A topic based document relevance ranking model

Topic modelling has been widely used in the fields of information retrieval, text mining, machine learning, etc. In this paper, we propose a novel model, Pattern Enhanced Topic Model (PETM), which makes improvements to topic modelling by semantically representing topics with discriminative patterns, and also makes innovative contributions to information filtering by utilising the proposed PETM to determine document relevance based on topics distribution and maximum matched patterns proposed in this paper. Extensive experiments are conducted to evaluate the effectiveness of PETM by using the TREC data collection Reuters Corpus Volume 1. The results show that the proposed model significantly outperforms both state-of-the-art term-based models and pattern-based models.

The α5 subunit regulates the expression and function of α4*-containing neuronal nicotinic acetylcholine receptors in the ventral-tegmental area

Human genetic association studies have shown gene variants in the α5 subunit of the neuronal nicotinic receptor (nAChR) influence both ethanol and nicotine dependence. The α5 subunit is an accessory subunit that facilitates α4* nAChRs assembly in vitro. However, it is unknown whether this occurs in the brain, as there are few research tools to adequately address this question. As the α4*-containing nAChRs are highly expressed in the ventral tegmental area (VTA) we assessed the molecular, functional and pharmacological roles of α5 in α4*-containing nAChRs in the VTA. We utilized transgenic mice α5+/+(α4YFP) and α5-/-(α4YFP) that allow the direct visualization and measurement of α4-YFP expression and the effect of the presence (α5+/+) and absence of α5 (-/-) subunit, as the antibodies for detecting the α4* subunits of the nAChR are not specific. We performed voltage clamp electrophysiological experiments to study baseline nicotinic currents in VTA dopaminergic neurons. We show that in the presence of the α5 subunit, the overall expression of α4 subunit is increased significantly by 60% in the VTA. Furthermore, the α5 subunit strengthens baseline nAChR currents, suggesting the increased expression of α4* nAChRs to be likely on the cell surface. While the presence of the α5 subunit blunts the desensitization of nAChRs following nicotine exposure, it does not alter the amount of ethanol potentiation of VTA dopaminergic neurons. Our data demonstrates a major regulatory role for the α5 subunit in both the maintenance of α4*-containing nAChRs expression and in modulating nicotinic currents in VTA dopaminergic neurons. Additionally, the α5α4* nAChR in VTA dopaminergic neurons regulates the effect of nicotine but not ethanol on currents. Together, the data suggest that the α5 subunit is critical for controlling the expression and functional role of a population of α4*-containing nAChRs in the VTA.

Pattern-based topics for document modelling in information filtering

Many mature term-based or pattern-based approaches have been used in the field of information filtering to generate users’ information needs from a collection of documents. A fundamental assumption for these approaches is that the documents in the collection are all about one topic. However, in reality users’ interests can be diverse and the documents in the collection often involve multiple topics. Topic modelling, such as Latent Dirichlet Allocation (LDA), was proposed to generate statistical models to represent multiple topics in a collection of documents, and this has been widely utilized in the fields of machine learning and information retrieval, etc. But its effectiveness in information filtering has not been so well explored. Patterns are always thought to be more discriminative than single terms for describing documents. However, the enormous amount of discovered patterns hinder them from being effectively and efficiently used in real applications, therefore, selection of the most discriminative and representative patterns from the huge amount of discovered patterns becomes crucial. To deal with the above mentioned limitations and problems, in this paper, a novel information filtering model, Maximum matched Pattern-based Topic Model (MPBTM), is proposed. The main distinctive features of the proposed model include: (1) user information needs are generated in terms of multiple topics; (2) each topic is represented by patterns; (3) patterns are generated from topic models and are organized in terms of their statistical and taxonomic features, and; (4) the most discriminative and representative patterns, called Maximum Matched Patterns, are proposed to estimate the document relevance to the user’s information needs in order to filter out irrelevant documents. Extensive experiments are conducted to evaluate the effectiveness of the proposed model by using the TREC data collection Reuters Corpus Volume 1. The results show that the proposed model significantly outperforms both state-of-the-art term-based models and pattern-based models

Comparing methods for modelling spreading cell fronts

Spreading cell fronts play an essential role in many physiological processes. Classically, models of this process are based on the Fisher-Kolmogorov equation; however, such continuum representations are not always suitable as they do not explicitly represent behaviour at the level of individual cells. Additionally, many models examine only the large time asymptotic behaviour, where a travelling wave front with a constant speed has been established. Many experiments, such as a scratch assay, never display this asymptotic behaviour, and in these cases the transient behaviour must be taken into account. We examine the transient and asymptotic behaviour of moving cell fronts using techniques that go beyond the continuum approximation via a volume-excluding birth-migration process on a regular one-dimensional lattice. We approximate the averaged discrete results using three methods: (i) mean-field, (ii) pair-wise, and (iii) one-hole approximations. We discuss the performace of these methods, in comparison to the averaged discrete results, for a range of parameter space, examining both the transient and asymptotic behaviours. The one-hole approximation, based on techniques from statistical physics, is not capable of predicting transient behaviour but provides excellent agreement with the asymptotic behaviour of the averaged discrete results, provided that cells are proliferating fast enough relative to their rate of migration. The mean-field and pair-wise approximations give indistinguishable asymptotic results, which agree with the averaged discrete results when cells are migrating much more rapidly than they are proliferating. The pair-wise approximation performs better in the transient region than does the mean-field, despite having the same asymptotic behaviour. Our results show that each approximation only works in specific situations, thus we must be careful to use a suitable approximation for a given system, otherwise inaccurate predictions could be made.

