Using the R package Shiny to create web applications that facilitate quantitative gene expression analysis

Thesis (Master's)--University of Washington, 2016-06

The relationship between non-orthographic language abilities and reading performance: An exploration of the primary systems hypothesis in chronic aphasia

Thesis (Ph.D.)--University of Washington, 2016-06

Two empirical hydrocyclone models revisited

There has been an abundance of literature on the modelling of hydrocyclones over the past 30 years. However, in the comminution area at least, the more popular commercially available packages (e.g. JKSimMet, Limn, MODSIM) use the models developed by Nageswararao and Plitt in the 1970s, either as published at that time, or with minor modification. With the benefit of 30 years of hindsight, this paper discusses the assumptions and approximations used in developing these models. Differences in model structure and the choice of dependent and independent variables are also considered. Redundancies are highlighted and an assessment made of the general applicability of each of the models, their limitations and the sources of error in their model predictions. This paper provides the latest version of the Nageswararao model based on the above analysis, in a form that can readily be implemented in any suitable programming language, or within a spreadsheet. The Plitt model is also presented in similar form. (C) 2004 Elsevier Ltd. All rights reserved.

The real-time refinement calculus: A foundation for machine-independent real-time programming

The real-time refinement calculus is an extension of the standard refinement calculus in which programs are developed from a precondition plus post-condition style of specification. In addition to adapting standard refinement rules to be valid in the real-time context, specific rules are required for the timing constructs such as delays and deadlines. Because many real-time programs may be nonterminating, a further extension is to allow nonterminating repetitions. A real-time specification constrains not only what values should be output, but when they should be output. Hence for a program to implement such a specification, it must guarantee to output values by the specified times. With standard programming languages such guarantees cannot be made without taking into account the timing characteristics of the implementation of the program on a particular machine. To avoid having to consider such details during the refinement process, we have extended our real-time programming language with a deadline command. The deadline command takes no time to execute and always guarantees to meet the specified time; if the deadline has already passed the deadline command is infeasible (miraculous in Dijkstra's terminology). When such a realtime program is compiled for a particular machine, one needs to ensure that all execution paths leading to a deadline are guaranteed to reach it by the specified time. We consider this checking as part of an extended compilation phase. The addition of the deadline command restores for the real-time language the advantage of machine independence enjoyed by non-real-time programming languages.

Interhemispheric differences of spectral power in expressive language:a MEG study with clinical applications

In the last decade we have seen an exponential growth of functional imaging studies investigating multiple aspects of language processing. These studies have sparked an interest in applying some of the paradigms to various clinically relevant questions, such as the identification of the cortical regions mediating language function in surgical candidates for refractory epilepsy. Here we present data from a group of adult control participants in order to investigate the potential of using frequency specific spectral power changes in MEG activation patterns to establish lateralisation of language function using expressive language tasks. In addition, we report on a paediatric patient whose language function was assessed before and after a left hemisphere amygdalo-hippocampectomy. Our verb generation task produced left hemisphere decreases in beta-band power accompanied by right hemisphere increases in low beta-band power in the majority of the control group, a previously unreported phenomenon. This pattern of spectral power was also found in the patient's post-surgery data, though not her pre-surgery data. Comparison of pre and post-operative results also provided some evidence of reorganisation in language related cortex both inter- and intra-hemispherically following surgery. The differences were not limited to changes in localisation of language specific cortex but also changes in the spectral and temporal profile of frontal brain regions during verb generation. While further investigation is required to establish concordance with invasive measures, our data suggest that the methods described may serve as a reliable lateralisation marker for clinical assessment. Furthermore, our findings highlight the potential utility of MEG for the investigation of cortical language functioning in both healthy development and pathology.

An expert system for the development of a health and safety policy/risk assessment in the plastics industry

Health and safety policies may be regarded as the cornerstone for positive prevention of occupational accidents and diseases. The Health and Safety at Work, etc Act 1974 makes it a legal duty for employers to prepare and revise a written statement of a general policy with respect to the health and safety at work of employees as well as the organisation and arrangements for carrying out that policy. Despite their importance and the legal equipment to prepare them, health and safety policies have been found, in a large number of plastics processing companies (particularly small companies), to be poorly prepared, inadequately implemented and monitored. An important cause of these inadequacies is the lack of necessary health and safety knowledge and expertise to prepare, implement and monitor policies. One possible way of remedying this problem is to investigate the feasibility of using computers to develop expert system programs to simulate the health and safety (HS) experts' task of preparing the policies and assisting companies implement and monitor them. Such programs use artificial intelligence (AI) techniques to solve this sort of problems which are heuristic in nature and require symbolic reasoning. Expert systems have been used successfully in a variety of fields such as medicine and engineering. An important phase in the feasibility of development of such systems is the engineering of knowledge which consists of identifying the knowledge required, eliciting, structuring and representing it in an appropriate computer programming language.

