Pub Date : 2021-01-01DOI: 10.4230/LIPIcs.SEA.2021.12
S. Puglisi, Bella Zhukova
Given a collection of strings, document listing refers to the problem of finding all the strings (or documents) where a given query string (or pattern) appears. Index data structures that support efficient document listing for string collections have been the focus of intense research in the last decade, with dozens of papers published describing exotic and elegant compressed data structures. The problem is now quite well understood in theory and many of the solutions have been implemented and evaluated experimentally. A particular recent focus has been on highly repetitive document collections, which have become prevalent in many areas (such as version control systems and genomics – to name just two very different sources). The aim of this paper is to describe simple and efficient document listing algorithms that can be used in combination with more sophisticated techniques, or as baselines against which the performance of new document listing indexes can be measured. Our approaches are based on simple combinations of scanning and hashing, which we show to combine very well with dictionary compression to achieve small space usage. Our experiments show these methods to be often much faster and less space consuming than the best specialized indexes for the problem.
{"title":"Document Retrieval Hacks","authors":"S. Puglisi, Bella Zhukova","doi":"10.4230/LIPIcs.SEA.2021.12","DOIUrl":"https://doi.org/10.4230/LIPIcs.SEA.2021.12","url":null,"abstract":"Given a collection of strings, document listing refers to the problem of finding all the strings (or documents) where a given query string (or pattern) appears. Index data structures that support efficient document listing for string collections have been the focus of intense research in the last decade, with dozens of papers published describing exotic and elegant compressed data structures. The problem is now quite well understood in theory and many of the solutions have been implemented and evaluated experimentally. A particular recent focus has been on highly repetitive document collections, which have become prevalent in many areas (such as version control systems and genomics – to name just two very different sources). The aim of this paper is to describe simple and efficient document listing algorithms that can be used in combination with more sophisticated techniques, or as baselines against which the performance of new document listing indexes can be measured. Our approaches are based on simple combinations of scanning and hashing, which we show to combine very well with dictionary compression to achieve small space usage. Our experiments show these methods to be often much faster and less space consuming than the best specialized indexes for the problem.","PeriodicalId":9448,"journal":{"name":"Bulletin of the Society of Sea Water Science, Japan","volume":"65 1","pages":"12:1-12:12"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82812154","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}
Pub Date : 2021-01-01DOI: 10.4230/LIPIcs.SEA.2021.21
M. Hermann
We present several experimental algorithms for fast computation of variadic polynomials over non-negative integers. 2012 ACM Subject Classification Theory of computation → Theory and algorithms for application domains
{"title":"How to Find the Exit from a 3-Dimensional Maze","authors":"M. Hermann","doi":"10.4230/LIPIcs.SEA.2021.21","DOIUrl":"https://doi.org/10.4230/LIPIcs.SEA.2021.21","url":null,"abstract":"We present several experimental algorithms for fast computation of variadic polynomials over non-negative integers. 2012 ACM Subject Classification Theory of computation → Theory and algorithms for application domains","PeriodicalId":9448,"journal":{"name":"Bulletin of the Society of Sea Water Science, Japan","volume":"3 1","pages":"21:1-21:12"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85507678","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}
Pub Date : 2021-01-01DOI: 10.4230/LIPIcs.SEA.2021.23
G. Brodal, Rolf Fagerberg, David Hammer, U. Meyer, M. Penschuck, Hung Tran
