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Marker-Directed Optimization of UnCAL Graph Transformations [chapter]

Soichiro Hidaka, Zhenjiang Hu, Kazuhiro Inaba, Hiroyuki Kato, Kazutaka Matsuda, Keisuke Nakano, Isao Sasano
2012 Lecture Notes in Computer Science  
UnCAL graph model includes the concept of markers, which correspond to recursive function call in the structural recursion.  ...  Buneman et al. proposed a graph algebra called UnCAL (Unstructured CALculus) for compositional graph transformations based on structural recursion, and we have recently applied to model transformations  ...  The research was supported in part by the Grand-Challenging Project on "Linguistic Foundation for Bidirectional Model Transformation" from the National Institute of Informatics, Grantin-Aid for Scientific  ... 
doi:10.1007/978-3-642-32211-2_9 fatcat:m5ce2ttaujbw7e5cwiffjiiydu

A functional reformulation of UnCAL graph-transformations: or, graph transformation as graph reduction

Kazutaka Matsuda, Kazuyuki Asada
2017 Proceedings of the 2017 ACM SIGPLAN Workshop on Partial Evaluation and Program Manipulation - PEPM 2017  
This paper proposes FUnCAL, a functional redesign of the graph transformation language UnCAL.  ...  In this paper, following the observation that markers can be emulated by tuples and λ-abstractions, we transform UnCAL programs to a restricted class of usual (thus, marker-free) functional ones.  ...  " of the National Institute of Informatics.  ... 
doi:10.1145/3018882.3018883 fatcat:kdhaazshrzbc3m2nd6prkrk3d4

Pregel meets UnCAL: A systematic framework for transforming big graphs

Le-Duc Tung
2015 2015 31st IEEE International Conference on Data Engineering Workshops  
In this thesis we are developing Gito, a systematic framework on top of Pregel to do transformations over big graphs.  ...  In particular, in this paper, we show the feasibility of integrating UnCAL and Pregel, and propose a scalable Pregel-based computation for a subclass of UnCAL.  ...  Graph Data Model UnCAL's data model is a directed edge-labeled graph extended by markers and ε-edges [2] .  ... 
doi:10.1109/icdew.2015.7129585 dblp:conf/icde/Tung15 fatcat:f2mkt5yborhzbnwoyvghu3gjva

Towards a compositional approach to model transformation for software development

Soichiro Hidaka, Zhenjiang Hu, Hiroyuki Kato, Keisuke Nakano
2009 Proceedings of the 2009 ACM symposium on Applied Computing - SAC '09  
Despite a large amount of theoretical work and a lot of experience with research prototypes on graph-based model transformations, it remains an open issue how to compose model transformations.  ...  Although models may have different notations and representations, they are basically graphs, and model transformations are thus nothing but graph transformations.  ...  ACKNOWLEDGEMENTS We would like to thank Mary Fernandez from AT&T Labs Research, who kindly provided us with the SML source codes of an UnQL system, which helped us a lot in implementing our extended system  ... 
doi:10.1145/1529282.1529383 dblp:conf/sac/HidakaHKN09 fatcat:clkgltnrpbcj7bcxtj2jvaqbx4

Bidirectionalizing graph transformations

Soichiro Hidaka, Zhenjiang Hu, Kazuhiro Inaba, Hiroyuki Kato, Kazutaka Matsuda, Keisuke Nakano
2010 Proceedings of the 15th ACM SIGPLAN international conference on Functional programming - ICFP '10  
We challenge the problem of bidirectional transformations within the context of graphs, by proposing a formal definition of a well-behaved bidirectional semantics for UnCAL, i.e., a graph algebra for the  ...  The key to our successful formalization is full utilization of both the recursive and bulk semantics of structural recursion on graphs.  ...  The research was supported in part by the Grand-Challenging Project on "Linguistic Foundation for Bidirectional Model Transformation" from the National Institute of Informatics, Grant-in-Aid for Scientific  ... 
doi:10.1145/1863543.1863573 dblp:conf/icfp/HidakaHIKMN10 fatcat:towkjjz2fvchji45qam2rcy76y

Bidirectionalizing graph transformations

Soichiro Hidaka, Zhenjiang Hu, Kazuhiro Inaba, Hiroyuki Kato, Kazutaka Matsuda, Keisuke Nakano
2010 SIGPLAN notices  
We challenge the problem of bidirectional transformations within the context of graphs, by proposing a formal definition of a well-behaved bidirectional semantics for UnCAL, i.e., a graph algebra for the  ...  The key to our successful formalization is full utilization of both the recursive and bulk semantics of structural recursion on graphs.  ...  The research was supported in part by the Grand-Challenging Project on "Linguistic Foundation for Bidirectional Model Transformation" from the National Institute of Informatics, Grant-in-Aid for Scientific  ... 
doi:10.1145/1932681.1863573 fatcat:luhkqdfnljglbm3pkztihcnini

Towards Systematic Parallelization of Graph Transformations Over Pregel

Le-Duc Tung, Zhenjiang Hu
2016 International journal of parallel programming  
Although Pregel is simple to understand and use, it is of low-level in programming and requires developers to write programs that are hard to maintain and need to be carefully optimized.  ...  Graphs are flexible in modelling many kinds of data from traditional datasets to social networks or semi-structured datasets.  ...  The second direction is to optimize the core of our framework.  ... 
doi:10.1007/s10766-016-0418-5 fatcat:yfixwlim7zh5vagrcyxka24ge4