Parallel implementation of image segmentation algorithms on a network of transputers

Image segmentation is one of the most computationally intensive operations in image processing and computer vision. This is because a large volume of data is involved and many different features have to be extracted from the image data. This thesis is concerned with the investigation of practical issues related to the implementation of several classes of image segmentation algorithms on parallel architectures. The Transputer is used as the basic building block of hardware architectures and Occam is used as the programming language. The segmentation methods chosen for implementation are convolution, for edge-based segmentation; the Split and Merge algorithm for segmenting non-textured regions; and the Granlund method for segmentation of textured images. Three different convolution methods have been implemented. The direct method of convolution, carried out in the spatial domain, uses the array architecture. The other two methods, based on convolution in the frequency domain, require the use of the two-dimensional Fourier transform. Parallel implementations of two different Fast Fourier Transform algorithms have been developed, incorporating original solutions. For the Row-Column method the array architecture has been adopted, and for the Vector-Radix method, the pyramid architecture. The texture segmentation algorithm, for which a system-level design is given, demonstrates a further application of the Vector-Radix Fourier transform. A novel concurrent version of the quad-tree based Split and Merge algorithm has been implemented on the pyramid architecture. The performance of the developed parallel implementations is analysed. Many of the obtained speed-up and efficiency measures show values close to their respective theoretical maxima. Where appropriate comparisons are drawn between different implementations. The thesis concludes with comments on general issues related to the use of the Transputer system as a development tool for image processing applications; and on the issues related to the engineering of concurrent image processing applications.

UncertWeb processing service:making models easer to access on the web

Models are central tools for modern scientists and decision makers, and there are many existing frameworks to support their creation, execution and composition. Many frameworks are based on proprietary interfaces, and do not lend themselves to the integration of models from diverse disciplines. Web based systems, or systems based on web services, such as Taverna and Kepler, allow composition of models based on standard web service technologies. At the same time the Open Geospatial Consortium has been developing their own service stack, which includes the Web Processing Service, designed to facilitate the executing of geospatial processing - including complex environmental models. The current Open Geospatial Consortium service stack employs Extensible Markup Language as a default data exchange standard, and widely-used encodings such as JavaScript Object Notation can often only be used when incorporated with Extensible Markup Language. Similarly, no successful engagement of the Web Processing Service standard with the well-supported technologies of Simple Object Access Protocol and Web Services Description Language has been seen. In this paper we propose a pure Simple Object Access Protocol/Web Services Description Language processing service which addresses some of the issues with the Web Processing Service specication and brings us closer to achieving a degree of interoperability between geospatial models, and thus realising the vision of a useful 'model web'.

Goal detection from natural language queries

This paper aims to identify the communication goal(s) of a user's information-seeking query out of a finite set of within-domain goals in natural language queries. It proposes using Tree-Augmented Naive Bayes networks (TANs) for goal detection. The problem is formulated as N binary decisions, and each is performed by a TAN. Comparative study has been carried out to compare the performance with Naive Bayes, fully-connected TANs, and multi-layer neural networks. Experimental results show that TANs consistently give better results when tested on the ATIS and DARPA Communicator corpora.

Distinctive Features of Mobile Messages Processing

World’s mobile market pushes past 2 billion lines in 2005. Success in these competitive markets requires operational excellence with product and service innovation to improve the mobile performance. Mobile users very often prefer to send a mobile instant message or text messages rather than talking on a mobile. Well developed “written speech analysis” does not work not only with “verbal speech” but also with “mobile text messages”. The main purpose of our paper is, firstly, to highlight the problems of mobile text messages processing and, secondly, to show the possible ways of solving these problems.

Information Processing in a Cognitive Model of NLP

A model of the cognitive process of natural language processing has been developed using the formalism of generalized nets. Following this stage-simulating model, the treatment of information inevitably includes phases, which require joint operations in two knowledge spaces – language and semantics. In order to examine and formalize the relations between the language and the semantic levels of treatment, the language is presented as an information system, conceived on the bases of human cognitive resources, semantic primitives, semantic operators and language rules and data. This approach is applied for modeling a specific grammatical rule – the secondary predication in Russian. Grammatical rules of the language space are expressed as operators in the semantic space. Examples from the linguistics domain are treated and several conclusions for the semantics of the modeled rule are made. The results of applying the information system approach to the language turn up to be consistent with the stages of treatment modeled with the generalized net.

Applied Problems of Functional Homonymy Resolution for Russian Language

Applied problems of functional homonymy resolution for Russian language are investigated in the work. The results obtained while using the method of functional homonymy resolution based on contextual rules are presented. Structural characteristics of minimal contextual rules for different types of functional homonymy are researched. Particular attention is paid to studying the control structure of the rules, which allows for the homonymy resolution accuracy not less than 95%. The contextual rules constructed have been realized in the system of technical text analysis.

Ontology-Based Model of Representation of Knowledge about Language Mappings

The paper presents a short review of some systems for program transformations performed on the basis of the internal intermediate representations of these programs. Many systems try to support several languages of representation of the source texts of programs and solve the task of their translation into the internal representation. This task is still a challenge as it is effort-consuming. To reduce the effort, different systems of translator construction, ready compilers with ready grammars of outside designers are used. Though this approach saves the effort, it has its drawbacks and constraints. The paper presents the general idea of using the mapping approach to solve the task within the framework of program transformations and overcome the disadvantages of the existing systems. The paper demonstrates a fragment of the ontology model of high-level languages mappings onto the single representation and gives the example of how the description of (a fragment) a particular mapping is represented in accordance with the ontology model.

Educational Games for Learning Programming Languages

A concept of educational game for learning programming languages is presented. The idea of learning programming languages and improving programming skills through programming game characters’ behavior is described. The learning course description rules for using in games are suggested. The concept is implemented in a game for learning C# programming language. A common game architecture is modified for using in the educational game. The game engine is built on the base of the graphical engine Ogre3D and extended with game logic. The game has been developed as an industry level commercial product and is planned for sale to educational institutions.

Hierarchical Three-level Ontology for Text Processing

The principal feature of ontology, which is developed for a text processing, is wider knowledge representation of an external world due to introduction of three-level hierarchy. It allows to improve semantic interpretation of natural language texts.