Experimental verification of the modified spring-mass theory of fiber Bragg grating accelerometers using transverse forces

A fiber Bragg grating (FBG) accelerometer using transverse forces is more sensitive than one using axial forces with the same mass of the inertial object, because a barely stretched FBG fixed at its two ends is much more sensitive to transverse forces than axial ones. The spring-mass theory, with the assumption that the axial force changes little during the vibration, cannot accurately predict its sensitivity and resonant frequency in the gravitational direction because the assumption does not hold due to the fact that the FBG is barely prestretched. It was modified but still required experimental verification due to the limitations in the original experiments, such as the (1) friction between the inertial object and shell; (2) errors involved in estimating the time-domain records; (3) limited data; and (4) large interval ∼5 Hz between the tested frequencies in the frequency-response experiments. The experiments presented here have verified the modified theory by overcoming those limitations. On the frequency responses, it is observed that the optimal condition for simultaneously achieving high sensitivity and resonant frequency is at the infinitesimal prestretch. On the sensitivity at the same frequency, the experimental sensitivities of the FBG accelerometer with a 5.71 gram inertial object at 6 Hz (1.29, 1.19, 0.88, 0.64, and 0.31 nm/g at the 0.03, 0.69, 1.41, 1.93, and 3.16 nm prestretches, respectively) agree with the static sensitivities predicted (1.25, 1.14, 0.83, 0.61, and 0.29 nm/g, correspondingly). On the resonant frequency, (1) its assumption that the resonant frequencies in the forced and free vibrations are similar is experimentally verified; (2) its dependence on the distance between the FBG’s fixed ends is examined, showing it to be independent; (3) the predictions of the spring-mass theory and modified theory are compared with the experimental results, showing that the modified theory predicts more accurately. The modified theory can be used more confidently in guiding its design by predicting its static sensitivity and resonant frequency, and may have applications in other fields for the scenario where the spring-mass theory fails.

Perception Quality Evaluation with Visual and Infrared Cameras in Challenging Environmental Conditions

This work aims to contribute to the reliability and integrity of perceptual systems of unmanned ground vehicles (UGV). A method is proposed to evaluate the quality of sensor data prior to its use in a perception system by utilising a quality metric applied to heterogeneous sensor data such as visual and infrared camera images. The concept is illustrated specifically with sensor data that is evaluated prior to the use of the data in a standard SIFT feature extraction and matching technique. The method is then evaluated using various experimental data sets that were collected from a UGV in challenging environmental conditions, represented by the presence of airborne dust and smoke. In the first series of experiments, a motionless vehicle is observing a ’reference’ scene, then the method is extended to the case of a moving vehicle by compensating for its motion. This paper shows that it is possible to anticipate degradation of a perception algorithm by evaluating the input data prior to any actual execution of the algorithm.

A near-to-far non-parametric learning approach for estimating traversability in deformable terrain

It is well recognized that many scientifically interesting sites on Mars are located in rough terrains. Therefore, to enable safe autonomous operation of a planetary rover during exploration, the ability to accurately estimate terrain traversability is critical. In particular, this estimate needs to account for terrain deformation, which significantly affects the vehicle attitude and configuration. This paper presents an approach to estimate vehicle configuration, as a measure of traversability, in deformable terrain by learning the correlation between exteroceptive and proprioceptive information in experiments. We first perform traversability estimation with rigid terrain assumptions, then correlate the output with experienced vehicle configuration and terrain deformation using a multi-task Gaussian Process (GP) framework. Experimental validation of the proposed approach was performed on a prototype planetary rover and the vehicle attitude and configuration estimate was compared with state-of-the-art techniques. We demonstrate the ability of the approach to accurately estimate traversability with uncertainty in deformable terrain.

