Hierarchical models for 2D presence/absence data having ambiguous zeroes: With a biogeographical case study on dingo behaviour

This dissertation is primarily an applied statistical modelling investigation, motivated by a case study comprising real data and real questions. Theoretical questions on modelling and computation of normalization constants arose from pursuit of these data analytic questions. The essence of the thesis can be described as follows. Consider binary data observed on a two-dimensional lattice. A common problem with such data is the ambiguity of zeroes recorded. These may represent zero response given some threshold (presence) or that the threshold has not been triggered (absence). Suppose that the researcher wishes to estimate the effects of covariates on the binary responses, whilst taking into account underlying spatial variation, which is itself of some interest. This situation arises in many contexts and the dingo, cypress and toad case studies described in the motivation chapter are examples of this. Two main approaches to modelling and inference are investigated in this thesis. The first is frequentist and based on generalized linear models, with spatial variation modelled by using a block structure or by smoothing the residuals spatially. The EM algorithm can be used to obtain point estimates, coupled with bootstrapping or asymptotic MLE estimates for standard errors. The second approach is Bayesian and based on a three- or four-tier hierarchical model, comprising a logistic regression with covariates for the data layer, a binary Markov Random field (MRF) for the underlying spatial process, and suitable priors for parameters in these main models. The three-parameter autologistic model is a particular MRF of interest. Markov chain Monte Carlo (MCMC) methods comprising hybrid Metropolis/Gibbs samplers is suitable for computation in this situation. Model performance can be gauged by MCMC diagnostics. Model choice can be assessed by incorporating another tier in the modelling hierarchy. This requires evaluation of a normalization constant, a notoriously difficult problem. Difficulty with estimating the normalization constant for the MRF can be overcome by using a path integral approach, although this is a highly computationally intensive method. Different methods of estimating ratios of normalization constants (N Cs) are investigated, including importance sampling Monte Carlo (ISMC), dependent Monte Carlo based on MCMC simulations (MCMC), and reverse logistic regression (RLR). I develop an idea present though not fully developed in the literature, and propose the Integrated mean canonical statistic (IMCS) method for estimating log NC ratios for binary MRFs. The IMCS method falls within the framework of the newly identified path sampling methods of Gelman & Meng (1998) and outperforms ISMC, MCMC and RLR. It also does not rely on simplifying assumptions, such as ignoring spatio-temporal dependence in the process. A thorough investigation is made of the application of IMCS to the three-parameter Autologistic model. This work introduces background computations required for the full implementation of the four-tier model in Chapter 7. Two different extensions of the three-tier model to a four-tier version are investigated. The first extension incorporates temporal dependence in the underlying spatio-temporal process. The second extensions allows the successes and failures in the data layer to depend on time. The MCMC computational method is extended to incorporate the extra layer. A major contribution of the thesis is the development of a fully Bayesian approach to inference for these hierarchical models for the first time. Note: The author of this thesis has agreed to make it open access but invites people downloading the thesis to send her an email via the 'Contact Author' function.

