1828938
Crimson: a data management system to support evaluating phylogenetic tree reconstruction algorithms
Evolutionary and systems biology increasingly rely on the construction of large phylogenetic trees which represent the relationships between species of interest. As the number and size of such trees increases, so does the need for efficient data storage and query capabilities. Although much attention has been focused on XML as a tree data model, phylogenetic trees differ from document-oriented applications in their size and depth, and their need for structure-based queries rather than path-based queries.This paper focuses on Crimson, a tree storage system for phylogenetic trees used to evaluate phylogenetic tree reconstruction algorithms within the context of the NSF CIPRes project. A goal of the modeling component of the CIPRes project is to construct a huge simulation tree representing a "gold standard" of evolutionary history against which phylogenetic tree reconstruction algorithms can be tested.In this demonstration, we highlight our storage and indexing strategies and show how Crimson is used for benchmarking phylogenetic tree reconstruction algorithms. We also show how our design can be used to support more general queries over phylogenetic trees.
129842
BLAS: an efficient XPath processing system
We present BLAS, a Bi-LAbeling based System, for efficiently processing complex XPath queries over XML data. BLAS uses P-labeling to process queries involving consecutive child axes, and D-labeling to process queries involving descendant axes traversal. The XML data is stored in labeled form, and indexed to optimize descendent axis traversals. Three algorithms are presented for translating complex XPath queries to SQL expressions, and two alternate query engines are provided. Experimental results demonstrate that the BLAS system has a substantial performance improvement compared to traditional XPath processing using D-labeling.
6047065
Efficiently Supporting Structure Queries on Phylogenetic Trees
With phylogenetics becoming increasingly important in biomedical research, the number of phylogenetic studies is increasing rapidly and huge mount of phylogenetic data has been generated and stored in databases. How to efficiently extract information from the data has become an important research problem. In this paper, we focus on a class of important queries on phylogenetic trees: structure queries which include least common ancestor, minimal spanning clade, tree pattern match and tree projection. After analyzing the characteristics of the phylogenetic tree as well as structure queries, we propose a storage system based on labeling using RDBMS and design algorithms for query evaluation. We implement these algorithms and compare them with existing techniques. Performance studies prove the efficiency of our strategy.
8394681
ViteX: a streaming XPath processing system
We present ViteX, an XPath processing system on XML streams with polynomial time complexity. ViteX uses a polynomial-space data structure to encode an exponential number of pattern matches (in the query size) which are required to process queries correctly during a single sequential scan of XML. Then ViteX computes query solutions by probing the data structure in a lazy fashion without enumerating pattern matches.
11596303
A Practical Digital Multisignature Scheme Based on Discrete Logarithms
This paper proposes a practical digital multisignature scheme based on the C sig * cryptosystem derived from the C sig cryptosystem of Zheng and Seberry (1993). The simple scheme consists of three phases. In the first phase the issuer of the document prepares the document, the list of prospective signatories and a pad on which signatories are to write their signatures. In the second phase each signatory verifies the document, signs it and forwards it to the next signatory. In the third phase a trusted verifier or notary decides on the validity of the signatures. The scheme prevents cheating by dishonest signatories from going undetected. The scheme is practical and offers at least the same security level afforded by its underlying cryptosystem against external attacks. Internal attacks in the form of forging or cheating by a dishonest issuer or by one or more of the signatories (alone or by collaboration) requires the solving of instances of the discrete logarithm problem.
5415824
Shared memory programming for large scale machines
This paper describes the design and implementation of a scalable run-time system and an optimizing compiler for Unified Parallel C (UPC). An experimental evaluation on BlueGene/L®, a distributed-memory machine, demonstrates that the combination of the compiler with the runtime system produces programs with performance comparable to that of efficient MPI programs and good performance scalability up to hundreds of thousands of processors.Our runtime system design solves the problem of maintaining shared object consistency efficiently in a distributed memory machine. Our compiler infrastructure simplifies the code generated for parallel loops in UPC through the elimination of affinity tests, eliminates several levels of indirection for accesses to segments of shared arrays that the compiler can prove to be local, and implements remote update operations through a lower-cost asynchronous message. The performance evaluation uses three well-known benchmarks --- HPC RandomAccess, HPC STREAM and NAS CG --- to obtain scaling and absolute performance numbers for these benchmarks on up to 131072 processors, the full BlueGene/L machine. These results were used to win the HPC Challenge Competition at SC05 in Seattle WA, demonstrating that PGAS languages support both productivity and performance.
15530803
Formal Proofs for the Security of Signcryption
Signcryption is a public key or asymmetric cryptographic method that provides simultaneously both message confidentiality and unforgeability at a lower computational and communication overhead. In this paper, we propose a sound security model for signcryption that admits rigorous formal proofs for the confidentiality and unforgeablity of signcryption. A conclusion that comes out naturally from this work is that, as an asymmetric encryption scheme, signcryption is secure against adaptive chosen ciphertext attack in the random oracle model relative to, quite interestingly, the Gap Diffie-Hellman problem, and as a digital signature scheme, signcryption is existentially unforgeable against adaptive chosen message attack in the random oracle model relative to the discrete logarithm problem.
1196113
Feature-based wavelet shrinkage algorithm for image denoising
A selective wavelet shrinkage algorithm for digital image denoising is presented. The performance of this method is an improvement upon other methods proposed in the literature and is algorithmically simple for large computational savings. The improved performance and computational speed of the proposed wavelet shrinkage algorithm is presented and experimentally compared with established methods. The denoising method incorporated in the proposed algorithm involves a two-threshold validation process for real-time selection of wavelet coefficients. The two-threshold criteria selects wavelet coefficients based on their absolute value, spatial regularity, and regularity across multiresolution scales. The proposed algorithm takes image features into consideration in the selection process. Statistically, most images have regular features resulting in connected subband coefficients. Therefore, the resulting subbands of wavelet transformed images in large part do not contain isolated coefficients. In the proposed algorithm, coefficients are selected due to their magnitude, and only a subset of those selected coefficients which exhibit a spatially regular behavior remain for image reconstruction. Therefore, two thresholds are used in the coefficient selection process. The first threshold is used to distinguish coefficients of large magnitude and the second is used to distinguish coefficients of spatial regularity. The performance of the proposed wavelet denoising technique is an improvement upon several other established wavelet denoising techniques, as well as being computationally efficient to facilitate real-time image-processing applications.
8204880
Privacy aware data generation for testing database applications
Testing of database applications is of great importance. A significant issue in database application testing consists in the availability of representative data. In this paper, we investigate the problem of generating a synthetic database based on a-priori knowledge about a production database. Our approach is to fit general location model using various characteristics (e.g., constraints, statistics, rules) extracted from the production database and then generate the synthetic data using model learnt. The generated data is valid and similar to real data in terms of statistical distribution, hence it can be used for functional and performance testing. As characteristics extracted may contain information which may be used by attacker to derive some confidential information about individuals, we present our disclosure analysis method which applies cell suppression technique for identity disclosure analysis and perturbation for value disclosure.