EMD performance comparison: single vs double floating points

Empirical mode decomposition (EMD) is a data-driven method used to decompose data into oscillatory components. This paper examines to what extent the defined algorithm for EMD might be susceptible to data format. Two key issues with EMD are its stability and computational speed. This paper shows that for a given signal there is no significant difference between results obtained with single (binary32) and double (binary64) floating points precision. This implies that there is no benefit in increasing floating point precision when performing EMD on devices optimised for single floating point format, such as graphical processing units (GPUs).

Objective Empirical Mode Decomposition metric

Empirical Mode Decomposition (EMD) is a data driven technique for extraction of oscillatory components from data. Although it has been introduced over 15 years ago, its mathematical foundations are still missing which also implies lack of objective metrics for decomposed set evaluation. Most common technique for assessing results of EMD is their visual inspection, which is very subjective. This article provides objective measures for assessing EMD results based on the original definition of oscillatory components.

Regulation of early steps of GPVI signal transduction by phosphatases: a systems biology approach

We present a data-driven mathematical model of a key initiating step in platelet activation, a central process in the prevention of bleeding following Injury. In vascular disease, this process is activated inappropriately and causes thrombosis, heart attacks and stroke. The collagen receptor GPVI is the primary trigger for platelet activation at sites of injury. Understanding the complex molecular mechanisms initiated by this receptor is important for development of more effective antithrombotic medicines. In this work we developed a series of nonlinear ordinary differential equation models that are direct representations of biological hypotheses surrounding the initial steps in GPVI-stimulated signal transduction. At each stage model simulations were compared to our own quantitative, high-temporal experimental data that guides further experimental design, data collection and model refinement. Much is known about the linear forward reactions within platelet signalling pathways but knowledge of the roles of putative reverse reactions are poorly understood. An initial model, that includes a simple constitutively active phosphatase, was unable to explain experimental data. Model revisions, incorporating a complex pathway of interactions (and specifically the phosphatase TULA-2), provided a good description of the experimental data both based on observations of phosphorylation in samples from one donor and in those of a wider population. Our model was used to investigate the levels of proteins involved in regulating the pathway and the effect of low GPVI levels that have been associated with disease. Results indicate a clear separation in healthy and GPVI deficient states in respect of the signalling cascade dynamics associated with Syk tyrosine phosphorylation and activation. Our approach reveals the central importance of this negative feedback pathway that results in the temporal regulation of a specific class of protein tyrosine phosphatases in controlling the rate, and therefore extent, of GPVI-stimulated platelet activation.

Aspects of particle filtering in high-dimensional spaces

Nonlinear data assimilation is high on the agenda in all fields of the geosciences as with ever increasing model resolution and inclusion of more physical (biological etc.) processes, and more complex observation operators the data-assimilation problem becomes more and more nonlinear. The suitability of particle filters to solve the nonlinear data assimilation problem in high-dimensional geophysical problems will be discussed. Several existing and new schemes will be presented and it is shown that at least one of them, the Equivalent-Weights Particle Filter, does indeed beat the curse of dimensionality and provides a way forward to solve the problem of nonlinear data assimilation in high-dimensional systems.

