The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing

A Survey on Metric Learning for Feature Vectors and Structured Data

The need for appropriate ways to measure the distance or similarity between data is ubiquitous in machine learning, pattern recognition and data mining, but handcrafting such good metrics for specific problems is generally difficult. This has led to the emergence of metric learning, which aims at automatically learning a metric from data and has attracted a lot of interest in machine learning and related fields for the past ten years. This survey paper proposes a systematic review of the metric learning literature, highlighting the pros and cons of each approach. We pay particular attention to Mahalanobis distance metric learning, a well-studied and successful framework, but additionally present a wide range of methods that have recently emerged as powerful alternatives, including nonlinear metric learning, similarity learning and local metric learning. Recent trends and extensions, such as semi-supervised metric learning, metric learning for histogram data and the derivation of generalization guarantees, are also covered. Finally, this survey addresses metric learning for structured data, in particular edit distance learning, and attempts to give an overview of the remaining challenges in metric learning for the years to come.Comment: Technical report, 59 pages. Changes in v2: fixed typos and improved presentation. Changes in v3: fixed typos. Changes in v4: fixed typos and new method

TUMK-ELM: A fast unsupervised heterogeneous data learning approach

© 2013 IEEE. Advanced unsupervised learning techniques are an emerging challenge in the big data era due to the increasing requirements of extracting knowledge from a large amount of unlabeled heterogeneous data. Recently, many efforts of unsupervised learning have been done to effectively capture information from heterogeneous data. However, most of them are with huge time consumption, which obstructs their further application in the big data analytics scenarios, where an enormous amount of heterogeneous data are provided but real-time learning are strongly demanded. In this paper, we address this problem by proposing a fast unsupervised heterogeneous data learning algorithm, namely two-stage unsupervised multiple kernel extreme learning machine (TUMK-ELM). TUMK-ELM alternatively extracts information from multiple sources and learns the heterogeneous data representation with closed-form solutions, which enables its extremely fast speed. As justified by theoretical evidence, TUMK-ELM has low computational complexity at each stage, and the iteration of its two stages can be converged within finite steps. As experimentally demonstrated on 13 real-life data sets, TUMK-ELM gains a large efficiency improvement compared with three state-of-the-art unsupervised heterogeneous data learning methods (up to 140 000 times) while it achieves a comparable performance in terms of effectiveness