12948988
Parallelization of Multiple Genome Alignment
In this work, we implement a genome alignment system which applies parallelization schemes to the ClustalW algorithm and the interface of database querying. Parallel construction of the distance matrices and parallelization of progressive alignment in the ClustalW algorithm are performed on PC-based Linux cluster with message-passing interface libraries. Achieved experiments show good speedup and significant parallel performance.
18159266
A Distributed Simulation-Based Computational Intelligence Algorithm for Nanoscale Semiconductor Device Inverse Problem
In this paper, a distributed simulation-based computational intelligence algorithm for inverse problem of nanoscale semiconductor device is presented. This approach features a simulation-based optimization strategy, and mainly integrates the semiconductor process simulation, semiconductor device simulation, evolutionary strategy, and empirical knowledge on a distributed computing environment. For a set of given target current-voltage (I-V) curves of metal-oxide-semiconductor field effect transistors (MOSFETs) devices, the developed prototype executes evolutionary tasks to solve an inverse doping profile problem, and therefore optimize fabrication recipes. In the evolutionary loop, the established management server allocates the jobs of process simulation and device simulation on a PC-based Linux cluster with message passing interface (MPI) libraries. Good benchmark results including the speed-up, the load balancing, and the parallel efficiency are presented. Computed results, compared with the realistic measured data of 65 nm n-type MOSFET, show the accuracy and robustness of the method.
9693361
Query translation scheme for heterogeneous XML data sources
In order to formulate a meaningful XML query, a user must have some knowledge of the schema of the XML documents to be queried. The query will succeed only if the schema of the actual documents is consistent with the user's information. When a user queries a collection of documents collected from heterogeneous XML data sources, there is a high possibility that these documents do not all conform to the same schema assumed by the user, thus causing the query to fail. In this paper, we try to solve this query and data schema mismatching problem by proposing a query translation scheme. Without attempting to solve the general problem of schema integration, we present an inclusion mapping algorithm that decides how compatible the schema of the query and the schema of the target XML documents are. Based upon the compatibility, the query will be executed directly, or translated according to the target schema and then executed, or rejected.
41020572
Cycle Partitions in Graphs
In this paper, we prove that every graph contains a cycle intersecting all maximum independent sets. Using this, we further prove that every graph with stability number α is spanned by α disjoint cycles. Here, the empty set, the graph of order 1 and the path of order 2 are all considered as degenerate cycles.
6056437
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics
WormBase (http://www.wormbase.org), the model organism database for information about Caenorhabditis elegans and related nematodes, continues to expand in breadth and depth. Over the past year, WormBase has added multiple large-scale datasets including SAGE, interactome, 3D protein structure datasets and NCBI KOGs. To accommodate this growth, the International WormBase Consortium has improved the user interface by adding new features to aid in navigation, visualization of large-scale datasets, advanced searching and data mining. Internally, we have restructured the database models to rationalize the representation of genes and to prepare the system to accept the genome sequences of three additional Caenorhabditis species over the coming year.
27714693
Efficient Parallel Processing for K-Nearest-Neighbor Search in Spatial Databases
Even though the problem of k nearest neighbor (kNN) query is well-studied in serial environment, there is little prior work on parallel kNN search processing in parallel one. In this paper, we present the first Best-First based Parallel kNN (BFPkNN) query algorithm in a multi-disk setting, for efficient handling of kNN retrieval with arbitrary values of k by parallelization. The core of our method is to access more entries from multiple disks simultaneously and enable several effective pruning heuristics to discard non-qualifying entries. Extensive experiments with real and synthetic datasets confirm that BFPkNN significantly outperforms its competitors in both efficiency and scalability.
21308144
EmoEars: An Emotion Recognition System for Mandarin Speech
In this paper, an emotion recognition system for mandarin speech is presented. Five basic human emotions including angry, fear, happy, neutral and sad are investigated. The recognizer is based on neural network with OCON and ACON architecture. Some novel feature selection methods are also added as optional tool to enhance the efficiency and classification accuracy. The system can train speaker dependent emotion speech model through online emotional utterance recording. Experiment results show that emotion can be recognized through neural network model, the best mean accuracy is 86.7%. In addition, the feature selection module is effective to reduce the compute load and increase the generalization ability of the recognizer.