Mira: A Framework for Static Performance Analysis

The performance model of an application can pro- vide understanding about its runtime behavior on particular hardware. Such information can be analyzed by developers for performance tuning. However, model building and analyzing is frequently ignored during software development until perfor- mance problems arise because they require significant expertise and can involve many time-consuming application runs. In this paper, we propose a fast, accurate, flexible and user-friendly tool, Mira, for generating performance models by applying static program analysis, targeting scientific applications running on supercomputers. We parse both the source code and binary to estimate performance attributes with better accuracy than considering just source or just binary code. Because our analysis is static, the target program does not need to be executed on the target architecture, which enables users to perform analysis on available machines instead of conducting expensive exper- iments on potentially expensive resources. Moreover, statically generated models enable performance prediction on non-existent or unavailable architectures. In addition to flexibility, because model generation time is significantly reduced compared to dynamic analysis approaches, our method is suitable for rapid application performance analysis and improvement. We present several scientific application validation results to demonstrate the current capabilities of our approach on small benchmarks and a mini application

List Decoding Tensor Products and Interleaved Codes

We design the first efficient algorithms and prove new combinatorial bounds for list decoding tensor products of codes and interleaved codes. We show that for {\em every} code, the ratio of its list decoding radius to its minimum distance stays unchanged under the tensor product operation (rather than squaring, as one might expect). This gives the first efficient list decoders and new combinatorial bounds for some natural codes including multivariate polynomials where the degree in each variable is bounded. We show that for {\em every} code, its list decoding radius remains unchanged under $m$-wise interleaving for an integer $m$. This generalizes a recent result of Dinur et al \cite{DGKS}, who proved such a result for interleaved Hadamard codes (equivalently, linear transformations). Using the notion of generalized Hamming weights, we give better list size bounds for {\em both} tensoring and interleaving of binary linear codes. By analyzing the weight distribution of these codes, we reduce the task of bounding the list size to bounding the number of close-by low-rank codewords. For decoding linear transformations, using rank-reduction together with other ideas, we obtain list size bounds that are tight over small fields.Comment: 32 page

Identification of SNP interactions using logic regression

Interactions of single nucleotide polymorphisms (SNPs) are assumed to be responsible for complex diseases such as sporadic breast cancer. Important goals of studies concerned with such genetic data are thus to identify combinations of SNPs that lead to a higher risk of developing a disease and to measure the importance of these interactions. There are many approaches based on classification methods such as CART and Random Forests that allow measuring the importance of single variables. But with none of these methods the importance of combinations of variables can be quantified directly. In this paper, we show how logic regression can be employed to identify SNP interactions explanatory for the disease status in a case- control study and propose two measures for quantifying the importance of these interactions for classification. These approaches are then applied, on the one hand, to simulated data sets, and on the other hand, to the SNP data of the GENICA study, a study dedicated to the identification of genetic and gene-environment interactions associated with sporadic breast cancer. --Single Nucleotide Polymorphism,Feature Selection,Variable Importance Measure,GENICA