573449
Recent progress on selected topics in database research — A report by nine young Chinese researchers working in the United States
The study on database technologies, or more generally, the technologies of data and information management, is an important and active research field. Recently, many exciting results have been reported. In this fast growing field, Chinese researchers play more and more active roles. Research papers from Chinese scholars, both in China and abroad, appear in prestigious academic forums.In this paper, we, nine young Chinese researchers working in the United States, present concise surveys and report our recent progress on the selected fields that we are working on. Although the paper covers only a small number of topics and the selection of the topics is far from balanced, we hope that such an effort would attract more and more researchers, especially those in China, to enter the frontiers of database research and promote collaborations. For the obvious reason, the authors are listed alphabetically, while the sections are arranged in the order of the author list.
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
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.
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.
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.
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 .
16609668
Throughput vs. Distance Tradeoffs and Deployment Considerations for a Multi-Hop IEEE 802.16e Railroad Test Bed
Throughput vs. distance analysis and coverage requirements are critical issues in planning wireless network deployments. With the recent availability of IEEE 802.16e and its promise of larger coverage areas for high-speed data communication, evaluating it in a real-world environment is very important to us in our ongoing study of standards based wireless technologies for the Federal Railroad Administration (FRA). In this paper, we present results obtained with our IEEE 802.16e module for NS-2, particularly throughput vs. distance performance, and its consideration for designing a real-world multi-hop IEEE 802.16e testbed. Firstly, a quantitative analysis of throughput vs. distance performance is conducted via extensive simulation, and the optimal modulation and coding scheme as well as channel bandwidth profiles are identified for specific distances. Secondly, we present a real-world multi-hop IEEE 802.16e testbed design intended for installation along BNSF Railway track in Nebraska. We apply our findings towards selecting various base station deployment locations and their appropriate communications parameters in order achieve best possible multi-hop throughput performance. We also provide a client access coverage analysis for the various locations.
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.
876538
Dependent link padding algorithms for low latency anonymity systems
Low latency anonymity systems are susceptive to traffic analysis attacks. In this paper, we propose a dependent link padding scheme to protect anonymity systems from traffic analysis attacks while providing a strict delay bound. The covering traffic generated by our scheme uses the minimum sending rate to provide full anonymity for a given set of flows. The relationship between user anonymity and the minimum covering traffic rate is then studied via analysis and simulation. When user flows are Poisson processes with the same sending rate, the minimum covering traffic rate to provide full anonymity to m users is O(log m). For Pareto traffic, we show that the rate of the covering traffic converges to a constant when the number of flows goes to infinity. Finally, we use real Internet trace files to study the behavior of our algorithm when user flows have different rates.
6564567
Stabbing the sky: efficient skyline computation over sliding windows
We consider the problem of efficiently computing the skyline against the most recent N elements in a data stream seen so far. Specifically, we study the n-of-N skyline queries; that is, computing the skyline for the most recent n (/spl forall/n/spl les/N) elements. Firstly, we developed an effective pruning technique to minimize the number of elements to be kept. It can be shown that on average storing only O(log/sup d/ N) elements from the most recent N elements is sufficient to support the precise computation of all n-of-N skyline queries in a d-dimension space if the data distribution on each dimension is independent. Then, a novel encoding scheme is proposed, together with efficient update techniques, for the stored elements, so that computing an n-of-N skyline query in a d-dimension space takes O(log N+s) time that is reduced to O(d log log N+s) if the data distribution is independent, where s is the number of skyline points. Thirdly, a novel trigger based technique is provided to process continuous n-of-N skyline queries with O(/spl delta/) time to update the current result per new data element and O(log s) time to update the trigger list per result change, where /spl delta/ is the number of element changes from the current result to the new result. Finally, we extend our techniques to computing the skyline against an arbitrary window in the most recent N element. Besides theoretical performance guarantees, our extensive experiments demonstrated that the new techniques can support on-line skyline query computation over very rapid data streams.