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Engineering an Efficient Canonical Labeling Tool for Large and Sparse Graphs [chapter]

Tommi Junttila, Petteri Kaski
2007 2007 Proceedings of the Ninth Workshop on Algorithm Engineering and Experiments (ALENEX)  
The problem of canonically labeling a graph is studied.  ...  Within the general framework of backtracking algorithms based on individualization and refinement, data structures, subroutines, and pruning heuristics especially for fast handling of large and sparse  ...  The authors thank Jani Jaakkola and Pekka Niklander at the Department of Computer Science of University of Helsinki for providing computing resources for the experiments.  ... 
doi:10.1137/1.9781611972870.13 dblp:conf/alenex/JunttilaK07 fatcat:c5tcgchf5jfjbg5ww5l65k6gvu

Detection of Network Motif Based on a Novel Graph Canonization Algorithm from Transcriptional Regulation Networks

Jialu Hu, Xuequn Shang
2017 Molecules  
To quickly and effectively count subgraphs of a large biological network, we propose a novel graph canonization algorithm based on resolving sets.  ...  Results on several simulated datasets and transcriptional regulation networks indicate that sgip outperforms nauty on many graph cases.  ...  The founding sponsors had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish the results.  ... 
doi:10.3390/molecules22122194 pmid:29232861 fatcat:x2jidlmdordrno7ubhfq43qcqi

DyNet: The Dynamic Neural Network Toolkit [article]

Graham Neubig, Chris Dyer, Yoav Goldberg, Austin Matthews, Waleed Ammar, Antonios Anastasopoulos, Miguel Ballesteros, David Chiang, Daniel Clothiaux, Trevor Cohn, Kevin Duh, Manaal Faruqui (+12 others)
2017 arXiv   pre-print
are fed into an engine that executes this computation and computes its derivatives.  ...  To achieve this, DyNet has an optimized C++ backend and lightweight graph representation.  ...  Efficiency Tools DyNet contains a number of features to improve computational efficiency, including sparse updates, minibatching, and multi-processing across CPUs.  ... 
arXiv:1701.03980v1 fatcat:q3lmo4l4h5csticqfhns3dexm4

Fast Canonical Labelling for Graph based Data Mining

D. Kavitha, V. Kamakshi Prasad, J. V. R. Murthy
2017 International Journal of Advanced Research in Computer Science and Software Engineering  
In this work, we present an algorithm to discover isomorphic graphs using canonical labelling that overcomes this problem based on the symmetries present in the graph, which eliminates the permutation  ...  For subgraphs with symmetric and non-symmetric structures, the algorithm reduces search space and computation feasible to perform isomorphism testing on large datasets for frequent pattern mining.  ...  VF2 is more efficient, especially for large graph sizes.  ... 
doi:10.23956/ijarcsse/sv7i5/0145 fatcat:w3d4l2ft4jg4hkm2yarhvxtv5u

Search Space Contraction in Canonical Labeling of Graphs [article]

Adolfo Piperno
2011 arXiv   pre-print
The individualization-refinement paradigm for computing a canonical labeling and the automorphism group of a graph is investigated.  ...  It is shown that the approach presented here leads to a huge reduction in the search space, thereby making computation feasible for several classes of graphs which are hard for all the main canonical labeling  ...  Acknowledgments I would like to thank my friends and colleagues Maurizio Bonuccelli, Angelo Monti and Riccardo Silvestri for their suggestions and discussions about the topics of this paper.  ... 
arXiv:0804.4881v2 fatcat:wuyn4nnhbfeh3nbstcypecouem

Graph Data Mining with Arabesque

Eslam Hussein, Mohammed Zaki, Abdurrahman Ghanem, Vinicius Vitor dos Santos Dias, Carlos H.C. Teixeira, Ghadeer AbuOda, Marco Serafini, Georgos Siganos, Gianmarco De Francisci Morales, Ashraf Aboulnaga
2017 Proceedings of the 2017 ACM International Conference on Management of Data - SIGMOD '17  
Graph data mining is defined as searching in an input graph for all subgraphs that satisfy some property that makes them interesting to the user.  ...  Arabesque provides a simple programming model to express graph data mining computations, and a highly scalable and efficient implementation of this model, scaling to billions of subgraphs on hundreds of  ...  We use an external tool called UCSF Chimera 8 [13] for visualization.  ... 
doi:10.1145/3035918.3058742 dblp:conf/sigmod/HusseinGDTASSMA17 fatcat:yfesugez3rcqhjsbusxixb423m

Probabilistic symbolic model checking with PRISM: a hybrid approach

Marta Kwiatkowska, Gethin Norman, David Parker
2004 International Journal on Software Tools for Technology Transfer (STTT)  
In this paper we present efficient symbolic techniques for probabilistic model checking.  ...  These have been implemented in PRISM, a tool for the analysis of probabilistic models such as discrete-time Markov chains, continuous-time Markov chains and Markov decision processes using specifications  ...  Usually, the reason for maintaining canonicity is for the efficient implementation of lookups in a cache of previously performed operations. This is crucial for efficient manipulation of MTBDDs.  ... 
doi:10.1007/s10009-004-0140-2 fatcat:xqud3lfsgbhnbm4zaqe3cdkgqi

Canonical Symbolic Analysis of Large Analog Circuits with Determinant Decision Diagrams [chapter]

