Bulletin of the Society of Sea Water Science, Japan最新文献_第10页

Reduction of Supercooling of Heavy Water with Silver Iodide 用碘化银还原重水过冷

Bulletin of the Society of Sea Water Science, Japan Pub Date : 2018-01-01 DOI: 10.11457/SWSJ.72.1_41

Shoko Naruke, K. Fujiwara, T. Sugo, S. Kawai-Noma, D. Umeno, Kyoichi Saito

引用次数: 0

Speeding up Dualization in the Fredman-Khachiyan Algorithm B 加速fredman - kachiyan算法的二象化B

Bulletin of the Society of Sea Water Science, Japan Pub Date : 2018-01-01 DOI: 10.4230/LIPIcs.SEA.2018.6

N. Sedaghat, Tamon Stephen, L. Chindelevitch

{"title":"Speeding up Dualization in the Fredman-Khachiyan Algorithm B","authors":"N. Sedaghat, Tamon Stephen, L. Chindelevitch","doi":"10.4230/LIPIcs.SEA.2018.6","DOIUrl":"https://doi.org/10.4230/LIPIcs.SEA.2018.6","url":null,"abstract":"The problem of computing the dual of a monotone Boolean function f is a fundamental problem in theoretical computer science with numerous applications. The related problem of duality testing (given two monotone Boolean functions f and g, declare that they are dual or provide a certificate that shows they are not) has a complexity that is not yet known. However, two quasi-polynomial time algorithms for it, often referred to as FK-A and FK-B, were proposed by Fredman and Khachiyan in 1996, with the latter having a better complexity guarantee. These can be naturally used as a subroutine in computing the dual of f . In this paper, we investigate this use of the FK-B algorithm for the computation of the dual of a monotone Boolean function, and present practical improvements to its performance. First, we show how FK-B can be modified to produce multiple certificates (Boolean vectors on which the functions defined by the original f and the current dual g do not provide outputs consistent with duality). Second, we show how the number of redundancy tests one of the more costly and time-consuming steps of FK-B can be substantially reduced in this context. Lastly, we describe a simple memoization technique that avoids the solution of multiple identical subproblems. We test our approach on a number of inputs coming from computational biology as well as combinatorics. These modifications provide a substantial speed-up, as much as an order of magnitude, for FK-B dualization relative to a naive implementation. Although other methods may end up being faster in practice, our work paves the way for a principled optimization process for the generation of monotone Boolean functions and their duals from an oracle. 2012 ACM Subject Classification Computing methodologies → Boolean algebra algorithms","PeriodicalId":9448,"journal":{"name":"Bulletin of the Society of Sea Water Science, Japan","volume":"42 1","pages":"6:1-6:13"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87563201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Monovalent Selective Cation-exchange Membranes Prepared from PVA-based Block Copolymers 聚乙烯醇基嵌段共聚物制备的一价选择性阳离子交换膜

Bulletin of the Society of Sea Water Science, Japan Pub Date : 2018-01-01 DOI: 10.11457/SWSJ.72.6_338

Saeko Harada, Yuriko Kakihana, Mitsuru Higa

引用次数: 1

High-performance Liquid Chromatographic Evaluation of Effect of Metal Ion on Amyloid Fibril Formation 高效液相色谱法评价金属离子对淀粉样纤维形成的影响

Bulletin of the Society of Sea Water Science, Japan Pub Date : 2018-01-01 DOI: 10.11457/SWSJ.72.6_336

K. Nagashima, H. Minamisawa, T. Nakagama, K. Saitoh, Hiromichi Asamoto

引用次数: 0

Real-Time Traffic Assignment Using Fast Queries in Customizable Contraction Hierarchies 在可定制的收缩层次结构中使用快速查询的实时流量分配

Bulletin of the Society of Sea Water Science, Japan Pub Date : 2018-01-01 DOI: 10.4230/LIPIcs.SEA.2018.27

