17656600
BIOKDD 2005 workshop report
Bioinformatics is the science of managing, mining, and interpreting information from biological entities. Genome sequencing projects have contributed to an exponential growth in complete and partial sequence databases. The structural genomics initiative aims to catalog the structure-function information for proteins. Advances in technology such as microarrays have launched the subfield of genomics and proteomics to study the genes, proteins, and the regulatory gene expression circuitry inside the cell. What characterizes the state of the field is the flood of data that exists today or that is anticipated in the future; data that needs to be mined to help unlock the secrets of the cell. Knowledge extracted from such analysis can be used effectively to better design new drugs, offer better medical care via diagnostic tests that combine information from multiple sources, and improve scientific and clinical practice.
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.
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.
8292023
Fuzzy Multi-Dimensional Search in the Wayfinder File System
With the explosion in the amount of semi-structured data users access and store, there is a need for complex search tools to retrieve often very heterogeneous data in a simple and efficient way. Existing tools usually index text content, allowing for some IR-style ranking on the textual part of the query, but only consider structure (e.g., file directory) and metadata (e.g., date, file type) as filtering conditions. We propose a novel multidimensional querying approach to semi-structured data searches in personal information systems by allowing users to provide fuzzy structure and metadata conditions in addition to traditional keyword conditions. The provided query interface is more comprehensive than content-only searches as it considers three query dimensions (content, structure, metadata) in the search. We have implemented our proposed approach in the Wayfinder file system. In this demo, we will use this implementation to both present an overview of the unified scoring framework underlying the fuzzy multi-dimensional querying approach and demonstrate its potential in improving search results.
6043120
Optimal Image Component Transmissions in Multirate Wireless Sensor Networks
In image transmission applications over wireless sensor networks (WSN), energy efficiency and image quality are both important factors for joint optimization. In this paper, we propose a new position-value (P-V) oriented cross layer optimization approach to minimize energy consumption with distortion bounds for image transmission applications in WSN, by exploring importance level diversity for position-magnitude information. To put more effort on transmitting important position information and relatively less effort on unimportant magnitude information, desirable BER, ARQ retry limit, transmission rate and distortion reduction of image are jointly optimized cross PHY, MAC and APP layers, and image quality is assured while energy consumption is minimized. Simulation results demonstrate the effectiveness of the proposed approach in achieving energy efficiency while maintaining image quality.
15366915
PictureBook: A Text-and-Image Summary System for Web Search Result
Search engine technology plays an important role in Web information retrieval. However, with Internet information explosion, traditional searching techniques cannot provide satisfactory result due to problems such as huge number of result Web pages, unintuitive ranking, etc. Therefore, the reorganization and post-processing of Web search results have been extensively studied to help user effectively obtain useful information. Previous studies mainly focused on Web page clustering, document summary, visualization of search results, etc, which are applied separately to either text or image search. In this paper, we propose a demo to illustrate a new Web search result summary system - PictureBook, which combines text and image retrieval using techniques of multiple document summarization and image semantics analysis. Particularly, audience can interactively investigate the effect of the combined text and image summary in Web information searching and knowledge acquisition. We also introduce our new image semantic analysis method based on generalized discriminant analysis (GDA).
1916291
A Novel Anonymous Communication Strategy with Respect to Payment Mechanism
Anonymous communication systems are vulnerable to free-riders who use the systems while provide little or no service to other users in the systems. An anonymous communication strategy is proposed to promote and encourage participants to provide service to the systems. We analyze the number of coins that a sender uses to pay for the peers on its anonymous route, and propose a new measure in the payment mechanism that is suitable to a next-hop anonymous system. Theoretical analysis shows that the system with the new payment mechanism promotes anonymous communication effectively while it keeps the system performance comparable to the existing anonymous systems such as Crowds. Moreover, the new system avoids the drawback of existing anonymous systems that enforces no upper bound on the length of anonymous routes.
1107425
Information Coverage in Randomly Deployed Wireless Sensor Networks
Coverage is an important issue in wireless sensor networks. The most commonly used coverage model in the literature defines a point to be covered if its Euclidian distance to at least one sensor is less than a fixed threshold. This is a conservative definition of coverage which implicitly assumes that each sensor makes a decision independent of other sensors in the field. Sensors can cooperate to make an accurate estimation, even if any single sensor is unable to do so. We have previously proposed a new notion of information coverage and investigated its properties. In this paper, we study sensor density requirements for complete information coverage of a field with random sensor deployment. We provide an upper bound on the probability that an arbitrary point in a randomly deployed sensor field is not information covered and find the relationship between the sensor density and the average field vacancy. Simulation results validate our theoretical analysis and show that significant savings in terms of sensor density for complete coverage can be achieved with information coverage.