Model refinement through high-performance computing: an agent-based HIV example

Background Recent advances in Immunology highlighted the importance of local properties on the overall progression of HIV infection. In particular, the gastrointestinal tract is seen as a key area during early infection, and the massive cell depletion associated with it may influence subsequent disease progression. This motivated the development of a large-scale agent-based model. Results Lymph nodes are explicitly implemented, and considerations on parallel computing permit large simulations and the inclusion of local features. The results obtained show that GI tract inclusion in the model leads to an accelerated disease progression, during both the early stages and the long-term evolution, compared to a theoretical, uniform model. Conclusions These results confirm the potential of treatment policies currently under investigation, which focus on this region. They also highlight the potential of this modelling framework, incorporating both agent-based and network-based components, in the context of complex systems where scaling-up alone does not result in models providing additional insights.

A probabilistic framework for analysing the compositionality of conceptual combinations

Conceptual combination performs a fundamental role in creating the broad range of compound phrases utilised in everyday language. While the systematicity and productivity of language provide a strong argument in favour of assuming compositionality, this very assumption is still regularly questioned in both cognitive science and philosophy. This article provides a novel probabilistic framework for assessing whether the semantics of conceptual combinations are compositional, and so can be considered as a function of the semantics of the constituent concepts, or not. Rather than adjudicating between different grades of compositionality, the framework presented here contributes formal methods for determining a clear dividing line between compositional and non-compositional semantics. Compositionality is equated with a joint probability distribution modelling how the constituent concepts in the combination are interpreted. Marginal selectivity is emphasised as a pivotal probabilistic constraint for the application of the Bell/CH and CHSH systems of inequalities (referred to collectively as Bell-type). Non-compositionality is then equated with either a failure of marginal selectivity, or, in the presence of marginal selectivity, with a violation of Bell-type inequalities. In both non-compositional scenarios, the conceptual combination cannot be modelled using a joint probability distribution with variables corresponding to the interpretation of the individual concepts. The framework is demonstrated by applying it to an empirical scenario of twenty-four non-lexicalised conceptual combinations.

Probabilistic orthographic cues to grammatical category in the brain

What helps us determine whether a word is a noun or a verb, without conscious awareness? We report on cues in the way individual English words are spelled, and, for the first time, identify their neural correlates via functional magnetic resonance imaging (fMRI). We used a lexical decision task with trisyllabic nouns and verbs containing orthographic cues that are either consistent or inconsistent with the spelling patterns of words from that grammatical category. Significant linear increases in response times and error rates were observed as orthography became less consistent, paralleled by significant linear decreases in blood oxygen level dependent (BOLD) signal in the left supramarginal gyrus of the left inferior parietal lobule, a brain region implicated in visual word recognition. A similar pattern was observed in the left superior parietal lobule. These findings align with an emergentist view of grammatical category processing which results from sensitivity to multiple probabilistic cues.

Probabilistic multi-tensor estimation using the tensor distribution function

Diffusion weighted magnetic resonance (MR) imaging is a powerful tool that can be employed to study white matter microstructure by examining the 3D displacement profile of water molecules in brain tissue. By applying diffusion-sensitized gradients along a minimum of 6 directions, second-order tensors can be computed to model dominant diffusion processes. However, conventional DTI is not sufficient to resolve crossing fiber tracts. Recently, a number of high-angular resolution schemes with greater than 6 gradient directions have been employed to address this issue. In this paper, we introduce the Tensor Distribution Function (TDF), a probability function defined on the space of symmetric positive definite matrices. Here, fiber crossing is modeled as an ensemble of Gaussian diffusion processes with weights specified by the TDF. Once this optimal TDF is determined, the diffusion orientation distribution function (ODF) can easily be computed by analytic integration of the resulting displacement probability function.

The development and refinement of the practice domain framework as a conceptual tool for understanding and guiding social care practice

This study identified the common factors that influence social care practice across disciplines (such as social work and psychology), practice fields, and geographical contexts and further developed the Practice Domain Framework as an empirically-based conceptual framework to assist practitioners in understanding practice complexities. The framework has application in critical reflection, professional supervision, interdisciplinary understanding, teamwork, management, teaching and research. A mixed-methods design was used to identify the components and structure of the refined framework. Eighteen influential factors were identified and organised into eight domains: the Societal, Structural, Organisational, Practice Field, Professional Practice, Accountable Practice, Community of Place, and Personal.

