词： Markov random fields computer vision combinatorial algorithms graph algorithms stereo motion image restoration

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A survey of approximately optimal solutions to some covering and packing problems

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ACM COMPUTING SURVEYS 1997年第2期29卷 171-209页

作者： Paschos, VT Lamsade Université Paris-Dauphine

We survey approximation algorithms for some well-known and very natural combinatorial optimization problems, the minimum set covering, the minimum vertex covering, the maximum set packing, and maximum independent set problems;we discuss their approximation performance and their complexity. For already known results, any time we have conceived simpler proofs than those already published, we give these proofs, and, for the rest, we cite the simpler published ones. Finally, we discuss how one can relate the approximability behavior (from both a positive and a negative point of view) of vertex covering to the approximability behavior of a restricted class of independent set problems.

关键词： algorithm analysis approximation algorithms combinatorial algorithms constrained optimization problem complexity

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Trimming Gene Deletion Strategies for Growth-Coupled Production in Constraint-Based Metabolic Networks: TrimGdel

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IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023年第2期20卷 1540-1549页

作者： Tamura, Takeyuki Kyoto Univ Inst Chem Res Bioinformat Ctr Uji Kyoto 6110011 Japan

When simulating genome-scale metabolite production using constraint-based metabolic networks, it is often necessary to find gene deletion strategies which lead to growth-coupled production, which means that target metabolites are produced when cell growth is maximized. Existing methods are effective when the number of gene deletions is relatively small, but when the number of required gene deletions exceeds approximately 1% of whole genes, the time required for the calculation is often unfeasible. Therefore, a complementing algorithm that is effective even when the required number of gene deletions is approximately 1% to 5% of whole genes would be helpful because the number of deletable genes in a strain is increasing with advances in genetic engineering technology. In this study, the author developed an algorithm, TrimGdel, which first computes a strategy with many gene deletions that results in growth-coupled production and then gradually reduces the number of gene deletions while ensuring the original production rate and growth rate. The results of the computer experiments showed that TrimGdel can calculate stoichiometrically feasible gene deletion strategies, especially those whose sizes are 1 to 5% of whole genes, which lead to growth-coupled production of many target metabolites, which include useful vitamins such as biotin and pantothenate, for which existing methods could not.

关键词： Biology and genetics chemistry combinatorial algorithms graphs and network linear programming

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MetNetComp: Database for Minimal and Maximal Gene-Deletion Strategies for Growth-Coupled Production of Genome-Scale Metabolic Networks

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IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023年第6期20卷 3748-3758页

作者： Tamura, Takeyuki Kyoto Univ Inst Chem Res Bioinformat Ctr Uji Kyoto 6110011 Japan

Growth-coupled production, in which cell growth forces the production of target metabolites, plays an essential role in the production of substances by microorganisms. The strains are first designed using computational simulation and then validated by biological experiments. In the simulations, gene-deletion strategies are often necessary because many metabolites are not produced in the natural state of the microorganisms. However, such information is not available for many metabolites owing to the requirement of heavy computation, especially when many gene deletions are required for genome-scale models. A database for such information will be helpful. However, developing such a database is not straightforward because heavy computation and the existence of replaceable genes render difficulty in efficient enumeration. In this study, the author developed efficient methods for enumerating minimal and maximal gene-deletion strategies and a web-based database system. MetNetComp provides information on 1) a total of 85,611 gene-deletion strategies excluding apparent duplicate counting for replaceable genes for 1,735 target metabolites, 11 constraint-based models, and 10 species;2) necessary substrates and products in the process;and 3) reaction rates that can be used for visualization. MetNetComp is helpful for strain design and for new research paradigms using machine learning.

