Constructing minimal acyclic deterministic finite automata

This thesis is submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Ph.D) in the FASTAR group of the Department of Computer Science, University of Pretoria, South Africa. I present a number of algorithms for constructing minimal acyclic deterministic finite automata (MADFAs), most of which I originally derived/designed or co-discovered. Being acyclic, such automata represent finite languages and have proven useful in applications such as spellchecking, virus-searching and text indexing. In many of those applications, the automata grow to billions of states, making them difficult to store without using various compression techniques — the most important of which is minimization. Results from the late 1950’s show that minimization yields a unique automaton (for a given language), and later results show that minimization of acyclic automata is possible in time linear in the number of states. These two results make for a rich area of algorithmics research; automata and algorithmics research are relatively old fields of computing science and the discovery/invention of new algorithms in the field is an exciting result. I present both incremental and nonincremental algorithms. With nonincremental techniques, the unminimized acyclic deterministic finite automaton (ADFA) is first constructed and then minimized. As mentioned above, the unminimized ADFA can be very large indeed — often even too large to fit within the virtual memory space of the computer. As a result, incremental techniques for minimization (i.e. the ADFA is minimized during its construction) become interesting. Incremental algorithms frequently have some overhead: if the unminimized ADFA fits easily within physical memory, it may still be faster to use nonincremental techniques. The presentation used in this thesis has a few unusual characteristics: Few other presentations follow a correctness-by-construction style for presenting and deriving algorithms. The presentations given here include correctness arguments or sketches thereof. The presentation is taxonomic — emphasizing the similarities and differences between the algorithms at a fundamental level. While it is possible to present these algorithms in a formal-language-theoretic setting, this thesis remains somewhat closer to the actual implementation issues. In several chapters, new algorithms and interesting new variants of existing algorithms are presented. It gives new presentations of many existing algorithms — all in a common format with common examples. There are extensive links to the existing literature. Thesis (PhD)--University of Pretoria, 2010.Computer Scienceunrestricte

Model-based passive testing of safety-critical components

Passive testing is a complementary technique to active testing. For some types of systems, for example dynamic or adaptive distributed systems which are able to re-configure themselves at runtime in response to changes in their environments, exhaustive active testing before deployment is either theoretically impossible or practically not feasible. For such types of systems the additional application of the technique of passive testing is recommendable. However, a comprehensive theory and taxonomy of methods and techniques for model-based passive testing does –as far as we know– not yet exist and is from today’s perspective still very much a topic for future research in this domain. For this reason the presentation of the topic in this chapter is very much example-based such as to provide the reader with some first intuitions about what model-based passive testing is, what kinds of techniques could be used to implement it, and what could be some typical application scenarios for model-based passive testing in the domains of software systems, hardware systems, as well as embedded software+hardware systems.Note: Section 5 of our chapter, as well as several Figures and a number of Acknowledgments, which will appear in the above-mentioned book, are OMITTED in this pre-print version.http://www.crcpress.com/product/isbn/978143981845

Quality in software development : a pragmatic approach using metrics

As long as software has been produced, there have been e orts to strive for quality in software products. In order to understand quality in software products, researchers have built models of software quality that rely on metrics in an attempt to provide a quantitative view of software quality. The aim of these models is to provide software producers with the capability to de ne and evaluate metrics related to quality and use these metrics to improve the quality of the software they produce over time. The main disadvantage of these models is that they require e ort and resources to de ne and evaluate metrics from software projects. This article brie y describes some prominent models of software quality in the literature and continues to describe a new approach to gaining insight into quality in software development projects. A case study based on this new approach is described and results from the case study are discussed.http://www.journals.co.za/ej/ejour_comp.htmlam201

Weak factor automata : the failure of failure factor oracles?

In indexing of, and pattern matching on, DNA and text sequences, it is often important to represent all factors of a sequence. One e cient, compact representation is the factor oracle (FO). At the same time, any classical deterministic nite automaton (DFA) can be transformed to a so-called failure one (FDFA), which may use failure transitions to replace multiple symbol transitions, potentially yielding a more compact representation. We combine the two ideas and directly construct a failure factor oracle (FFO) from a given sequence, in contrast to ex post facto transformation to an FDFA. The algorithm is suitable for both short and long sequences. We empirically compared the resulting FFOs and FOs on number of transitions for many DNA sequences of lengths 4 - 512, showing gains of up to 10% in total number of transitions, with failure transitions also taking up less space than symbol transitions. The resulting FFOs can be used for indexing, as well as in a variant of the FO-using backward oracle matching algorithm. We discuss and classify this pattern matching algorithm in terms of the keyword pattern matching taxonomies of Watson, Cleophas and Zwaan. We also empirically compared the use of FOs and FFOs in such backward reading pattern matching algorithms, using both DNA and natural language (English) data sets. The results indicate that the decrease in pattern matching performance of an algorithm using an FFO instead of an FO may outweigh the gain in representation space by using an FFO instead of an FO.http://www.journals.co.za/ej/ejour_comp.htmlam201

