Hierarchical classification of G-protein-coupled receptors with data-driven selection of attributes and classifiers

We address the important bioinformatics problem of predicting protein function from a protein's primary sequence. We consider the functional classification of G-Protein-Coupled Receptors (GPCRs), whose functions are specified in a class hierarchy. We tackle this task using a novel top-down hierarchical classification system where, for each node in the class hierarchy, the predictor attributes to be used in that node and the classifier to be applied to the selected attributes are chosen in a data-driven manner. Compared with a previous hierarchical classification system selecting classifiers only, our new system significantly reduced processing time without significantly sacrificing predictive accuracy.

Natural images dominate in binocular rivalry

Ecological approaches to perception have demonstrated that information encoding by the visual system is informed by the natural environment, both in terms of simple image attributes like luminance and contrast, and more complex relationships corresponding to Gestalt principles of perceptual organization. Here, we ask if this optimization biases perception of visual inputs that are perceptually bistable. Using the binocular rivalry paradigm, we designed stimuli that varied in either their spatiotemporal amplitude spectra or their phase spectra. We found that noise stimuli with “natural” amplitude spectra (i.e., amplitude content proportional to 1/f, where f is spatial or temporal frequency) dominate over those with any other systematic spectral slope, along both spatial and temporal dimensions. This could not be explained by perceived contrast measurements, and occurred even though all stimuli had equal energy. Calculating the effective contrast following attenuation by a model contrast sensitivity function suggested that the strong contrast dependency of rivalry provides the mechanism by which binocular vision is optimized for viewing natural images. We also compared rivalry between natural and phase-scrambled images and found a strong preference for natural phase spectra that could not be accounted for by observer biases in a control task. We propose that this phase specificity relates to contour information, and arises either from the activity of V1 complex cells, or from later visual areas, consistent with recent neuroimaging and single-cell work. Our findings demonstrate that human vision integrates information across space, time, and phase to select the input most likely to hold behavioral relevance.

Measuring the benefits of a psychology placement year

Placement programmes are considered to provide students with an induction into the work environment and a valuable learning experience. Aston University maintains one of the highest success rates of any UK university for graduate employment and it is thought that the placement year plays a large role in this success. However, the benefits of placements in theoretical subjects like Psychology are often less obvious than those for practical subjects like Optometry or Engineering. Here we compared Psychology students on the 3-year vs. the 4-year sandwich course on a number of attributes using both quantitative and qualitative methodologies. Final year students who had taken a placement year achieved significantly higher marks in their final year (F 1,407=31.52, p<0.001) and were rated more favourably by academic staff on a measure of transferable skills (F1,43= 11.08, p<0.005). In addition, post-graduation, students who had taken a placement year reported a better idea of their career direction and could be argued to be further on in terms of their career progression and pay levels. Qualitatively, focus groups of placement and non-placement students suggested a number of benefits of taking a placement year, including better time management, confidence and responsibility. Whether the benefits of a sandwich placement in a psychology degree outweigh the costs to students and their families, and the need for further research to identify the scope and longevity of possible early career benefits are discussed. © 2006 Taylor & Francis.

Semantics of query-driven communication of exact values

We address the question of how to communicate among distributed processes valuessuch as real numbers, continuous functions and geometrical solids with arbitrary precision, yet efficiently. We extend the established concept of lazy communication using streams of approximants by introducing explicit queries. We formalise this approach using protocols of a query-answer nature. Such protocols enable processes to provide valid approximations with certain accuracy and focusing on certain locality as demanded by the receiving processes through queries. A lattice-theoretic denotational semantics of channel and process behaviour is developed. Thequery space is modelled as a continuous lattice in which the top element denotes the query demanding all the information, whereas other elements denote queries demanding partial and/or local information. Answers are interpreted as elements of lattices constructed over suitable domains of approximations to the exact objects. An unanswered query is treated as an error anddenoted using the top element. The major novel characteristic of our semantic model is that it reflects the dependency of answerson queries. This enables the definition and analysis of an appropriate concept of convergence rate, by assigning an effort indicator to each query and a measure of information content to eachanswer. Thus we capture not only what function a process computes, but also how a process transforms the convergence rates from its inputs to its outputs. In future work these indicatorscan be used to capture further computational complexity measures. A robust prototype implementation of our model is available.