Science of winning soccer : emergent pattern-forming dynamics in association football

Quantitative analysis is increasingly being used in team sports to better understand performance in these stylized, delineated, complex social systems. Here we provide a first step toward understanding the pattern-forming dynamics that emerge from collective offensive and defensive behavior in team sports. We propose a novel method of analysis that captures how teams occupy sub-areas of the field as the ball changes location. We used the method to analyze a game of association football (soccer) based upon a hypothesis that local player numerical dominance is key to defensive stability and offensive opportunity. We found that the teams consistently allocated more players than their opponents in sub-areas of play closer to their own goal. This is consistent with a predominantly defensive strategy intended to prevent yielding even a single goal. We also find differences between the two teams' strategies: while both adopted the same distribution of defensive, midfield, and attacking players (a 4:3:3 system of play), one team was significantly more effective both in maintaining defensive and offensive numerical dominance for defensive stability and offensive opportunity. That team indeed won the match with an advantage of one goal (2 to 1) but the analysis shows the advantage in play was more pervasive than the single goal victory would indicate. Our focus on the local dynamics of team collective behavior is distinct from the traditional focus on individual player capability. It supports a broader view in which specific player abilities contribute within the context of the dynamics of multiplayer team coordination and coaching strategy. By applying this complex system analysis to association football, we can understand how players' and teams' strategies result in successful and unsuccessful relationships between teammates and opponents in the area of play.

The science behind the “stain”

It has been almost fi ve years since I fi rst published the article entitled “Much Ado About Staining” in Review of Optometry, which explored what we really knew in 2006 about the relationship between “corneal staining” and contact lens multipurpose solutions (MPS). This was published just prior to the controversial “staining grid.” While the Grid showed MPS-associated hyperfl uorescence under the slitlamp at two hours, it did not explain the “what” or “why” behind it; even so, many proponents of the Grid continue to suggest that it shows us which solution/lens combinations are “biocompatible” and which are not. New evidence suggests that the preservative-associated transient hyperfl uorescence (or PATH) observed at two hours after lens insertion is a benign phenomenon due to an interaction between fl uorescein, MPS preservatives, and corneal cell membranes. The misinterpretation of PATH as “real” corneal staining, like that observed in pathological conditions, may be due in part to the fact that there is not a lot of teaching regarding the true properties of fl uorescein and what is actually occurring when we see either PATH or corneal staining. To discuss the science of fl uorescein, corneal staining, and PATH, I have asked some of the preeminent research experts in the study of fl uorescence spectroscopy and corneal staining from around the world to share their new research and personal opinions on these topics...

The science of compliance

A survey conducted in Australia and the Asian region of the way in which contact lens wearers use and maintain their lenses reveals disturbingly low levels of compliance with recommended practice. Key problem areas are identified, and a plea is made for practitioners to help reverse this trend.

Scepticism and trust: two counterpoint essentials in science education for complex socio-scientific issues

In this response to Tom G. K. Bryce and Stephen P. Day’s (Cult Stud Sci Educ. doi:10.1007/s11422-013-9500-0, 2013) original article, I share with them their interest in the teaching of climate change in school science, but I widen it to include other contemporary complex socio-scientific issues that also need to be discussed. I use an alternative view of the relationship between science, technology and society, supported by evidence from both science and society, to suggest science-informed citizens as a more realistic outcome image of school science than the authors’ one of mini-scientists. The intellectual independence of students Bryce and Day assume, and intend for school science, is countered with an active intellectual dependence. It is only in relation to emerging and uncertain scientific contexts that students should be taught about scepticism, but they also need to learn when, and why to trust science as an antidote to the expressions of doubting it. Some suggestions for pedagogies that could lead to these new learnings are made. The very recent fifth report of the IPCC answers many of their concerns about climate change.

Distinguishing between mechanisms of cell aggregation using pair-correlation functions

Many cell types form clumps or aggregates when cultured in vitro through a variety of mechanisms including rapid cell proliferation, chemotaxis, or direct cell-to-cell contact. In this paper we develop an agent-based model to explore the formation of aggregates in cultures where cells are initially distributed uniformly, at random, on a two-dimensional substrate. Our model includes unbiased random cell motion, together with two mechanisms which can produce cell aggregates: (i) rapid cell proliferation, and (ii) a biased cell motility mechanism where cells can sense other cells within a finite range, and will tend to move towards areas with higher numbers of cells. We then introduce a pair-correlation function which allows us to quantify aspects of the spatial patterns produced by our agent-based model. In particular, these pair-correlation functions are able to detect differences between domains populated uniformly at random (i.e. at the exclusion complete spatial randomness (ECSR) state) and those where the proliferation and biased motion rules have been employed - even when such differences are not obvious to the naked eye. The pair-correlation function can also detect the emergence of a characteristic inter-aggregate distance which occurs when the biased motion mechanism is dominant, and is not observed when cell proliferation is the main mechanism of aggregate formation. This suggests that applying the pair-correlation function to experimental images of cell aggregates may provide information about the mechanism associated with observed aggregates. As a proof of concept, we perform such analysis for images of cancer cell aggregates, which are known to be associated with rapid proliferation. The results of our analysis are consistent with the predictions of the proliferation-based simulations, which supports the potential usefulness of pair correlation functions for providing insight into the mechanisms of aggregate formation.