Modelling the perceptual similarity of facial expressions from image statistics and neural responses

The ability to perceive facial expressions of emotion is essential for effective social communication. We investigated how the perception of facial expression emerges from the image properties that convey this important social signal, and how neural responses in face-selective brain regions might track these properties. To do this, we measured the perceptual similarity between expressions of basic emotions, and investigated how this is reflected in image measures and in the neural response of different face-selective regions. We show that the perceptual similarity of different facial expressions (fear, anger, disgust, sadness, happiness) can be predicted by both surface and feature shape information in the image. Using block design fMRI, we found that the perceptual similarity of expressions could also be predicted from the patterns of neural response in the face-selective posterior superior temporal sulcus (STS), but not in the fusiform face area (FFA). These results show that the perception of facial expression is dependent on the shape and surface properties of the image and on the activity of specific face-selective regions

Robotic geometric and volumetric inspection of high value and large scale aircraft wings

Increased demands in performance and production rates require a radical new approach to the design and manufacturing of aircraft wings. Performance of modern robotic manipulators has enabled research and development of fast automated non-destructive testing (NDT) systems for complex geometries. This paper presents recent outcomes of work aimed at removing the bottleneck due to data acquisition rates, to fully exploit the scanning speed of modern 6-DoF manipulators. The geometric assessment of the parts is carried out with a robotised dynamic laser scanner encoded through an absolute laser tracker. This method allows scanning speeds up to 330mm/s at 1mm pitch. State of the art ultrasonic instrumentation has been integrated into a large robot cell to enable fast data acquisition, high scan resolutions and accurate positional encoding. A fibre optic connection between the ultrasonic instrument and the server computer enables data transfer rates up to 1.6 GB/s. The robotic inspection system presented herein is currently being tested for industrial exploitation. The adopted system integration strategies allow traditional ultrasonic phased array scanning as well as full matrix capture (FMC) and other novel scanning approaches (e.g. multi-Tx phased array). Scan results, relative to a 1.2m x 3m carbon fibre sample, are presented. The system shows a reference scanning rate of 25.3m2/hour with an 8Tx/8Rx PA approach and an ultrasonically reachable scanning rate over 100m2/hour with the novel techniques

Rates Of Amyloid Imaging Positivity In Patients With Primary Progressive Aphasia

IMPORTANCE The ability to predict the pathology underlying different neurodegenerative syndromes is of critical importance owing to the advent of molecule-specific therapies. OBJECTIVE To determine the rates of positron emission tomography (PET) amyloid positivity in the main clinical variants of primary progressive aphasia (PPA). DESIGN, SETTING, AND PARTICIPANTS This prospective clinical-pathologic case series was conducted at a tertiary research clinic specialized in cognitive disorders. Patients were evaluated as part of a prospective, longitudinal research study between January 2002 and December 2015. Inclusion criteria included clinical diagnosis of PPA; availability of complete speech, language, and cognitive testing; magnetic resonance imaging performed within 6 months of the cognitive evaluation; and PET carbon 11-labeled Pittsburgh Compound-B or florbetapir F 18 brain scan results. Of 109 patients referred for evaluation of language symptoms who underwent amyloid brain imaging, 3 were excluded because of incomplete language evaluations, 5 for absence of significant aphasia, and 12 for presenting with significant initial symptoms outside of the language domain, leaving a cohort of 89 patients with PPA. MAIN OUTCOMES AND MEASURES Clinical, cognitive, neuroimaging, and pathology results. RESULTS Twenty-eight cases were classified as imaging-supported semantic variant PPA (11 women [39.3%]; mean [SD] age, 64 [7] years), 31 nonfluent/agrammatic variant PPA (22 women [71.0%]; mean [SD] age, 68 [7] years), 26 logopenic variant PPA (17 women [65.4%]; mean [SD] age, 63 [8] years), and 4 mixed PPA cases. Twenty-four of 28 patients with semantic variant PPA (86%) and 28 of 31 patients with nonfluent/agrammatic variant PPA (90%) had negative amyloid PET scan results, while 25 of 26 patients with logopenic variant PPA (96%) and 3 of 4 mixed PPA cases (75%) had positive scan results. The amyloid positive semantic variant PPA and nonfluent/agrammatic variant PPA cases with available autopsy data (2 of 4 and 2 of 3, respectively) all had a primary frontotemporal lobar degeneration and secondary Alzheimer disease pathologic diagnoses, whereas autopsy of 2 patients with amyloid PET-positive logopenic variant PPA confirmed Alzheimer disease. One mixed PPA patient with a negative amyloid PET scan had Pick disease at autopsy. CONCLUSIONS AND RELEVANCE Primary progressive aphasia variant diagnosis according to the current classification scheme is associated with Alzheimer disease biomarker status, with the logopenic variant being associated with carbon 11-labeled Pittsburgh Compound-B positivity in more than 95% of cases. Furthermore, in the presence of a clinical syndrome highly predictive of frontotemporal lobar degeneration pathology, biomarker positivity for Alzheimer disease may be associated more with mixed pathology rather than primary Alzheimer disease