Orientation masking and cross-orientation suppression (XOS):implications for estimates of channel bandwidth

Most contemporary models of spatial vision include a cross-oriented route to suppression (masking from a broadly tuned inhibitory pool), which is most potent at low spatial and high temporal frequencies (T. S. Meese & D. J. Holmes, 2007). The influence of this pathway can elevate orientation-masking functions without exciting the target mechanism, and because early psychophysical estimates of filter bandwidth did not accommodate this, it is likely that they have been overestimated for this corner of stimulus space. Here we show that a transient 40% contrast mask causes substantial binocular threshold elevation for a transient vertical target, and this declines from a mask orientation of 0° to about 40° (indicating tuning), and then more gently to 90°, where it remains at a factor of ∼4. We also confirm that cross-orientation masking is diminished or abolished at high spatial frequencies and for sustained temporal modulation. We fitted a simple model of pedestal masking and cross-orientation suppression (XOS) to our data and those of G. C. Phillips and H. R. Wilson (1984) and found the dependency of orientation bandwidth on spatial frequency to be much less than previously supposed. An extension of our linear spatial pooling model of contrast gain control and dilution masking (T. S. Meese & R. J. Summers, 2007) is also shown to be consistent with our results using filter bandwidths of ±20°. Both models include tightly and broadly tuned components of divisive suppression. More generally, because XOS and/or dilution masking can affect the shape of orientation-masking curves, we caution that variations in bandwidth estimates might reflect variations in processes that have nothing to do with filter bandwidth.

The impact of context on pattern category learning and representation

Context traditionally has been regarded in vision research as a determinant for the interpretation of sensory information on the basis of previously acquired knowledge. Here we propose a novel, complementary perspective by showing that context also specifically affects visual category learning. In two experiments involving sets of Compound Gabor patterns we explored how context, as given by the stimulus set to be learned, affects the internal representation of pattern categories. In Experiment 1, we changed the (local) context of the individual signal classes by changing the configuration of the learning set. In Experiment 2, we varied the (global) context of a fixed class configuration by changing the degree of signal accentuation. Generalization performance was assessed in terms of the ability to recognize contrast-inverted versions of the learning patterns. Both contextual variations yielded distinct effects on learning and generalization thus indicating a change in internal category representation. Computer simulations suggest that the latter is related to changes in the set of attributes underlying the production rules of the categories. The implications of these findings for phenomena of contrast (in)variance in visual perception are discussed.

Early warnings of heart rate deterioration

Hospitals can experience difficulty in detecting and responding to early signs of patient deterioration leading to late intensive care referrals, excess mortality and morbidity, and increased hospital costs. Our study aims to explore potential indicators of physiological deterioration by the analysis of vital-signs. The dataset used comprises heart rate (HR) measurements from MIMIC II waveform database, taken from six patients admitted to the Intensive Care Unit (ICU) and diagnosed with severe sepsis. Different indicators were considered: 1) generic early warning indicators used in ecosystems analysis (autocorrelation at-1-lag (ACF1), standard deviation (SD), skewness, kurtosis and heteroskedasticity) and 2) entropy analysis (kernel entropy and multi scale entropy). Our preliminary findings suggest that when a critical transition is approaching, the equilibrium state changes what is visible in the ACF1 and SD values, but also by the analysis of the entropy. Entropy allows to characterize the complexity of the time series during the hospital stay and can be used as an indicator of regime shifts in a patient’s condition. One of the main problems is its dependency of the scale used. Our results demonstrate that different entropy scales should be used depending of the level of entropy verified.

Pyrolysis and combustion of municipal solid wastes:evaluation of synergistic effects using TGA-MS

A thermogravimetric methodology was developed to investigate and semi-quantify the extent of synergistic effects during pyrolysis and combustion of municipal solid waste (MSW). Results from TGA-MS were used to compare the pyrolysis and combustion characteristics of single municipal solid waste components (polyvinyl chloride (PVC), polypropylene (PP), polystyrene (PS), branches (BR), leaves (LV), grass (GR), packaging paper (PK), hygienic paper (HP) and cardboard (CB)) and a mixture (MX) of PP, BR and CB. Samples were heated under dynamic conditions at 20°C/min from 25°C to 1000°C with the continuous record of their main evolved fragments. Synergistic effects were evaluated by comparing experimental and calculated weight losses and relative areas of MS peaks. Pyrolysis of the mixture happened in two stages, with the release of H2, CH4, H2O, CO and CO2 between 200 and 415°C and the release of CH4, CxHy, CO and CO2 between 415 and 525°C. Negative synergistic effect in the 1st stage was attributed to the presence of PP where the release of hydrocarbons and CO2 from BR and CB was inhibited, whereas positive synergistic effects were observed during the 2nd degradation stage. In a second part of the study, synergistic effects were related to the dependency of the effective activation energy (Eα) versus the conversion (α). Higher Eαs were obtained for MX during its 1st stage of pyrolysis and lower Eαs for the 2nd stage when compared to the individual components. On the other hand, mostly positive synergistic effects were observed during the combustion of the same mixture, for which lower Eαs were recorded.

