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A scalable approach to computing representative lowest common ancestor in directed acyclic graphs

Santanu Kumar Dash, Sven-Bodo Scholz, Stephan Herhut, Bruce Christianson
2013 Theoretical Computer Science  
A directed acyclic graph with all vertices annotated with the corresponding clusterhead Proof Straightforward.  ...  Introduction The set of Lowest Common Ancestors (LCA) of two vertices u and v in a DAG is a set of vertices L = {l 1 , l 2 · · · , l n } such that all vertices in L are common ancestors of u and v and  ... 
doi:10.1016/j.tcs.2013.09.030 fatcat:ndspszb2qraajcvdfv57fbqzq4

Large-Scale, Exhaustive Lattice-Based Structural Auditing of SNOMED CT [chapter]

Guo-Qiang Zhang
2010 Lecture Notes in Computer Science  
Formal Concept Analysis (FCA) has been used as a technique for assessing the quality of ontologies, but is not scalable to large ontologies such as SNOMED CT (>300k concepts).  ...  We developed a methodology called Lattice-based Structural Auditing (LaSA), for auditing biomedical ontologies, implemented through automated SPARQL queries, in order to exhaustively identify all non-lattice  ...  Acknowledgements This research was supported in part by the Intramural Research Program of the National Institutes of Health (NIH), National Library of Medicine (NLM).  ... 
doi:10.1007/978-3-642-15280-1_61 fatcat:ojfaeawtf5hjponz2vs7cgontu

Citations, Sequence Alignments, Contagion, and Semantics: On Acyclic Structures and their Randomness [article]

Sandeep Gupta
2014 arXiv   pre-print
Increasingly, as a consequence, there is a need to build and evaluate various strategies for processing acyclic structured graphs.  ...  These datasets, particularly those in bio-informatics and computational epidemiology, have grown tremendously over the last decade or so.  ...  In computational epidemiology, the graph representing the (plausible) spread of contagion from person to person in a population is acyclic [21] .  ... 
arXiv:1204.6535v6 fatcat:l7ggpjip2zcurhbickxopdmqim

ONLAY: Online Layering for scalable asynchronous BFT system [article]

Quan Nguyen, Andre Cronje
2019 arXiv   pre-print
At the core of L_ϕ protocol, it introduces to use layering algorithm to achieve practical Byzantine fault tolerance (pBFT) in leaderless asynchronous Directed Acyclic Graph (DAG).  ...  This paper presents a new framework, namely , for scalable asynchronous distributed systems.  ...  These approaches utilize directed acyclic graphs (DAG) [17, 4, 5, 18, 19] to facilitate consensus.  ... 
arXiv:1905.04867v1 fatcat:brympc64abc7xe5cfl64snr2vq

MG7: Configurable and scalable 16S metagenomics data analysis [article]

Alexey Alekhin, Evdokim Kovach, Marina Manrique, Pablo Pareja-Tobes, Eduardo Pareja, Raquel Tobes, Eduardo Pareja-Tobes
2015 bioRxiv   pre-print
Cloud computing, in its Amazon Web Services incarnation, when coupled with these ideas, produces a robust, safely configurable, scalable tool.  ...  The basic principle is a new approach to data analysis, where configuration, processes, or data locations are static, type-checked and subject to the standard evolution of a well-maintained software project  ...  Figure 2 : 2 Lowest Common Ancestor algorithm for taxonomic assignment. The Left panel displays an example of the application of LCA algorithm in a sensu stricto mode.  ... 
doi:10.1101/027714 fatcat:tye5wklrjvetzhnrlhy6qr6o5q

Using SPARQL to Test for Lattices: Application to Quality Assurance in Biomedical Ontologies [chapter]

Guo-Qiang Zhang, Olivier Bodenreider
2010 Lecture Notes in Computer Science  
We present a scalable, SPARQL-based computational pipeline for testing the lattice-theoretic properties of partial orders represented as RDF triples.  ...  Our technical contribution is the coding of NuMi completely in SPARQL. To show its scalability, we applied NuMi to the entirety of SNOMED CT, the largest clinical ontology (over 300,000 conepts).  ...  Acknowledgements This research was supported in part by the Intramural Research Program of the National Library of Medicine (NLM), and in part by Clinical and Translational Science Award (UL1 RR024989)  ... 
doi:10.1007/978-3-642-17749-1_18 pmid:25699294 pmcid:PMC4330995 fatcat:srdrq2xsmff53bgw3cmugzbyxe

Parallel Depth-First Search for Directed Acyclic Graphs

Maxim Naumov, Alysson Vrielink, Michael Garland
2017 Proceedings of the Seventh Workshop on Irregular Applications: Architectures and Algorithms - IA3'17  
In the literature, most works focus on the DFS-Tree maintenance problem in undirected graphs and directed acyclic graphs.  ...  Motivated by this, we propose a framework and corresponding algorithms for both edge insertion and deletion in general directed graphs.  ...  [3] extend the incremental algorithm for directed acyclic graphs presented in [10] to general directed graphs. For undirected graphs, Baswana et al.  ... 
doi:10.1145/3149704.3149764 dblp:conf/sc/NaumovVG17 fatcat:6cf2usa3yzaj3el7ixi546lvoe

Cyclic Bayesian Attack Graphs: A Systematic Computational Approach [article]

