5664354
Association analysis with one scan of databases
Mining frequent patterns with an FP-tree avoids costly candidate generation and repeatedly occurrence frequency checking against the support threshold. It therefore achieves better performance and efficiency than Apriori-like algorithms. However the database still needs to be scanned twice to get the FP-tree. This can be very time-consuming when new data are added to an existing database because two scans may be needed for not only the new data but also the existing data. This paper presents a new data structure P-tree, Pattern Tree, and a new technique, which can get the P-tree through only one scan of the database and can obtain the corresponding FP-tree with a specified support threshold. Updating a P-tree with new data needs one scan of the new data only, and the existing data do not need to be re-scanned.
18616381
The Cost of Transparency: Grid-Based File Access on the Avaki Data Grid
Grid computing has been a hot topic for a decade. Several systems have been developed. Despite almost a decade of research and tens of millions of dollars spent, uptake of grid technology has been slow. Most deployed grids are based on a toolkit approach that requires significant software modification or development. An operating system technique used for over 30 years has been to reduce application complexity by providing transparency, e.g. file systems mask details of devices, virtual machines mask finite memory, etc. It has been argued that providing transparency in a grid environment is too costly in terms of performance. This paper examines that question in the context of data grids by measuring the performance of a commercially available data grid product – the Avaki Data Grid (ADG). We present the architecture of the ADG, describe our experimental setup, and provide performance results, comparing the ADG to a native NFS V3 implementation for both local and wide area access cases. The results were mixed, though encouraging. For single client local file operations, native NFS outperformed the ADG by 15% to 45% for smaller files, though for files larger than 32 MB ADG outperformed native NFS.
10305231
The Protein Information Resource: an integrated public resource of functional annotation of proteins
The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. The PIR, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the PIR-International Protein Sequence Database (PSD), the major annotated protein sequence database in the public domain, containing about 250 000 proteins. To improve protein annotation and the coverage of experimentally validated data, a bibliography submission system is developed for scientists to submit, categorize and retrieve literature information. Comprehensive protein information is available from iProClass, which includes family classification at the superfamily, domain and motif levels, structural and functional features of proteins, as well as cross-references to over 40 biological databases. To provide timely and comprehensive protein data with source attribution, we have introduced a non-redundant reference protein database, PIR-NREF. The database consists of about 800 000 proteins collected from PIR-PSD, SWISS-PROT, TrEMBL, GenPept, RefSeq and PDB, with composite protein names and literature data. To promote database interoperability, we provide XML data distribution and open database schema, and adopt common ontologies. The PIR web site (http://pir.georgetown.edu/) features data mining and sequence analysis tools for information retrieval and functional identification of proteins based on both sequence and annotation information. The PIR databases and other files are also available by FTP (ftp://nbrfa.georgetown.edu/pir_databases).
14288907
RgS-Miner: A Biological Data Warehousing, Analyzing and Mining System for Identifying Transcriptional Regulatory Sites in Human Genome
Recently, biological databases and analytical methods have become available for analyzing gene expression and transcriptional regulatory sequences. However, users must make the complicated analyses to query the data in various databases, and then they must analyze the gene upstreams using various predictive tools, before finally converting date among formats. Beyond methods for predicting transcriptional regulatory sites, new automated and integrated methods for analyzing gene upstream sequences on a higher level are urgently required. Efficient and integrated data management methods are essential, too. We present an integrated system, namely RgS-Miner, to predict transcriptional regulatory sites and detect co-occurrence of these regulatory sites. RgS-Miner comprises a biological data warehousing system, pattern discovery programs, pattern occurrence association detectors and user interfaces. The system is available at http://rgsminer.csie.ncu.edu.tw/.
197229
The PIR integrated protein databases and data retrieval system
The Protein Information Resource (PIR) provides many databases and tools to support genomic and proteomic research. PIR is a member of UniProt—Universal Protein Resource—the central repository of protein sequence and function, which maintains UniProt Knowledgebase with extensively curated annotation, UniProt Reference databases to speed sequence searches, and UniProt Archive to reflect sequence history. PIR also provides PIRSF family classification system based on evolutionary relationships of full-length proteins, and iProClass integrated database of protein family, function, and structure. These databases are easily accessible from PIR web site using a centralized data retrieval system for information retrieval and knowledge discovery.
7392928
Finding short DNA motifs using permuted markov models
Many short DNA motifs such as transcription factor binding sites (TFBS) and splice sites exhibit strong local as well as non-local dependence. We introduce permuted variable length Markov models (PVLMM) which could capture the potentially important dependencies among positions, and apply them to the problem of detecting splice and TFB sites. They have been satisfactory from the viewpoint of prediction performance, and also give ready biological interpretations of the sequence dependence observed. The issue of model selection is also studied.
11189498
On the spanning connectivity of graphs
Abstract A k-container C ( u , v ) of G between u and v is a set of k internally disjoint paths between u and v . A k -container C ( u , v ) of G is a k * - container if it contains all vertices of G . A graph G is k * - connected if there exists a k * -container between any two distinct vertices. The spanning connectivity of G , κ * ( G ) , is defined to be the largest integer k such that G is w * -connected for all 1 ⩽ w ⩽ k if G is a 1 * -connected graph. In this paper, we prove that κ * ( G ) ⩾ 2 δ ( G ) - n ( G ) + 2 if ( n ( G ) / 2 ) + 1 ⩽ δ ( G ) ⩽ n ( G ) - 2 . Furthermore, we prove that κ * ( G - T ) ⩾ 2 δ ( G ) - n ( G ) + 2 - | T | if T is a vertex subset with | T | ⩽ 2 δ ( G ) - n ( G ) - 1 .