V. Buchhold, P. Sanders, D. Wagner

{"title":"Real-Time Traffic Assignment Using Fast Queries in Customizable Contraction Hierarchies","authors":"V. Buchhold, P. Sanders, D. Wagner","doi":"10.4230/LIPIcs.SEA.2018.27","DOIUrl":"https://doi.org/10.4230/LIPIcs.SEA.2018.27","url":null,"abstract":"Given an urban road network and a set of origin-destination (OD) pairs, the traffic assignment problem asks for the traffic flow on each road segment. A common solution employs a feasible-direction method, where the direction-finding step requires many shortest-path computations. In this paper, we significantly accelerate the computation of flow patterns, enabling interactive transportation and urban planning applications. We achieve this by revisiting and carefully engineering known speedup techniques for shortest paths, and combining them with customizable contraction hierarchies. In particular, our accelerated elimination tree search is more than an order of magnitude faster for local queries than the original algorithm, and our centralized search speeds up batched point-to-point shortest paths by a factor of up to 6. These optimizations are independent of traffic assignment and can be generally used for (batched) point-to-point queries. In contrast to prior work, our evaluation uses real-world data for all parts of the problem. On a metropolitan area encompassing more than 2.7 million inhabitants, we reduce the flow-pattern computation for a typical two-hour morning peak from 76.5 to 10.5 seconds on one core, and 4.3 seconds on four cores. This represents a speedup of 18 over the state of the art, and three orders of magnitude over the Dijkstra-based baseline.","PeriodicalId":9448,"journal":{"name":"Bulletin of the Society of Sea Water Science, Japan","volume":"19 4","pages":"27:1-27:15"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91456563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 13

Engineering Motif Search for Large Motifs 大型Motif的工程Motif搜索

Bulletin of the Society of Sea Water Science, Japan Pub Date : 2018-01-01 DOI: 10.4230/LIPIcs.SEA.2018.28

P. Kaski, Juho Lauri, Suhas Thejaswi

{"title":"Engineering Motif Search for Large Motifs","authors":"P. Kaski, Juho Lauri, Suhas Thejaswi","doi":"10.4230/LIPIcs.SEA.2018.28","DOIUrl":"https://doi.org/10.4230/LIPIcs.SEA.2018.28","url":null,"abstract":"Given a vertex-colored graph H and a multiset M of colors as input, the graph motif problem asks us to decide whether H has a connected induced subgraph whose multiset of colors agrees with M. The graph motif problem is NP-complete but known to admit randomized algorithms based on constrained multilinear sieving over GF(2^b) that run in time O(2^kk^2m {M({2^b})}) and with a false-negative probability of at most k/2^{b-1} for a connected m-edge input and a motif of size k. On modern CPU microarchitectures such algorithms have practical edge-linear scalability to inputs with billions of edges for small motif sizes, as demonstrated by Bjorklund, Kaski, Kowalik, and Lauri [ALENEX'15]. This scalability to large graphs prompts the dual question whether it is possible to scale to large motif sizes. We present a vertex-localized variant of the constrained multilinear sieve that enables us to obtain, in time O(2^kk^2m{M({2^b})}) and for every vertex simultaneously, whether the vertex participates in at least one match with the motif, with a per-vertex probability of at most k/2^{b-1} for a false negative. Furthermore, the algorithm is easily vector-parallelizable for up to 2^k threads, and parallelizable for up to 2^kn threads, where n is the number of vertices in H. Here {M({2^b})} is the time complexity to multiply in GF(2^b). We demonstrate with an open-source implementation that our variant of constrained multilinear sieving can be engineered for vector-parallel microarchitectures to yield hardware utilization that is bound by the available memory bandwidth. Our main engineering contributions are (a) a version of the recurrence for tightly labeled arborescences that can be executed as a sequence of memory-and-arithmetic coalescent parallel workloads on multiple GPUs, and (b) a bit-sliced low-level implementation for arithmetic in characteristic 2 to support (a).","PeriodicalId":9448,"journal":{"name":"Bulletin of the Society of Sea Water Science, Japan","volume":"70 1","pages":"28:1-28:19"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79171735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

A Computational Investigation on the Strength of Dantzig-Wolfe Reformulations dantzigg - wolfe重构强度的计算研究

Bulletin of the Society of Sea Water Science, Japan Pub Date : 2018-01-01 DOI: 10.4230/LIPIcs.SEA.2018.11

