Context-aware visual exploration of molecular databases

Facilitating the visual exploration of scientific data has received increasing attention in the past decade or so. Especially in life science related application areas the amount of available data has grown at a breath taking pace. In this paper we describe an approach that allows for visual inspection of large collections of molecular compounds. In contrast to classical visualizations of such spaces we incorporate a specific focus of analysis, for example the outcome of a biological experiment such as high throughout screening results. The presented method uses this experimental data to select molecular fragments of the underlying molecules that have interesting properties and uses the resulting space to generate a two dimensional map based on a singular value decomposition algorithm and a self organizing map. Experiments on real datasets show that the resulting visual landscape groups molecules of similar chemical properties in densely connected regions.

Fast training of self organizing maps for the visual exploration of molecular compounds

Visual exploration of scientific data in life science area is a growing research field due to the large amount of available data. The Kohonen’s Self Organizing Map (SOM) is a widely used tool for visualization of multidimensional data. In this paper we present a fast learning algorithm for SOMs that uses a simulated annealing method to adapt the learning parameters. The algorithm has been adopted in a data analysis framework for the generation of similarity maps. Such maps provide an effective tool for the visual exploration of large and multi-dimensional input spaces. The approach has been applied to data generated during the High Throughput Screening of molecular compounds; the generated maps allow a visual exploration of molecules with similar topological properties. The experimental analysis on real world data from the National Cancer Institute shows the speed up of the proposed SOM training process in comparison to a traditional approach. The resulting visual landscape groups molecules with similar chemical properties in densely connected regions.

Students’ perception of the safety and value of a herbal vs. a conventional medicine for treating insomnia

University students suffer from variable sleep patterns including insomnia;[1] furthermore, the highest incidence of herbal use appears to be among college graduates.[2] Our objective was to test the perception of safety and value of herbal against conventional medicine for the treatment of insomnia in a non-pharmacy student population. We used an experimental design and bespoke vignettes that relayed the same effectiveness information to test our hypothesis that students would give higher ratings of safety and value to herbal product compared to conventional medicine. We tested another hypothesis that the addition of side-effect information would lower people’s perception of the safety and value of the herbal product to a greater extent than it would with the conventional medicine.

Judgments of path, not heading, guide locomotion

To steer a course through the world, people are almost entirely dependent on visual information, of which a key component is optic flow. In many models of locomotion, heading is described as the fundamental control variable; however, it has also been shown that fixating points along or near one's future path could be the basis of an efficient control solution. Here, the authors aim to establish how well observers can pinpoint instantaneous heading and path, by measuring their accuracy when looking at these features while traveling along straight and curved paths. The results showed that observers could identify both heading and path accurately (similar to 3 degrees) when traveling along straight paths, but on curved paths they were more accurate at identifying a point on their future path (similar to 5 degrees) than indicating their instantaneous heading (similar to 13 degrees). Furthermore, whereas participants could track changes in the tightness of their path, they were unable to accurately track the rate of change of heading. In light of these results, the authors suggest it is unlikely that heading is primarily used by the visual system to support active steering.

The distinct contributions of age of acquisition and word frequency in auditory word perception

We report two studies of the distinct effects that a word's age of acquisition (AoA) and frequency have on the mental lexicon. In the first study, a purely statistical analysis, we show that AoA and frequency are related in different ways to the phonological form and imageability of different words. In the second study, three groups of participants (34 seven-year-olds, 30 ten-year-olds, and 17 adults) took part in an auditory lexical decision task, with stimuli varying in AoA, frequency, length, neighbourhood density, and imageability. The principal result is that the influence of these different variables changes as a function of AoA: Neighbourhood density effects are apparent for early and late AoA words, but not for intermediate AoA, whereas imageability effects are apparent for intermediate AoA words but not for early or late AoA. These results are discussed from the perspective that AoA affects a word's representation, but frequency affects processing biases.

