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

Measuring the similarity of PML documents with RFID-based sensors

The Electronic Product Code (EPC) Network is an important part of the Internet of Things. The Physical Mark-Up Language (PML) is to represent and de-scribe data related to objects in EPC Network. The PML documents of each component to exchange data in EPC Network system are XML documents based on PML Core schema. For managing theses huge amount of PML documents of tags captured by Radio frequency identification (RFID) readers, it is inevitable to develop the high-performance technol-ogy, such as filtering and integrating these tag data. So in this paper, we propose an approach for meas-uring the similarity of PML documents based on Bayesian Network of several sensors. With respect to the features of PML, while measuring the similarity, we firstly reduce the redundancy data except information of EPC. On the basis of this, the Bayesian Network model derived from the structure of the PML documents being compared is constructed.Comment: International Journal of Ad Hoc and Ubiquitous Computin

Query-Driven Sampling for Collective Entity Resolution

Probabilistic databases play a preeminent role in the processing and management of uncertain data. Recently, many database research efforts have integrated probabilistic models into databases to support tasks such as information extraction and labeling. Many of these efforts are based on batch oriented inference which inhibits a realtime workflow. One important task is entity resolution (ER). ER is the process of determining records (mentions) in a database that correspond to the same real-world entity. Traditional pairwise ER methods can lead to inconsistencies and low accuracy due to localized decisions. Leading ER systems solve this problem by collectively resolving all records using a probabilistic graphical model and Markov chain Monte Carlo (MCMC) inference. However, for large datasets this is an extremely expensive process. One key observation is that, such exhaustive ER process incurs a huge up-front cost, which is wasteful in practice because most users are interested in only a small subset of entities. In this paper, we advocate pay-as-you-go entity resolution by developing a number of query-driven collective ER techniques. We introduce two classes of SQL queries that involve ER operators --- selection-driven ER and join-driven ER. We implement novel variations of the MCMC Metropolis Hastings algorithm to generate biased samples and selectivity-based scheduling algorithms to support the two classes of ER queries. Finally, we show that query-driven ER algorithms can converge and return results within minutes over a database populated with the extraction from a newswire dataset containing 71 million mentions

Saber: window-based hybrid stream processing for heterogeneous architectures

Modern servers have become heterogeneous, often combining multicore CPUs with many-core GPGPUs. Such heterogeneous architectures have the potential to improve the performance of data-intensive stream processing applications, but they are not supported by current relational stream processing engines. For an engine to exploit a heterogeneous architecture, it must execute streaming SQL queries with sufficient data-parallelism to fully utilise all available heterogeneous processors, and decide how to use each in the most effective way. It must do this while respecting the semantics of streaming SQL queries, in particular with regard to window handling. We describe SABER, a hybrid high-performance relational stream processing engine for CPUs and GPGPUs. SABER executes windowbased streaming SQL queries in a data-parallel fashion using all available CPU and GPGPU cores. Instead of statically assigning query operators to heterogeneous processors, SABER employs a new adaptive heterogeneous lookahead scheduling strategy, which increases the share of queries executing on the processor that yields the highest performance. To hide data movement costs, SABER pipelines the transfer of stream data between different memory types and the CPU/GPGPU. Our experimental comparison against state-ofthe-art engines shows that SABER increases processing throughput while maintaining low latency for a wide range of streaming SQL queries with small and large windows sizes