We empirically investigate algorithms for solving Connected Components in the external memory model. In particular, we study whether the randomized O(Sort(E)) algorithm by Karger, Klein, and Tarjan can be implemented to compete with practically promising and simpler algorithms having only slightly worse theoretical cost, namely Borůvka’s algorithm and the algorithm by Sibeyn and collaborators. For all algorithms, we develop and test a number of tuning options. Our experiments are executed on a large set of different graph classes including random graphs, grids, geometric graphs, and hyperbolic graphs. Among our findings are: The Sibeyn algorithm is a very strong contender due to its simplicity and due to an added degree of freedom in its internal workings when used in the Connected Components setting. With the right tunings, the Karger-Klein-Tarjan algorithm can be implemented to be competitive in many cases. Higher graph density seems to benefit Karger-Klein-Tarjan relative to Sibeyn. Borůvka’s algorithm is not competitive with the two others. 2012 ACM Subject Classification Mathematics of computing → Paths and connectivity problems; Theory of computation → Graph algorithms analysis
我们实证研究了解决外部存储器模型中连接组件的算法。我们特别研究了Karger, Klein和Tarjan的随机化O(Sort(E))算法是否可以实现，以与理论成本稍差的具有实际前景和更简单的算法，即Borůvka的算法和Sibeyn及其合作者的算法竞争。对于所有算法，我们开发和测试了许多调优选项。我们的实验是在大量不同的图类上进行的，包括随机图、网格图、几何图和双曲图。我们的发现包括:Sibeyn算法是一个非常强大的竞争者，因为它的简单性，并且在连接组件设置中使用时，它的内部工作增加了自由度。通过适当的调整，kager - klein - tarjan算法可以在许多情况下具有竞争力。相对于Sibeyn，更高的图形密度似乎对kager - klein - tarjan有利。Borůvka的算法与其他两种算法没有竞争关系。2012 ACM学科分类计算数学→路径和连通性问题;计算理论→图算法分析
{"title":"An Experimental Study of External Memory Algorithms for Connected Components","authors":"G. Brodal, Rolf Fagerberg, David Hammer, U. Meyer, M. Penschuck, Hung Tran","doi":"10.4230/LIPIcs.SEA.2021.23","DOIUrl":"https://doi.org/10.4230/LIPIcs.SEA.2021.23","url":null,"abstract":"We empirically investigate algorithms for solving Connected Components in the external memory model. In particular, we study whether the randomized O(Sort(E)) algorithm by Karger, Klein, and Tarjan can be implemented to compete with practically promising and simpler algorithms having only slightly worse theoretical cost, namely Borůvka’s algorithm and the algorithm by Sibeyn and collaborators. For all algorithms, we develop and test a number of tuning options. Our experiments are executed on a large set of different graph classes including random graphs, grids, geometric graphs, and hyperbolic graphs. Among our findings are: The Sibeyn algorithm is a very strong contender due to its simplicity and due to an added degree of freedom in its internal workings when used in the Connected Components setting. With the right tunings, the Karger-Klein-Tarjan algorithm can be implemented to be competitive in many cases. Higher graph density seems to benefit Karger-Klein-Tarjan relative to Sibeyn. Borůvka’s algorithm is not competitive with the two others. 2012 ACM Subject Classification Mathematics of computing → Paths and connectivity problems; Theory of computation → Graph algorithms analysis","PeriodicalId":9448,"journal":{"name":"Bulletin of the Society of Sea Water Science, Japan","volume":"75 1","pages":"23:1-23:23"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91029855","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}
Pub Date : 2020-06-16DOI: 10.4230/LIPICS.SEA.2020.18
Ali Al Zoobi, D. Coudert, N. Nisse
The k shortest simple path problem (kSSP) asks to compute a set of top-k shortest simple paths from a vertex s to a vertex t in a digraph. Yen (1971) proposed the first algorithm with the best known theoretical complexity of O(kn(m + n log n)) for a digraph with n vertices and m arcs. Since then, the problem has been widely studied from an algorithm engineering perspective, and impressive improvements have been achieved. In particular, Kurz and Mutzel (2016) proposed a sidetracks-based (SB) algorithm which is currently the fastest solution. In this work, we propose two improvements of this algorithm. We first show how to speed up the SB algorithm using dynamic updates of shortest path trees. We did experiments on some road networks of the 9th DIMAC'S challenge with up to about half a million nodes and one million arcs. Our computational results show an average speed up by a factor of 1.5 to 2 with a similar working memory consumption as SB. We then propose a second algorithm enabling to significantly reduce the working memory at the cost of an increase of the running time (up to two times slower). Our experiments on the same data set show, on average, a reduction by a factor of 1.5 to 2 of the working memory.
