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The Local Outlier Factor (LOF) is a very powerful anomaly detection method available in machine learning and classification. The algorithm defines the notion of local outlier in which the degree to which an object is outlying is dependent on the density of its local neighborhood, and each object can be assigned an LOF which represents the likelihood of that object being an outlier. Although this concept of a local outlier is a useful one, the computation of LOF values for every data object requires a large number of k-nearest neighbor queries -this overhead can limit the use of LOF due to the computational overhead involved.Due to the growing popularity of Graphics Processing Units (GPU) in general-purpose computing domains, and equipped with a high-level programming language designed specifically for general-purpose applications (e.g., CUDA), we look to apply this parallel computing approach to accelerate LOF. In this paper we explore how to utilize a CUDA-based GPU implementation of the k-nearest neighbor algorithm to accelerate LOF classification. We achieve more than a 100X speedup over a multi-threaded dual-core CPU implementation. We also consider the impact of input data set size, the neighborhood size (i.e., the value of k) and the feature space dimension, and report on their impact on execution time.

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The fundamental principle of precision oncology is centralized on identification of therapeutically exploitable targets that provides individual cancer patients an opportunity to make informed decisions on a personalized level. To facilitate and adopt such concepts within clinical practice, we have initiated a nation-wide, multi-institutional precision oncology screening program to examine and enroll patients into the most appropriate clinical trial based on their unique molecular properties. To determine prevalence of essential major driver mutations and to explore their dynamic associations at both single molecular and pathway levels, we first present a comprehensive overview on the genomic properties of East Asian cancer patients. We further delineated the extent of genomic diversity as well as clinical utility between patients from western and eastern cultures at the pan-cancer and single tumor entity levels. To support fellow oncology communities in future investigations involving largescale analysis, all data have been made accessible to the public (https://kmportal.or.kr).

Optimizing program execution targeted for Graphics Processing Units (GPUs) can be very challenging. Our ability to efficiently map serial code to a GPU or stream processing platform is a time consuming task and is greatly hampered by a lack of detail about the underlying hardware. Programmers are left to attempt trial and error to produce optimized codes.Recent publication of the underlying instruction set architecture (ISA) of the AMD/ATI GPU has allowed researchers to begin to propose aggressive optimizations. In this work, we present an optimization methodology that utilizes this information to accelerate programs on AMD/ATI GPUs. We start by defining optimization spaces that guide our work. We begin with disassembled machine code and collect program statistics provided by the AMD Graphics Shader Analyzer (GSA) profiling toolset. We explore optimizations targeting three different computing resources: 1) ALUs, 2) fetch bandwidth, and 3) thread usage, and present optimization techniques that consider how to better utilize each resource.We demonstrate the effectiveness of our proposed optimization approach on an AMD Radeon HD3870 GPU using the Brook+ stream programming language. We describe our optimizations using two commonly-used GPGPU applications that present very different program characteristics and optimization spaces: matrix multiplication and back-projection for medical image reconstruction. Our results show that optimized code can improve performance by 1.45x-6.7x as compared to unoptimized code run on the same GPU platform.Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. The speedup obtained with our optimized implementations are 882x (matrix multiply) and 19x (back-projection) faster as compared with serial implementations run on an Intel 2.66 GHz Core 2 Duo with a 2 GB main memory. Second Workshop on General-Purpose Computation on Graphics Processing Units (GPGPU