Timing continuous or discontinuous movements across effectors specified by different pacing modalities and intervals

Sensorimotor synchronization is hypothesized to arise through two different processes, associated with continuous or discontinuous rhythmic movements. This study investigated synchronization of continuous and discontinuous movements to different pacing signals (auditory or visual), pacing interval (500, 650, 800, 950 ms) and across effectors (non-dominant vs. non-dominant hand). The results showed that mean and variability of asynchronization errors were consistently smaller for discontinuous movements compared to continuous movements. Furthermore, both movement types were timed more accurately with auditory pacing compared to visual pacing and were more accurate with the dominant hand. Shortening the pacing interval also improved sensorimotor synchronization accuracy in both continuous and discontinuous movements. These results show the dependency of temporal control of movements on the nature of the motor task, the type and rate of extrinsic sensory information as well as the efficiency of the motor actuators for sensory integration.

Comparing dissimilarity measures for content-based image retrieval

Dissimilarity measurement plays a crucial role in content-based image retrieval, where data objects and queries are represented as vectors in high-dimensional content feature spaces. Given the large number of dissimilarity measures that exist in many fields, a crucial research question arises: Is there a dependency, if yes, what is the dependency, of a dissimilarity measure’s retrieval performance, on different feature spaces? In this paper, we summarize fourteen core dissimilarity measures and classify them into three categories. A systematic performance comparison is carried out to test the effectiveness of these dissimilarity measures with six different feature spaces and some of their combinations on the Corel image collection. From our experimental results, we have drawn a number of observations and insights on dissimilarity measurement in content-based image retrieval, which will lay a foundation for developing more effective image search technologies.

Fully probabilistic control for stochastic nonlinear control systems with input dependent noise

Robust controllers for nonlinear stochastic systems with functional uncertainties can be consistently designed using probabilistic control methods. In this paper a generalised probabilistic controller design for the minimisation of the Kullback-Leibler divergence between the actual joint probability density function (pdf) of the closed loop control system, and an ideal joint pdf is presented emphasising how the uncertainty can be systematically incorporated in the absence of reliable systems models. To achieve this objective all probabilistic models of the system are estimated from process data using mixture density networks (MDNs) where all the parameters of the estimated pdfs are taken to be state and control input dependent. Based on this dependency of the density parameters on the input values, explicit formulations to the construction of optimal generalised probabilistic controllers are obtained through the techniques of dynamic programming and adaptive critic methods. Using the proposed generalised probabilistic controller, the conditional joint pdfs can be made to follow the ideal ones. A simulation example is used to demonstrate the implementation of the algorithm and encouraging results are obtained.

An unsupervised Bayesian modelling approach to storyline detection from news articles

Storyline detection from news articles aims at summarizing events described under a certain news topic and revealing how those events evolve over time. It is a difficult task because it requires first the detection of events from news articles published in different time periods and then the construction of storylines by linking events into coherent news stories. Moreover, each storyline has different hierarchical structures which are dependent across epochs. Existing approaches often ignore the dependency of hierarchical structures in storyline generation. In this paper, we propose an unsupervised Bayesian model, called dynamic storyline detection model, to extract structured representations and evolution patterns of storylines. The proposed model is evaluated on a large scale news corpus. Experimental results show that our proposed model outperforms several baseline approaches.

Transaction attributes and buyer-supplier relationships in AMT acquisition and implementation:the case of Malaysia

This paper explores how transaction attributes of technology affect differences in the relationship between technology buyers and suppliers. It also examines the impact on performance of different patterns of relationship between technology buyers and suppliers. Data obtained from 147 manufacturing firms in Malaysia are used to test several hypotheses, which were derived from a review of the literature on technology, transaction cost theory and buyer–supplier relationships (BSR). The research results indicate that the higher the level of technological complexity, specificity and uncertainty, the more firms are likely to engage in a closer relationship with technology suppliers. Even though the majority of firms reported improvements in their performance, results indicate that firms demonstrating a closer relationship with technology suppliers are more likely to achieve higher levels of performance than those that do not. It is also shown that with high levels of transaction attribute, implementation performance suffers more when firms have weak relationships with technology suppliers than with moderate and low levels of transaction attribute.

Valuing transferred machine tool technology:Relating value to product attributes and preferences of acquirers

The value of technology and the appropriate form of transfer arrangement are important questions to be resolved when transferring technology between Western manufacturing firms and partners in industrialising and developing countries. This article reports on surveys carried out in the machine tool industries in the UK and China to establish the differences and similarities between owners and acquirers of technology regarding the relative importance of the factors they evaluate, and the assessments they make, when considering a technology transfer. It also outlines the development of a framework for technology valuation. The survey results indicate that the value of product technology is related to superior technical performance, especially on reliability and functionality, and the prospects of premium prices and increased sales of the technology transfer based machine tools. Access to markets is the main objective of UK companies, while Chinese companies are concerned about improving their technological capability. There are significant risks, especially related to performance in the market, and while owners and acquirers have benefited in the short term, the long term collaboration required for strategic benefits has been difficult to achieve because of the different priorities of the owners and the acquirers.