Probability distributed time delays: integrating spatial effects into temporal models

Background In order to provide insights into the complex biochemical processes inside a cell, modelling approaches must find a balance between achieving an adequate representation of the physical phenomena and keeping the associated computational cost within reasonable limits. This issue is particularly stressed when spatial inhomogeneities have a significant effect on system's behaviour. In such cases, a spatially-resolved stochastic method can better portray the biological reality, but the corresponding computer simulations can in turn be prohibitively expensive. Results We present a method that incorporates spatial information by means of tailored, probability distributed time-delays. These distributions can be directly obtained by single in silico or a suitable set of in vitro experiments and are subsequently fed into a delay stochastic simulation algorithm (DSSA), achieving a good compromise between computational costs and a much more accurate representation of spatial processes such as molecular diffusion and translocation between cell compartments. Additionally, we present a novel alternative approach based on delay differential equations (DDE) that can be used in scenarios of high molecular concentrations and low noise propagation. Conclusions Our proposed methodologies accurately capture and incorporate certain spatial processes into temporal stochastic and deterministic simulations, increasing their accuracy at low computational costs. This is of particular importance given that time spans of cellular processes are generally larger (possibly by several orders of magnitude) than those achievable by current spatially-resolved stochastic simulators. Hence, our methodology allows users to explore cellular scenarios under the effects of diffusion and stochasticity in time spans that were, until now, simply unfeasible. Our methodologies are supported by theoretical considerations on the different modelling regimes, i.e. spatial vs. delay-temporal, as indicated by the corresponding Master Equations and presented elsewhere.

The use of temporal speech and lip information for multi-modal speaker identification via multi-stream HMMs

Investigates the use of temporal lip information, in conjunction with speech information, for robust, text-dependent speaker identification. We propose that significant speaker-dependent information can be obtained from moving lips, enabling speaker recognition systems to be highly robust in the presence of noise. The fusion structure for the audio and visual information is based around the use of multi-stream hidden Markov models (MSHMM), with audio and visual features forming two independent data streams. Recent work with multi-modal MSHMMs has been performed successfully for the task of speech recognition. The use of temporal lip information for speaker identification has been performed previously (T.J. Wark et al., 1998), however this has been restricted to output fusion via single-stream HMMs. We present an extension to this previous work, and show that a MSHMM is a valid structure for multi-modal speaker identification

Butterpaper, sweat & tears : the affective dimension of engaging students during the architectural critique

Considering how dominant a feature of architectural education the critique has been, and continues to be, little has been written about the affective dimension of engaging students during this key final stage of the design or documentation process. For most students, the critique is unlike any previous educational or life experience that they have ever confronted, and the abrupt change in the instructor’s role, from tutor to judge, can be disconcerting at a time when the student is feeling their most vulnerable. The fact that the period immediately leading up to the critique habitually entails not only a focused and sustained effort, but also sleepless nights of intensive work, further exacerbates this. The purpose of this paper is to recognise the affective phenomena influencing student engagement, during the critique. The participants of this research were second to fourth year architecture students at a major Australian university. Following the implementation of trials in alternative modes of critique in architectural design and technology studios, qualitative data was obtained from students, through questionnaires and interviews. Six indicators of engagement were investigated through this research: motivation and agency, transactional engagement with staff, transactional engagement with students, institutional support, active citizenship, and non-institutional support. This research confirms that affective phenomena play a significant role in the events of the critique; the relationship between instructor and student influences student engagement, as does the choreography and spatial planning of the critique environment; and these factors ultimately have an impact on the depth of student learning.