Algebraic attacks on clock-controlled stream ciphers

Stream ciphers are encryption algorithms used for ensuring the privacy of digital telecommunications. They have been widely used for encrypting military communications, satellite communications, pay TV encryption and for voice encryption of both fixed lined and wireless networks. The current multi year European project eSTREAM, which aims to select stream ciphers suitable for widespread adoptation, reflects the importance of this area of research. Stream ciphers consist of a keystream generator and an output function. Keystream generators produce a sequence that appears to be random, which is combined with the plaintext message using the output function. Most commonly, the output function is binary addition modulo two. Cryptanalysis of these ciphers focuses largely on analysis of the keystream generators and of relationships between the generator and the keystream it produces. Linear feedback shift registers are widely used components in building keystream generators, as the sequences they produce are well understood. Many types of attack have been proposed for breaking various LFSR based stream ciphers. A recent attack type is known as an algebraic attack. Algebraic attacks transform the problem of recovering the key into a problem of solving multivariate system of equations, which eventually recover the internal state bits or the key bits. This type of attack has been shown to be effective on a number of regularly clocked LFSR based stream ciphers. In this thesis, algebraic attacks are extended to a number of well known stream ciphers where at least one LFSR in the system is irregularly clocked. Applying algebriac attacks to these ciphers has only been discussed previously in the open literature for LILI-128. In this thesis, algebraic attacks are first applied to keystream generators using stop-and go clocking. Four ciphers belonging to this group are investigated: the Beth-Piper stop-and-go generator, the alternating step generator, the Gollmann cascade generator and the eSTREAM candidate: the Pomaranch cipher. It is shown that algebraic attacks are very effective on the first three of these ciphers. Although no effective algebraic attack was found for Pomaranch, the algebraic analysis lead to some interesting findings including weaknesses that may be exploited in future attacks. Algebraic attacks are then applied to keystream generators using (p; q) clocking. Two well known examples of such ciphers, the step1/step2 generator and the self decimated generator are investigated. Algebraic attacks are shown to be very powerful attack in recovering the internal state of these generators. A more complex clocking mechanism than either stop-and-go or the (p; q) clocking keystream generators is known as mutual clock control. In mutual clock control generators, the LFSRs control the clocking of each other. Four well known stream ciphers belonging to this group are investigated with respect to algebraic attacks: the Bilateral-stop-and-go generator, A5/1 stream cipher, Alpha 1 stream cipher, and the more recent eSTREAM proposal, the MICKEY stream ciphers. Some theoretical results with regards to the complexity of algebraic attacks on these ciphers are presented. The algebraic analysis of these ciphers showed that generally, it is hard to generate the system of equations required for an algebraic attack on these ciphers. As the algebraic attack could not be applied directly on these ciphers, a different approach was used, namely guessing some bits of the internal state, in order to reduce the degree of the equations. Finally, an algebraic attack on Alpha 1 that requires only 128 bits of keystream to recover the 128 internal state bits is presented. An essential process associated with stream cipher proposals is key initialization. Many recently proposed stream ciphers use an algorithm to initialize the large internal state with a smaller key and possibly publicly known initialization vectors. The effect of key initialization on the performance of algebraic attacks is also investigated in this thesis. The relationships between the two have not been investigated before in the open literature. The investigation is conducted on Trivium and Grain-128, two eSTREAM ciphers. It is shown that the key initialization process has an effect on the success of algebraic attacks, unlike other conventional attacks. In particular, the key initialization process allows an attacker to firstly generate a small number of equations of low degree and then perform an algebraic attack using multiple keystreams. The effect of the number of iterations performed during key initialization is investigated. It is shown that both the number of iterations and the maximum number of initialization vectors to be used with one key should be carefully chosen. Some experimental results on Trivium and Grain-128 are then presented. Finally, the security with respect to algebraic attacks of the well known LILI family of stream ciphers, including the unbroken LILI-II, is investigated. These are irregularly clock- controlled nonlinear filtered generators. While the structure is defined for the LILI family, a particular paramater choice defines a specific instance. Two well known such instances are LILI-128 and LILI-II. The security of these and other instances is investigated to identify which instances are vulnerable to algebraic attacks. The feasibility of recovering the key bits using algebraic attacks is then investigated for both LILI- 128 and LILI-II. Algebraic attacks which recover the internal state with less effort than exhaustive key search are possible for LILI-128 but not for LILI-II. Given the internal state at some point in time, the feasibility of recovering the key bits is also investigated, showing that the parameters used in the key initialization process, if poorly chosen, can lead to a key recovery using algebraic attacks.

Calculating shades of meaning in semantic spaces

This thesis introduces the problem of conceptual ambiguity, or Shades of Meaning (SoM) that can exist around a term or entity. As an example consider President Ronald Reagan the ex-president of the USA, there are many aspects to him that are captured in text; the Russian missile deal, the Iran-contra deal and others. Simply finding documents with the word “Reagan” in them is going to return results that cover many different shades of meaning related to "Reagan". Instead it may be desirable to retrieve results around a specific shade of meaning of "Reagan", e.g., all documents relating to the Iran-contra scandal. This thesis investigates computational methods for identifying shades of meaning around a word, or concept. This problem is related to word sense ambiguity, but is more subtle and based less on the particular syntactic structures associated with or around an instance of the term and more with the semantic contexts around it. A particularly noteworthy difference from typical word sense disambiguation is that shades of a concept are not known in advance. It is up to the algorithm itself to ascertain these subtleties. It is the key hypothesis of this thesis that reducing the number of dimensions in the representation of concepts is a key part of reducing sparseness and thus also crucial in discovering their SoMwithin a given corpus.

Pandemic (H1N1) 2009 Influenza Outbreak in Australia: Impact on Emergency Departments.

