Navigating, recognizing and describing urban spaces with vision and lasers

In this paper we describe a body of work aimed at extending the reach of mobile navigation and mapping. We describe how running topological and metric mapping and pose estimation processes concurrently, using vision and laser ranging, has produced a full six-degree-of-freedom outdoor navigation system. It is capable of producing intricate three-dimensional maps over many kilometers and in real time. We consider issues concerning the intrinsic quality of the built maps and describe our progress towards adding semantic labels to maps via scene de-construction and labeling. We show how our choices of representation, inference methods and use of both topological and metric techniques naturally allow us to fuse maps built from multiple sessions with no need for manual frame alignment or data association.

Look before you leap : a confidence-based method for selecting species criticality while avoiding negative populations in τ-leaping

The stochastic simulation algorithm was introduced by Gillespie and in a different form by Kurtz. There have been many attempts at accelerating the algorithm without deviating from the behavior of the simulated system. The crux of the explicit τ-leaping procedure is the use of Poisson random variables to approximate the number of occurrences of each type of reaction event during a carefully selected time period, τ. This method is acceptable providing the leap condition, that no propensity function changes “significantly” during any time-step, is met. Using this method there is a possibility that species numbers can, artificially, become negative. Several recent papers have demonstrated methods that avoid this situation. One such method classifies, as critical, those reactions in danger of sending species populations negative. At most, one of these critical reactions is allowed to occur in the next time-step. We argue that the criticality of a reactant species and its dependent reaction channels should be related to the probability of the species number becoming negative. This way only reactions that, if fired, produce a high probability of driving a reactant population negative are labeled critical. The number of firings of more reaction channels can be approximated using Poisson random variables thus speeding up the simulation while maintaining the accuracy. In implementing this revised method of criticality selection we make use of the probability distribution from which the random variable describing the change in species number is drawn. We give several numerical examples to demonstrate the effectiveness of our new method.

Bayesian models for the determination of resonant frequencies in a DI diesel engine

A time series method for the determination of combustion chamber resonant frequencies is outlined. This technique employs the use of Markov-chain Monte Carlo (MCMC) to infer parameters in a chosen model of the data. The development of the model is included and the resonant frequency is characterised as a function of time. Potential applications for cycle-by-cycle analysis are discussed and the bulk temperature of the gas and the trapped mass in the combustion chamber are evaluated as a function of time from resonant frequency information.

Systematics of the Ustilago-Sporisorium-Macalpinomyces complex of smut fungi

Smut fungi are important pathogens of grasses, including the cultivated crops maize, sorghum and sugarcane. Typically, smut fungi infect the inflorescence of their host plants. Three genera of smut fungi (Ustilago, Sporisorium and Macalpinomyces) form a complex with overlapping morphological characters, making species placement problematic. For example, the newly described Macalpinomyces mackinlayi possesses a combination of morphological characters such that it cannot be unambiguously accommodated in any of the three genera. Previous attempts to define Ustilago, Sporisorium and Macalpinomyces using morphology and molecular phylogenetics have highlighted the polyphyletic nature of the genera, but have failed to produce a satisfactory taxonomic resolution. A detailed systematic study of 137 smut species in the Ustilago-Sporisorium- Macalpinomyces complex was completed in the current work. Morphological and DNA sequence data from five loci were assessed with maximum likelihood and Bayesian inference to reconstruct a phylogeny of the complex. The phylogenetic hypotheses generated were used to identify morphological synapomorphies, some of which had previously been dismissed as a useful way to delimit the complex. These synapomorphic characters are the basis for a revised taxonomic classification of the Ustilago-Sporisorium-Macalpinomyces complex, which takes into account their morphological diversity and coevolution with their grass hosts. The new classification is based on a redescription of the type genus Sporisorium, and the establishment of four genera, described from newly recognised monophyletic groups, to accommodate species expelled from Sporisorium. Over 150 taxonomic combinations have been proposed as an outcome of this investigation, which makes a rigorous and objective contribution to the fungal systematics of these important plant pathogens.

