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PARSEC: PAtteRn SEarch and Contextualization

Alexis Allot, Yannick-Noël Anno, Laetitia Poidevin, Raymond Ripp, Olivier Poch, Odile Lecompte
2013 Computer applications in the biosciences : CABIOS  
We present PARSEC (PAtteRn Search and Contextualization), a new open source platform for guided discovery, allowing localization and biological characterization of short genomic sites in entire eukaryotic  ...  PARSEC can search for a sequence or a degenerated pattern.  ...  ACKNOWLEDGEMENTS The authors are grateful to Vincent Laudet and Ce´cile Rochette-Egly for helpful discussions during the development of PARSEC.  ... 
doi:10.1093/bioinformatics/btt455 pmid:23929031 fatcat:4a5dz23e3zcaph75slvnovi6ku

Auto-X3D: Ultra-Efficient Video Understanding via Finer-Grained Neural Architecture Search [article]

Yifan Jiang, Xinyu Gong, Junru Wu, Humphrey Shi, Zhicheng Yan, Zhangyang Wang
2021 arXiv   pre-print
This paper bypasses existing 2D architectures, and directly searched for 3D architectures in a fine-grained space, where block type, filter number, expansion ratio and attention block are jointly searched  ...  A probabilistic neural architecture search method is adopted to efficiently search in such a large space.  ...  In this work, we employ PARSEC as the search procedure to search efficient 3.1.  ... 
arXiv:2112.04710v1 fatcat:p3dxpblcx5f5xlohmas5odwu7e

Star Classification Under Data Variability: An Emerging Challenge in Astroinformatics [chapter]

Ricardo Vilalta, Kinjal Dhar Gupta, Ashish Mahabal
2015 Lecture Notes in Computer Science  
One relevant subarea is the use of machine learning for analysis of large astronomical repositories and surveys.  ...  parsecs, and L is the star luminosity.  ...  Machine learning is already an indispensable resource to modern astronomy, serving as an instrumental aid during the process of data integration and fusion, pattern discovery, classification, regression  ... 
doi:10.1007/978-3-319-23461-8_22 fatcat:axxmk2xl5nff3j2emtkfz27374

Evaluating Auto-Vectorizing Compilers through Objective Withdrawal of Useful Information

Sergi Siso, Wes Armour, Jeyarajan Thiyagalingam
2019 ACM Transactions on Architecture and Code Optimization (TACO)  
CCS Concepts: • Software and its engineering → Compilers;  ...  AltiVec; using the adapted TSVC suite and applicationlevel proxy kernels.  ...  The Searching was only vectorized by the Intel compiler on x86 platforms and by the PGI compiler exclusively on AVX2.  ... 
doi:10.1145/3356842 fatcat:iztjlyb7lffvrehu4mcx3dgroy

Data-driven spatial locality

Svetozar Miucin, Alexandra Fedorova
2018 Proceedings of the International Symposium on Memory Systems - MEMSYS '18  
Our contribution is a set of tools, techniques and algorithms for automatic extraction of correlations between data and access patterns of programs.  ...  Experts often use correlations between the access pattern of an algorithm and properties of the objects it operates on to devise new ways to lay data out in memory.  ...  A search path corresponds to access pattern locality, and colour groups in figure 3.9 correspond to payload value similarity.  ... 
doi:10.1145/3240302.3240417 dblp:conf/memsys/MiucinF18 fatcat:ay76jpnd3jcfzjpqyw42c4vemm

Staged selective parser combinators

Jamie Willis, Nicolas Wu, Matthew Pickering
2020 Proceedings of the ACM on Programming Languages (PACMPL)  
Parser combinators are a middle ground between the fine control of hand-rolled parsers and the high-level almost grammar-like appearance of parsers created via parser generators.  ...  Selective functors can help recover lost functionality in the absence of monads, and the parser tree can be partially evaluated with staging. This is implemented in a library called Parsley.  ...  This work has been supported by EPSRC grant number EP/S028129/1 on łSCOPE: Scoped Contextual Operations and Effectsž.  ... 
doi:10.1145/3409002 fatcat:6xi6jzi4inho3oerpjt62jjuwq

From patterns to frameworks to parallel programs

S. MacDonald, J. Anvik, S. Bromling, J. Schaeffer, D. Szafron, K. Tan
2002 Parallel Computing  
This dissertation shows a new approach to writing object-oriented parallel programs based on design patterns, frameworks, and multiple layers of abstraction.  ...  Lower layers gradually provide access to the generated structural code and other low-level  ...  A UML model does not have the same contextual information.  ... 
doi:10.1016/s0167-8191(02)00190-4 fatcat:judxriww25fcralmmrsyizgv4e

Scalable Speculative Parallelization on Commodity Clusters

Hanjun Kim, Arun Raman, Feng Liu, Jae W. Lee, David I. August
2010 2010 43rd Annual IEEE/ACM International Symposium on Microarchitecture  
with regular and independent units of work.  ...  In particular, high inter-node communication cost and lack of globally shared memory appear to make clusters suitable only for server applications with abundant task-level parallelism and scientific applications  ...  CCF-0811580 and OCI-0849512, and the Air Force Research Laboratory.  ... 
doi:10.1109/micro.2010.19 dblp:conf/micro/KimRLLA10 fatcat:jj6chf5ucree7crvhqmscy7xae

