7865354
Modifying the DPClus algorithm for identifying protein complexes based on new topological structures
BackgroundIdentification of protein complexes is crucial for understanding principles of cellular organization and functions. As the size of protein-protein interaction set increases, a general trend is to represent the interactions as a network and to develop effective algorithms to detect significant complexes in such networks.ResultsBased on the study of known complexes in protein networks, this paper proposes a new topological structure for protein complexes, which is a combination of subgraph diameter (or average vertex distance) and subgraph density. Following the approach of that of the previously proposed clustering algorithm DPClus which expands clusters starting from seeded vertices, we present a clustering algorithm IPCA based on the new topological structure for identifying complexes in large protein interaction networks. The algorithm IPCA is applied to the protein interaction network of Sacchromyces cerevisiae and identifies many well known complexes. Experimental results show that the algorithm IPCA recalls more known complexes than previously proposed clustering algorithms, including DPClus, CFinder, LCMA, MCODE, RNSC and STM.ConclusionThe proposed algorithm based on the new topological structure makes it possible to identify dense subgraphs in protein interaction networks, many of which correspond to known protein complexes. The algorithm is robust to the known high rate of false positives and false negatives in data from high-throughout interaction techniques. The program is available at http://netlab.csu.edu.cn/bioinformatics/limin/IPCA.
8340253
UGE4B: An Universal Grid Environment for Bioinformatics Research
Recent years, grid technology has been used widely in the fields of scientific research. In this paper, we present a universal grid environment for bioinformatics research (UGE4B). Although there have been several similar projects successfully constructed in the world, we need to meet some unique requirements from bioinformatics research in China. UGE4B consists of 6 components, including portal, task management, data management, information server, security and computing node. As a national-wide bioinformatics research platform, UGE4B is built through interconnecting multiple sub grids provided by each bioinformatics institutes. Besides provides a universal portal to end users for bioinformatics computing and data accessing, UGE4B also supported some special bioinformatics applications
8051159
A Web-based Framework For On-line Collaborative Learning
This paper presents a framework for design of online courses and collaborative learning based on Web technologies. It provides the following features: construction of structured learning materials in a distributed environment; personalization of course contents in the run-time that adapts to the progress of individual students; it can supply relevant Web resources to the students by analyzing the learning history dynamically; students in a group could exchange their learning experiences and discover relevant knowledge via the communication channels provided by the framework. The proposed techniques could be deployed to a variety of online computer-assisted modules to improve the effectiveness of Web-based e-learning
26669443
Bottom-up discovery of frequent rooted unordered subtrees
In the past decade, XML has emerged as the standard language for information exchanging over the Internet. Due to its tree-structure paradigm, XML is superior for its capability of storing, querying, and manipulating complex data. Therefore, discovering frequent tree patterns over tree-structured data has become an interesting topic for XML data management. In this paper, we propose a tree mining algorithm, named BUXMiner, for finding a special class of frequent trees, called rooted unordered trees, from a tree-structured database. BUXMiner employs an efficient bottom-up approach to enumerate all candidate trees over a compact global tree guide and computes the frequent trees based on the tree guide. In addition to BUXMiner, we also propose a mining approach called BUMXMiner to discover the maximal frequent rooted unordered trees. We compare BUXMiner with previous tree-structure mining algorithms, namely XQPMinerTID and FastXMiner, which were also proposed to discover rooted unordered trees. The experimental results show that our algorithm outperforms XQPMinerTID and FastXMiner in terms of efficiency. The performance results from real-world applications also indicate the usefulness of our proposed tree mining algorithms in a variety of web applications, such as analysis of web page access patterns and mining frequent XML query patterns for caching.
116588251
On-line evolutionary exponential family mixture
This paper deals with evolutionary clustering, which refers to the problem of clustering data with distribution drifting along time. Starting from a density estimation view to clustering problems, we propose two general on-line frameworks. In the first framework, i.e., historical data dependent (HDD), current model distribution is designed to approximate both current and historical data distributions. In the second framework, i.e., historical model dependent (HMD), current model distribution is designed to approximate both current data distribution and historical model distribution. Both frameworks are based on the general exponential family mixture (EFM) model. As a result, all conventional clustering algorithms based on EFMs can be extended to evolutionary setting under the two frameworks. Empirical results validate the two frameworks.
