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An Efficient Staging Algorithm for Binding-Time Analysis [chapter]

Takuma Murakami, Zhenjiang Hu, Kazuhiko Kakehi, Masato Takeichi
2004 Lecture Notes in Computer Science  
Introduction Binding-Time Analysis (BTA) is one of the compile time program analyses which is a general framework for program optimization and program generation [1] .  ...  Then we can give the binding-time specification of the desired function as An Optimal Staging Algorithm Our basic policy is to develop an algorithm to solve the staging problem in terms of algorithm  ... 
doi:10.1007/978-3-540-25938-1_9 fatcat:l6dsqqppmrgvlm3ncenc42qflq

Early Quality Assessment for Low Power Behavioral Synthesis

Eren Kursun, Rajarshi Mukherjee, Seda Ogrenci Memik
2005 Journal of Low Power Electronics  
In this paper, we present an efficient technique to evaluate the power dissipation of scheduled Data Flow Graphs (DFGs).  ...  Fast and effective exploration at the early stages of the design flow can yield significant improvement in the quality of the design and substantial reduction in design time.  ...  The algorithm offers both running time improvement and power efficiency.  ... 
doi:10.1166/jolpe.2005.028 fatcat:rmumzjht7rhlvh3surki67oege

Stochastic Adaptive Robust Dispatch for Virtual Power Plants Using the Binding Scenario Identification Approach

Guoqiang Sun, Weihang Qian, Wenjin Huang, Zheng Xu, Zhongxing Fu, Zhinong Wei, Sheng Chen
2019 Energies  
The binding scenario subset is identified in the sub-problem, which greatly reduces the number of iterations required for solving the model, and thereby increases the computational efficiency.  ...  In addition, the results demonstrate that the binding scenario identification algorithm is accurate, and its computation time increases slowly with increasing scenario set size, so the approach is adaptable  ...  Figure 8 . 8 scenarios Computation time of binding scenario approach Computation time of standard scenario-based approach [32] Comparison of the computational efficiencies of the two algorithms for solving  ... 
doi:10.3390/en12101918 fatcat:u6rnvqwpmvg2nbceqa77wkvsai

Fast binding-time analysis for multi-level specialization [chapter]

Robert Glück, Jesper Jørgensen
1996 Lecture Notes in Computer Science  
We present the key ingredient of our approach to multi-level specialization: an accurate and fast multi-level binding-time analysis.  ...  Experiments with widely-available example programs confirm the excellent run-time behavior of the normalization algorithms.  ...  The work was also supported by the project "Design, Analysis and Reasoning about Tools" funded by the Danish Natural Sciences Research Council.  ... 
doi:10.1007/3-540-62064-8_22 fatcat:56q7y55lnrcg3m574ig4fl6mfe

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

Morgane Thomas-Chollier, Carl Herrmann, Matthieu Defrance, Olivier Sand, Denis Thieffry, Jacques van Helden
2011 Nucleic Acids Research  
It relies on time-and memory-efficient algorithms enabling the treatment of several thousand peaks within minutes.  ...  an extensive report suited for both naive and expert users.  ...  Node labels refer to the algorithm used to discover the motif: L (local-words), P (position-analysis), O (oligo-analysis), D (dyad-analysis) as well as the considered word length (6 or 7).  ... 
doi:10.1093/nar/gkr1104 pmid:22156162 pmcid:PMC3287167 fatcat:uxtmsfltwngohedr6ebpgbzm6e

Binding-Time Analysis for MetaML via Type Inference and Constraint Solving [chapter]

Nathan Linger, Tim Sheard
2004 Lecture Notes in Computer Science  
The two predominant program specialization techniques, partial evaluation and staged programming, take opposite approaches to automating binding-time analysis (BTA).  ...  Such an algorithm provides a basis for a system integrating staged programming and partial evaluation because it allows programmers to switch between automatic and manual staging.  ...  First, that the input to binding time analysis is really a staged type.  ... 
doi:10.1007/978-3-540-24730-2_22 fatcat:qnxcxeczyvczzcaahw7zhiac3y

BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments

Lu-yong Wang, Michael Snyder, Mark Gerstein
2006 Genome Biology  
Our method (BoCaTFBS) uses boosted cascades of classifiers for optimum efficiency, in which components are alternating decision trees; it exploits interpositional correlations; and it explicitly integrates  ...  For this, we propose a mining approach combining noisy data from ChIP (chromatin immunoprecipitation)-chip experiments with known binding site patterns.  ...  Acknowledgements We thank the anonymous reviewers for their advice and comments.  ... 
doi:10.1186/gb-2006-7-11-r102 pmid:17078876 pmcid:PMC1794589 fatcat:njcjy6s4hjb7xde4foj7s2dt4q

Automatic Pipeline Construction for Real-Time Annotation [chapter]

Henning Wachsmuth, Mirko Rose, Gregor Engels
2013 Lecture Notes in Computer Science  
Based on an abstract ontological model, we use partial order planning to select a pipeline's algorithms and informed search to obtain an efficient pipeline schedule.  ...  This paper presents an artificial intelligence approach to automatically construct annotation pipelines for given information needs and quality prioritizations.  ...  Different algorithms for an analysis may vary in their requirements, thereby placing different constraints on π.  ... 
doi:10.1007/978-3-642-37247-6_4 fatcat:pzq2i47dzfhobnsl2nhdjvjfqe