Sparse temporal representations for facial expression recognition

In automatic facial expression recognition, an increasing number of techniques had been proposed for in the literature that exploits the temporal nature of facial expressions. As all facial expressions are known to evolve over time, it is crucially important for a classifier to be capable of modelling their dynamics. We establish that the method of sparse representation (SR) classifiers proves to be a suitable candidate for this purpose, and subsequently propose a framework for expression dynamics to be efficiently incorporated into its current formulation. We additionally show that for the SR method to be applied effectively, then a certain threshold on image dimensionality must be enforced (unlike in facial recognition problems). Thirdly, we determined that recognition rates may be significantly influenced by the size of the projection matrix \Phi. To demonstrate these, a battery of experiments had been conducted on the CK+ dataset for the recognition of the seven prototypic expressions - anger, contempt, disgust, fear, happiness, sadness and surprise - and comparisons have been made between the proposed temporal-SR against the static-SR framework and state-of-the-art support vector machine.

Unusual Event Detection in Crowded Scenes Using Bag of LBPs in spatio-temporal patches

Modelling events in densely crowded environments remains challenging, due to the diversity of events and the noise in the scene. We propose a novel approach for anomalous event detection in crowded scenes using dynamic textures described by the Local Binary Patterns from Three Orthogonal Planes (LBP-TOP) descriptor. The scene is divided into spatio-temporal patches where LBP-TOP based dynamic textures are extracted. We apply hierarchical Bayesian models to detect the patches containing unusual events. Our method is an unsupervised approach, and it does not rely on object tracking or background subtraction. We show that our approach outperforms existing state of the art algorithms for anomalous event detection in UCSD dataset.

Temporal tracking of mineralization and transcriptional developments of shell formation during the early life history of pearl oyster Pinctada maxima

Molluscan larval ontogeny is a highly conserved process comprising three principal developmental stages. A characteristic unique to each of these stages is shell design, termed prodissoconch I, prodissoconch II and dissoconch. These shells vary in morphology, mineralogy and microstructure. The discrete temporal transitions in shell biomineralization between these larval stages are utilized in this study to investigate transcriptional involvement in several distinct biomineralization events. Scanning electron microscopy and X-ray diffraction analysis of P. maxima larvae and juveniles collected throughout post-embryonic ontogenesis, document the mineralogy and microstructure of each shelled stage as well as establishing a timeline for transitions in biomineralization. P. maxima larval samples most representative of these biomineralization distinctions and transitions were analyzed for differential gene expression on the microarray platform PmaxArray 1.0. A number of transcripts are reported as differentially expressed in correlation to the mineralization events of P. maxima larval ontogeny. Some of those isolated are known shell matrix genes while others are novel; these are discussed in relation to potential shell formation roles. This interdisciplinary investigation has linked the shell developments of P. maxima larval ontogeny with corresponding gene expression profiles, furthering the elucidation of shell biomineralization.

A temporal comparison of AltaVista Web searching

Major Web search engines, such as AltaVista, are essential tools in the quest to locate online information. This article reports research that used transaction log analysis to examine the characteristics and changes in AltaVista Web searching that occurred from 1998 to 2002. The research questions we examined are (1) What are the changes in AltaVista Web searching from 1998 to 2002? (2) What are the current characteristics of AltaVista searching, including the duration and frequency of search sessions? (3) What changes in the information needs of AltaVista users occurred between 1998 and 2002? The results of our research show (1) a move toward more interactivity with increases in session and query length, (2) with 70% of session durations at 5 minutes or less, the frequency of interaction is increasing, but it is happening very quickly, and (3) a broadening range of Web searchers' information needs, with the most frequent terms accounting for less than 1% of total term usage. We discuss the implications of these findings for the development of Web search engines. © 2005 Wiley Periodicals, Inc.

Charting the system : the integrated master schedule as a multi-level and poly-temporal boundary object in complex projects

This paper investigates the use of visual artifacts to represent a complex adaptive system (CAS). The integrated master schedule (IMS) is one of those visuals widely used in complex projects for scheduling, budgeting, and project management. In this paper, we discuss how the IMS outperforms the traditional timelines and acts as a ‘multi-level and poly-temporal boundary object’ that visually represents the CAS. We report the findings of a case study project on the way the IMS mapped interactions, interdependencies, constraints and fractal patterns in a complex project. Finally, we discuss how the IMS was utilised as a complex boundary object by eliciting commitment and development of shared mental models, and facilitating negotiation through the layers of multiple interpretations from stakeholders.