Bayesian refinement of association signals for 14 loci in 3 common diseases

To further investigate susceptibility loci identified by genome-wide association studies, we genotyped 5,500 SNPs across 14 associated regions in 8,000 samples from a control group and 3 diseases: type 2 diabetes (T2D), coronary artery disease (CAD) and Graves' disease. We defined, using Bayes theorem, credible sets of SNPs that were 95% likely, based on posterior probability, to contain the causal disease-associated SNPs. In 3 of the 14 regions, TCF7L2 (T2D), CTLA4 (Graves' disease) and CDKN2A-CDKN2B (T2D), much of the posterior probability rested on a single SNP, and, in 4 other regions (CDKN2A-CDKN2B (CAD) and CDKAL1, FTO and HHEX (T2D)), the 95% sets were small, thereby excluding most SNPs as potentially causal. Very few SNPs in our credible sets had annotated functions, illustrating the limitations in understanding the mechanisms underlying susceptibility to common diseases. Our results also show the value of more detailed mapping to target sequences for functional studies. © 2012 Nature America, Inc. All rights reserved.

Predicting tours and probabilistic simulation for BKZ lattice reduction algorithm

We investigate the terminating concept of BKZ reduction first introduced by Hanrot et al. [Crypto'11] and make extensive experiments to predict the number of tours necessary to obtain the best possible trade off between reduction time and quality. Then, we improve Buchmann and Lindner's result [Indocrypt'09] to find sub-lattice collision in SWIFFT. We illustrate that further improvement in time is possible through special setting of SWIFFT parameters and also through the combination of different reduction parameters adaptively. Our contribution also include a probabilistic simulation approach top-up deterministic simulation described by Chen and Nguyen [Asiacrypt'11] that can able to predict the Gram-Schmidt norms more accurately for large block sizes.

Probabilistic assessment of herbicide runoff from Japanese rice paddies: The effects of local meteorological conditions and site-specific water management

Uncertainty assessments of herbicide losses from rice paddies in Japan associated with local meteorological conditions and water management practices were performed using a pesticide fate and transport model, PCPF-1, under the Monte Carlo (MC) simulation scheme. First, MC simulations were conducted for five different cities with a prescribed water management scenario and a 10-year meteorological dataset of each city. The effectiveness of water management was observed regarding the reduction of pesticide runoff. However, a greater potential of pesticide runoff remained in Western Japan. Secondly, an extended analysis was attempted to evaluate the effects of local water management and meteorological conditions between the Chikugo River basin and the Sakura River basin using uncertainty inputs processed from observed water management data. The results showed that because of more severe rainfall events, significant pesticide runoff occurred in the Chikugo River basin even when appropriate irrigation practices were implemented. © Pesticide Science Society of Japan.

Permissions in Deontic Event-Calculus

Permissions are special case of deontic effects and play important role compliance. Essentially they are used to determine the obligations or prohibitions to contrary. A formal language e.g., temporal logic, event-calculus et., not able to represent permissions is doomed to be unable to represent most of the real-life legal norms. In this paper we address this issue and extend deontic-event-calculus (DEC) with new predicates for modelling permissions enabling it to elegantly capture the intuition of real-life cases of permissions.

Probabilistic load flow for distribution systems with uncertain PV generation

Large integration of solar Photo Voltaic (PV) in distribution network has resulted in over-voltage problems. Several control techniques are developed to address over-voltage problem using Deterministic Load Flow (DLF). However, intermittent characteristics of PV generation require Probabilistic Load Flow (PLF) to introduce variability in analysis that is ignored in DLF. The traditional PLF techniques are not suitable for distribution systems and suffer from several drawbacks such as computational burden (Monte Carlo, Conventional convolution), sensitive accuracy with the complexity of system (point estimation method), requirement of necessary linearization (multi-linear simulation) and convergence problem (Gram–Charlier expansion, Cornish Fisher expansion). In this research, Latin Hypercube Sampling with Cholesky Decomposition (LHS-CD) is used to quantify the over-voltage issues with and without the voltage control algorithm in the distribution network with active generation. LHS technique is verified with a test network and real system from an Australian distribution network service provider. Accuracy and computational burden of simulated results are also compared with Monte Carlo simulations.