关键词： Biology and genetics chemistry combinatorial algorithms graphs and networks linear programming scientific databases

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Time-varying Reeb graphs for continuous space-time data

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COMPUTATIONAL GEOMETRY-THEORY AND APPLICATIONS 2008年第3期41卷 149-166页

作者： Edelsbrunner, Herbert Harer, John Mascarenhas, Ajith Pascucci, Valerio Snoeyink, Jack Lawrence Livermore Natl Lab Ctr Appl Sci Comp Livermore CA 94550 USA Raindrop Geomag Res Triangle Pk NC USA Duke Univ Dept Math & Comp Sci Durham NC 27706 USA Univ N Carolina Dept Comp Sci Chapel Hill NC USA

The Reeb graph is a useful tool in visualizing real-valued data obtained from computational simulations of physical processes. We characterize the evolution of the Reeb graph of a time-varying continuous function defined in three-dimensional space. We show how to maintain the Reeb graph over time and compress the entire sequence of Reeb graphs into a single, partially persistent data structure, and augment this data structure with Betti numbers to describe the topology of level sets and with path seeds to assist in the fast extraction of level sets for visualization. (c) 2008 Elsevier B.V. All rights reserved.

关键词： differential and computational topology Morse functions critical points level sets Reeb graph triangulations combinatorial algorithms

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Parallel Graph Partitioning for Complex Networks

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IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS 2017年第9期28卷 2625-2638页

作者： Meyerhenke, Henning Sanders, Peter Schulz, Christian Karlsruhe Inst Technol D-76131 Karlsruhe Germany Univ Vienna A-1010 Vienna Austria

Processing large complex networks like social networks or web graphs has attracted considerable interest. To do this in parallel, we need to partition them into pieces of roughly equal size. Unfortunately, previous parallel graph partitioners originally developed for more regular mesh-like networks do not work well for complex networks. Here we address this problem by parallelizing and adapting the label propagation technique originally developed for graph clustering. By introducing size constraints, label propagation becomes applicable for both the coarsening and the refinement phase of multilevel graph partitioning. This way we exploit the hierarchical cluster structure present in many complex networks. We obtain very high quality by applying a highly parallel evolutionary algorithm to the coarsest graph. The resulting system is both more scalable and achieves higher quality than state-of-theart systems like ParMetis or PT-Scotch. For large complex networks the performance differences are very big. As an example, our algorithm partitions a web graph with 3.3 G edges in 16 seconds using 512 cores of a high-performance cluster while producing a high quality partition-none of the competing systems can handle this graph on our system.

关键词： Load balancing and task assignment graph algorithms combinatorial algorithms algorithm design and analysis

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Efficient Capacity Constrained Assignment for Dynamic Network Coverage

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IEEE TRANSACTIONS ON MOBILE COMPUTING 2024年第5期23卷 5111-5129页

作者： Ao, Eerdemotai Xin, Shiqing Li, Feng Tu, Changhe Wang, Wenping Univ Hong Kong Fac Engn Dept Comp Sci Hong Kong Peoples R China Shandong Univ Sch Comp Sci & Technol Qingdao 266237 Shandong Peoples R China Texas A&M Univ Coll Engn Dept Comp Sci & Engn College Stn TX 77843 USA

With the fast development of the 5G wireless communications, the Internet of Things (IoT) becomes a hot research topic. Unmanned aerial vehicles (UAVs), due to the high mobility and low labor cost, have a big potential to be applied in the future IoT communication networks, e.g., data collection in remote areas. In this paper, we take a UAV as a monitor and an IoT device as an agent, and study how to utilize UAVs to establish network coverage and enhance the overall performance. Given ground agents and aerial monitors, each agent needs to be supervised by one monitor that can at most take charge of certain amount, while such assignment should guarantee the required service quality. This is much different from the conventional assumption that each monitor owns exactly a fixed number of agents without considering sensing quality under limited transmit power. Suppose that a monitor supervises an agent with a cost as the negative value of transmission rate in Rician fading, we then maximize the sum of transmission induced by every monitor-agent connection constrained with workload capacity for each monitor. To achieve the above goals, we first present a fast algorithm to report the least-cost assignment plan. Then, we seek for the minimum number of monitors to maintain the required service quality. Last, we discuss the assignment problem in the scenario of dynamic agents and dynamic monitors. We also give a set of strategies on how to initialize assignment, optimize monitor locations and manage power consumption. Extensive experimental results on both simulated datasets and real-life traffic data demonstrate our effectiveness and high performance.

