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Internal Representation (internal + representation)
Selected AbstractsCIRSE: A solvation energy estimator compatible with flexible protein docking and design applicationsPROTEIN SCIENCE, Issue 7 2006David S. Cerutti Abstract We present the Coordinate Internal Representation of Solvation Energy (CIRSE) for computing the solvation energy of protein configurations in terms of pairwise interactions between their atoms with analytic derivatives. Currently, CIRSE is trained to a Poisson/surface-area benchmark, but CIRSE is not meant to fit this benchmark exclusively. CIRSE predicts the overall solvation energy of protein structures from 331 NMR ensembles with 0.951 ± 0.047 correlation and predicts relative solvation energy changes between members of individual ensembles with an accuracy of 15.8 ± 9.6 kcal/mol. The energy of individual atoms in any of CIRSE's 17 types is predicted with at least 0.98 correlation. We apply the model in energy minimization, rotamer optimization, protein design, and protein docking applications. The CIRSE model shows some propensity to accumulate errors in energy minimization as well as rotamer optimization, but these errors are consistent enough that CIRSE correctly identifies the relative solvation energies of designed sequences as well as putative docked complexes. We analyze the errors accumulated by the CIRSE model during each type of simulation and suggest means of improving the model to be generally useful for all-atom simulations. [source] Cortical mechanisms of smooth pursuit eye movements with target blanking.EUROPEAN JOURNAL OF NEUROSCIENCE, Issue 5 2004An fMRI study Abstract Smooth pursuit eye movements are evoked by retinal image motion of visible moving objects and can also be driven by the internal representation of a target due to extraretinal mechanisms (e.g. efference copy). To delineate the corresponding neuronal correlates, functional magnetic resonance imaging at 1.5 T was applied during smooth pursuit at 10 °/s with continuous target presentation and target blanking for 1 s to 16 right-handed healthy males. Eye movements were assessed during scanning sessions by infra-red reflection oculography. Smooth pursuit performance was optimal when the target was visible but decreased to a residual velocity of about 30% of the velocity observed during continuous target presentation. Random effects analysis of the imaging data yielded an activation pattern for smooth pursuit in the absence of a visual target (in contrast to continuous target presentation) which included a number of cortical areas in which extraretinal information is available such as the frontal eye field, the superior parietal lobe, the anterior and the posterior intraparietal sulcus and the premotor cortex, and also the supplementary and the presupplementary eye field, the supramarginal gyrus, the dorsolateral prefrontal cortex, cerebellar areas and the basal ganglia. We suggest that cortical mechanisms such as prediction, visuo-spatial attention and transformation, multimodal visuomotor control and working memory are of special importance for maintaining smooth pursuit eye movements in the absence of a visible target. [source] A connectionist inference model for pattern-directed knowledge representationEXPERT SYSTEMS, Issue 2 2000I Mitchell In this paper we propose a connectionist model for variable binding. The model is topology dependent on the graph it builds based on the predicates available. The irregular connections between perceptron-like assemblies facilitate forward and backward chaining. The model treats the symbolic data as a sequence and represents the training set as a partially connected network using basic set and graph theory to form the internal representation. Inference is achieved by opportunistic reasoning via the bidirectional connections. Consequently, such activity stabilizes to a multigraph. This multigraph is composed of isomorphic subgraphs which all represent solutions to the query made. Such a model has a number of advantages over other methods in that irrelevant connections are avoided by superimposing positionally dependent sub-structures that are identical, variable binding can be encoded and multiple solutions can be extracted simultaneously. The model also has the ability to adapt its existing architecture when presented with new clauses and therefore add new relationships/rules to the model explicitly; this is done by some partial retraining of the network due to the superimposition properties. [source] Regional differences in hippocampal PKA immunoreactivity after training and reversal training in a spatial Y-maze taskHIPPOCAMPUS, Issue 5 2007Robbert Havekes Abstract It is suggested that the hippocampus functions as a comparator by making a comparison between the internal representation and actual sensory information from the environment (for instance, comparing a previously learned location of a food reward with an actual novel location of a food reward in a Y-maze). However, it remains unclear to what extent the various hippocampal regions contribute to this comparator function. One of the proteins known to be crucially involved in the formation of hippocampus-dependent long-term memory is the adenosine 3,,5, cyclic monophosphate dependent protein kinase (PKA). Here, we examined region-specific changes in immunoreactivity (ir) of the regulatory II,,, subunits of PKA (PKA RII,,,-ir) in the hippocampus during various stages of spatial learning in a Y-maze reference task. Thereafter, we compared changes in hippocampal PKA RII,,,-ir induced by training and reversal training in which the food reward was relocated to the previously unrewarded arm. We show that: (1) There was a clear correlation between behavioral performance and elevated PKA RII,,,-ir during the acquisition phase of both training and reversal training in area CA3 and dentate gyrus (DG), (2) PKA RII,,,-ir was similarly enhanced in area CA1 during the acquisition