Efficient probabilistic contingency analysis through a stability measure considering wind perturbation

The integration of stochastic wind power has accentuated a challenge for power system stability assessment. Since the power system is a time-variant system under wind generation fluctuations, pure time-domain simulations are difficult to provide real-time stability assessment. As a result, the worst-case scenario is simulated to give a very conservative assessment of system transient stability. In this study, a probabilistic contingency analysis through a stability measure method is proposed to provide a less conservative contingency analysis which covers 5-min wind fluctuations and a successive fault. This probabilistic approach would estimate the transfer limit of a critical line for a given fault with stochastic wind generation and active control devices in a multi-machine system. This approach achieves a lower computation cost and improved accuracy using a new stability measure and polynomial interpolation, and is feasible for online contingency analysis.

Development of probabilistic understanding in fourth grade

We analyzed the development of 4th-grade students’ understanding of the transition from experimental relative frequencies of outcomes to theoretical probabilities with a focus on the foundational statistical concepts of variation and expectation. We report students’ initial and changing expectations of the outcomes of tossing one and two coins, how they related the relative frequency from their physical and computersimulated trials to the theoretical probability, and how they created and interpreted theoretical probability models. Findings include students’ progression from an initial apparent equiprobability bias in predicting outcomes of tossing two coins through to representing the outcomes of increasing the number of trials. After observing the decreasing variation from the theoretical probability as the sample size increased, students developed a deeper understanding of the relationship between relative frequency of outcomes and theoretical probability as well as their respective associations with variation and expectation. Students’ final models indicated increasing levels of probabilistic understanding.

Numerical approximation of a fractional-in-space diffusion equation (II) - with nonhomogeneous boundary conditions

In this paper, a space fractional di®usion equation (SFDE) with non- homogeneous boundary conditions on a bounded domain is considered. A new matrix transfer technique (MTT) for solving the SFDE is proposed. The method is based on a matrix representation of the fractional-in-space operator and the novelty of this approach is that a standard discretisation of the operator leads to a system of linear ODEs with the matrix raised to the same fractional power. Analytic solutions of the SFDE are derived. Finally, some numerical results are given to demonstrate that the MTT is a computationally e±cient and accurate method for solving SFDE.

Integrating science through Bayesian Belief Networks : case study of Lyngbya in Moreton Bay

Bayesian Belief Networks (BBNs) are emerging as valuable tools for investigating complex ecological problems. In a BBN, the important variables in a problem are identified and causal relationships are represented graphically. Underpinning this is the probabilistic framework in which variables can take on a finite range of mutually exclusive states. Associated with each variable is a conditional probability table (CPT), showing the probability of a variable attaining each of its possible states conditioned on all possible combinations of it parents. Whilst the variables (nodes) are connected, the CPT attached to each node can be quantified independently. This allows each variable to be populated with the best data available, including expert opinion, simulation results or observed data. It also allows the information to be easily updated as better data become available ----- ----- This paper reports on the process of developing a BBN to better understand the initial rapid growth phase (initiation) of a marine cyanobacterium, Lyngbya majuscula, in Moreton Bay, Queensland. Anecdotal evidence suggests that Lyngbya blooms in this region have increased in severity and extent over the past decade. Lyngbya has been associated with acute dermatitis and a range of other health problems in humans. Blooms have been linked to ecosystem degradation and have also damaged commercial and recreational fisheries. However, the causes of blooms are as yet poorly understood.

Delay-dependent robust H-infinity control for uncertain systems with time-varying delay

This paper proposes a new approach for delay-dependent robust H-infinity stability analysis and control synthesis of uncertain systems with time-varying delay. The key features of the approach include the introduction of a new Lyapunov–Krasovskii functional, the construction of an augmented matrix with uncorrelated terms, and the employment of a tighter bounding technique. As a result, significant performance improvement is achieved in system analysis and synthesis without using either free weighting matrices or model transformation. Examples are given to demonstrate the effectiveness of the proposed approach.