NRG-loops: adjusting power from within applications

Melanie Kambadur, Martha A. Kim
2016 Proceedings of the 2016 International Symposium on Code Generation and Optimization - CGO 2016  
NRG-Loops are portable across different hardware platforms and operating systems and are complementary to existing system-level efficiency techniques, such as DVFS and idle states.  ...  NRG-Loops are source-level abstractions that allow an application to dynamically manage its power and energy through adjustments to functionality, performance, and accuracy.  ...  This work is partially supported by the DARPA PERFECT program (HR0011-13-C-0003) and the National Science Foundation (CCF-1253772).  ... 
doi:10.1145/2854038.2854045 dblp:conf/cgo/KambadurK16 fatcat:hfqta5daxjdvvjwchbccvaprm4

Cybercosm: New Foundations for a Converged Science Data Ecosystem [article]

Mark Asch, François Bodin, Micah Beck, Terry Moore, Michela Taufer, Martin Swany, Jean-Pierre Vilotte
2021 arXiv   pre-print
composability, and data ecosystem convergence.  ...  By building on a common, universal interface into which the problems that infect today's data-intensive workflows can be decomposed and attacked, Cybercosm aims to support scalable, portable and composable  ...  In it we will be adding and updating relevant explanations and material.  ... 
arXiv:2105.10680v3 fatcat:m2vytmdkdvdvzc2deal5odte4u

When organisations and ecosystems interact: toward a law of requisite fractality in firms

Bill McKelvey, Benyamin B. Lichtenstein, Pierpaolo Andriani
2012 International Journal of Complexity in Leadership and Management  
now to it's most recent focus on power laws and their basis in Scale-free theory.  ...  Implications for organizations and managers are discussed. 'I think the next century will be the century of complexity'.  ...  The first lesson from Ashby is that for strategists to find emerging patterns in what appear to be chaotic environments, they need to uncover the contextual constraints.  ... 
doi:10.1504/ijclm.2012.050398 fatcat:zerp6mchvvaprohe7vfcovlk3u

The Deep Lens Survey Transient Search. I. Short Timescale and Astrometric Variability

A. C. Becker, D. M. Wittman, P. C. Boeshaar, A. Clocchiatti, I. P. Dell'Antonio, D. A. Frail, J. Halpern, V. E. Margoniner, D. Norman, J. A. Tyson, R. A. Schommer
2004 Astrophysical Journal  
We report on the methodology and first results from the Deep Lens Survey transient search.  ...  The DLS is the first survey to classify and report all types of photometric and astrometric variability detected, including solar system objects, variable stars, supernovae, and short timescale phenomena  ...  Navarro, and R. Wilcox. We thank G. Bernstein for orbit calculations, R. Sari and S. Hawley for useful discussions, and G. Bravo, M. Hamui, D. Kirkman, C. Smith, and C. Stubbs for assistance.  ... 
doi:10.1086/421994 fatcat:r2iijrafwfc7hjdccz222eod54

Self‐adaptation on parallel stream processing: A systematic review

Adriano Vogel, Dalvan Griebler, Marco Danelutto, Luiz Gustavo Fernandes
2021 Concurrency and Computation  
Finally, applying the taxonomy made it possible to characterize the state-of-the-art, identify trends, and discuss open research challenges and future opportunities.  ...  On the one hand, stream processing applications are becoming more complex, dynamic, and long-running.  ...  Then, we contextualize our search strategy and protocol.  ... 
doi:10.1002/cpe.6759 fatcat:4qa2hlnhijbjbhmf73de5qa2re

Pythia: A Customizable Hardware Prefetching Framework Using Online Reinforcement Learning [article]

Rahul Bera, Konstantinos Kanellopoulos, Anant V. Nori, Taha Shahroodi, Sreenivas Subramoney, Onur Mutlu
2021 pre-print
context and system-level feedback information into account while prefetching.  ...  Pythia uses this reward to reinforce the correlation between program context information and prefetch decision to generate highly accurate, timely, and system-aware prefetch requests in the future.  ...  First, CP uses the contextual-bandit (CB) algorithm [38] , a simplified version of RL.  ... 
doi:10.1145/3466752.3480114 arXiv:2109.12021v1 fatcat:fovtyfbtwbfztken2n47xzrada

Communication as fair distribution of knowledge

Jean-Marc Andreoli, Remo Pareschi
1991 Conference proceedings on Object-oriented programming systems, languages, and applications - OOPSLA '91  
the well-established blackboard-based communication (see for instance [lo]): as it will be shown, forumbased communication can both be viewed as a logical version of blackboard-based communication and  ...  1990), which exploits the proof-theory of Linear Logic also to achieve a powerful form of knowledge-sharing. thermore, we shall characterize the relationship between such a novel form of communication and  ...  Acknowledgement We are grateful to Gerard Comyn and Alexander Herold for helpful comments on this paper. We also thank Nabiel Elshiewy for helpful discussions. References  ... 
doi:10.1145/117954.117971 dblp:conf/oopsla/AndreoliP91 fatcat:bfep25zuarb2taulaxbp3tpbu4
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