Isaac Matthews, John Mace, Sadegh Soudjani, Aad van Moorsel
2020 arXiv   pre-print
In this paper we provide a systematic approach to analyse and perform computations over cyclic Bayesian attack graphs.  ...  %thus providing a generic approach to handle cycles as well as unifying the theory of Bayesian attack graphs.  ...  INTRODUCTION An attack graph is a representation of a system and its vulnerabilities in the form of a directed acyclic graph.  ... 
arXiv:2005.06350v1 fatcat:nlbsukvixfcpvijanbagly2uru

Supporting Window Analytics over Large-scale Dynamic Graphs [article]

Qi Fan, Zhengkui Wang, Chee-Yong Chan, Kian-Lee Tan
2015 arXiv   pre-print
In this paper, we formally introduce window queries for graph analytics. In such queries, for each vertex, the analysis is performed on a window of vertices defined based on the graph structure.  ...  In relational DBMS, window functions have been widely used to facilitate data analytics.  ...  K-reach: who is in your small world. In VLDB’12. [10] A. Czumaj, M. Kowaluk, and A. Lingas. Faster algorithms for finding lowest common ancestors in directed acyclic graphs.  ... 
arXiv:1510.07104v1 fatcat:lxxedk3fc5ab5izyv5yejgado4

Validating Dominator Trees for a Fast, Verified Dominance Test [chapter]

Sandrine Blazy, Delphine Demange, David Pichardie
2015 Lecture Notes in Computer Science  
The problem of computing dominators in a control flow graph is central to numerous modern compiler optimizations.  ...  In contrast, production compilers, like GCC or LLVM, implement the classic, efficient Lengauer-Tarjan algorithm [12] , to compute dominator trees.  ...  In a direct acyclic graph, d is an ancestor of n if and only if I(n) ⊆ I(d).  ... 
doi:10.1007/978-3-319-22102-1_6 fatcat:noeesvjn4zcflllnp2ecc4z2da

A hierarchical Bayesian network approach for linkage disequilibrium modeling and data-dimensionality reduction prior to genome-wide association studies

Raphaël Mourad, Christine Sinoquet, Philippe Leray
2011 BMC Bioinformatics  
Discovering the genetic basis of common genetic diseases in the human genome represents a public health issue.  ...  In order to tackle the learning of both forest structure and probability distributions, a generic algorithm has been proposed.  ...  Acknowledgements The authors are grateful to two anonymous referees for constructive comments and help in improving their manuscript.  ... 
doi:10.1186/1471-2105-12-16 pmid:21226914 pmcid:PMC3033325 fatcat:dbgrxmj46zcn5cr52e2x47hrsa

A distributed placement service for graph-structured and tree-structured data

Gregory Buehrer, Srinivasan Parthasarathy, Shirish Tatikonda
2010 Proceedings of the 15th ACM SIGPLAN symposium on Principles and practice of parallel programming - PPoPP '10  
XML database) and other specialized graph data types -bi-partite (query-click graphs), directed acyclic graphs etc.  ...  Such strategies can have a significant impact in localizing the computation, in minimizing synchronization (communication) costs, in enhancing reliability (via strategic replication policies), and in ensuring  ...  Acknowledgments: This work is supported in part by grants from National Science Foundation CAREER-IIS-0347662, RI-CNS-0403342, CCF-0702587, and IIS-0917070.  ... 
doi:10.1145/1693453.1693511 dblp:conf/ppopp/BuehrerPT10 fatcat:yyr4yybalfbujatqyqcgew4zou

Multidimensional cyclic graph approach: Representing a data cube without common sub-graphs

Joubert de Castro Lima, Celso Massaki Hirata
2011 Information Sciences  
In general, redundant sub-graphs are quite common in a data cube, but eliminating them is a hard problem. Dwarf, Star and MDAG approaches only eliminate some specific common sub-graphs.  ...  The MCG approach efficiently eliminates all common sub-graphs from the entire cube, based on an exact sub-graph matching solution.  ...  Efficient cube approaches, such as the multidimensional direct acyclic graph (MDAG) approach [20] , the Dwarf approach [28] , and the Star approach [34] use graphs to represent a data cube.  ... 
doi:10.1016/j.ins.2010.05.012 fatcat:5tc5guji2jajfj3bn5wabxewla

Deterministic parallel fixpoint computation

Sung Kook Kim, Arnaud J. Venet, Aditya V. Thakur
2019 Proceedings of the ACM on Programming Languages (PACMPL)  
It reduces the problem of extracting properties of a program to computing an approximation of the least fixpoint of a system of equations.  ...  The de facto approach for computing this approximation uses a sequential algorithm based on weak topological order (WTO).  ...  ACKNOWLEDGMENTS The authors would like to thank Maxime Arthaud for help with IKOS.  ... 
doi:10.1145/3371082 fatcat:ari64jy7xrcdxe36liainvtw3u

Improving quality and performance of schema matching in large scale

Fabien Duchateau, Zohra Bellahsene, Mathieu Roche
2008 Ingénierie des Systèmes d'Information  
In this article, we present the BMatch approach to efficiently match a large number of schemas. The quality aspect is based on the combination of terminological and contextual methods.  ...  Finally, experiments with real sets of schemas show that our approach is scalable and outperforms the most referenced matching tools both in quality of matches and performance time. RÉSUMÉ.  ...  When loading a schema, COMA++ transforms it into a rooted directed acyclic graph.  ... 
doi:10.3166/isi.13.5.59-82 fatcat:hwli4c6l6zem5kqubnzra3w6bi
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