k个最短简单路径问题(kSSP)要求计算有向图中从顶点s到顶点t的top-k个最短简单路径的集合。Yen(1971)提出了第一个算法，其最著名的理论复杂度为O(kn(m + n log n))，用于具有n个顶点和m条弧的有向图。从那时起，从算法工程的角度对这个问题进行了广泛的研究，并取得了令人印象深刻的改进。特别是，Kurz和Mutzel(2016)提出了一种基于侧边的(SB)算法，这是目前最快的解决方案。在这项工作中，我们对该算法提出了两个改进。我们首先展示了如何使用最短路径树的动态更新来加速SB算法。我们在第九届DIMAC挑战赛的一些道路网络上做了实验，其中有大约50万个节点和100万个弧线。我们的计算结果表明，在工作记忆消耗与SB相似的情况下，平均速度提高了1.5到2倍。然后，我们提出了第二种算法，能够以增加运行时间为代价显著减少工作记忆(最多慢两倍)。我们在相同数据集上的实验显示，平均而言，工作记忆减少了1.5到2倍。
{"title":"Space and Time Trade-Off for the k Shortest Simple Paths Problem","authors":"Ali Al Zoobi, D. Coudert, N. Nisse","doi":"10.4230/LIPICS.SEA.2020.18","DOIUrl":"https://doi.org/10.4230/LIPICS.SEA.2020.18","url":null,"abstract":"The k shortest simple path problem (kSSP) asks to compute a set of top-k shortest simple paths from a vertex s to a vertex t in a digraph. Yen (1971) proposed the first algorithm with the best known theoretical complexity of O(kn(m + n log n)) for a digraph with n vertices and m arcs. Since then, the problem has been widely studied from an algorithm engineering perspective, and impressive improvements have been achieved. In particular, Kurz and Mutzel (2016) proposed a sidetracks-based (SB) algorithm which is currently the fastest solution. In this work, we propose two improvements of this algorithm. We first show how to speed up the SB algorithm using dynamic updates of shortest path trees. We did experiments on some road networks of the 9th DIMAC'S challenge with up to about half a million nodes and one million arcs. Our computational results show an average speed up by a factor of 1.5 to 2 with a similar working memory consumption as SB. We then propose a second algorithm enabling to significantly reduce the working memory at the cost of an increase of the running time (up to two times slower). Our experiments on the same data set show, on average, a reduction by a factor of 1.5 to 2 of the working memory.","PeriodicalId":9448,"journal":{"name":"Bulletin of the Society of Sea Water Science, Japan","volume":"5 1","pages":"18:1-18:13"},"PeriodicalIF":0.0,"publicationDate":"2020-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76952465","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}
Pub Date : 2020-04-07DOI: 10.4230/LIPIcs.SEA.2020.5
S. Fekete, Alexander Hill, Dominik Krupke, Tyler Mayer, Joseph S. B. Mitchell, Ojas D. Parekh, C. Phillips
We study a trajectory analysis problem we call the Trajectory Capture Problem (TCP), in which, for a given input set ${cal T}$ of trajectories in the plane, and an integer $kgeq 2$, we seek to compute a set of $k$ points (``portals'') to maximize the total weight of all subtrajectories of ${cal T}$ between pairs of portals. This problem naturally arises in trajectory analysis and summarization. We show that the TCP is NP-hard (even in very special cases) and give some first approximation results. Our main focus is on attacking the TCP with practical algorithm-engineering approaches, including integer linear programming (to solve instances to provable optimality) and local search methods. We study the integrality gap arising from such approaches. We analyze our methods on different classes of data, including benchmark instances that we generate. Our goal is to understand the best performing heuristics, based on both solution time and solution quality. We demonstrate that we are able to compute provably optimal solutions for real-world instances.