Mobile systems for monitoring Parkinson's disease

A challenge for the clinical management of Parkinson's disease (PD) is the large within- and between-patient variability in symptom profiles as well as the emergence of motor complications which represent a significant source of disability in patients. This thesis deals with the development and evaluation of methods and systems for supporting the management of PD by using repeated measures, consisting of subjective assessments of symptoms and objective assessments of motor function through fine motor tests (spirography and tapping), collected by means of a telemetry touch screen device. One aim of the thesis was to develop methods for objective quantification and analysis of the severity of motor impairments being represented in spiral drawings and tapping results. This was accomplished by first quantifying the digitized movement data with time series analysis and then using them in data-driven modelling for automating the process of assessment of symptom severity. The objective measures were then analysed with respect to subjective assessments of motor conditions. Another aim was to develop a method for providing comparable information content as clinical rating scales by combining subjective and objective measures into composite scores, using time series analysis and data-driven methods. The scores represent six symptom dimensions and an overall test score for reflecting the global health condition of the patient. In addition, the thesis presents the development of a web-based system for providing a visual representation of symptoms over time allowing clinicians to remotely monitor the symptom profiles of their patients. The quality of the methods was assessed by reporting different metrics of validity, reliability and sensitivity to treatment interventions and natural PD progression over time. Results from two studies demonstrated that the methods developed for the fine motor tests had good metrics indicating that they are appropriate to quantitatively and objectively assess the severity of motor impairments of PD patients. The fine motor tests captured different symptoms; spiral drawing impairment and tapping accuracy related to dyskinesias (involuntary movements) whereas tapping speed related to bradykinesia (slowness of movements). A longitudinal data analysis indicated that the six symptom dimensions and the overall test score contained important elements of information of the clinical scales and can be used to measure effects of PD treatment interventions and disease progression. A usability evaluation of the web-based system showed that the information presented in the system was comparable to qualitative clinical observations and the system was recognized as a tool that will assist in the management of patients.

Automatic spiral analysis for objective assessment of motor symptoms in Parkinson's disease

Objective: To develop a method for objective quantification of PD motor symptoms related to Off episodes and peak dose dyskinesias, using spiral data gathered by using a touch screen telemetry device. The aim was to objectively characterize predominant motor phenotypes (bradykinesia and dyskinesia), to help in automating the process of visual interpretation of movement anomalies in spirals as rated by movement disorder specialists. Background: A retrospective analysis was conducted on recordings from 65 patients with advanced idiopathic PD from nine different clinics in Sweden, recruited from January 2006 until August 2010. In addition to the patient group, 10 healthy elderly subjects were recruited. Upper limb movement data were collected using a touch screen telemetry device from home environments of the subjects. Measurements with the device were performed four times per day during week-long test periods. On each test occasion, the subjects were asked to trace pre-drawn Archimedean spirals, using the dominant hand. The pre-drawn spiral was shown on the screen of the device. The spiral test was repeated three times per test occasion and they were instructed to complete it within 10 seconds. The device had a sampling rate of 10Hz and measured both position and time-stamps (in milliseconds) of the pen tip. Methods: Four independent raters (FB, DH, AJ and DN) used a web interface that animated the spiral drawings and allowed them to observe different kinematic features during the drawing process and to rate task performance. Initially, a number of kinematic features were assessed including ‘impairment’, ‘speed’, ‘irregularity’ and ‘hesitation’ followed by marking the predominant motor phenotype on a 3-category scale: tremor, bradykinesia and/or choreatic dyskinesia. There were only 2 test occasions for which all the four raters either classified them as tremor or could not identify the motor phenotype. Therefore, the two main motor phenotype categories were bradykinesia and dyskinesia. ‘Impairment’ was rated on a scale from 0 (no impairment) to 10 (extremely severe) whereas ‘speed’, ‘irregularity’ and ‘hesitation’ were rated on a scale from 0 (normal) to 4 (extremely severe). The proposed data-driven method consisted of the following steps. Initially, 28 spatiotemporal features were extracted from the time series signals before being presented to a Multilayer Perceptron (MLP) classifier. The features were based on different kinematic quantities of spirals including radius, angle, speed and velocity with the aim of measuring the severity of involuntary symptoms and discriminate between PD-specific (bradykinesia) and/or treatment-induced symptoms (dyskinesia). A Principal Component Analysis was applied on the features to reduce their dimensions where 4 relevant principal components (PCs) were retained and used as inputs to the MLP classifier. Finally, the MLP classifier mapped these components to the corresponding visually assessed motor phenotype scores for automating the process of scoring the bradykinesia and dyskinesia in PD patients whilst they draw spirals using the touch screen device. For motor phenotype (bradykinesia vs. dyskinesia) classification, the stratified 10-fold cross validation technique was employed. Results: There were good agreements between the four raters when rating the individual kinematic features with intra-class correlation coefficient (ICC) of 0.88 for ‘impairment’, 0.74 for ‘speed’, 0.70 for ‘irregularity’, and moderate agreements when rating ‘hesitation’ with an ICC of 0.49. When assessing the two main motor phenotype categories (bradykinesia or dyskinesia) in animated spirals the agreements between the four raters ranged from fair to moderate. There were good correlations between mean ratings of the four raters on individual kinematic features and computed scores. The MLP classifier classified the motor phenotype that is bradykinesia or dyskinesia with an accuracy of 85% in relation to visual classifications of the four movement disorder specialists. The test-retest reliability of the four PCs across the three spiral test trials was good with Cronbach’s Alpha coefficients of 0.80, 0.82, 0.54 and 0.49, respectively. These results indicate that the computed scores are stable and consistent over time. Significant differences were found between the two groups (patients and healthy elderly subjects) in all the PCs, except for the PC3. Conclusions: The proposed method automatically assessed the severity of unwanted symptoms and could reasonably well discriminate between PD-specific and/or treatment-induced motor symptoms, in relation to visual assessments of movement disorder specialists. The objective assessments could provide a time-effect summary score that could be useful for improving decision-making during symptom evaluation of individualized treatment when the goal is to maximize functional On time for patients while minimizing their Off episodes and troublesome dyskinesias.

