Parameterized Construction of Program Representations for Sparse Dataflow Analyses

Data-flow analyses usually associate information with control flow regions. Informally, if these regions are too small, like a point between two consecutive statements, we call the analysis dense. On the other hand, if these regions include many such points, then we call it sparse. This paper presents a systematic method to build program representations that support sparse analyses. To pave the way to this framework we clarify the bibliography about well-known intermediate program representations. We show that our approach, up to parameter choice, subsumes many of these representations, such as the SSA, SSI and e-SSA forms. In particular, our algorithms are faster, simpler and more frugal than the previous techniques used to construct SSI - Static Single Information - form programs. We produce intermediate representations isomorphic to Choi et al.'s Sparse Evaluation Graphs (SEG) for the family of data-flow problems that can be partitioned per variables. However, contrary to SEGs, we can handle - sparsely - problems that are not in this family

A NOVEL COMPUTATIONAL FRAMEWORK FOR TRANSCRIPTOME ANALYSIS WITH RNA-SEQ DATA

The advance of high-throughput sequencing technologies and their application on mRNA transcriptome sequencing (RNA-seq) have enabled comprehensive and unbiased profiling of the landscape of transcription in a cell. In order to address the current limitation of analyzing accuracy and scalability in transcriptome analysis, a novel computational framework has been developed on large-scale RNA-seq datasets with no dependence on transcript annotations. Directly from raw reads, a probabilistic approach is first applied to infer the best transcript fragment alignments from paired-end reads. Empowered by the identification of alternative splicing modules, this framework then performs precise and efficient differential analysis at automatically detected alternative splicing variants, which circumvents the need of full transcript reconstruction and quantification. Beyond the scope of classical group-wise analysis, a clustering scheme is further described for mining prominent consistency among samples in transcription, breaking the restriction of presumed grouping. The performance of the framework has been demonstrated by a series of simulation studies and real datasets, including the Cancer Genome Atlas (TCGA) breast cancer analysis. The successful applications have suggested the unprecedented opportunity in using differential transcription analysis to reveal variations in the mRNA transcriptome in response to cellular differentiation or effects of diseases

Optimal Control Dependence Computation and the Roman Chariots Problem

this article, we introduce the augmented postdominator tree (APT ), a data structure which can be constructed in space and time proportional to the size of the program and which supports enumeration of a number of useful control dependence sets in time proportional to their size. Therefore, APT provides an optimal representation of control dependence. Specifically, the AP