关键词： Wireless sensor networks coherence and coordination autonomous vehicles combinatorial algorithms

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THE MINIMAL HITTING SET GENERATION PROBLEM: algorithms AND COMPUTATION

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SIAM JOURNAL ON DISCRETE MATHEMATICS 2017年第1期31卷 63-100页

作者： Gainer-Dewar, Andrew Vera-Licona, Paola UConn Hlth Ctr Quantitat Med Farmington CT 06030 USA

Finding inclusion-minimal hitting sets (MHSs) for a given family of sets is a fundamental combinatorial problem with applications in domains as diverse as Boolean algebra, computational biology, and data mining. Although many algorithms are available in the literature to generate these MHSs, application papers typically consider only a few before selecting one (or introducing a novel algorithm), suggesting the need for a comprehensive survey and performance comparison. We introduce several of these applications, discussing how MHS generation is applied in each domain and which algorithms have been used, providing a unified view of these applications for researchers from diverse areas. We survey twenty-one algorithms for MHS generation from across a variety of domains, considering their history, classification, and useful features. We provide the results of a comprehensive suite of benchmarks of public software implementations of seventeen of these algorithms, including six we implemented ourselves in C++, emphasizing problem instances taken from real applications in the literature. We find that the fastest algorithms in practice are not those with the tightest complexity bounds or those most commonly used in applications, suggesting that, for a given application, benchmarking from across the broad span of available algorithms will enable a better choice. Finally, we provide a public repository of these software implementations as ready-to-use, platform-agnostic Docker containers based on the AlgoRun framework, so interested computational scientists can easily perform similar tests with inputs from their own research areas, either on their own computers or through a convenient Web interface or deploy the algorithms in their own analysis pipelines.

关键词： minimal hitting set Boolean dualization combinatorial algorithms hypergraph transversal set cover problem

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A method for counting models on grid Boolean formulas

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JOURNAL OF INTELLIGENT & FUZZY SYSTEMS 2022年第5期42卷 4719-4726页

作者： Lopez-Medina, Marco A. Raymundo Marcial-Romero, J. De Ita Luna, Guillermo Hernandez, Jose A. BUAP Fac Ingn UAEMex Puebla Mexico BUAP Fac Ciencias Comp Puebla Mexico

We present a novel algorithm based on combinatorial operations on lists for computing the number of models on two conjunctive normal form Boolean formulas whose restricted graph is represented by a grid graph G(m, n). We show that our algorithm is correct and its time complexity is O(root t . 1.618(root t+2) + t . 1.6182(root t+4)), where t = n . m is the total number of vertices in the graph. For this class of formulas, we show that our proposal improves the asymptotic behavior of the time-complexity with respect of the current leader algorithm for counting models on two conjunctive form formulas of this kind.

关键词： #SAT #2SAT models of boolean formulas combinatorial algorithms complexity theory

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Computing distance-based topological descriptors of complex chemical networks: New theoretical techniques

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CHEMICAL PHYSICS LETTERS 2017年 688卷 51-58页

作者： Hayat, Sakander USTC Sch Math Sci Hefei Anhui Peoples R China

Structure-based topological descriptors/indices of complex chemical networks enable prediction of physico-chemical properties and the bioactivities of these compounds through QSAR/QSPR methods. In this paper, we have developed a rigorous computational and theoretical technique to compute various distance-based topological indices of complex chemical networks. A fullerene is called the IPR (Isolated-Pentagon-Rule) fullerene, if every pentagon in it is surrounded by hexagons only. To ensure the applicability of our technique, we compute certain distance-based indices of an infinite family of IPR fullerenes. Our results show that the proposed technique is more diverse and bears less algorithmic and combinatorial complexity. (C) 2017 Elsevier B.V. All rights reserved.

关键词： combinatorial algorithms Distance-based topological descriptors Chemical networks IPR fullerenes QSAR of fullerenes

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