13324501
Local Structure Comparison of Proteins
Abstract Protein local structure comparison aims to recognize structural similarities between parts of proteins. It is an active topic in bioinformatics research, integrating computer science concepts in computational geometry and graph theory with empirical observations and physical principles from biochemistry. It has important biological applications, including protein function prediction. In this chapter, we provide an introduction to the protein local structure comparison problem including challenges and applications. Current approaches to the problem are reviewed. Particular consideration is given to the discovery of local structure common to a group of related proteins. We present a new algorithm for this problem that uses a graph-based representation of protein structure and finds recurring subgraphs among a group of protein graphs.
62615149
Mining Asynchronous Periodic Patterns in Time Series Data
Periodicy detection in time series data is a challenging problem of great importance in many applications. Most previous work focused on mining synchronous periodic patterns and did not recognize the misaligned presence of a pattern due to the intervention of random noise. In this paper, we propose a more flexible model of asynchronous periodic pattern that may be present only within a subsequence and whose occurrences may be shifted due to disturbance. Two parameters min/spl I.bar/rep and max/spl I.bar/dis are employed to specify the minimum number of repetitions that is required within each segment of nondisrupted pattern occurrences and the maximum allowed disturbance between any two successive valid segments. Upon satisfying these two requirements, the longest valid subsequence of a pattern is returned. A two-phase algorithm is devised to first generate potential periods by distance-based pruning followed by an iterative procedure to derive and validate candidate patterns and locate the longest valid subsequence. We also show that this algorithm cannot only provide linear time complexity with respect to the length of the sequence but also achieve space efficiency.
14969897
Dynamic adaptive file management in a local area network
In light of advances in processor and networking technology, especially the emergence of network attached disks, the traditional client-server architecture of file systems has become suboptimal for many computation/data intensive applications. We introduce a revised architecture for file management employing network attached storage: the dynamic file server environment (Dynamo). Dynamo introduces two main architectural innovations: to provide high scalability, the file management functions are mainly performed cooperatively by the clients in the system. Furthermore, data is transferred directly to the client's cache from network-attached disks, thus avoiding copies from a disk to the server buffer and then over the network to the client. Secondly, Dynamo uses a cooperative cache management which employs a decentralized lottery-based page replacement strategy. We show via performance benchmarks run on the Dynamo system and simulation results how this architecture increases the system's adaptability, scalability and cost performance.
5788516
Efficient genome ancestry inference in complex pedigrees with inbreeding
Motivation: High-density SNP data of model animal resources provides opportunities for fine-resolution genetic variation studies. These genetic resources are generated through a variety of breeding schemes that involve multiple generations of matings derived from a set of founder animals. In this article, we investigate the problem of inferring the most probable ancestry of resulting genotypes, given a set of founder genotypes. Due to computational difficulty, existing methods either handle only small pedigree data or disregard the pedigree structure. However, large pedigrees of model animal resources often contain repetitive substructures that can be utilized in accelerating computation. Results: We present an accurate and efficient method that can accept complex pedigrees with inbreeding in inferring genome ancestry. Inbreeding is a commonly used process in generating genetically diverse and reproducible animals. It is often carried out for many generations and can account for most of the computational complexity in real-world model animal pedigrees. Our method builds a hidden Markov model that derives the ancestry probabilities through inbreeding process without explicit modeling in every generation. The ancestry inference is accurate and fast, independent of the number of generations, for model animal resources such as the Collaborative Cross (CC). Experiments on both simulated and real CC data demonstrate that our method offers comparable accuracy to those methods that build an explicit model of the entire pedigree, but much better scalability with respect to the pedigree size. Contact: weiwang@cs.unc.edu
2548187
Mining asynchronous periodic patterns in time series data
Periodicy detection in time series data is a challenging problem of great importance in many applications. Most previous work focused on mining synchronous periodic patterns and did not recognize the misaligned presence of a pattern due to the intervention of random noise. In this paper, we propose a more flexible model of asynchronous periodic pattern that may be present only within a subsequence and whose occurrences may be shifted due to disturbance. Two parameters min rep and max dis are employed to specify the minimum number of repetitions that is required within each segment of nondisrupted pattern occurrences and the maximum allowed disturbance between any two successive valid segments. Upon satisfying these two requirements, the longest valid subsequence of a pattern is returned. A two-phase algorithm is devised to first generate potential periods by distance-based pruning followed by an iterative procedure to derive and validate candidate patterns and locate the longest valid subsequence. We also show that this algorithm cannot only provide linear time complexity with respect to the length of the sequence but also achieve space
7408751
Quantitative Association Analysis Using Tree Hierarchies
Association analysis arises in many important applications such as bioinformatics and business intelligence. Given a large collection of measurements over a set of samples, association analysis aims to find dependencies of target variables to subsets of measurements. Most previous algorithms adopt a two-stage approach; they first group samples based on the similarity in the subset of measurements, and then they examine the association between these groups and the specified target variables without considering the inter-group similarities or alternative groupings. This can lead to cases where the strength of association depends significantly on arbitrary clustering choices. In this paper, we propose a tree-based method for quantitative association analysis. Tree hierarchies derived from sample similarities represent many possible sample groupings. They also provide a natural way to incorporate domain knowledge such as ontologies and to identify and remove outliers. Given a tree hierarchy, our association analysis evaluates all possible groupings and selects the one with strongest association to the target variable. We introduce an efficient algorithm, TreeQA, to systematically explore the search-space of all possible groupings in a set of input trees, with integrated permutation tests. Experimental results show that TreeQA is able to handlelarge-scale association analysis very efficiently and is more effective and robust in association analysis than previous methods.