Executive summary Objective: The aims of this study were to identify the impact of Pandemic (H1N1) 2009 Influenza on Australian Emergency Departments (EDs) and their staff, and to inform planning, preparedness, and response management arrangements for future pandemics, as well as managing infectious patients presenting to EDs in everyday practice. Methods This study involved three elements: 1. The first element of the study was an examination of published material including published statistics. Standard literature research methods were used to identify relevant published articles. In addition, data about ED demand was obtained from Australian Government Department of Health and Ageing (DoHA) publications, with several state health departments providing more detailed data. 2. The second element of the study was a survey of Directors of Emergency Medicine identified with the assistance of the Australasian College for Emergency Medicine (ACEM). This survey retrieved data about demand for ED services and elicited qualitative comments on the impact of the pandemic on ED management. 3. The third element of the study was a survey of ED staff. A questionnaire was emailed to members of three professional colleges—the ACEM; the Australian College of Emergency Nursing (ACEN); and the College of Emergency Nursing Australasia (CENA). The overall response rate for the survey was 18.4%, with 618 usable responses from 3355 distributed questionnaires. Topics covered by the survey included ED conditions during the (H1N1) 2009 influenza pandemic; information received about Pandemic (H1N1) 2009 Influenza; pandemic plans; the impact of the pandemic on ED staff with respect to stress; illness prevention measures; support received from others in work role; staff and others’ illness during the pandemic; other factors causing ED staff to miss work during the pandemic; and vaccination against Pandemic (H1N1) 2009 Influenza. Both qualitative and quantitative data were collected and analysed. Results: The results obtained from Directors of Emergency Medicine quantifying the impact of the pandemic were too limited for interpretation. Data sourced from health departments and published sources demonstrated an increase in influenza-like illness (ILI) presentations of between one and a half and three times the normal level of presentations of ILIs. Directors of Emergency Medicine reported a reasonable level of preparation for the pandemic, with most reporting the use of pandemic plans that translated into relatively effective operational infection control responses. Directors reported a highly significant impact on EDs and their staff from the pandemic. Growth in demand and related ED congestion were highly significant factors causing distress within the departments. Most (64%) respondents established a ‘flu clinic’ either as part of Pandemic (H1N1) 2009 Influenza Outbreak in Australia: Impact on Emergency Departments. the ED operations or external to it. They did not note a significantly higher rate of sick leave than usual. Responses relating to the impact on staff were proportional to the size of the colleges. Most respondents felt strongly that Pandemic (H1N1) 2009 Influenza had a significant impact on demand in their ED, with most patients having low levels of clinical urgency. Most respondents felt that the pandemic had a negative impact on the care of other patients, and 94% revealed some increase in stress due to lack of space for patients, increased demand, and filling staff deficits. Levels of concern about themselves or their family members contracting the illness were less significant than expected. Nurses displayed significantly higher levels of stress overall, particularly in relation to skill-mix requirements, lack of supplies and equipment, and patient and patients’ family aggression. More than one-third of respondents became ill with an ILI. Whilst respondents themselves reported taking low levels of sick leave, respondents cited difficulties with replacing absent staff. Ranked from highest to lowest, respondents gained useful support from ED colleagues, ED administration, their hospital occupational health department, hospital administration, professional colleges, state health department, and their unions. Respondents were generally positive about the information they received overall; however, the volume of information was considered excessive and sometimes inconsistent. The media was criticised as scaremongering and sensationalist and as being the cause of many unnecessary presentations to EDs. Of concern to the investigators was that a large proportion (43%) of respondents did not know whether a pandemic plan existed for their department or hospital. A small number of staff reported being redeployed from their usual workplace for personal risk factors or operational reasons. As at the time of survey (29 October –18 December 2009), 26% of ED staff reported being vaccinated against Pandemic (H1N1) 2009 Influenza. Of those not vaccinated, half indicated they would ‘definitely’ or ‘probably’ not get vaccinated, with the main reasons being the vaccine was ‘rushed into production’, ‘not properly tested’, ‘came out too late’, or not needed due to prior infection or exposure, or due to the mildness of the disease. Conclusion: Pandemic (H1N1) 2009 Influenza had a significant impact on Australian Emergency Departments. The pandemic exposed problems in existing plans, particularly a lack of guidelines, general information overload, and confusion due to the lack of a single authoritative information source. Of concern was the high proportion of respondents who did not know if their hospital or department had a pandemic plan. Nationally, the pandemic communication strategy needs a detailed review, with more engagement with media networks to encourage responsible and consistent reporting. Also of concern was the low level of immunisation, and the low level of intention to accept vaccination. This is a problem seen in many previous studies relating to seasonal influenza and health care workers. The design of EDs needs to be addressed to better manage infectious patients. Significant workforce issues were confronted in this pandemic, including maintaining appropriate staffing levels; staff exposure to illness; access to, and appropriate use of, personal protective equipment (PPE); and the difficulties associated with working in PPE for prolonged periods. An administrative issue of note was the reporting requirement, which created considerable additional stress for staff within EDs. Peer and local support strategies helped ensure staff felt their needs were provided for, creating resilience, dependability, and stability in the ED workforce. Policies regarding the establishment of flu clinics need to be reviewed. The ability to create surge capacity within EDs by considering staffing, equipment, physical space, and stores is of primary importance for future pandemics.

Focus-score weighted super-resolution for uncooperative iris recognition at a distance and on the move

Uncooperative iris identification systems at a distance and on the move often suffer from poor resolution and poor focus of the captured iris images. The lack of pixel resolution and well-focused images significantly degrades the iris recognition performance. This paper proposes a new approach to incorporate the focus score into a reconstruction-based super-resolution process to generate a high resolution iris image from a low resolution and focus inconsistent video sequence of an eye. A reconstruction-based technique, which can incorporate middle and high frequency components from multiple low resolution frames into one desired super-resolved frame without introducing false high frequency components, is used. A new focus assessment approach is proposed for uncooperative iris at a distance and on the move to improve performance for variations in lighting, size and occlusion. A novel fusion scheme is then proposed to incorporate the proposed focus score into the super-resolution process. The experiments conducted on the The Multiple Biometric Grand Challenge portal database shows that our proposed approach achieves an EER of 2.1%, outperforming the existing state-of-the-art averaging signal-level fusion approach by 19.2% and the robust mean super-resolution approach by 8.7%.