Predicting the distribution of discrete spatial events using artificial neural networks

Although the development of geographic information system (GIS) technology and digital data manipulation techniques has enabled practitioners in the geographical and geophysical sciences to make more efficient use of resource information, many of the methods used in forming spatial prediction models are still inherently based on traditional techniques of map stacking in which layers of data are combined under the guidance of a theoretical domain model. This paper describes a data-driven approach by which Artificial Neural Networks (ANNs) can be trained to represent a function characterising the probability that an instance of a discrete event, such as the presence of a mineral deposit or the sighting of an endangered animal species, will occur over some grid element of the spatial area under consideration. A case study describes the application of the technique to the task of mineral prospectivity mapping in the Castlemaine region of Victoria using a range of geological, geophysical and geochemical input variables. Comparison of the maps produced using neural networks with maps produced using a density estimation-based technique demonstrates that the maps can reliably be interpreted as representing probabilities. However, while the neural network model and the density estimation-based model yield similar results under an appropriate choice of values for the respective parameters, the neural network approach has several advantages, especially in high dimensional input spaces.

Optimization of MLP parameters on mineral potential mapping tasks

Mineral potential mapping is the process of combining a set of input maps, each representing a distinct geo-scientific variable, to produce a single map which ranks areas according to their potential to host deposits of a particular type. The maps are combined using a mapping function which must be either provided by an expert (knowledge-driven approach), or induced from sample data (data-driven approach). Current data-driven approaches using multilayer perceptrons (MLPs) to represent the mapping function have several inherent problems: they rely heavily on subjective judgment in selecting training data and are highly sensitive to this selection; they do not utilize the contextual information provided by unlabeled data; and, there is no objective interpretation of the values output by the MLP. This paper presents a novel approach which overcomes these three problems.

Adjacency cache : an efficient P2P web cache indexing and lookup system

This paper describes the design and evaluation of an efficient per-to-peer (P2P) web cache indexing and lookup system, which can be used to integrate the resources of locally available web pages into globally addressable index using a distributed hash table. The salient feature of the indexing system’s design is the efficient dissemination of cache index information using a next-url index which allows cache clients to determine ahead of time whether linked content is also available at a remote cache. In addition, conventional optimizations such as in browser caching and batching of index write requests are also used. These optimizations are evaluated using trace-driven simulation and the results show that these design trade-offs improve cache lookup performance.