The effect of colored lenses on the visual evoked response in children with visual stress

Purpose. Some children with visual stress and/or headaches have fewer symptoms when wearing colored lenses. Although subjective reports of improved perception exist, few objective correlates of these effects have been established. Methods. In a pilot study, 10 children who wore Intuitive Colorimeter lenses, and claimed benefit, and two asymptomatic children were tested. Steady-state potentials were measured in response to low contrast patterns modulating at a frequency of 12 Hz. Four viewing conditions were compared: 1) no lens; 2) Colorimeter lens; 3) lens of complementary color; and 4) spectrally neutral lens with similar photopic transmission. Results. The asymptomatic children showed little or no difference between the lens and no lens conditions. When all the symptomatic children were tested together, a similar result was found. However, when the symptomatic children were divided into two groups depending on their symptoms, an interaction emerged. Children with visual stress but no headaches showed the largest amplitude visual evoked potential response in the no lens condition, whereas those children whose symptoms included severe headaches or migraine showed the largest amplitude visual evoked potential response when wearing their prescribed lens. Conclusions. The results suggest that it is possible to measure objective correlates of the beneficial subjective perceptual effects of colored lenses, at least in some children who have a history of migraine or severe headaches.

Optokinetic stimulation induces illusory movement of both out-of-the-body and on-the-body hand-held visual objects

The coding of body part location may depend upon both visual and proprioceptive information, and allows targets to be localized with respect to the body. The present study investigates the interaction between visual and proprioceptive localization systems under conditions of multisensory conflict induced by optokinetic stimulation (OKS). Healthy subjects were asked to estimate the apparent motion speed of a visual target (LED) that could be located either in the extrapersonal space (visual encoding only, V), or at the same distance, but stuck on the subject's right index finger-tip (visual and proprioceptive encoding, V-P). Additionally, the multisensory condition was performed with the index finger kept in position both passively (V-P passive) and actively (V-P active). Results showed that the visual stimulus was always perceived to move, irrespective of its out- or on-the-body location. Moreover, this apparent motion speed varied consistently with the speed of the moving OKS background in all conditions. Surprisingly, no differences were found between V-P active and V-P passive conditions in the speed of apparent motion. The persistence of the visual illusion during the active posture maintenance reveals a novel condition in which vision totally dominates over proprioceptive information, suggesting that the hand-held visual stimulus was perceived as a purely visual, external object despite its contact with the hand.

Picture book exposure elicits positive visual preferences in toddlers

Although the relationship between "mere exposure" and attitude enhancement is well established in the adult domain, there has been little similar work with children. This article examines whether toddlers' visual attention toward pictures of foods can be enhanced by repeated visual exposure to pictures of foods in a parent-administered picture book. We describe three studies that explored the number and nature of exposures required to elicit positive visual preferences for stimuli and the extent to which induced preferences generalize to other similar items. Results show that positive preferences for stimuli are easily and reliably induced in children and, importantly, that this effect of exposure is not restricted to the exposed stimulus per se but also applies to new representations of the exposed item. (C) 2009 Elsevier Inc. All rights reserved.

Neural systems in the visual control of steering

Visual control of locomotion is essential for most mammals and requires coordination between perceptual processes and action systems. Previous research on the neural systems engaged by self-motion has focused on heading perception, which is only one perceptual subcomponent. For effective steering, it is necessary to perceive an appropriate future path and then bring about the required change to heading. Using function magnetic resonance imaging in humans, we reveal a role for the parietal eye fields (PEFs) in directing spatially selective processes relating to future path information. A parietal area close to PEFs appears to be specialized for processing the future path information itself. Furthermore, a separate parietal area responds to visual position error signals, which occur when steering adjustments are imprecise. A network of three areas, the cerebellum, the supplementary eye fields, and dorsal premotor cortex, was found to be involved in generating appropriate motor responses for steering adjustments. This may reflect the demands of integrating visual inputs with the output response for the control device.

Adaptive control of event integration

Identifying 2 target stimuli in a rapid stream of visual symbols is much easier if the 2nd target appears immediately after the 1st target (i.e., at Lag 1) than if distractor stimuli intervene. As this phenomenon comes with a strong tendency to confuse the order of the targets, it seems to be due to the integration of both targets into the same attentional episode or object file. The authors investigated the degree to which people can control the temporal extension of their (episodic) integration windows by manipulating the expectations participants had with regard to the time available for target processing. As predicted, expecting more time to process increased the number of order confusions at Lag 1. This was true for between-subjects and within-subjects (trial-to-trial) manipulations, suggesting that integration windows can be adapted actively and rather quickly.