Altered topology of the functional speech production network in non-fluent/agrammatic variant of PPA

Non-fluent/agrammatic primary progressive aphasia (nfvPPA) is caused by neuro-degeneration within the left fronto-insular speech and language production network (SPN). Graph theory is a branch of mathematics that studies network architecture (topology) by quantifying features based on its elements (nodes and connections). This approach has been recently applied to neuroimaging data to explore the complex architecture of the brain connectome, though few studies have exploited this technique in PPA. Here, we used graph theory on functional MRI resting state data from a group of 20 nfvPPA patients and 20 matched controls to investigate topological changes in response to focal neuro-degeneration. We hypothesized that changes in the network architecture would be specific to the affected SPN in nfvPPA, while preserved in the spared default mode network (DMN). Topological configuration was quantified by hub location and global network metrics. Our findings showed a less efficiently wired and less optimally clustered SPN, while no changes were detected in the DMN. The SPN in the nfvPPA group showed a loss of hubs in the left fronto-parietal-temporal area and new critical nodes in the anterior left inferior-frontal and right frontal regions. Behaviorally, speech production score and rule violation errors correlated with the strength of functional connectivity of the left (lost) and right (new) regions respectively. This study shows that focal neurodegeneration within the SPN in nfvPPA is associated with network-specific topological alterations, with the loss and gain of crucial hubs and decreased global efficiency that were better accounted for through functional rather than structural changes. These findings support the hypothesis of selective network vulnerability in nfvPPA and may offer biomarkers for future behavioral intervention

The Giant Accreting Protoplanet Survey (GAPlanetS) -- Results from a Six Year Campaign to Image Accreting Protoplanets

Accreting protoplanets represent a window into planet formation processes. We report H{\alpha} differential imaging results from the deepest and most comprehensive accreting protoplanet survey to date, acquired with the Magellan Adaptive Optics (MagAO) system's VisAO camera. The fourteen transitional disks targeted are ideal candidates for protoplanet discovery due to their wide, heavily depleted central cavities, wealth of non-axisymmetric circumstellar disk features evocative of ongoing planet formation, and ongoing stellar accretion. To address the twin challenges of morphological complexity in the target systems and PSF instability, we develop novel approaches for frame selection and optimization of the Karhounen-Loeve Image Processing algorithm pyKLIP. We detect one new candidate protoplanet, CS Cha "c", at a separation of 75mas and a {\Delta}mag of 5.1 and robustly recover the HD142527 B and HD100453 B low mass stellar companions across multiple epochs. Though we cannot rule out a substantial scattered light contribution to its emission, we also recover LkCa 15 b. Its presence inside of the cleared disk cavity and consistency with a forward-modeled point source suggest that it remains a viable protoplanet candidate. The protoplanet PDS 70 c was marginally recovered under our conservative general methodology. However, through targeted optimization in H{\alpha} imagery, we tentatively recover PDS 70 c in three epochs and PDS 70 b in one epoch. Of the many other previously-reported companions and companion candidates around objects in the sample, we do not recover any additional robust candidates. However, lack of recovery at moderate H{\alpha} contrast does not rule out the presence of protoplanets at these locations, and we report limiting H{\alpha} contrasts in such cases.Comment: Accepted for publication in A

First-Year Spectroscopy for the SDSS-II Supernova Survey

This paper presents spectroscopy of supernovae discovered in the first season of the Sloan Digital Sky Survey-II Supernova Survey. This program searches for and measures multi-band light curves of supernovae in the redshift range z = 0.05 - 0.4, complementing existing surveys at lower and higher redshifts. Our goal is to better characterize the supernova population, with a particular focus on SNe Ia, improving their utility as cosmological distance indicators and as probes of dark energy. Our supernova spectroscopy program features rapid-response observations using telescopes of a range of apertures, and provides confirmation of the supernova and host-galaxy types as well as precise redshifts. We describe here the target identification and prioritization, data reduction, redshift measurement, and classification of 129 SNe Ia, 16 spectroscopically probable SNe Ia, 7 SNe Ib/c, and 11 SNe II from the first season. We also describe our efforts to measure and remove the substantial host galaxy contamination existing in the majority of our SN spectra.Comment: Accepted for publication in The Astronomical Journal(47pages, 9 figures