{"title":"Probing a Set of Trajectories to Maximize Captured Information","authors":"S. Fekete, Alexander Hill, Dominik Krupke, Tyler Mayer, Joseph S. B. Mitchell, Ojas D. Parekh, C. Phillips","doi":"10.4230/LIPIcs.SEA.2020.5","DOIUrl":"https://doi.org/10.4230/LIPIcs.SEA.2020.5","url":null,"abstract":"We study a trajectory analysis problem we call the Trajectory Capture Problem (TCP), in which, for a given input set ${cal T}$ of trajectories in the plane, and an integer $kgeq 2$, we seek to compute a set of $k$ points (``portals'') to maximize the total weight of all subtrajectories of ${cal T}$ between pairs of portals. This problem naturally arises in trajectory analysis and summarization. \u0000We show that the TCP is NP-hard (even in very special cases) and give some first approximation results. Our main focus is on attacking the TCP with practical algorithm-engineering approaches, including integer linear programming (to solve instances to provable optimality) and local search methods. We study the integrality gap arising from such approaches. We analyze our methods on different classes of data, including benchmark instances that we generate. Our goal is to understand the best performing heuristics, based on both solution time and solution quality. We demonstrate that we are able to compute provably optimal solutions for real-world instances.","PeriodicalId":9448,"journal":{"name":"Bulletin of the Society of Sea Water Science, Japan","volume":"89 2 1","pages":"5:1-5:14"},"PeriodicalIF":0.0,"publicationDate":"2020-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90976799","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}
Pub Date : 2020-04-01DOI: 10.4230/LIPIcs.SEA.2020.22
Kengo Nakamura, Shuhei Denzumi, Masaaki Nishino
The Sentential Decision Diagram (SDD) is a tractable representation of Boolean functions that subsumes the famous Ordered Binary Decision Diagram (OBDD) as a strict subset. SDDs are attracting much attention because they are more succinct than OBDDs, as well as having canonical forms and supporting many useful queries and transformations such as model counting and Apply operation. In this paper, we propose a more succinct variant of SDD named Variable Shift SDD (VS-SDD). The key idea is to create a unique representation for Boolean functions that are equivalent under a specific variable substitution. We show that VS-SDDs are never larger than SDDs and there are cases in which the size of a VS-SDD is exponentially smaller than that of an SDD. Moreover, despite such succinctness, we show that numerous basic operations that are supported in polytime with SDD are also supported in polytime with VS-SDD. Experiments confirm that VS-SDDs are significantly more succinct than SDDs when applied to classical planning instances, where inherent symmetry exists.
{"title":"Variable Shift SDD: A More Succinct Sentential Decision Diagram","authors":"Kengo Nakamura, Shuhei Denzumi, Masaaki Nishino","doi":"10.4230/LIPIcs.SEA.2020.22","DOIUrl":"https://doi.org/10.4230/LIPIcs.SEA.2020.22","url":null,"abstract":"The Sentential Decision Diagram (SDD) is a tractable representation of Boolean functions that subsumes the famous Ordered Binary Decision Diagram (OBDD) as a strict subset. SDDs are attracting much attention because they are more succinct than OBDDs, as well as having canonical forms and supporting many useful queries and transformations such as model counting and Apply operation. In this paper, we propose a more succinct variant of SDD named Variable Shift SDD (VS-SDD). The key idea is to create a unique representation for Boolean functions that are equivalent under a specific variable substitution. We show that VS-SDDs are never larger than SDDs and there are cases in which the size of a VS-SDD is exponentially smaller than that of an SDD. Moreover, despite such succinctness, we show that numerous basic operations that are supported in polytime with SDD are also supported in polytime with VS-SDD. Experiments confirm that VS-SDDs are significantly more succinct than SDDs when applied to classical planning instances, where inherent symmetry exists.","PeriodicalId":9448,"journal":{"name":"Bulletin of the Society of Sea Water Science, Japan","volume":"5 1","pages":"22:1-22:13"},"PeriodicalIF":0.0,"publicationDate":"2020-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75226379","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}
Pub Date : 2020-04-01DOI: 10.4230/LIPIcs.SEA.2020.17
A. Kleff, F. Schulz, Jakob Wagenblatt, Tim Zeitz
We study the problem of planning routes in road networks when certain streets or areas are closed at certain times. For heavy vehicles, such areas may be very large since many European countries impose temporary driving bans during the night or on weekends. In this setting, feasible routes may require waiting at parking areas, and several feasible routes with different trade-offs between waiting and driving detours around closed areas may exist. We propose a novel model in which driving and waiting are assigned abstract costs, and waiting costs are location-dependent to reflect the different quality of the parking areas. Our goal is to find Pareto-optimal routes with regards to arrival time at the destination and total cost. We investigate the complexity of the model and determine a necessary constraint on the cost parameters such that the problem is solvable in polynomial time. We present a thoroughly engineered implementation and perform experiments on a production-grade real world data set. The experiments show that our implementation can answer realistic queries in around a second or less which makes it feasible for practical application.
