Digital Commons Network^™

An Intelligent System For Automated Dna Base Calling, Mohamad T. Musavi

University of Maine Office of Research Administration: Grant Reports

An investigation into improving the performance of DNA base calling algorithms was conducted. The results have shown that the preprocessing steps performed by ABI sequencer on raw data adversely affects the accuracy of DNA sequencing. This adverse effect has been responsible for relatively high error rates, between 3.5% to 6%, in both ABI and Phred sequencing software. Please note that Phred also uses the processed data generated by ABI sequencer; only their base-calling algorithm is different. To remedy this effect, we have developed and implemented a new filtering technique that preserves the initial information contained in the raw data. This …

Method And Apparatus For Adaptive Filtering By Counting Acoustic Sample Zeroes In Ultrasound Imaging, Gregory R. Bashford, Edward D. Nonnweiler, David D. Becker, David John Muzilla

Biomedical Imaging and Biosignal Analysis Laboratory

An ultrasound imaging system having an adaptive spatial filter the filter coefficients of which, for particular image parameter sample, are determined by counting the number of neighboring image parameter samples having zero or near-zero values. If the number of zero or near-zero values in a data window is greater than a predetermined threshold, the data in the window is passed, not filtered. This filter has two advantages over other spatial filters. First, image parameter data samples having only zero or near-zero neighboring values (i.e., isolated "point noise") are not smeared. Second, boundaries such as the edge of color in a …

Classes Of Logic Programs Which Possess Unique Supported Models, Anthony K. Seda, Pascal Hitzler

Computer Science and Engineering Faculty Publications

Logic programming is concerned with the use of logic as a programming language. The main manifestation of this computing paradigm is in the various versions of Prolog which are now available, in which computation is viewed as deduction from sets of Horn clauses, although there is also growing interest in the related form known as answer set programming, see [10]. The reference [1] contains a good survey of the growth of logic programming over the last twenty-five years both as a stand-alone programming language and as a software component of large information systems. One advantage a logic program P has …

Semantic Web And Information Brokering: Opportunities, Commercialization, And Challenges, Amit P. Sheth

Kno.e.sis Publications

From the chairs' report published in SIGMOD record: The keynote address entitled 'Semantic Web and Information Brokering: Opportunities, Early Commercializations, and Challenges' was delivered by Amit Sheth (University of Georgia and Taalee Corp). Sheth characterized semantics as the next step in the evolution of the WWW and stressed the importance of semantically organized information for supporting ubiquitous, powerful, accurate and efficient access to this information. Sheth also reviewed proposals for semantic interoperability frameworks such as the DAML(DARPA Agent Mark-Up Language), the Oingo family of tools for defining concepts and extracting knowledge from large databases, as well as several scenarios on …

Exception Handling In Workflow Systems, Zongwei Luo, Amit P. Sheth, Krzysztof J. Kochut, John A. Miller

Kno.e.sis Publications

In this paper, defeasible workflow is proposed as a framework to support exception handling for workflow management. By using the “justified” ECA rules to capture more contexts in workflow modeling, defeasible workflow uses context dependent reasoning to enhance the exception handling capability of workflow management systems. In particular, this limits possible alternative exception handler candidates in dealing with exceptional situations. Furthermore, a case-based reasoning (CBR) mechanism with integrated human involvement is used to improve the exception handling capabilities. This involves collecting cases to capture experiences in handling exceptions, retrieving similar prior exception handling cases, and reusing the exception handling experiences …

Dimensionality Reduction Using Genetic Algorithms, Michael L. Raymer, William F. Punch, Erik D. Goodman, Leslie A. Kuhn, Anil K. Jain

Kno.e.sis Publications

Pattern recognition generally requires that objects be described in terms of a set of measurable features. The selection and quality of the features representing each pattern affect the success of subsequent classification. Feature extraction is the process of deriving new features from original features to reduce the cost of feature measurement, increase classifier efficiency, and allow higher accuracy. Many feature extraction techniques involve linear transformations of the original pattern vectors to new vectors of lower dimensionality. While this is useful for data visualization and classification efficiency, it does not necessarily reduce the number of features to be measured since each …

A New Fixed-Point Theorem For Logic Programming Semantics, Anthony K. Seda, Pascal Hitzler

Computer Science and Engineering Faculty Publications

We present a new fixed-point theorem akin to the Banach contraction mapping theorem, but in the context of a novel notion of generalized metric space, and show how it can be applied to analyse the denotational semantics of certain logic programs. The theorem is obtained by generalizing a theorem of Priess-Crampe and Ribenboim, which grew out of applications within valuation theory, but is also inspired by a theorem of S.G. Matthews which grew out of applications to conventional programming language semantics. The class of programs to which we apply our theorem was defined previously by us in terms of operators …

Method And Apparatus For Controlling Acoustic Signal Bandwidth In An Ultrasonic Diagnostic Imaging System, Jeffrey R. Resnick, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

An ultrasonic imaging system includes a receive beamformer that generates analog receive signals and a scan converter. A receive signal processing path interconnects the receive beamformer and the scan converter, and this processing path included both an A/D converter characterized by a selectable sampling rate and at least one filter characterized by at least one filter parameter. The filter parameter is selected as a function of the sampling rate to provide enhanced image quality.

