A Synthetic Lethal (SL) interaction is a functional relationship between two genes or functional entities where the loss of either entity is viable but the loss of both is lethal. Such pairs can be used to develop targeted anticancer therapies with fewer side effects and reduced overtreatment. However, finding clinically relevant SL interactions remains challenging. Leveraging unified gene expression data of both disease-free and cancerous samples, we design a new technique based on statistical hypothesis testing, called ASTER, to identify SL pairs. We empirically find that the patterns of mutually exclusivity ASTER finds using genomic and transcriptomic data provides a strong signal of synthetic lethality. For large-scale multiple hypothesis testing, we develop an extension called ASTER++ that can utilize additional input gene features within the hypothesis testing framework. Our computational and functional experiments demonstrate the efficacy of ASTER in identifying SL pairs with potential therapeutic benefits.

Frequent Item set Mining (FIM) is a classic data mining topic with many real world applications such as market basket analysis. Many algorithms including Apriori, FP-Growth, and Eclat were proposed in the FIM field. As the dataset size grows, researchers have proposed MapReduce version of FIM algorithms to meet the big data challenge. This paper proposes new improvements to the MapReduce implementation of FIM algorithm by introducing a cache layer and a selective online analyzer. We have evaluated the effectiveness and efficiency of Smart Cache via extensive experiments on four public datasets. Smart Cache can reduce on average 45.4%, and up to 97.0% of the total execution time compared with the state-of-the-art solution.

Unlike in the consumer electronics and personal computing areas, in the HPC environment hard disks can hardly be replaced by SSDs. The reasons include hard disk's large capacity, very low price, and decent peak throughput. However, when latency dominates the I/O performance (e.g., when accessing random data), the hard disk's performance can be compromised. If the issue of high latency could be effectively solved, the HPC community would enjoy a large, affordable and fast storage without having to replace disks completely with expensive SSDs. In this paper, we propose an almost latency-free hard-disk dominated storage system called LiU for HPC. The key technique is leveraging limited amount of SSD storage for its low-latency access, and changing data layout in a hybrid storage hierarchy with low-latency SSD at the top and high-latency hard disk at the bottom. If a segment of data would be randomly accessed, we lift its top part (the head) up in the hierarchy to the SSD and leave the remaining part (the body) untouched on the disk. As a result, the latency of accessing this whole segment can be removed because access latency of the body can be hidden by the access time of the head on the SSD. Combined with the effect of prefetching a large segment, LiU (Lift it Up) can effectively remove disk access latency so disk's high peak throughput can now be fully exploited for data-intensive HPC applications. We have implemented a prototype of LiU in the PVFS parallel file system and evaluated it with representative MPI-IO micro benchmarks, including mpi-io-test, mpi-tile-io, and ior-mpi-io, and one macro-benchmark BTIO. Our experimental results show that LiU can effectively improve the I/O performance for HPC applications, with the throughput improvement ratio up to 5.8. Furthermore, LiU can bring much more benefits to sequential-I/O MPI applications when the applications are interfered by other workloads. For example, LiU improves the I/O throughput of mpi-io-test, which is under interference, by 1.1-3.4 times, while improving the same workload without interference by 15%.

MapReduce programming model is emerging as an efficient tool for data-intensive applications. Hadoop, an open-source implementation of MapReduce, has been widely adopted and experienced by both academia and enterprise. Recently, lots of efforts have been done on improving the performance of MapReduce system and on analyzing the MapReduce process based on the log files generated during the Hadoop execution. Visualizing log files seems to be a very useful tool to understand the behavior of the Hadoop process. In this paper, we present MR-Scope, a real-time MapReduce tracing tool. MR-Scope provides a real-time insight of the MapReduce process, including the ongoing progress of every task hosted in Task Tracker. In addition, it displays the health of the Hadoop cluster data nodes, the distribution of the file system's blocks and their replicas and the content of the different block splits of the file system. We implement MR-Scope in native Hadoop 0.1. Experimental results demonstrat that MR-Scope's overhead is less than 4% when running wordcount benchmark.