Structural recursion for querying ordered graphs

Soichiro Hidaka, Kazuyuki Asada, Zhenjiang Hu, Hiroyuki Kato, Keisuke Nakano
2013 Proceedings of the 18th ACM SIGPLAN international conference on Functional programming - ICFP '13  
We propose a new graph transformation language called λFG for transforming and querying ordered graphs, based on the well-defined bisimulation relation on ordered graphs with special ε-edges.  ...  the help of the bisimilarity for ordered graphs with ε-edges.  ...  The research was supported in part by the Grand-Challenging Project on the "Linguistic Foundation for Bidi-rectional Model Transformation" of the National Institute of Informatics, and a Grant-in-Aid for  ... 
doi:10.1145/2500365.2500608 dblp:conf/icfp/HidakaAHKN13 fatcat:2st3rc5cwbdrbfvjshm3c2ukle

Structural recursion for querying ordered graphs

Soichiro Hidaka, Kazuyuki Asada, Zhenjiang Hu, Hiroyuki Kato, Keisuke Nakano
2013 SIGPLAN notices  
We propose a new graph transformation language called λFG for transforming and querying ordered graphs, based on the well-defined bisimulation relation on ordered graphs with special ε-edges.  ...  the help of the bisimilarity for ordered graphs with ε-edges.  ...  The research was supported in part by the Grand-Challenging Project on the "Linguistic Foundation for Bidi-rectional Model Transformation" of the National Institute of Informatics, and a Grant-in-Aid for  ... 
doi:10.1145/2544174.2500608 fatcat:blf5rnoqwfhpzg3x6fioui7ujy

Maintaining invariant traceability through bidirectional transformations

Yijun Yu, Yu Lin, Zhenjiang Hu, Soichiro Hidaka, Hiroyuki Kato, Lionel Montrieux
2012 2012 34th International Conference on Software Engineering (ICSE)  
in both directions.  ...  In this paper, we propose a two-layered invariant traceability framework that reduces the number of mismatches through bidirectional transformations.  ...  Derivation of a One-Pass Transformation The automatically generated UnQL+ transformations are not optimal.  ... 
doi:10.1109/icse.2012.6227162 dblp:conf/icse/YuLHHKM12 fatcat:ibc7nmqypjaidm2jhn2smm57xi

UnQL: a query language and algebra for semistructured data based on structural recursion

Peter Buneman, Mary Fernandez, Dan Suciu
2000 The VLDB journal  
We show that the composition of two structural recursion queries can be expressed as a single such query, and this is used as the basis of an optimization method for mediator systems.  ...  This paper presents structural recursion as the basis of the syntax and semantics of query languages for semistructured data and XML.  ...  GOOD uses a graph model of data that conforms to a functional data model and has a query/transformation language that exploits pattern matching of graphs.  ... 
doi:10.1007/s007780050084 fatcat:k7vm6qng6nhbvosf3cwpanfsxe

Toward Bidirectionalization of ATL with GRoundTram [chapter]

Isao Sasano, Zhenjiang Hu, Soichiro Hidaka, Kazuhiro Inaba, Hiroyuki Kato, Keisuke Nakano
2011 Lecture Notes in Computer Science  
In our previous work we have shown that transformations of graph structures given in some form can be bidirectionalized and have implemented a system called GRoundTram system for bidirectional graph transformations  ...  ATL is a language for describing model transformations currently in uni-direction.  ...  Formally, when encoding models with cycles as in Fig. 4 , we use the cycle construct and markers in UnCAL language [8] , which we omit for simplifying the presentation.  ... 
doi:10.1007/978-3-642-21732-6_10 fatcat:pufzh3ioyjcrtm2rsfcpyfgumu

Cross-Kernel Control-Flow--Graph Analysis for Event-Driven Real-Time Systems

Christian Dietrich, Martin Hoffmann, Daniel Lohmann
2015 Proceedings of the 16th ACM SIGPLAN/SIGBED Conference on Languages, Compilers and Tools for Embedded Systems 2015 CD-ROM - LCTES'15  
On the example of a real-world safety-critical control system, we present two possible use cases: Run-time optimizations, by means of specialized system calls for each call site, allow to speed up the  ...  Modern compilers can extract and exploit this information to perform extensive whole-program analyses and interprocedural optimizations.  ...  Figure 4a shows a state-transition graph for a system consisting of three ABBs. This graph is the direct result of the SSE stepping function.  ... 
doi:10.1145/2670529.2754963 dblp:conf/lctrts/0001HL15 fatcat:xj7vui2hgzdizit5gw3krq355u

The hippocampi of children with chromosome 22q11.2 deletion syndrome have localized anterior alterations that predict severity of anxiety
EN

Julia A. Scott, Naomi Goodrich-Hunsaker, Kristopher Kalish, Aaron Lee, Michael R. Hunsaker, Cynthia M. Schumann, Owen T. Carmichael, Tony J. Simon
2016 Journal of Psychiatry & Neuroscience  
Acknowledgements: The study was funded by National Institute of  ...  , pri-mate uncal CA1 and prosubicular regions have direct connections to the amygdala. 53 The basis vectors associated with 22q11.2DS and anxiety severity were localized to the homologous regions of  ...  Parameters were optimized for the characteristics of the data set and are detailed in Appendix 1.  ... 
doi:10.1503/jpn.140299 fatcat:ukmjpx4nsfhnljq6ee4ocyljtu

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

Ana Elena Pérez-Cobas, Laura Gomez-Valero, Carmen Buchrieser
2020 Microbial Genomics  
Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology.  ...  It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge.  ...  Similarly, PEAR joins the paired-end reads and allows us to define different parameters, such as the minimum and maximum length of output sequences or the maximum proportion of uncalled bases.  ... 
doi:10.1099/mgen.0.000409 pmid:32706331 fatcat:lv23zgejzzf45pmetzsb52kdlm
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