Process-variation aware mapping of real-time streaming applications to MPSoCs for improved yield

Davit Mirzoyan, Benny Akesson, Kees Goossens
2012 Thirteenth International Symposium on Quality Electronic Design (ISQED)  
terms of clock cycles (which is independent of variation) and seconds (which does depend on the variation of the resource), which we connect by an explicit binding. 2) We present two approaches for optimizing  ...  The three main contributions of this paper are: 1) Using data flow graphs that are well-suited for modeling and analysis of real-time streaming applications, we explicitly model task execution both in  ...  They proposed an effective statistical static timing analysis technique, which schedules and binds tasks in an acyclic task graph to the resources in an MPSoC in the presence of resource sharing, such  ... 
doi:10.1109/isqed.2012.6187472 dblp:conf/isqed/MirzoyanAG12 fatcat:xvqyh43ykbgapfu7w7q7ctjxzq

Simultaneous Peak Temperature and Average Power Minimization during Behavioral Synthesis

Vyas Krishnan, Srinivas Katkoori
2009 2009 22nd International Conference on VLSI Design  
We present an algorithm for thermally-aware low-power behavioral synthesis that concurrently minimizes average power and peak chip temperature.  ...  Our algorithm uses accurate floorplan-based temperature estimates to guide behavioral synthesis.  ...  The main algorithm comprises of an HLS synthesis system tightly integrated with an incremental floorplanner and a thermal analysis tool.  ... 
doi:10.1109/vlsi.design.2009.78 dblp:conf/vlsid/KrishnanK09 fatcat:whdkit7emjau7lafsteqslvx5m

Concurrent and Adaptive Extreme Scale Binding Free Energy Calculations

Jumana Dakka, Kristof Farkas-Pall, Matteo Turilli, David W. Wright, Peter V. Coveney, Shantenu Jha
2018 2018 IEEE 14th International Conference on e-Science (e-Science)  
This demands advances in algorithms, scalable software systems, and efficient utilization of supercomputing resources.  ...  For this predictive accuracy to impact clinical decision making, binding free energy computational campaigns must provide results rapidly and without loss of accuracy.  ...  ACKNOWLEDGMENTS JD acknowledges Dept. of Education Award P200A150217 for her fellowship.  ... 
doi:10.1109/escience.2018.00034 dblp:conf/eScience/DakkaFTWCJ18 fatcat:jotwrti6vbhuvjti6klhzpm67e

Efficient Integrative Multi-SNP Association Analysis via Deterministic Approximation of Posteriors

Xiaoquan Wen, Yeji Lee, Francesca Luca, Roger Pique-Regi
2016 American Journal of Human Genetics  
In particular, we propose an algorithm, named deterministic approximation of posteriors (DAP), which enables highly efficient and accurate joint enrichment analysis and identification of multiple causal  ...  In this paper, we propose a rigorous inference procedure to perform integrative association analysis incorporating genomic annotations for both traditional GWASs and emerging molecular QTL mapping studies  ...  Acknowledgments We thank the GTEx consortium and the GEUVADIS RNA sequencing project for releasing valuable data in a timely fashion.  ... 
doi:10.1016/j.ajhg.2016.03.029 pmid:27236919 pmcid:PMC4908152 fatcat:pvkcejd2izajffnkxv23uv35fi

Adaptive Ensemble Biomolecular Simulations at Scale [article]

Vivek Balasubramanian, Travis Jensen, Matteo Turilli, Peter Kasson, Michael Shirts, Shantenu Jha
2019 arXiv   pre-print
Thus, there is a need for scalable software systems to support adaptive ensemble-based applications.  ...  Recent advances in both theory and methods have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations.  ...  The first stage generates sufficient amount of MD trajectory data for an analysis.  ... 
arXiv:1804.04736v5 fatcat:qn7zyrturrd5rpq4h336obi2xa

Toward introducing binding-time analysis to MetaOCaml

Kenichi Asai
2016 Proceedings of the 2016 ACM SIGPLAN Workshop on Partial Evaluation and Program Manipulation - PEPM 2016  
It forms a basis for introducing binding-time analysis to full-fledged staged languages such as MetaOCaml.  ...  This paper relates 2-level λ-calculus and staged λ-calculus (restricted to 2 stages) to obtain monovariant binding-time analysis for λ-calculus that produces the output in the form of staging annotations  ...  There is an efficient such algorithm [4] , which can be further simplified in case the input term is already well typed.  ... 
doi:10.1145/2847538.2847547 dblp:conf/pepm/Asai16 fatcat:fxjy4pbwb5dtfipv4w5gk3n3ry

Principles of flexible protein-protein docking

Nelly Andrusier, Efrat Mashiach, Ruth Nussinov, Haim J. Wolfson
2008 Proteins: Structure, Function, and Bioinformatics  
ACKNOWLEDGMENTS The authors thank Dina Schneidman-Duhovny and Michael Farkash for the helpful comments. E.M. was supported in part by a fellowship from the Edmond J.  ...  This analysis is more efficient both in CPU time and in memory than the ANM analysis and therefore it can be applied on larger systems.  ...  The time efficiency of the R3 and SCWRL methods was better than of MILP for these cases.  ... 
doi:10.1002/prot.22170 pmid:18655061 pmcid:PMC2574623 fatcat:iyu4ebl7lrbaxcasxtqrzzlibm
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