16209599
Extend SRML schema based on DEVS: an executable DEVS language
This paper analyzes the significance of the representation and reusability of SRML when being used in simulation models as well as its drawbacks. The paper also discusses the ways to extend SRML schema based on DEVS. The emphasis is placed on the elaboration of mapping DEVS onto SRML schema to formulate SRML's basic syntax and semantics for the structure and behavior representation of atomic model and coupled model. The model structure, such as property, input interface, output interface and sub-model composition, are described by a group of XML marks. The model behavior, such as external transition, internal transition, output and time-advance functions are described by script language and a group of standard interface offered by SRML simulator in script marks. The paper then reviews the SRML element architecture and finally gives a simulation demo of using SRML to build differential equation model.
15939515
GraphMiner: a structural pattern-mining system for large disk-based graph databases and its applications
Mining frequent structural patterns from graph databases is an important research problem with broad applications. Recently, we developed an effective index structure, ADI, and efficient algorithms for mining frequent patterns from large, disk-based graph databases [5], as well as constraint-based mining techniques. The techniques have been integrated into a research prototype system--- GraphMiner. In this paper, we describe a demo of GraphMiner which showcases the technical details of the index structure and the mining algorithms including their efficient implementation, the mining performance and the comparison with some state-of-the-art methods, the constraint-based graph-pattern mining techniques and the procedure of constrained graph mining, as well as mining real data sets in novel applications.
18533711
A New Approach for Detecting Anonymity of Patterns
Information sharing becomes more frequently and easily than before. However, it also brings serious threats towards individual's privacy. It is no doubt that sharing personal data can cause privacy breaches. Moreover, sharing the knowledge discovered by data mining may also pose threats to personal privacy. In this paper, we consider the anonymity of patterns derived from the result of frequent itemset mining. A new projection-based approach for detecting anonymity of patterns is presented. We prove that the approach can detect all the maximal inference channels for non-k-anonymous patterns. The experimental results show that our approach is more efficient than previous work especially when the number of closed frequent itemsets in the mining result is close to or larger than the number of transactions in a database.
5421333
Modulo deflation in (2n+1, 2n, 2n-1) converters
In this paper, a new modulo reduction theorem is introduced to decompose the base of the modulo operation. As one of possible applications, this new theorem can be used to further reduce the modulo size of the modified Chinese remainder theorem (CRT). Based on this new theorem, an improved modulo size reduced CRT algorithm for M={2 n +1, 2, 2 n -1} is presented. For the most popular three-moduli set M, the design and FPGA implementation show that the proposed modulo part of the residue-to-binary(R/B) converter is almost twice faster and needs 50% less hardware and power than the modulo operation of the two converters previously published in the literature.
5733267
KemaDom: a web server for domain prediction using kernel machine with local context
Predicting domains of proteins is an important and challenging problem in computational biology because of its significant role in understanding the complexity of proteomes. Although many template-based prediction servers have been developed, ab initio methods should be designed and further improved to be the complementarity of the template-based methods. In this paper, we present a novel domain prediction system KemaDom by ensembling three kernel machines with the local context information among neighboring amino acids. KemaDom, an alternative ab initio predictor, can achieve high performance in predicting the number of domains in proteins. It is freely accessible at and .