A highly efficient multi-core algorithm for clustering extremely large datasets

<p>Abstract</p> <p>Background</p> <p>In recent years, the demand for computational power in computational biology has increased due to rapidly growing data sets from microarray and other high-throughput technologies. This demand is likely to increase. Standard algorithms for analyzing data, such as cluster algorithms, need to be parallelized for fast processing. Unfortunately, most approaches for parallelizing algorithms largely rely on network communication protocols connecting and requiring multiple computers. One answer to this problem is to utilize the intrinsic capabilities in current multi-core hardware to distribute the tasks among the different cores of one computer.</p> <p>Results</p> <p>We introduce a multi-core parallelization of the k-means and k-modes cluster algorithms based on the design principles of transactional memory for clustering gene expression microarray type data and categorial SNP data. Our new shared memory parallel algorithms show to be highly efficient. We demonstrate their computational power and show their utility in cluster stability and sensitivity analysis employing repeated runs with slightly changed parameters. Computation speed of our Java based algorithm was increased by a factor of 10 for large data sets while preserving computational accuracy compared to single-core implementations and a recently published network based parallelization.</p> <p>Conclusions</p> <p>Most desktop computers and even notebooks provide at least dual-core processors. Our multi-core algorithms show that using modern algorithmic concepts, parallelization makes it possible to perform even such laborious tasks as cluster sensitivity and cluster number estimation on the laboratory computer.</p

Transactional Lock-Free Execution of Lock-Based Programs

This paper is motivated by the difficulty in writing correct high-performance programs. Writing shared-memory multithreaded programs imposes a complex trade-off between programming ease and performance, largely due to subtleties in coordinating access to shared data. To ensure correctness programmers often rely on conservative locking at the expense of performance. The resulting serialization of threads is a performance bottleneck. Locks also interact poorly with thread scheduling and faults, resulting in poor system performance

Uterine prolapse prevention in Eastern Nepal: the perspectives of women and health care professionals

Christina M Rad,l Ranjita Rajwar, Arja R AroUniversity of Southern Denmark, Esbjerg, DenmarkAbstract: Uterine prolapse is a major reproductive health issue in Nepal. There is a wide range of literature available on the causes and risk factors of uterine prolapse and on the ways to prevent and treat it. There is still a lack of published evidence on what prevention and treatment services are working well or the attitudes toward them. This paper presents the findings of a qualitative study on primary and secondary prevention of uterine prolapse in Eastern Nepal.Method: The study involved eight focus group discussions with 71 women in six villages of the eastern districts of Siraha and Saptari and 14 qualitative interviews with health professionals from the local to central level. The group discussions and interviews covered the awareness levels of uterine prolapse and its prevention and treatment, as well as participants&amp;#39; opinions on and experiences with the services offered.Results: It was found that patriarchy, gender discrimination, and cultural traditions such as early marriage and pregnancy make it difficult for people to discontinue uterine prolapse risk behaviors. Women are aware of risk factors, prevention, and treatment, but are powerless to change their situations. Health professionals and women are fond of surgery as treatment, but opinions on the use of ring pessaries and pelvic floor muscle training are split.Conclusion: The main recommendation that can be drawn from this study is that research on the effectiveness of early treatments, such as ring pessaries and exercise, should be conducted. Furthermore, the involvement of other target groups (husbands, adolescents, and mothers-in-law) needs to be increased in order to make it easier for women to adapt low-risk behaviors. Finally, uterine prolapse prevention should be better integrated in national reproductive health services. Enforcing transparency, monitoring systems, and collaborations are important factors that should be considered as well.Keywords: uterine prolapse, primary prevention, secondary prevention, awareness, Nepa

Using Speculative Push for Unnecessary Checkpoint Creation Avoidance

Abstract. This paper discusses a way of incorporating speculation techniques into Distributed Shared Memory (DSM) systems with checkpointing mechanism without creating unnecessary checkpoints. Speculation is a general technique involving prediction of the future of a computation, namely accesses to shared objects unavailable on the accessing node (read faults). Thanks to such predictions objects can be pushed to requesting nodes before the actual access operation is performed, resulting, at least potentially, in a considerable performance improvement. This mechanism is a foundation for the proposed SpecCkpt protocol based on independent checkpointing integrated with a coherence protocol for a given consistency model introducing little overhead. It ensures the consistency of checkpoints, at the same time allowing a fast recovery from failures.