2009 Computer-Aided Design of Analog Integrated Circuits and Systems  
We describe an efficient DDD-vertex-ordering heuristic and prove that it is optimum for ladder-structured circuits.  ...  Richard Shi (M'91-SM'99) received the B.S. and M.S. degrees in electrical engineering from Fudan University, Shanghai, China, in 1985 and 1988, respectively, the M.A.  ...  Gielen of Katholieke Universiteit Leuven, Belgium, and Prof. M. Hassoun of Iowa State University, Ames, for providing them their symbolic circuit analysis packages ISAAC and SCAPP.  ... 
doi:10.1109/9780470544310.ch28 fatcat:ybkgnhqimzfzvmh2ocfpefsoru

Canonical symbolic analysis of large analog circuits with determinant decision diagrams

C.-J.R. Shi, Xiang-Dong Tan
2000 IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems  
We describe an efficient DDD-vertex-ordering heuristic and prove that it is optimum for ladder-structured circuits.  ...  Richard Shi (M'91-SM'99) received the B.S. and M.S. degrees in electrical engineering from Fudan University, Shanghai, China, in 1985 and 1988, respectively, the M.A.  ...  Gielen of Katholieke Universiteit Leuven, Belgium, and Prof. M. Hassoun of Iowa State University, Ames, for providing them their symbolic circuit analysis packages ISAAC and SCAPP.  ... 
doi:10.1109/43.822616 fatcat:zwg6napwvrbmratocjxga7s4eu

10 Reasons to Get Interested in Graph Drawing [chapter]

Carla Binucci, Ulrik Brandes, Tim Dwyer, Martin Gronemann, Reinhard von Hanxleden, Marc van Kreveld, Petra Mutzel, Marcus Schaefer, Falk Schreiber, Bettina Speckmann
2019 Lecture Notes in Computer Science  
This is an invitation to the research area of graph drawing.  ...  It encompasses basic research such as graph theory, complexity theory, data structures, and graph algorithms as well as applied research such as software libraries, implementations, and applications.  ...  For undirected triconnected non-planar graphs, Schmidt [70] showed how to efficiently obtain a Mondshein sequence, a special non-separating ear decomposition similar to canonical orderings.  ... 
doi:10.1007/978-3-319-91908-9_6 fatcat:wchqxlk4fbfqdmhdjhhks74joe

Efficient algorithm for computing large scale systems of differential algebraic equations [article]

Xiaolin Qin, Juan Tang, Yong Feng, Bernhard Bachmann, Peter Fritzson
2015 arXiv   pre-print
To make use of its sparsity, this paper provides a simple and efficient algorithm for computing the large scale DAEs system.  ...  In general, the feature of DAEs is a sparse large scale system of fully nonlinear and high index.  ...  It shows that our algorithm is efficient for the large scale system of DAEs.  ... 
arXiv:1506.03963v1 fatcat:j3n7vrsum5amna5o3pxn2e2rhu

Architecture synthesis of high-performance application-specific processors

Mauricio Breternitz, John Paul Shen
1990 Conference proceedings on 27th ACM/IEEE design automation conference - DAC '90  
Implementation optimization is performed to allocate functional units and register files. Graph-coloring algorithms minimize the amount of hardware needed to exploit available parallelism.  ...  The results and experiences from this project served as the basis of and the model for the architecture synthesis method presented herein, called Application-Specific Processor Design (ASPD).  ...  The White Dwarf design also indicates that the VLIW-like [4] architectural model can serve as an effective and efficient architecture template for ASP synthesis for scientific. engineering and embedded  ... 
doi:10.1145/123186.123398 dblp:conf/dac/BreternitzS90 fatcat:h5lhg46wtzhijefjimgjwczz5i

HYENA-live: Fine-Grained Online Entity Type Classification from Natural-language Text

Mohamed Amir Yosef, Sandro Bauer, Johannes Hoffart, Marc Spaniol, Gerhard Weikum
2013 Annual Meeting of the Association for Computational Linguistics  
Our system offers an online interface where natural-language text can be inserted, which returns semantic type labels for entity mentions.  ...  Thanks to its efficient implementation and compacted feature representation, the system is able to process text inputs on-the-fly while still achieving equally high precision as leading state-ofthe-art  ...  The system is based on an SVM classifier using a comprehensive set of features and provides results for all classes of a large data set.  ... 
dblp:conf/acl/YosefBHSW13 fatcat:6xtvqtcx2nd2tncrn3lowrdse4

Timed Automata: Semantics, Algorithms and Tools [chapter]

Johan Bengtsson, Wang Yi
2004 Lecture Notes in Computer Science  
As an example, we give a brief introduction to the tool UPPAAL. As in verification tools e.g.  ...  We present the concrete and abstract semantics of timed automata (based on transition rules, regions and zones), decision problems, and algorithms for verification.  ...  Acknowledgements We would like to thank Pavel Krcal for pointing out an error in an early version of this document.  ... 
doi:10.1007/978-3-540-27755-2_3 fatcat:r3bghehpinbhrcuvih5l4qufja

A Generic Framework for Engineering Graph Canonization Algorithms [chapter]

Jakob L. Andersen, Daniel Merkle
2018 2018 Proceedings of the Twentieth Workshop on Algorithm Engineering and Experiments (ALENEX)  
The state-of-the-art tools for practical graph canonization are all based on the individualization-refinement paradigm, and their difference is primarily in the choice of heuristics they include and in  ...  the actual tool implementation.  ...  Computation for the work described in this paper was supported by the DeiC National HPC Centre, SDU.  ... 
doi:10.1137/1.9781611975055.13 dblp:conf/alenex/AndersenM18 fatcat:u5qocxlotzdd3bhn2cshcwcsuq
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