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Exploiting symmetries for scaling loopy belief propagation and relational training

Babak Ahmadi, Kristian Kersting, Martin Mladenov, Sriraam Natarajan
2013 Machine Learning  
Often, however, we face inference and training problems with symmetries and redundancies in the graph structure.  ...  Often, we encounter inference and training problems with symmetries and redundancies in the graph structure. A prominent example are relational models that capture complexity.  ...  We ran BPCOUNT and LBPCOUNT on the circuit synthesis problem 2bit-max_6 with damping factor 0.5 and convergence threshold 10 −8 .  ... 
doi:10.1007/s10994-013-5385-0 fatcat:tzyy7cagjzhhxccvsw6smdjsom

The Highly Efficient Translation Initiation Region from the Escherichia coli rpsA Gene Lacks a Shine-Dalgarno Element

P. Skorski, P. Leroy, O. Fayet, M. Dreyfus, S. Hermann-Le Denmat
2006 Journal of Bacteriology  
These findings suggest that, under these conditions, the SD-anti-SD interaction plays a significant but not essential role for the synthesis of bulk cellular proteins.  ...  Here, we have tested this hypothesis with the "specialized ribosome" approach.  ...  As a control, the same mutations were also introduced in the (loopIϩII wt ,UUG) TIR.  ... 
doi:10.1128/jb.00591-06 pmid:16923895 pmcid:PMC1595398 fatcat:cj3mbnkhx5corpiei6rvnoenuq

Image completion with structure propagation

Jian Sun, Lu Yuan, Jiaya Jia, Heung-Yeung Shum
2005 ACM Transactions on Graphics  
Figure 1: Image completion with structure propagation.  ...  If only a single curve is specified, structure propagation is solved using Dynamic Programming.  ...  Loopy BP For a graph with loops, the belief propagation algorithm can still be applied without modification, using loopy belief propagation.  ... 
doi:10.1145/1073204.1073274 fatcat:2cgfixxypjeh3llcp33zzlspfa

Image completion with structure propagation

Jian Sun, Lu Yuan, Jiaya Jia, Heung-Yeung Shum
2005 ACM SIGGRAPH 2005 Papers on - SIGGRAPH '05  
Figure 1: Image completion with structure propagation.  ...  If only a single curve is specified, structure propagation is solved using Dynamic Programming.  ...  Loopy BP For a graph with loops, the belief propagation algorithm can still be applied without modification, using loopy belief propagation.  ... 
doi:10.1145/1186822.1073274 fatcat:ae5aeg6dt5djfiqdcxksajvjiu

Identification of plant α-tubulin amino acids playing a key role in specific binding of nitroaniline compounds

S. P. Ozheredov, O. M. Demchuk, P. A. Karpov, S. I. Spivak, Ya. B. Blume
2019 Faktori eksperimentalʹnoï evolûcìï organìzmìv  
These computations allow us to select a.a. residues playing key role in specific interaction with nitro- and dinitroaniline compounds in plant α-tubulin. Conclusions.  ...  The structural model of plant α-tubulin from Avena sativa was build. Also, the virtual library of 25 nitroaniline compounds was prepared.  ...  This loopis associated with GTP hydrolysis in β-tubulin of neighboring б/в-dimer in protofilament.  ... 
doi:10.7124/feeo.v24.1125 fatcat:fxfp5d6q4vg3jf2w74apn6rzri

From relational verification to SIMD loop synthesis

Gilles Barthe, Juan Manuel Crespo, Sumit Gulwani, Cesar Kunz, Mark Marron
2013 SIGPLAN notices  
We present a new program synthesis based technique for auto-vectorizing performance critical innermost loops.  ...  Our technique is able to quickly produce SIMD implementations (up to 9 instructions in 0.12 seconds) for a wide range of fundamental looping structures.  ...  Relational Hoare Logic is effective for proving the correctness of structure-preserving optimizations, and simple optimizations that alter the control flow of programs.  ... 
doi:10.1145/2517327.2442529 fatcat:w2vktstyqveipdvq6eeffocgzu

From relational verification to SIMD loop synthesis

Gilles Barthe, Juan Manuel Crespo, Cesar Kunz, Sumit Gulwani, Mark Marron
2013 Proceedings of the 18th ACM SIGPLAN symposium on Principles and practice of parallel programming - PPoPP '13  
We present a new program synthesis based technique for auto-vectorizing performance critical innermost loops.  ...  Our technique is able to quickly produce SIMD implementations (up to 9 instructions in 0.12 seconds) for a wide range of fundamental looping structures.  ...  Relational Hoare Logic is effective for proving the correctness of structure-preserving optimizations, and simple optimizations that alter the control flow of programs.  ... 
doi:10.1145/2442516.2442529 dblp:conf/ppopp/BartheCKGM13 fatcat:dke54m2jgje2nhfpf5sf5bt4j4

Spiroindolines Identify the Vesicular Acetylcholine Transporter as a Novel Target for Insecticide Action