The implementation of performance based planning in Queensland under the integrated planning act 1997 : an evaluation of perceptions and planning schemes

Performance based planning is a form of planning regulation that is not well understood and the theoretical advantages of this type of planning are rarely achieved in practice. Normatively, this type of regulation relies on performance standards that are quantifiable and technically based which are designed to manage the effects of development, where performance standards provide certainty in respect of the level of performance and the means of achievement is flexible. Few empirical studies have attempted to examine how performance based planning has been conceptualised and implemented in practice. Existing literature is predominately anecdotal and consultant based (Baker et al. 2006) and has not sought to quantitatively examine how land use has been managed or determine how context influences implementation. The Integrated Planning Act 1997 (IPA) operated as Queensland’s principal planning legislation between March 1998 and December 2009. The IPA prevented Local Governments from prohibiting development or use and the term zone was absent from the legislation. While the IPA did not use the term performance based planning, the system is widely considered to be performance based in practice (e.g. Baker et al. 2006; Steele 2009a, 2009b). However, the degree to which the IPA and the planning system in Queensland is performance based is debated (e.g. Yearbury 1998; England 2004). Four research questions guided the research framework using Queensland as the case study. The questions sought to: determine if there is a common understanding of performance based planning; identify how performance based planning was expressed under the IPA; understand how performance based planning was implemented in plans; and explore the experiences of participants in the planning system. The research developed a performance adoption spectrum. The spectrum describes how performance based planning is implemented, ranging between pure and hybrid interpretations. An ex-post evaluation of seventeen IPA plans sought to determine plan performativity within the conceptual spectrum. Land use was examined from the procedural dimension of performance (Assessment Tables) and the substantive dimension of performance (Codes). A documentary analysis and forty one interviews supplemented the research. The analytical framework considered how context influenced performance based planning, including whether: the location of the local government affected land use management techniques; temporal variation in implementation exists; plan-making guidelines affected implementation; different perceptions of the concept exist; this type of planning applies to a range of spatial scales. Outcomes were viewed as the medium for determining the acceptability of development in Queensland, a significant departure from pure approaches found in the United States. Interviews highlighted the absence of plan-making direction in the IPA, which contributed to the confusion about the intended direction of the planning system and the myth that the IPA would guarantee a performance based system. A hybridised form of performance based planning evolved in Queensland which was dependent on prescriptive land use zones and specification of land use type, with some local governments going to extreme lengths to discourage certain activities in a predetermined manner. Context had varying degrees of influence on plan-making methods. Decision-making was found to be inconsistent and the system created a range of unforeseen consequences including difficulties associated with land valuation, increased development speculation, and the role of planners in court was found to be less critical than in the previous planning system.

Efficient preconditioning of the method of lines for solving nonlinear two-sided space-fractional diffusion equations

A standard method for the numerical solution of partial differential equations (PDEs) is the method of lines. In this approach the PDE is discretised in space using �finite di�fferences or similar techniques, and the resulting semidiscrete problem in time is integrated using an initial value problem solver. A significant challenge when applying the method of lines to fractional PDEs is that the non-local nature of the fractional derivatives results in a discretised system where each equation involves contributions from many (possibly every) spatial node(s). This has important consequences for the effi�ciency of the numerical solver. First, since the cost of evaluating the discrete equations is high, it is essential to minimise the number of evaluations required to advance the solution in time. Second, since the Jacobian matrix of the system is dense (partially or fully), methods that avoid the need to form and factorise this matrix are preferred. In this paper, we consider a nonlinear two-sided space-fractional di�ffusion equation in one spatial dimension. A key contribution of this paper is to demonstrate how an eff�ective preconditioner is crucial for improving the effi�ciency of the method of lines for solving this equation. In particular, we show how to construct suitable banded approximations to the system Jacobian for preconditioning purposes that permit high orders and large stepsizes to be used in the temporal integration, without requiring dense matrices to be formed. The results of numerical experiments are presented that demonstrate the effectiveness of this approach.