A suspicious behaviour detection using a context space model for smart surveillance systems

Video surveillance systems using Closed Circuit Television (CCTV) cameras, is one of the fastest growing areas in the field of security technologies. However, the existing video surveillance systems are still not at a stage where they can be used for crime prevention. The systems rely heavily on human observers and are therefore limited by factors such as fatigue and monitoring capabilities over long periods of time. This work attempts to address these problems by proposing an automatic suspicious behaviour detection which utilises contextual information. The utilisation of contextual information is done via three main components: a context space model, a data stream clustering algorithm, and an inference algorithm. The utilisation of contextual information is still limited in the domain of suspicious behaviour detection. Furthermore, it is nearly impossible to correctly understand human behaviour without considering the context where it is observed. This work presents experiments using video feeds taken from CAVIAR dataset and a camera mounted on one of the buildings Z-Block) at the Queensland University of Technology, Australia. From these experiments, it is shown that by exploiting contextual information, the proposed system is able to make more accurate detections, especially of those behaviours which are only suspicious in some contexts while being normal in the others. Moreover, this information gives critical feedback to the system designers to refine the system.

Some empirical results for neo-Piagetian reasoning in novice programmers and the relationship to code explanation questions

Recent research on novice programmers has suggested that they pass through neo-Piagetian stages: sensorimotor, preoperational, and concrete operational stages, before eventually reaching programming competence at the formal operational stage. This paper presents empirical results in support of this neo-Piagetian perspective. The major novel contributions of this paper are empirical results for some exam questions aimed at testing novices for the concrete operational abilities to reason with quantities that are conserved, processes that are reversible, and properties that hold under transitive inference. While the questions we used had been proposed earlier by Lister, he did not present any data for how students performed on these questions. Our empirical results demonstrate that many students struggle to answer these problems, despite the apparent simplicity of these problems. We then compare student performance on these questions with their performance on six explain in plain English questions.

Data modelling with first-grade students

This paper argues for a renewed focus on statistical reasoning in the beginning school years, with opportunities for children to engage in data modelling. Results are reported from the first year of a 3-year longitudinal study in which three classes of first-grade children (6-year-olds) and their teachers engaged in data modelling activities. The theme of Looking after our Environment, part of the children’s science curriculum, provided the task context. The goals for the two activities addressed here included engaging children in core components of data modelling, namely, selecting attributes, structuring and representing data, identifying variation in data, and making predictions from given data. Results include the various ways in which children represented and re represented collected data, including attribute selection, and the metarepresentational competence they displayed in doing so. The “data lenses” through which the children dealt with informal inference (variation and prediction) are also reported.

L1 Learning Strategy Instruction does make a difference in EFL listening: An empirical study.

In language learning, listening is the basic skill which learners should begin to develop other skills, namely speaking, reading and writing. This sequence of language learning in most English as Foreign Language (EFL) settings goes against the stream, learning first reading and writing and later listening and speaking. This study investigates the effects of cognitive, process-based approach to instructing EFL listening strategies over 11 weeks during a semester in Persian (L1). Lower intermediate female participants (N = 50) came from a couple of EFL classrooms in an English Language Institute in Iran. The experimental group (n = 25) listened to their classroom activities using a methodology that led learners through four cognitive processes (guessing, making inference, identifying topics and repetition) in Persian was basically successful in EFL listening. The same teacher taught the control group (n = 25), which listened to the same classroom listening activities without any guided attention to the learning strategy process in Persian. A pre and post listening test made by a group of experts in the language institute tracked any development in light of cognitive learning strategy instruction in EFL listening through L1. The hypothesis was that the experimental group received the guided attention in L1 during the classroom listening activities made greater gains and was verified despite the partial improvement of the control group.