Ann Sluder, Sheetal Shah, Jérôme Cassayre, Ralph Clover, Peter Maienfisch, Louis-Pierre Molleyres, Elizabeth A. Hirst, Anthony J. Flemming, Min Shi, Penny Cutler, Carole Stanger, Richard S. Roberts (+12 others)
2012 PLoS ONE  
Here we describe a novel class of insecticides (Spiroindolines) encompassing molecules that combine excellent activity against major agricultural pest species with low mammalian toxicity.  ...  We confidently assign the vesicular acetylcholine transporter as the molecular target of Spiroindolines through the combination of molecular genetics in model organisms with a pharmacological approach  ...  Sally Cleere and Katrin Lauenberger, for technical support, Janet Phillips for project management, Christoph Vock and Philipp Eilinger for field biology data, Eddie McIndoe and Keith Ward for support with  ... 
doi:10.1371/journal.pone.0034712 pmid:22563457 pmcid:PMC3341389 fatcat:kxubk46xtzd5lc5b664kakzbrq

pH Tunable Thin Film Gradients of Magnetic Polymer Colloids for MRI Diagnostics

Sumera Khizar, Nasir M Ahmad
2020 Polymers  
The characteristics of films were controlled by changing the pH and level of the adsorbing solutions that lead to the development of gradient films having 5.5, 10.5 and 15.5 bilayers.  ...  Magnetic polymer colloids (MPC) and polyacrylic acid (PAA) with stimuli-responsive cationic and anionic functional groups respectively facilitate the formation of thin film gradients via layer by layer  ...  Sumera Khizar acknowledges the financial support of HEC for the scholarship and IRSIP program grant No. 9046 for visit to Univ Lyon, University Claude Bernard Lyon-1, CNRS, LAGEP-UMR, Lyon, France.  ... 
doi:10.3390/polym12092116 pmid:32957488 pmcid:PMC7569873 fatcat:oazpnujsdvf6jceqwosd5koreq

A mechanism for balancing accuracy and scope in cross-machine black-box GPU performance modeling [article]

James D. Stevens, Andreas Klöckner
2019 arXiv   pre-print
Bill Gropp for helpful discussions and feedback on an earlier version of the manuscript, and express appreciation to Matt Wala for significant contributions to our underlying transformation engine Loopy  ...  . • By making use of a polyhedrally-based program representation, we obtain precise counts of various units of work performed by the static-control part of a program.  ...  From these program objects, Loopy generates and executes source code in a range of output languages, including OpenCL, the output language we use for Loopy programs demonstrated in this work.  ... 
arXiv:1904.09538v2 fatcat:y3koovga2ncpvm4bnberjjiflq

On Plans With Loops and Noise [article]

Vaishak Belle
2018 arXiv   pre-print
While the characterisation does not immediately yield a practical algorithm, the specification serves as a general skeleton to explore the synthesis of program-like plans for reasonable, tractable fragments  ...  Increasingly, classical plan structures are being applied to stochastic environments such as robotics applications.  ...  Algorithmic proposals to synthesise plans that generalise varied widely in methodology, ranging from interactive theorem proving [28] to learning from examples [29] .  ... 
arXiv:1809.05309v1 fatcat:ctk726yp5nhnjpo7db3npxc7lq

Automating string processing in spreadsheets using input-output examples

Sumit Gulwani
2011 Proceedings of the 38th annual ACM SIGPLAN-SIGACT symposium on Principles of programming languages - POPL '11  
The synthesis algorithm is interactive and has several desirable features: it can rank multiple solutions and has fast convergence, it can detect noise in the user input, and it supports an active interaction  ...  The language is expressive enough to represent a wide variety of string manipulation tasks that end-users struggle with.  ...  Thanks to the Excel product team who kept engaging with us despite their initial skepticism whether such a "magical" technology can ever be possible.  ... 
doi:10.1145/1926385.1926423 dblp:conf/popl/Gulwani11 fatcat:ccpgno6lxjf7pmjrdglce2ct4e

Automating string processing in spreadsheets using input-output examples

Sumit Gulwani
2011 SIGPLAN notices  
The synthesis algorithm is interactive and has several desirable features: it can rank multiple solutions and has fast convergence, it can detect noise in the user input, and it supports an active interaction  ...  The language is expressive enough to represent a wide variety of string manipulation tasks that end-users struggle with.  ...  Thanks to the Excel product team who kept engaging with us despite their initial skepticism whether such a "magical" technology can ever be possible.  ... 
doi:10.1145/1925844.1926423 fatcat:aapkktoprnd5pnrnyotvptdwf4

Synthesizing data structure manipulations from storyboards

Rishabh Singh, Armando Solar-Lezama
2011 Proceedings of the 19th ACM SIGSOFT symposium and the 13th European conference on Foundations of software engineering - SIGSOFT/FSE '11  
We present the Storyboard Programming framework, a new synthesis system designed to help programmers write imperative low-level data-structure manipulations.  ...  The framework is based on a new approach for combining constraint-based synthesis and abstract-interpretationbased shape analysis.  ...  These techniques are not applicable in our setting as we deal with loopy programs.  ... 
doi:10.1145/2025113.2025153 dblp:conf/sigsoft/SinghS11 fatcat:hrukyz3pcbaevj2jsc7xwlkkci

The Caenorhabditis elegans Ldb/NLI/Clim Orthologue ldb-1 Is Required for Neuronal Function

Giuseppe Cassata, Sascha Röhrig, Franziska Kuhn, Hans-Peter Hauri, Ralf Baumeister, Thomas R Bürglin
2000 Developmental Biology  
is restricted to specific domains: the dimerization domain, the nuclear localization sequence, and the LIM interaction domain.  ...  The animals, in general, did not move much, but when moving they showed "loopy," exaggerated sinus wave movements. 53 The C. elegans ldb-1 Gene  ...  Sequence comparisons were performed with an interactive dot matrix program on the Macintosh (Bü rglin, 1998). GenBank searches were performed using Netblast at NCBI (Altschul et al., 1990) .  ... 
doi:10.1006/dbio.2000.9846 pmid:10993673 fatcat:rrzlnycjibbgjejkyckrmd5bhu
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