{"title":"Efficient Route Planning with Temporary Driving Bans, Road Closures, and Rated Parking Areas","authors":"A. Kleff, F. Schulz, Jakob Wagenblatt, Tim Zeitz","doi":"10.4230/LIPIcs.SEA.2020.17","DOIUrl":"https://doi.org/10.4230/LIPIcs.SEA.2020.17","url":null,"abstract":"We study the problem of planning routes in road networks when certain streets or areas are closed at certain times. For heavy vehicles, such areas may be very large since many European countries impose temporary driving bans during the night or on weekends. In this setting, feasible routes may require waiting at parking areas, and several feasible routes with different trade-offs between waiting and driving detours around closed areas may exist. We propose a novel model in which driving and waiting are assigned abstract costs, and waiting costs are location-dependent to reflect the different quality of the parking areas. Our goal is to find Pareto-optimal routes with regards to arrival time at the destination and total cost. We investigate the complexity of the model and determine a necessary constraint on the cost parameters such that the problem is solvable in polynomial time. We present a thoroughly engineered implementation and perform experiments on a production-grade real world data set. The experiments show that our implementation can answer realistic queries in around a second or less which makes it feasible for practical application.","PeriodicalId":9448,"journal":{"name":"Bulletin of the Society of Sea Water Science, Japan","volume":"268 Pt A 1","pages":"17:1-17:13"},"PeriodicalIF":0.0,"publicationDate":"2020-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90812403","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}
Pub Date : 2020-04-01DOI: 10.4230/LIPICS.SEA.2020.19
James Trimble
We present a novel algorithm for the minimum-depth elimination tree problem, which is equivalent to the optimal treedepth decomposition problem. Our algorithm makes use of two cheaply-computed lower bound functions to prune the search tree, along with symmetry-breaking and domination rules. We present an empirical study showing that the algorithm outperforms the current state-of-the-art solver (which is based on a SAT encoding) by orders of magnitude on a range of graph classes.
{"title":"An Algorithm for the Exact Treedepth Problem","authors":"James Trimble","doi":"10.4230/LIPICS.SEA.2020.19","DOIUrl":"https://doi.org/10.4230/LIPICS.SEA.2020.19","url":null,"abstract":"We present a novel algorithm for the minimum-depth elimination tree problem, which is equivalent to the optimal treedepth decomposition problem. Our algorithm makes use of two cheaply-computed lower bound functions to prune the search tree, along with symmetry-breaking and domination rules. We present an empirical study showing that the algorithm outperforms the current state-of-the-art solver (which is based on a SAT encoding) by orders of magnitude on a range of graph classes.","PeriodicalId":9448,"journal":{"name":"Bulletin of the Society of Sea Water Science, Japan","volume":"57 1","pages":"19:1-19:14"},"PeriodicalIF":0.0,"publicationDate":"2020-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77774287","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}
Pub Date : 2020-03-20DOI: 10.4230/LIPIcs.SEA.2020.21
Dmytro Antypov, Argyrios Deligkas, V. Gusev, M. Rosseinsky, P. Spirakis, Michail Theofilatos
We study Crystal Structure Prediction, one of the major problems in computational chemistry. This is essentially a continuous optimization problem, where many different, simple and sophisticated, methods have been proposed and applied. The simple searching techniques are easy to understand, usually easy to implement, but they can be slow in practice. On the other hand, the more sophisticated approaches perform well in general, however almost all of them have a large number of parameters that require fine tuning and, in the majority of the cases, chemical expertise is needed in order to properly set them up. In addition, due to the chemical expertise involved in the parameter-tuning, these approaches can be {em biased} towards previously-known crystal structures. Our contribution is twofold. Firstly, we formalize the Crystal Structure Prediction problem, alongside several other intermediate problems, from a theoretical computer science perspective. Secondly, we propose an oblivious algorithm for Crystal Structure Prediction that is based on local search. Oblivious means that our algorithm requires minimal knowledge about the composition we are trying to compute a crystal structure for. In addition, our algorithm can be used as an intermediate step by {em any} method. Our experiments show that our algorithms outperform the standard basin hopping, a well studied algorithm for the problem.