Michael Bastubbe, M. Lübbecke, Jonas T. Witt

{"title":"A Computational Investigation on the Strength of Dantzig-Wolfe Reformulations","authors":"Michael Bastubbe, M. Lübbecke, Jonas T. Witt","doi":"10.4230/LIPIcs.SEA.2018.11","DOIUrl":"https://doi.org/10.4230/LIPIcs.SEA.2018.11","url":null,"abstract":"In Dantzig-Wolfe reformulation of an integer program one convexifies a subset of the constraints, leading to potentially stronger dual bounds from the respective linear programming relaxation. As the subset can be chosen arbitrarily, this includes the trivial cases of convexifying no and all constraints, resulting in a weakest and strongest reformulation, respectively. Our computational study aims at better understanding of what happens in between these extremes. For a collection of integer programs with few constraints we compute, optimally solve, and evaluate the relaxations of all possible (exponentially many) Dantzig-Wolfe reformulations (with mild extensions to larger models from the MIPLIBs). We observe that only a tiny number of different dual bounds actually occur and that only a few inclusion-wise minimal representatives exist for each. This aligns with considerably different impacts of individual constraints on the strengthening the relaxation, some of which have almost no influence. In contrast, types of constraints that are convexified in textbook reformulations have a larger effect. We relate our experiments to what could be called a hierarchy of Dantzig-Wolfe reformulations.","PeriodicalId":9448,"journal":{"name":"Bulletin of the Society of Sea Water Science, Japan","volume":"4 1","pages":"11:1-11:12"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89303212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Isomorphism Test for Digraphs with Weighted Edges 加权边有向图的同构检验

Bulletin of the Society of Sea Water Science, Japan Pub Date : 2018-01-01 DOI: 10.4230/LIPIcs.SEA.2018.30

A. Piperno

引用次数: 7

Fast Spherical Drawing of Triangulations: An Experimental Study of Graph Drawing Tools 快速球面三角形绘图:图形绘图工具的实验研究

Bulletin of the Society of Sea Water Science, Japan Pub Date : 2018-01-01 DOI: 10.4230/LIPIcs.SEA.2018.24

L. C. Aleardi, Gaspard Denis, Éric Fusy

引用次数: 0

Dictionary Matching in Elastic-Degenerate Texts with Applications in Searching VCF Files On-line 弹性简并文本的字典匹配及其在VCF文件在线搜索中的应用

Bulletin of the Society of Sea Water Science, Japan Pub Date : 2018-01-01 DOI: 10.4230/LIPIcs.SEA.2018.16

S. Pissis, Ahmad Retha

{"title":"Dictionary Matching in Elastic-Degenerate Texts with Applications in Searching VCF Files On-line","authors":"S. Pissis, Ahmad Retha","doi":"10.4230/LIPIcs.SEA.2018.16","DOIUrl":"https://doi.org/10.4230/LIPIcs.SEA.2018.16","url":null,"abstract":"An elastic-degenerate string is a sequence of n sets of strings of total length N . It has been introduced to represent multiple sequence alignments of closely-related sequences in a compact form. For a standard pattern of length m, pattern matching in an elastic-degenerate text can be solved on-line in time O(nm2 +N) with pre-processing time and space O(m) (Grossi et al., CPM 2017). A fast bit-vector algorithm requiring time O(N · dmw e) with pre-processing time and space O(m·dmw e), where w is the size of the computer word, was also presented. In this paper we consider the same problem for a set of patterns of total length M . A straightforward generalization of the existing bit-vector algorithm would require time O(N · dMw e) with pre-processing time and space O(M · dMw e), which is prohibitive in practice. We present a new on-line O(N · d M w e)-time algorithm with pre-processing time and space O(M). We present experimental results using both synthetic and real data demonstrating the performance of the algorithm. We further demonstrate a real application of our algorithm in a pipeline for discovery and verification of minimal absent words (MAWs) in the human genome showing that a significant number of previously discovered MAWs are in fact false-positives when a population’s variants are considered. 2012 ACM Subject Classification Theory of computation → Pattern matching","PeriodicalId":9448,"journal":{"name":"Bulletin of the Society of Sea Water Science, Japan","volume":"25 1","pages":"16:1-16:14"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78245247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 13