10774024
Accurate Classification of Protein Structural Families Using Coherent Subgraph Analysis
Protein structural annotation and classification is an important problem in bioinformatics. We report on the development of an efficient subgraph mining technique and its application to finding characteristic substructural patterns within protein structural families. In our method, protein structures are represented by graphs where the nodes are residues and the edges connect residues found within certain distance from each other. Application of subgraph mining to proteins is challenging for a number reasons: (1) protein graphs are large and complex, (2) current protein databases are large and continue to grow rapidly, and (3) only a small fraction of the frequent subgraphs among the huge pool of all possible subgraphs could be significant in the context of protein classification. To address these challenges, we have developed an information theoretic model called coherent subgraph mining. From information theory, the entropy of a random variable X measures the information content carried by X and the Mutual Information (MI) between two random variables X and Y measures the correlation between X and Y. We define a subgraph X as coherent if it is strongly correlated with every sufficiently large sub-subgraph Y embedded in it. Based on the MI metric, we have designed a search scheme that only reports coherent subgraphs. To determine the significance of coherent protein subgraphs, we have conducted an experimental study in which all coherent subgraphs were identified in several protein structural families annotated in the SCOP database (Murzin et al, 1995). The Support Vector Machine algorithm was used to classify proteins from different families under the binary classification scheme. We find that this approach identifies spatial motifs unique to individual SCOP families and affords excellent discrimination between families.
28890
Extension of Lower Probabilities and Coherence of Belief Measures
Coherence is an important concept which is introduced and discussed in a new mathematics branch, Imprecise Probability Theory. By using the Choquet integral, belief measures can be extended to be coherent lower previsions on the linear space consisting of all bounded functions. As a special case, we establish that all belief measures are coherent imprecise probabilities.
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.
19868872
Management Assistance for Work First via a Dynamic Website
The purpose of the Work First project is to assist the state Dept. of Health and Human Services (DHHS) staff and each county Dept. of Social Services (DSS) across the state in the management of welfare reform initiatives. Work First is the cash assistance program in NC. One important objective is to encourage and support program managers to use data on outcomes to assess their performance. This is accomplished by providing them with easy to use and easy to understand comprehensive information on the experiences of families and individuals that have received assistance through their agency over time.
11841640
Accelerating Profile Queries in Elevation Maps
Elevation maps are a widely used spatial data representation in geographical information systems (GIS). Paths on elevation maps can be characterized by profiles, which describe relative elevation as a function of distance. In this research, we address the inverse of this mapping - given a profile, how to efficiently find paths that could have generated it. This is called the profile query problem. Profiles have a wide variety of uses that include registering tracking information, or even other maps, to a given map. We describe a probabilistic model to characterize the maximal likelihood that a point lying on a path matches the query profile. Propagation of such probabilities to neighboring points can effectively prune the search space. This model enables us to efficiently answer queries of arbitrary profiles with user-specified error tolerances. When compared to existing spatial index methods, our approach supports more flexible queries with orders of magnitude speedup.
9810371
The edge-face choosability of plane graphs
A plane graph G is said to be k-edge-face choosable if, for every list L of colors satisfying |L(x)|=k for every edge and face x, there exists a coloring which assigns to each edge and each face a color from its list so that any adjacent or incident elements receive different colors. We prove that every plane graph G with maximum degree Δ(G) is (Δ(G)+3)-edge-face choosable.
11539721
XParent: an efficient RDBMS-Based XML database system
Presents, XParent, an XML document management system built on top of RDBMS. It is based on an efficient, model-mapping-based approach that uses a fixed database schema to store any XML documents without assistance of DTD. The visual query interface of XParent provides both expressive power for professionals and user friendliness for naive users. The proposed multi-level query translation scheme makes it possible to develop a generic XML application that supports multiple XML query languages and mapping schemas.
15242556
AFOPT: An Efficient Implementation of Pattern Growth Approach
In this paper, we revisit the frequent itemset mining (FIM) problem and focus on studying the pattern growth approach. Existing pattern growth algorithms differ in several dimensions: (1) item search order; (2) conditional database representation; (3) conditional database construction strategy; and (4) tree traversal strategy. They adopted different strategies on these dimensions. Several adaptive algorithms were proposed to try to find good strategies for general situations. In this paper, we described the implementation techniques of an adaptive pattern growth algorithm, called AFOPT, which demonstrated good performance on all tested datasets. We also extended the algorithm to mine closed and maximal frequent itemsets. Comprehensive experiments were conducted to demonstrate the efficiency of the proposed algorithms.
2981606
Distributed Garbage Collection for Mobile Actor Systems: The Pseudo Root Approach
Automatic distributed garbage collection (GC) gives abstraction to grid application development, promoting code quality and improving resource management. Unreachability of active objects or actors from the root set is not a sufficient condition to collect actor garbage, making passive object GC algorithms unsafe when directly used on actor systems. In practical actor languages, all actors have references to the root set since they can interact with users, e.g., through standard input or output streams. Based on this observation, we introduce pseudo roots: a dynamic set of actors that can be viewed as the root set. Pseudo roots use protected (undeletable) references to ensure that no actors are erroneously collected even with messages in transit. Following this idea, we introduce a new direction of actor GC, and demonstrate it by developing a distributed GC framework. The framework can thus be used for automatic life time management of mobile reactive processes with unordered asynchronous communication.
8102164
XR-tree: indexing XML data for efficient structural joins
XML documents are typically queried with a combination of value search and structure search. While querying by values can leverage traditional database technologies, evaluating structural relationship, specifically parent-child or ancestor-descendant relationship, between XML element sets has imposed a great challenge on efficient XML query processing. We propose XR-tree, namely, XML region tree, which is a dynamic external memory index structure specially designed for strictly nested XML data. The unique feature of XR-tree is that, for a given element, all its ancestors (or descendants) in an element set indexed by an XR-tree can be identified with optimal worst case I/O cost. We then propose a new structural join algorithm that can evaluate the structural relationship between two XR-tree indexed element sets by effectively skipping ancestors and descendants that do not participate in the join. Our extensive performance study shows that the XR-tree based join algorithm significantly outperforms previous algorithms.