An efficient adaptive scheduling policy for high-performance computing

The advent of commodity-based high-performance clusters has raised parallel and distributed computing to a new level. However, in order to achieve the best possible performance improvements for large-scale computing problems as well as good resource utilization, efficient resource management and scheduling is required. This paper proposes a new two-level adaptive space-sharing scheduling policy for non-dedicated heterogeneous commodity-based high-performance clusters. Using trace-driven simulation, the performance of the proposed scheduling policy is compared with existing adaptive space-sharing policies. Results of the simulation show that the proposed policy performs substantially better than the existing policies.

The structural properties of sexual fantasies for sexual offenders : a preliminary model

While the phenomenon of sexual fantasy has been researched extensively, little contemporary inquiry has investigated the structural properties of sexual fantasy within the context of sexual offending. In this study, a qualitative analysis was used to develop a descriptive model of the phenomena of sexual fantasy during the offence process. Twenty-four adult males convicted of sexual offences provided detailed retrospective descriptions of their thoughts, emotions and behaviours—before, during and after their offences. A data-driven approach to model development, known as Grounded Theory, was undertaken to analyse the interview transcripts. A model was developed to elucidate the structural properties of sexual fantasy in the process of sexual offending, as well as the physiological and psychological variables associated with it. The Sexual Fantasy Structural Properties Model (SFSPM) comprises eight categories that describe various properties of sexual fantasy across the offence process. These categories are: origin, context, trigger, perceptual modality, clarity, motion, intensity and emotion. The strengths of the SFSPM are discussed and its clinical implications are reviewed. Finally, the limitations of the study are presented and future research directions discussed.

Geographical Information Systems (GIS) and their role in sustainable planning : a case study from a Local Government Area (LGA) in Australia

A case study is used to demonstrate the application of Geographical Information Systems (GIS) to inform sustainable development. The suitability of the landscape to support tourism accommodation in a Local Government Area (LGA) is modelled by integrating existing datasets, including conservation areas, residential zones, major roads and known locations of tourism operators into a logistic regression framework. By using a data-driven approach an indication of the relative importance of each explanatory variable can be accounted for, therefore informing planners of the importance of different assets. In a region where tourism is reliant upon natural features, this use of information systems in conjunction with quantitative statistical modelling can value-add to existing datasets. The provision of this kind of knowledge is important as it would otherwise not factor into the decision-making process had the datasets been considered independently of each other – a concept that applies to both the public and private sectors.

Eventscapes : visualizing events over time with emotive facets

The scale and dynamicity of social media, and interaction between traditional news sources and online communities, has created challenges to information retrieval approaches. Users may have no clear information need or be unable to express it in the appropriate idiom, requiring instead to be oriented in an unfamiliar domain, to explore and learn. We present a novel data-driven visualization, termed Eventscape, that combines time, visual media, mood, and controversy. Formative evaluation highlights the value of emotive facets for rapid evaluation of mixed news and social media topics, and a role for such visualizations as pre-cursors to deeper search. Copyright 2011 ACM.

Semi-supervised classification based on subspace sparse representation

Graph plays an important role in graph-based semi-supervised classification. However, due to noisy and redundant features in high-dimensional data, it is not a trivial job to construct a well-structured graph on high-dimensional samples. In this paper, we take advantage of sparse representation in random subspaces for graph construction and propose a method called Semi-Supervised Classification based on Subspace Sparse Representation, SSC-SSR in short. SSC-SSR first generates several random subspaces from the original space and then seeks sparse representation coefficients in these subspaces. Next, it trains semi-supervised linear classifiers on graphs that are constructed by these coefficients. Finally, it combines these classifiers into an ensemble classifier by minimizing a linear regression problem. Unlike traditional graph-based semi-supervised classification methods, the graphs of SSC-SSR are data-driven instead of man-made in advance. Empirical study on face images classification tasks demonstrates that SSC-SSR not only has superior recognition performance with respect to competitive methods, but also has wide ranges of effective input parameters.