M09---Program analysis tools for massively parallel applications

Author(s):  
Andreas Knuepfer ◽  
Dieter Kranzlmueller ◽  
Bernd W. Mohr ◽  
Wolfgang E. Nagel
2021 ◽  
Author(s):  
Eric Alcaide ◽  
Stella Biderman ◽  
Amalio Telenti ◽  
Michael Cyrus Maher

The conversion of proteins between internal and cartesian coordinates is a limiting step in many pipelines, such as molecular dynamics simulations and machine learning models. This conversion is typically carried out by sequential or parallel applications of the Natural extension of Reference Frame (NeRF) algorithm. This work proposes a massively parallel NeRF implementation which, depending on the polymer length, achieves speedups between 400-1000x over the previous state-of-the-art NeRF implementation. It accomplishes this by dividing the conversion into three main phases: a parallel composition of the monomer backbone, the assembly of backbone subunits, and the parallel elongation of sidechains; and by batching computations into a minimal number of efficient matrix operations. Special emphasis is placed on reusability and ease of use within diverse pipelines. We open source the code (available at https://github.com/EleutherAI/mp_nerf) and provide a corresponding python package.


Author(s):  
Takanori Fujiwara ◽  
Preeti Malakar ◽  
Khairi Reda ◽  
Venkatram Vishwanath ◽  
Michael E. Papka ◽  
...  

Author(s):  
Aibek Sarimbekov ◽  
Yudi Zheng ◽  
Danilo Ansaloni ◽  
Lubomir Bulej ◽  
Luka Marek ◽  
...  

Author(s):  
Ana Milanova ◽  
Barbara Cutler ◽  
Buster Holzbauer ◽  
Evan Maicus ◽  
Samuel Breese ◽  
...  

Author(s):  
Marco Pistoia ◽  
Omer Tripp ◽  
David Lubensky

Mobile devices have revolutionized many aspects of our lives. Without realizing it, we often run on them programs that access and transmit private information over the network. Integrity concerns arise when mobile applications use untrusted data as input to security-sensitive computations. Program-analysis tools for integrity and confidentiality enforcement have become a necessity. Static-analysis tools are particularly attractive because they do not require installing and executing the program, and have the potential of never missing any vulnerability. Nevertheless, such tools often have high false-positive rates. In order to reduce the number of false positives, static analysis has to be very precise, but this is in conflict with the analysis' performance and scalability, requiring a more refined model of the application. This chapter proposes Phoenix, a novel solution that combines static analysis with machine learning to identify programs exhibiting suspicious operations. This approach has been widely applied to mobile applications obtaining impressive results.


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