2891290
Sequence-driven features for prediction of subcellular localization of proteins
Prediction of the cellular location of a protein plays an important role in inferring the function of the protein. Feature extraction is a critical part in prediction systems, requiring raw sequence data to be transformed into appropriate numerical feature vectors while minimizing information loss. In this paper, we present a method for extracting useful features from protein sequence data. The method employs local and global pairwise sequence alignment scores as well as composition-based features. Five different features are used for training support vector machines (SVMs) separately and a weighted majority voting makes a final decision. The overall prediction accuracy evaluated by the 5-fold cross-validation reached 88.53% for the eukaryotic animal data set. Comparing the prediction accuracy of various feature extraction methods, provides a biological insight into the location of targeting information. Our experimental results confirm that our feature extraction methods are very useful for predicting subcellular localization of proteins.
16441621
Tree-Dependent Components of Gene Expression Data for Clustering
Tree-dependent component analysis (TCA) is a generalization of independent component analysis (ICA), the goal of which is to model the multivariate data by a linear transformation of latent variables, while latent variables fit by a tree-structured graphical model. In contrast to ICA, TCA allows dependent structure of latent variables and also consider non-spanning trees (forests). In this paper, we present a TCA-based method of clustering gene expression data. Empirical study with yeast cell cycle-related data, yeast metabolic shift data, and yeast sporulation data; shows that TCA is more suitable for gene clustering, compared to principal component analysis (PCA) as well as ICA.
6065142
On effective data clustering in bitemporal databases
Temporal databases provide built-in supports for efficient recording and querying of time-evolving data. In this paper, data clustering issues in temporal database environment are addressed. Data clustering is one of the most effective techniques that can improve performance of a database system. However, data clustering methods for conventional databases do not perform well in temporal databases because there exist crucial differences between their query patterns. We propose a data clustering measure, called Temporal Affinity, that can be used for the clustering of temporal data. The temporal affinity, which is based on the analysis of query patterns in temporal databases, reflects the closeness of temporal data objects in viewpoints of temporal query processing. We perform experiments to evaluate the proposed measure. The experimental results show that a data clustering method with the temporal affinity works better than other methods.
15935373
Random Matchings Which Induce Hamilton Cycles and Hamiltonian Decompositions of Random Regular Graphs
Select four perfect matchings of 2n vertices, independently at random. We find the asymptotic probability that each of the first and second matchings forms a Hamilton cycle with each of the third and fourth. This is generalised to embrace any fixed number of perfect matchings, where a prescribed set of pairs of matchings must each produce Hamilton cycles (with suitable restrictions on the prescribed set of pairs). We also show how the result with four matchings implies that a random d-regular graph for fixed even d?4 asymptotically almost surely decomposes into d/2 Hamilton cycles. This completes a general result on the edge-decomposition of a random regular graph into regular spanning subgraphs of given degrees together with Hamilton cycles and verifies conjectures of Janson and of Robinson and Wormald.
64537980
Design and analysis of an NoC architecture from performance, reliability and energy perspective
35659095
Asynchronous Genetic Algorithms on Parallel Computers
3492450
A framework for data prefetching using off-line training of Markovian predictors
An important technique for alleviating the memory bottleneck is data prefetching. Data prefetching solutions ranging from pure software approach by inserting prefetch instructions through program analysis to purely hardware mechanisms have been proposed. The degrees of success of those techniques are dependent on the nature of the applications. The need for innovative approach is rapidly growing with the introduction of applications such as object-oriented applications that show dynamically changing memory access behavior In this paper, we propose a novel framework for the use of data prefetchers that are trained off-line using smart learning algorithms to produce prediction models which captures hidden memory access patterns. Once built, those prediction models are loaded into a data prefetching unit in the CPU at the appropriate point during the runtime to drive the prefetching. On average by using table size of about 8KB size, we were able to achieve prediction accuracy of about 68% through our own proposed learning method and performance was boosted about 37% on average on the benchmarks we tested. Furthermore, we believe our proposed framework is amenable to other predictors and can be done as a phase of the profiling-optimizing-compiler.