First Principles Of Physio-Informatic Systems: Neurocosmology, David Jay Warner

Loma Linda University Electronic Theses, Dissertations & Projects

Physio-informatics is a new systems model for linking human physiologic systems to information systems in the most general way. Physio-informatics is used here to denote a systems based, physiologically robust reference architecture for designing and refining interactive human-computer interface systems in ways that increase operational throughput of information. In this dissertation, a systems model for interactive human-computer interface systems is developed. This model is a physiologically based reference architecture for designing and developing interactive human computer interface systems to match the human nervous system’s ability to transduce, transmit, and render to consciousness the necessary information to interact intelligently with information. …

On-Line Bayesian Speaker Adaptation By Using Tree-Structured Transformation And Robust Priors, Shaojun Wang, Yunxin Zhao

Kno.e.sis Publications

This paper presents new results by using our previously proposed on-line Bayesian learning approach for affine transformation parameter estimation in speaker adaptation. The on-line Bayesian learning technique allows updating parameter estimates after each utterance and it can accommodate flexible forms of transformation functions as well as prior probability density functions. We show through experimental results the robustness of heavy tailed priors to mismatch in prior density estimation. We also show that by properly choosing the transformation matrices and depths of hierarchical trees, recognition performance improved significantly.

Local Properties Of Query Languages, Guozhu Dong, Leonid Libkin, Limsoon Wong

Kno.e.sis Publications

In this paper we study the expressiveness of local queries. By locality we mean — informally — that in order to check if a tuple belongs to the result of a query, one only has to look at a certain predetermined portion of the input. Examples include all relational calculus queries. We start by proving a general result describing outputs of local queries. This result leads to many easy inexpressibility proofs for local queries. We then consider a closely related property, namely, the bounded degree property. It describes the outputs of local queries on structures that locally look “simple.” Every …

Method And Apparatus For Three-Dimensional Ultrasound Imaging Of Biopsy Needle, Syed Omar Ishrak, Mir Said Seyed-Bolorforosh, William Thomas Hatfield, Todd Michael Tillman, Brian Peter Geiser, Gregory R. Bashford, Michael Joseph Washburn

Biomedical Imaging and Biosignal Analysis Laboratory

A method and an apparatus for three-dimensional ultrasound imaging of a needle-like instrument, such as a biopsy needle, inserted in a human body. The instrument is visualized by transmitting ultrasound beams toward the instrument and then detecting the echo signals using a linear array of transducer elements. The problem of ultrasound being reflected from a biopsy needle in a direction away from the transducer array is solved by steering the transmitted ultrasound beams t increase the angle at which the beams impinge upon the biopsy needle. Ideally the ultrasound beams are perpendicular to the needle. This increases the system's sensitivity …

Integronlike Structures In Campylobacter Spp. Of Human And Animal Origin, Brigid Lucey, D. Crowley, P. Moloney, B. Cryan, M. Daly, F. O'Halloran, E. J. Threlfall, S. Fanning

Department of Biological Sciences Publications

Resistance to antimicrobial agents used to treat severe Campylobacter spp. gastroenteritis is increasing worldwide. We assessed the antimicrobial resistance patterns of Campylobacter spp. isolates of human and animal origin. More than half (n = 32) were resistant to sulphonamide, a feature known to be associated with the presence of integrons. Analysis of these integrons will further our understanding of Campylobacter spp. epidemiology.

The Space Of Jumping Emerging Patterns And Its Incremental Maintenance, Jinyan Li, Kotagiri Ramamohanarao, Guozhu Dong

Kno.e.sis Publications

The concept of jumping emerging patterns (JEPs) has been proposed to describe those discriminating features which only occur in the positive training instances but do not occur in the negative class at all; JEPs have been used to construct classifiers which generally provide better accuracy than the state-of-the-art classifiers such as C4.5. The algorithms for maintaining the space of jumping emerging patterns (JEP space) are presented in this paper. We prove that JEP spaces satisfy the property of convexity. Therefore JEP spaces can be concisely represented by two bounds: consisting respectively of the most general elements and the most specific …

Optimization Techniques For Data Intensive Decision Flows, Richard Hull, Francois Llirbat, Bharat Kumar, Gang Zhou, Guozhu Dong, Jianwen Su

Kno.e.sis Publications

For an enterprise to take advantage of the opportunities afforded by electronic commerce it must be able to make decisions about business transactions in near-real-time. In the coming era of segment-of-one marketing, these decisions will be quite intricate, so that customer treatments can be highly personalized, reflecting customer preferences, the customer's history with the enterprise, and targeted business objectives. This paper describes a paradigm called “decision flows” for specifying a form of incremental decision-making that can combine diverse business factors in near-real-time.

This paper introduces and empirically analyzes a variety of optimization strategies for decision flows that are “data-intensive”, i.e. …

Separating Auxiliary Arity Hierarchy Of First-Order Incremental Evaluation Using (3+1)-Ary Input Relations, Guozhu Dong, Louxin Zhang

Kno.e.sis Publications

Presents a first-order incremental evaluation system that uses first-order queries to maintain a database view defined by a non-first-order query. Reduction of the arity of queries to understand the power of foies; Use of a key lemma for proving a query which encodes the multiple parity problem.

Imprecise Answers In Distributed Environments: Estimation Of Information Loss For Multi-Ontology Based Query Processing, Eduardo Mena, Vipul Kashyap, Arantza Illarramendi, Amit P. Sheth

Kno.e.sis Publications

The World Wide Web is fast becoming a ubiquitous computing environment. Prevalent keyword-based search techniques are scalable, but are incapable of accessing information based on concepts. We investigate the use of concepts from multiple, real-world pre-existing, domain ontologies to describe the underlying data content and support information access at a higher level of abstraction. It is not practical to have a single domain ontology to describe the vast amounts of data on the Web. In fact, we expect multiple ontologies to be used as different world views and present an approach to "browse" ontologies as a paradigm for information access. …