883049
Functional Neighbors: Inferring Relationships between Non-Homologous Protein Families Using Family-Specific Packing Motifs
We describe a new approach for inferring the functional relationships between non-homologous protein families by looking at statistical enrichment of alternative function predictions in classification hierarchies such as Gene Ontology (GO) and Structural Classification of Proteins (SCOP). Protein structures are represented by robust graphs, and the Fast Frequent Subgraph Mining algorithm is applied to protein families to generate sets of family-specific packing motifs, i.e. amino acid residue packing patterns shared by most family members but infrequent in other proteins. The function of a protein is inferred by identifying in it motifs characteristic of a known family. We employ these family-specific motifs to elucidate functional relationships between families in the GO and SCOP hierarchies. Specifically, we postulate that two families are functionally related if one family is statistically enriched by motifs characteristic of another family, i.e. if the number of proteins in a family containing a motif from another family is greater than expected by chance. This function inference method can help annotate proteins of unknown function, establish functional neighbors of existing families, and help specify alternate functions for known proteins.
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.
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.
1764796
Mining Approximate Order Preserving Clusters in the Presence of Noise
Subspace clustering has attracted great attention due to its capability of finding salient patterns in high dimensional data. Order preserving subspace clusters have been proven to be important in high throughput gene expression analysis, since functionally related genes are often co-expressed under a set of experimental conditions. Such co-expression patterns can be represented by consistent orderings of attributes. Existing order preserving cluster models require all objects in a cluster have identical attribute order without deviation. However, real data are noisy due to measurement technology limitation and experimental variability which prohibits these strict models from revealing true clusters corrupted by noise. In this paper, we study the problem of revealing the order preserving clusters in the presence of noise. We propose a noise-tolerant model called approximate order preserving cluster (AOPC). Instead of requiring all objects in a cluster have identical attribute order, we require that (1) at least a certain fraction of the objects have identical attribute order; (2) other objects in the cluster may deviate from the consensus order by up to a certain fraction of attributes. We also propose an algorithm to mine AOPC. Experiments on gene expression data demonstrate the efficiency and effectiveness of our algorithm.
917867
Graph Database Indexing Using Structured Graph Decomposition
We introduce a novel method of indexing graph databases in order to facilitate subgraph isomorphism and similarity queries. The index is comprised of two major data structures. The primary structure is a directed acyclic graph which contains a node for each of the unique, induced subgraphs of the database graphs. The secondary structure is a hash table which cross-indexes each subgraph for fast isomorphic lookup. In order to create a hash key independent of isomorphism, we utilize a code-based canonical representation of adjacency matrices, which we have further refined to improve computation speed. We validate the concept by demonstrating its effectiveness in answering queries for two practical datasets. Our experiments show that for subgraph isomorphism queries, our method outperforms existing methods by more than an order of magnitude.
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
13632117
A Novel Intrusion Detection Method Based on Principle Component Analysis in Computer Security
Intrusion detection is an important technique in the defense-in-depth network security framework and a hot topic in computer security in recent years. In this paper, a new intrusion detection method based on Principle Component Analysis (PCA) with low overhead and high efficiency is presented. System call data and command sequences data are used as information sources to validate the proposed method. The frequencies of individual system calls in a trace and individual commands in a data block are computed and then data column vectors which represent the traces and blocks of the data are formed as data input. PCA is applied to reduce the high dimensional data vectors and distance between a vector and its projection onto the subspace reduced is used for anomaly detection. Experimental results show that the proposed method is promising in terms of detection accuracy, computational expense and implementation for real-time intrusion detection.
7156676
The design and implementation of scalable information services in a grid environment
This paper proposes an Extensible Monitoring and Discovery Service for grid environment MASSIVE (MEMDS). The MASSIVE project focuses on developing a multidisciplinary applications-oriented simulation and visualization environment. In the MEMDS, appropriate mechanisms make custom information services established and deployed easily, and the developed APIs simplify the access to the MDS and provide a uniform interface for programmers. Corresponding practices show that the MEMDS improves the extensibility and flexibility of the grid information service.
6835174
Optimal rate-oriented routing for distributed source coding in wireless sensor network
Recent Advances in Distributed Source Coding (DSC) motivate the mission-driven wireless sensor network application that relates to compression of multiple correlated sensor outputs, such as real time target tracking and environment monitoring. The characteristic of multiple rates in DSC applications requires the associated sensor network to support Rate-Oriented Routing (ROR) in order to extend the network life time. In this paper, we propose a novel optimal Rate-Oriented Routing based on the Distributed Energy Usage Scheduling (DEUS) for mission-driven DSC applications. The ROR adopts a new method called rate assignment instead of the traditional rate adaptation method in wireless networks to extend the network life time. The maximum network lifetime is achieved by constructing multiple rate-oriented paths between the source and sink, which balance the loads and lead to energy-efficient transmissions to meet the DSC application needs. Our simulation has shown that the Rate-Oriented Routing can extend the network life time and save energy significantly under the DSC application requirements
10807505
Refining Web authoritative resource by frequent structures
The Web resource is a rich collection of the dynamic information, which is useful in various disciplines. There has also been much research work related to improving the quality of information searching in the Web. However, most of the work is still inadequate to satisfy a diversified demand from users. In this paper, we exploit the hyperlinks in the Web and propose a new approach called SFP in order to improve the quality of research results obtain from search engines. The SFP algorithm evolves from the frequent pattern mining technique, which is a common data mining technique for conventional databases. The essential idea of our approach is to mine the frequent structures of links from a given Web topology. By using the SFP algorithm, we extract the authoritative pages and communities from the complex Web topology. We demonstrate our approach by running several experiments and show that the performance and functionalities of using the SFP in managing search results are better than other known methods such as HITS.
1043853
Scalable mining of large disk-based graph databases
Mining frequent structural patterns from graph databases is an interesting problem with broad applications. Most of the previous studies focus on pruning unfruitful search subspaces effectively, but few of them address the mining on large, disk-based databases. As many graph databases in applications cannot be held into main memory, scalable mining of large, disk-based graph databases remains a challenging problem. In this paper, we develop an effective index structure, ADI (for <u>ad</u>jacency <u>i</u>ndex), to support mining various graph patterns over large databases that cannot be held into main memory. The index is simple and efficient to build. Moreover, the new index structure can be easily adopted in various existing graph pattern mining algorithms. As an example, we adapt the well-known gSpan algorithm by using the ADI structure. The experimental results show that the new index structure enables the scalable graph pattern mining over large databases. In one set of the experiments, the new disk-based method can mine graph databases with one million graphs, while the original gSpan algorithm can only handle databases of up to 300 thousand graphs. Moreover, our new method is faster than gSpan when both can run in main memory.