71,971 research outputs found
gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution
One of the important questions in biological evolution is to know if certain
changes along protein coding genes have contributed to the adaptation of
species. This problem is known to be biologically complex and computationally
very expensive. It, therefore, requires efficient Grid or cluster solutions to
overcome the computational challenge. We have developed a Grid-enabled tool
(gcodeml) that relies on the PAML (codeml) package to help analyse large
phylogenetic datasets on both Grids and computational clusters. Although we
report on results for gcodeml, our approach is applicable and customisable to
related problems in biology or other scientific domains.Comment: 10 pages, 4 figures. To appear in the HealthGrid 2012 con
On a Catalogue of Metrics for Evaluating Commercial Cloud Services
Given the continually increasing amount of commercial Cloud services in the
market, evaluation of different services plays a significant role in
cost-benefit analysis or decision making for choosing Cloud Computing. In
particular, employing suitable metrics is essential in evaluation
implementations. However, to the best of our knowledge, there is not any
systematic discussion about metrics for evaluating Cloud services. By using the
method of Systematic Literature Review (SLR), we have collected the de facto
metrics adopted in the existing Cloud services evaluation work. The collected
metrics were arranged following different Cloud service features to be
evaluated, which essentially constructed an evaluation metrics catalogue, as
shown in this paper. This metrics catalogue can be used to facilitate the
future practice and research in the area of Cloud services evaluation.
Moreover, considering metrics selection is a prerequisite of benchmark
selection in evaluation implementations, this work also supplements the
existing research in benchmarking the commercial Cloud services.Comment: 10 pages, Proceedings of the 13th ACM/IEEE International Conference
on Grid Computing (Grid 2012), pp. 164-173, Beijing, China, September 20-23,
201
Visual and computational analysis of structure-activity relationships in high-throughput screening data
Novel analytic methods are required to assimilate the large volumes of structural and bioassay data generated by combinatorial chemistry and high-throughput screening programmes in the pharmaceutical and agrochemical industries. This paper reviews recent work in visualisation and data mining that can be used to develop structure-activity relationships from such chemical/biological datasets
Efficient resources assignment schemes for clustered multithreaded processors
New feature sizes provide larger number of transistors per chip that architects could use in order to further exploit instruction level parallelism. However, these technologies bring also new challenges that complicate conventional monolithic processor designs. On the one hand, exploiting instruction level parallelism is leading us to diminishing returns and therefore exploiting other sources of parallelism like thread level parallelism is needed in order to keep raising performance with a reasonable hardware complexity. On the other hand, clustering architectures have been widely studied in order to reduce the inherent complexity of current monolithic processors. This paper studies the synergies and trade-offs between two concepts, clustering and simultaneous multithreading (SMT), in order to understand the reasons why conventional SMT resource assignment schemes are not so effective in clustered processors. These trade-offs are used to propose a novel resource assignment scheme that gets and average speed up of 17.6% versus Icount improving fairness in 24%.Peer ReviewedPostprint (published version
Thirty Years of Machine Learning: The Road to Pareto-Optimal Wireless Networks
Future wireless networks have a substantial potential in terms of supporting
a broad range of complex compelling applications both in military and civilian
fields, where the users are able to enjoy high-rate, low-latency, low-cost and
reliable information services. Achieving this ambitious goal requires new radio
techniques for adaptive learning and intelligent decision making because of the
complex heterogeneous nature of the network structures and wireless services.
Machine learning (ML) algorithms have great success in supporting big data
analytics, efficient parameter estimation and interactive decision making.
Hence, in this article, we review the thirty-year history of ML by elaborating
on supervised learning, unsupervised learning, reinforcement learning and deep
learning. Furthermore, we investigate their employment in the compelling
applications of wireless networks, including heterogeneous networks (HetNets),
cognitive radios (CR), Internet of things (IoT), machine to machine networks
(M2M), and so on. This article aims for assisting the readers in clarifying the
motivation and methodology of the various ML algorithms, so as to invoke them
for hitherto unexplored services as well as scenarios of future wireless
networks.Comment: 46 pages, 22 fig
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