{"title":"Crystal Structure Prediction via Oblivious Local Search","authors":"Dmytro Antypov, Argyrios Deligkas, V. Gusev, M. Rosseinsky, P. Spirakis, Michail Theofilatos","doi":"10.4230/LIPIcs.SEA.2020.21","DOIUrl":"https://doi.org/10.4230/LIPIcs.SEA.2020.21","url":null,"abstract":"We study Crystal Structure Prediction, one of the major problems in computational chemistry. This is essentially a continuous optimization problem, where many different, simple and sophisticated, methods have been proposed and applied. The simple searching techniques are easy to understand, usually easy to implement, but they can be slow in practice. On the other hand, the more sophisticated approaches perform well in general, however almost all of them have a large number of parameters that require fine tuning and, in the majority of the cases, chemical expertise is needed in order to properly set them up. In addition, due to the chemical expertise involved in the parameter-tuning, these approaches can be {em biased} towards previously-known crystal structures. Our contribution is twofold. Firstly, we formalize the Crystal Structure Prediction problem, alongside several other intermediate problems, from a theoretical computer science perspective. Secondly, we propose an oblivious algorithm for Crystal Structure Prediction that is based on local search. Oblivious means that our algorithm requires minimal knowledge about the composition we are trying to compute a crystal structure for. In addition, our algorithm can be used as an intermediate step by {em any} method. Our experiments show that our algorithms outperform the standard basin hopping, a well studied algorithm for the problem.","PeriodicalId":9448,"journal":{"name":"Bulletin of the Society of Sea Water Science, Japan","volume":"15 1","pages":"21:1-21:14"},"PeriodicalIF":0.0,"publicationDate":"2020-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74939231","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}
Pub Date : 2020-02-03DOI: 10.4230/LIPIcs.SEA.2020.14
Kathrin Hanauer, M. Henzinger, Christian Schulz
The fully dynamic transitive closure problem asks to maintain reachability information in a directed graph between arbitrary pairs of vertices, while the graph undergoes a sequence of edge insertions and deletions. The problem has been thoroughly investigated in theory and many specialized algorithms for solving it have been proposed in the last decades. In two large studies [Frigioni ea, 2001; Krommidas and Zaroliagis, 2008], a number of these algorithms have been evaluated experimentally against simple static algorithms for graph traversal, showing the competitiveness and even superiority of the simple algorithms in practice, except for very dense random graphs or very high ratios of queries. A major drawback of those studies is that only small and mostly randomly generated graphs are considered. In this paper, we engineer new algorithms to maintain all-pairs reachability information which are simple and space-efficient. Moreover, we perform an extensive experimental evaluation on both generated and real-world instances that are several orders of magnitude larger than those in the previous studies. Our results indicate that our new algorithms outperform all state-of-the-art algorithms on all types of input considerably in practice.
{"title":"Faster Fully Dynamic Transitive Closure in Practice","authors":"Kathrin Hanauer, M. Henzinger, Christian Schulz","doi":"10.4230/LIPIcs.SEA.2020.14","DOIUrl":"https://doi.org/10.4230/LIPIcs.SEA.2020.14","url":null,"abstract":"The fully dynamic transitive closure problem asks to maintain reachability information in a directed graph between arbitrary pairs of vertices, while the graph undergoes a sequence of edge insertions and deletions. The problem has been thoroughly investigated in theory and many specialized algorithms for solving it have been proposed in the last decades. In two large studies [Frigioni ea, 2001; Krommidas and Zaroliagis, 2008], a number of these algorithms have been evaluated experimentally against simple static algorithms for graph traversal, showing the competitiveness and even superiority of the simple algorithms in practice, except for very dense random graphs or very high ratios of queries. A major drawback of those studies is that only small and mostly randomly generated graphs are considered. \u0000In this paper, we engineer new algorithms to maintain all-pairs reachability information which are simple and space-efficient. Moreover, we perform an extensive experimental evaluation on both generated and real-world instances that are several orders of magnitude larger than those in the previous studies. Our results indicate that our new algorithms outperform all state-of-the-art algorithms on all types of input considerably in practice.","PeriodicalId":9448,"journal":{"name":"Bulletin of the Society of Sea Water Science, Japan","volume":"43 1","pages":"14:1-14:14"},"PeriodicalIF":0.0,"publicationDate":"2020-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81435471","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}
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