Trust-based automated recommendation making

Recommender systems are one of the recent inventions to deal with ever growing information overload in relation to the selection of goods and services in a global economy. Collaborative Filtering (CF) is one of the most popular techniques in recommender systems. The CF recommends items to a target user based on the preferences of a set of similar users known as the neighbours, generated from a database made up of the preferences of past users. With sufficient background information of item ratings, its performance is promising enough but research shows that it performs very poorly in a cold start situation where there is not enough previous rating data. As an alternative to ratings, trust between the users could be used to choose the neighbour for recommendation making. Better recommendations can be achieved using an inferred trust network which mimics the real world "friend of a friend" recommendations. To extend the boundaries of the neighbour, an effective trust inference technique is required. This thesis proposes a trust interference technique called Directed Series Parallel Graph (DSPG) which performs better than other popular trust inference algorithms such as TidalTrust and MoleTrust. Another problem is that reliable explicit trust data is not always available. In real life, people trust "word of mouth" recommendations made by people with similar interests. This is often assumed in the recommender system. By conducting a survey, we can confirm that interest similarity has a positive relationship with trust and this can be used to generate a trust network for recommendation. In this research, we also propose a new method called SimTrust for developing trust networks based on user's interest similarity in the absence of explicit trust data. To identify the interest similarity, we use user's personalised tagging information. However, we are interested in what resources the user chooses to tag, rather than the text of the tag applied. The commonalities of the resources being tagged by the users can be used to form the neighbours used in the automated recommender system. Our experimental results show that our proposed tag-similarity based method outperforms the traditional collaborative filtering approach which usually uses rating data.

Statistical modelling of wind effects on signal propagation for wireless sensor networks

A wireless sensor network system must have the ability to tolerate harsh environmental conditions and reduce communication failures. In a typical outdoor situation, the presence of wind can introduce movement in the foliage. This motion of vegetation structures causes large and rapid signal fading in the communication link and must be accounted for when deploying a wireless sensor network system in such conditions. This thesis examines the fading characteristics experienced by wireless sensor nodes due to the effect of varying wind speed in a foliage obstructed transmission path. It presents extensive measurement campaigns at two locations with the approach of a typical wireless sensor networks configuration. The significance of this research lies in the varied approaches of its different experiments, involving a variety of vegetation types, scenarios and the use of different polarisations (vertical and horizontal). Non–line of sight (NLoS) scenario conditions investigate the wind effect based on different vegetation densities including that of the Acacia tree, Dogbane tree and tall grass. Whereas the line of sight (LoS) scenario investigates the effect of wind when the grass is swaying and affecting the ground-reflected component of the signal. Vegetation type and scenarios are envisaged to simulate real life working conditions of wireless sensor network systems in outdoor foliated environments. The results from the measurements are presented in statistical models involving first and second order statistics. We found that in most of the cases, the fading amplitude could be approximated by both Lognormal and Nakagami distribution, whose m parameter was found to depend on received power fluctuations. Lognormal distribution is known as the result of slow fading characteristics due to shadowing. This study concludes that fading caused by variations in received power due to wind in wireless sensor networks systems are found to be insignificant. There is no notable difference in Nakagami m values for low, calm, and windy wind speed categories. It is also shown in the second order analysis, the duration of the deep fades are very short, 0.1 second for 10 dB attenuation below RMS level for vertical polarization and 0.01 second for 10 dB attenuation below RMS level for horizontal polarization. Another key finding is that the received signal strength for horizontal polarisation demonstrates more than 3 dB better performances than the vertical polarisation for LoS and near LoS (thin vegetation) conditions and up to 10 dB better for denser vegetation conditions.

Using approximate Bayesian computation to estimate transmission rates of nosocomial pathogens

In this paper, we apply a simulation based approach for estimating transmission rates of nosocomial pathogens. In particular, the objective is to infer the transmission rate between colonised health-care practitioners and uncolonised patients (and vice versa) solely from routinely collected incidence data. The method, using approximate Bayesian computation, is substantially less computer intensive and easier to implement than likelihood-based approaches we refer to here. We find through replacing the likelihood with a comparison of an efficient summary statistic between observed and simulated data that little is lost in the precision of estimated transmission rates. Furthermore, we investigate the impact of incorporating uncertainty in previously fixed parameters on the precision of the estimated transmission rates.

Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation

In recent years, a number of phylogenetic methods have been developed for estimating molecular rates and divergence dates under models that relax the molecular clock constraint by allowing rate change throughout the tree. These methods are being used with increasing frequency, but there have been few studies into their accuracy. We tested the accuracy of several relaxed-clock methods (penalized likelihood and Bayesian inference using various models of rate change) using nucleotide sequences simulated on a nine-taxon tree. When the sequences evolved with a constant rate, the methods were able to infer rates accurately, but estimates were more precise when a molecular clock was assumed. When the sequences evolved under a model of autocorrelated rate change, rates were accurately estimated using penalized likelihood and by Bayesian inference using lognormal and exponential models of rate change, while other models did not perform as well. When the sequences evolved under a model of uncorrelated rate change, only Bayesian inference using an exponential rate model performed well. Collectively, the results provide a strong recommendation for using the exponential model of rate change if a conservative approach to divergence time estimation is required. A case study is presented in which we use a simulation-based approach to examine the hypothesis of elevated rates in the Cambrian period, and it is found that these high rate estimates might be an artifact of the rate estimation method. If this bias is present, then the ages of metazoan divergences would be systematically underestimated. The results of this study have implications for studies of molecular rates and divergence dates.

Relaxed phylogenetics and dating with confidence

In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of “relaxed phylogenetics.” Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.

Evolutionary relationships and divergence times among the native rats of Australia

Background The genus Rattus is highly speciose and has a complex taxonomy that is not fully resolved. As shown previously there are two major groups within the genus, an Asian and an Australo-Papuan group. This study focuses on the Australo-Papuan group and particularly on the Australian rats. There are uncertainties regarding the number of species within the group and the relationships among them. We analysed 16 mitochondrial genomes, including seven novel genomes from six species, to help elucidate the evolutionary history of the Australian rats. We also demonstrate, from a larger dataset, the usefulness of short regions of the mitochondrial genome in identifying these rats at the species level. Results Analyses of 16 mitochondrial genomes representing species sampled from Australo-Papuan and Asian clades of Rattus indicate divergence of these two groups ~2.7 million years ago (Mya). Subsequent diversification of at least 4 lineages within the Australo-Papuan clade was rapid and occurred over the period from ~ 0.9-1.7 Mya, a finding that explains the difficulty in resolving some relationships within this clade. Phylogenetic analyses of our 126 taxon, but shorter sequence (1952 nucleotides long), Rattus database generally give well supported species clades. Conclusions Our whole mitochondrial genome analyses are concordant with a taxonomic division that places the native Australian rats into the Rattus fuscipes species group. We suggest the following order of divergence of the Australian species. R. fuscipes is the oldest lineage among the Australian rats and is not part of a New Guinean radiation. R. lutreolus is also within this Australian clade and shallower than R. tunneyi while the R. sordidus group is the shallowest lineage in the clade. The divergences within the R. sordidus and R. leucopus lineages occurring about half a million years ago support the hypotheses of more recent interchanges of rats between Australia and New Guinea. While problematic for inference of deeper divergences, we report that the analysis of shorter mitochondrial sequences is very useful for species identification in rats.

Computationally efficient methods for solving time-variable-order time-space fractional reaction-diffusion equation

Fractional differential equations are becoming more widely accepted as a powerful tool in modelling anomalous diffusion, which is exhibited by various materials and processes. Recently, researchers have suggested that rather than using constant order fractional operators, some processes are more accurately modelled using fractional orders that vary with time and/or space. In this paper we develop computationally efficient techniques for solving time-variable-order time-space fractional reaction-diffusion equations (tsfrde) using the finite difference scheme. We adopt the Coimbra variable order time fractional operator and variable order fractional Laplacian operator in space where both orders are functions of time. Because the fractional operator is nonlocal, it is challenging to efficiently deal with its long range dependence when using classical numerical techniques to solve such equations. The novelty of our method is that the numerical solution of the time-variable-order tsfrde is written in terms of a matrix function vector product at each time step. This product is approximated efficiently by the Lanczos method, which is a powerful iterative technique for approximating the action of a matrix function by projecting onto a Krylov subspace. Furthermore an adaptive preconditioner is constructed that dramatically reduces the size of the required Krylov subspaces and hence the overall computational cost. Numerical examples, including the variable-order fractional Fisher equation, are presented to demonstrate the accuracy and efficiency of the approach.