5747087
Efficient Processing of Warping Time Series Join of Motion Capture Data
Discovering non-trivial matching subsequences from two time series is very useful in synthesizing novel time series. This can be applied to applications such as motion synthesis where smooth and natural motion sequences are often required to be generated from existing motion sequences. We first address this problem by defining it as a problem of l-e-join over two time series. Given two time series, the goal of l-e-join is to find those non-trivial matching subsequences by detecting maximal l-connections from the e-matching matrix of the two time series. Given a querying motion sequence, the l-e-join can be applied to retrieve all connectable motion sequences from a database of motion sequences. To support efficient l-e-join of time series, we propose a two-step filter-and-refine algorithm, called Warping Time Series Join (WTSJ) algorithm. The filtering step serves to prune those sparse regions of the e-matching matrix where there are no maximal l-connections without incurring costly computation. The refinement step serves to detect closed l-connections within regions that cannot be pruned by the filtering step. To speed up the computation of e-matching matrix, we propose a block-based time series summarization method, based on which the block-wise e-matching matrix is first computed. Lots of pairwise distance computation of elements can then be avoided by applying the filtering algorithm on the block-wise e-matching matrix.Extensive experiments on l-e-join of motion capture sequences are conducted. The results confirm the efficiency and effectiveness of our proposed algorithm in processing l-e-join of motion capture time series.
537363
Change propagation algorithm in a unified feature modeling scheme
Product lifecycle stages are inter-related and mutually constraining. Due to the sequential nature of the product development processes, some constraints or conflicts may emerge in a later stage and require modifications to the decisions made in earlier stages. The iterations between stages are hence unavoidable and must be managed carefully to maintain the consistency, integrity and validity of product information models. Due to the inter- or intra-stage relations, a chain of changes is very likely to occur as the consequence of an initial change. Modeling and maintaining these relations are important in collaborative engineering to evolve the state of the whole product model in a consistent manner. This paper introduces a new method of modeling associative engineering relations in a unified feature modeling scheme and elaborates a change propagation algorithm for the information consistency control among multiple applications of product lifecycle stages. The algorithm is established on a JTMS-based dependency network. Two case studies are used to illustrate the proposed dependency network and change propagation algorithm.
14482306
New procedures to identify redundant stuck-at faults and removal of redundant logic
We present new procedures for identifying redundant stuck-at faults including multiple line stuck-at faults on the branches of fan-out stems. The methods proposed include new procedures to identify stuck-at faults that are simultaneously redundant thus allowing simultaneous removal of logic associated with several redundant faults. Experimental results on benchmark as well as industrial circuits are also presented to demonstrate the effectiveness of the proposed methods.
14267344
Design and Development of Small-Size Stiffness Surveying Instrument for Sheet Metal
This paper explored the approach to solve the problems, such as instability of loading force and difficulty in measurement of deformation. A portable and high precision stiffness surveying instrument was developed for measuring the stiffness of large sheet metal. Combined with the mechanism, high accurate force sensor and grating sensor were used to measure the loading-force and the displacement. A special software named Stiffness Test(ST) was developed to process data and calculate the value of stiffness. In the practical test, the results indicate that this instrument is feasible and effective.
1048322
Soundness of Coercion in the Calculus of Constructions
A coercive subtyping system for the Calculus of Constructions is presented. The proposed system λC≤co is obtained essentially by adding coercions and η-conversion to λC≤, which is a subtyping extension to the Calculus of Constructions without coercions. We proved that a coercion c:A ≤ B is semantically sound. That is, (1) c is a term of type A → B; (2) c behaves like an identity function. This development follows the spirit of semantical interpretation of subtyping.
39222179
A New ART Neural Networks for Remote Sensing Image Classification
A new ART2A-C algorithm based on fuzzy operators to cluster the remote sensing images and aerials is proposed in this paper. By combining two ART ANNs with higher performance, the traditional ART2A-C is developed with the fuzzy operators introduced in matching rule. Then the proposed method is applied to the classification and the new network is implemented as well as two other existed ARTs respectively. Experimental results show that the new method outperforms the traditional ones.