Semantic-associative visual content labelling and retrieval: A multimodal approach

A novel framework referred to as collaterally confirmed labelling (CCL) is proposed, aiming at localising the visual semantics to regions of interest in images with textual keywords. Both the primary image and collateral textual modalities are exploited in a mutually co-referencing and complementary fashion. The collateral content and context-based knowledge is used to bias the mapping from the low-level region-based visual primitives to the high-level visual concepts defined in a visual vocabulary. We introduce the notion of collateral context, which is represented as a co-occurrence matrix of the visual keywords. A collaborative mapping scheme is devised using statistical methods like Gaussian distribution or Euclidean distance together with collateral content and context-driven inference mechanism. We introduce a novel high-level visual content descriptor that is devised for performing semantic-based image classification and retrieval. The proposed image feature vector model is fundamentally underpinned by the CCL framework. Two different high-level image feature vector models are developed based on the CCL labelling of results for the purposes of image data clustering and retrieval, respectively. A subset of the Corel image collection has been used for evaluating our proposed method. The experimental results to-date already indicate that the proposed semantic-based visual content descriptors outperform both traditional visual and textual image feature models. (C) 2007 Elsevier B.V. All rights reserved.

Collaterally cued labelling framework underpinning semantic-level visual content descriptor

In this paper, we introduce a novel high-level visual content descriptor devised for performing semantic-based image classification and retrieval. The work can be treated as an attempt for bridging the so called "semantic gap". The proposed image feature vector model is fundamentally underpinned by an automatic image labelling framework, called Collaterally Cued Labelling (CCL), which incorporates the collateral knowledge extracted from the collateral texts accompanying the images with the state-of-the-art low-level visual feature extraction techniques for automatically assigning textual keywords to image regions. A subset of the Corel image collection was used for evaluating the proposed method. The experimental results indicate that our semantic-level visual content descriptors outperform both conventional visual and textual image feature models.

Action preparation helps and hinders perception of action.

Several theories of the mechanisms linking perception and action require that the links are bidirectional, but there is a lack of consensus on the effects that action has on perception. We investigated this by measuring visual event-related brain potentials to observed hand actions while participants prepared responses that were spatially compatible (e.g., both were on the left side of the body) or incompatible and action type compatible (e.g., both were finger taps) or incompatible, with observed actions. An early enhanced processing of spatially compatible stimuli was observed, which is likely due to spatial attention. This was followed by an attenuation of processing for both spatially and action type compatible stimuli, likely to be driven by efference copy signals that attenuate processing of predicted sensory consequences of actions. Attenuation was not response-modality specific; it was found for manual stimuli when participants prepared manual and vocal responses, in line with the hypothesis that action control is hierarchically organized. These results indicate that spatial attention and forward model prediction mechanisms have opposite, but temporally distinct, effects on perception. This hypothesis can explain the inconsistency of recent findings on action-perception links and thereby supports the view that sensorimotor links are bidirectional. Such effects of action on perception are likely to be crucial, not only for the control of our own actions but also in sociocultural interaction, allowing us to predict the reactions of others to our own actions.

Visual motion interferes with lexical decision on motion words

Embodied theories of cognition propose that neural substrates used in experiencing the referent of a word, for example perceiving upward motion, should be engaged in weaker form when that word, for example ‘rise’, is comprehended. Motivated by the finding that the perception of irrelevant background motion at near-threshold, but not supra-threshold, levels interferes with task execution, we assessed whether interference from near-threshold background motion was modulated by its congruence with the meaning of words (semantic content) when participants completed a lexical decision task (deciding if a string of letters is a real word or not). Reaction times for motion words, such as ‘rise’ or ‘fall’, were slower when the direction of visual motion and the ‘motion’ of the word were incongruent — but only when the visual motion was at nearthreshold levels. When motion was supra-threshold, the distribution of error rates, not reaction times, implicated low-level motion processing in the semantic processing of motion words. As the perception of near-threshold signals is not likely to be influenced by strategies, our results support a close contact between semantic information and perceptual systems.