phase of reversal training, but did not correlate with behavioral performance, (3) PKA RII,,,-ir did not change during training or reversal training in the subiculum (SUB), (4) No changes in PKA RII,,, protein levels were found using Western blotting, and (5) AMPA receptor phosphorylation at serine 845 (S845p; the PKA site on the glutamate receptor 1 subunit (GluR1)), was enhanced selectively during the acquisition phase of reversal training. These findings reveal that training and reversal training induce region-specific changes in hippocampal PKA RII,,,-ir and suggest a differential involvement of hippocampal subregions in match-mismatch detection in case of Y-maze reference learning. Alterations in AMPA receptor regulation at the S845 site seems specifically related to the novelty detector function of the hippocampus important for match-mismatch detection. © 2007 Wiley-Liss, Inc. [source] Reorganizing web sites based on user access patternsINTELLIGENT SYSTEMS IN ACCOUNTING, FINANCE & MANAGEMENT, Issue 1 2002Yongjian Fu In this paper, an approach for reorganizing Web sites based on user access patterns is proposed. Our goal is to build adaptive Web sites by evolving site structure to facilitate user access. The approach consists of three steps: preprocessing, page classification, and site reorganization. In preprocessing, pages on a Web site are processed to create an internal representation of the site. Page access information of its users is extracted from the Web server log. In page classification, the Web pages on the site are classified into two categories, index pages and content pages, based on the page access information. After the pages are classified, in site reorganization, the Web site is examined to find better ways to organize and arrange the pages on the site. An algorithm for reorganizing Web sites has been developed. Our experiments on a large real data set show that the approach is efficient and practical for adaptive Web sites. Copyright © 2002 John Wiley & Sons, Ltd. [source] Error modeling and calibration of exteroceptive sensors for accurate mapping applicationsJOURNAL OF FIELD ROBOTICS (FORMERLY JOURNAL OF ROBOTIC SYSTEMS), Issue 1 2010James P. Underwood Reliable robotic perception and planning are critical to performing autonomous actions in uncertain, unstructured environments. In field robotic systems, automation is achieved by interpreting exteroceptive sensor information to infer something about the world. This is then mapped to provide a consistent spatial context, so that actions can be planned around the predicted future interaction of the robot and the world. The whole system is as reliable as the weakest link in this chain. In this paper, the term mapping is used broadly to describe the transformation of range-based exteroceptive sensor data (such as LIDAR or stereo vision) to a fixed navigation frame, so that it can be used to form an internal representation of the environment. The coordinate transformation from the sensor frame to the navigation frame is analyzed to produce a spatial error model that captures the dominant geometric and temporal sources of mapping error. This allows the mapping accuracy to be calculated at run time. A generic extrinsic calibration method for exteroceptive range-based sensors is then presented to determine the sensor location and orientation. This allows systematic errors in individual sensors to be minimized, and when multiple sensors are used, it minimizes the systematic contradiction between them to enable reliable multisensor data fusion. The mathematical derivations at the core of this model are not particularly novel or complicated, but the rigorous analysis and application to field robotics seems to be largely absent from the literature to date. The techniques in this paper are simple to implement, and they offer a significant improvement to the accuracy, precision, and integrity of mapped information. Consequently, they should be employed whenever maps are formed from range-based exteroceptive sensor data. © 2009 Wiley Periodicals, Inc. [source] Learning to Think: A Response to the Language of Thought Argument for InnatenessMIND & LANGUAGE, Issue 3 2005Christopher Viger I argue that because the logical/formal terms of natural languages are given a use-theory of meaning, unlike predicates, logical/formal terms might be learned without a mediating internal representation. In that case, our innate representational system might have less logical structure than a natural language, making it possible that we augment our innate representational system and improve our ability to think by learning a natural language. [source] Information Technology User Devices in Higher EducationNEW DIRECTIONS FOR HIGHER EDUCATION, Issue 115 2001Don McLaughlin System planners must understand that user devices serve as a translator between the technology's internal representation of information and what can be perceived, processed, and used by humans. [source] Motor foundations of higher cognition: similarities and differences in processing regular and violated perceptual sequences of different specificityEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 12 2009Andreja Bubic Abstract Processing perceptual sequences relies on the motor system, which is able to simulate the dynamics of the environment by developing internal representations of external events and using them to predict the incoming stimuli. Although it has previously been demonstrated that such models may incorporate predictions based on exact stimulus properties and single stimulus dimensions, it is not known whether they can also support abstract predictions pertaining to the level of stimulus categories. This issue was investigated within the present event-related functional magnetic resonance imaging study, which compared the processing of perceptual sequences of different specificity, namely those in which the sequential structure was based on the order of presentation of individual stimuli (token), and those in which such structure was defined by stimulus categories (type). The results obtained indicate a comparable engagement of the basic premotor,parietal network in processing both specific and categorical perceptual sequences. However, type sequences additionally elicited activations within the lateral prefrontal, occipital and posterior temporal regions that supported categorization in this task context. Introducing sequential deviants into token sequences activated parietotemporal and ventrolateral frontal cortices, whereas a less pronounced overall response, dominated by lateral prefrontal activation, was elicited by violations introduced into type sequences. Overall, the findings obtained suggest that, although forward models in perception may be able to incorporate expectations of lower specificity when compared to the motor domain, such processing is crucially dependent on additional contributions from lateral prefrontal as well as inferior occipital and temporal cortices that support categorization occurring in such a dynamic context. [source] Children's Insecure Representations of the Interparental Relationship and Their School Adjustment: The Mediating Role of Attention DifficultiesCHILD DEVELOPMENT, Issue 5 2008Patrick T. Davies This study examined the role of attention difficulties as a mediator of associations between children's insecure representations of the interparental relationship and their school adjustment in a sample of two hundred and sixteen 6-year-old children. Consistent with hypotheses, findings from structural equation models indicated that observer ratings of children's insecure representations of interparental relationships in a story completion task predicted computerized task assessments and parent reports of children's attention difficulties 1 year later. Children's attention difficulties, in turn, were associated with concurrent levels of school problems and increases in school problems over a 1-year period as indexed by teacher reports. Attention difficulties accounted for an average of 34% of the association between insecure internal representations and school problems. [source] Assessing Children's Emotional Security in the Interparental Relationship: The Security in the Interparental Subsystem ScalesCHILD DEVELOPMENT, Issue 2 2002Patrick T. Davies Guided by the emotional security hypothesis, this study reports on the development of a new self-report measure that assesses children's strategies for preserving emotional security in the context of interparental conflict. Participants were 924 sixth, seventh, and eighth graders and a subset of their mothers, fathers, and teachers. Exploratory and confirmatory factor analyses of the Security in the Interparental Subsystem (SIS) Scale supported a seven-factor solution, corresponding well to the three component processes (i.e., emotional reactivity, regulation of exposure to parent affect, and internal representations) outlined in the emotional security hypothesis. The SIS subscales demonstrated satisfactory internal consistency and test,retest reliability. Support for the validity of the SIS Scale is evidenced by its significant links with parent reports of children's overt reactivity to conflict, children's responses to interparental conflict simulations 6 months later, and children's psychological maladjustment and experiential histories with interparental conflict across multiple informants (i.e., child, mother, father, and teacher). Results are discussed in the context of developing recommendations for use of the SIS and advancing the emotional security hypothesis. [source] Evidence That Children and Adolescents Have Internal Models of Peer Interactions That Are Gender DifferentiatedCHILD DEVELOPMENT, Issue 3 2001Henry Markovits This study examined whether children's internal representations reflect gender differences that have been found in peer interactions. The dimensions examined were (1) preferences for dyadic or group situations, (2) whether children who are friends with a given target child are likely to be friends with each other, and (3) perceptions of the probability of knowing information about friends. Participants from preschool; grades 2, 6, 8, and 10; and college (N= 278) were asked questions about typical girls and boys. Results indicate that both girls and boys (1) rate typical boys as preferring group interactions more than do typical girls, a difference present as early as preschool; (2) rate typical boys as more likely than typical girls to be friends with one another if they are friends with the same target boy or gir,l respectively; and (3) rate typical girls as more likely than typical boys to know certain types of information about friends. These results are consistent with the existence of internal models of social interactions that are at least partially gender specific. [source] A Computational Model of Event Segmentation From Perceptual PredictionCOGNITIVE SCIENCE - A MULTIDISCIPLINARY JOURNAL, Issue 4 2007Jeremy R. Reynolds Abstract People tend to perceive ongoing continuous activity as series of discrete events. This partitioning of continuous activity may occur, in part, because events correspond to dynamic patterns that have recurred across different contexts. Recurring patterns may lead to reliable sequential dependencies in observers' experiences, which then can be used to guide perception. The current set of simulations investigated whether this statistical structure within events can be used 1) to develop stable internal representations that facilitate perception and 2) to learn when to update such representations in a self-organizing manner. These simulations demonstrate that experience with recurring patterns enables a system to accurately predict upcoming stimuli within an event, to identify boundaries between such events based on transient increases in prediction error, and to use such boundaries to improve prediction about subsequent activities. [source] | ||||||||||||||||