Machine learning for predictive condensed-phase simulation

We show how machine learning techniques based on Bayesian inference can be used to reach new levels of realism in the computer simulation of molecular materials, focusing here on water. We train our machine-learning algorithm using accurate, correlated quantum chemistry, and predict energies and forces in molecular aggregates ranging from clusters to solid and liquid phases. The widely used electronic-structure methods based on density-functional theory (DFT) give poor accuracy for molecular materials like water, and we show how our techniques can be used to generate systematically improvable corrections to DFT. The resulting corrected DFT scheme gives remarkably accurate predictions for the relative energies of small water clusters and of different ice structures, and greatly improves the description of the structure and dynamics of liquid water.

Reinforcement learning using a continuous time actor-critic framework with spiking neurons.

Animals repeat rewarded behaviors, but the physiological basis of reward-based learning has only been partially elucidated. On one hand, experimental evidence shows that the neuromodulator dopamine carries information about rewards and affects synaptic plasticity. On the other hand, the theory of reinforcement learning provides a framework for reward-based learning. Recent models of reward-modulated spike-timing-dependent plasticity have made first steps towards bridging the gap between the two approaches, but faced two problems. First, reinforcement learning is typically formulated in a discrete framework, ill-adapted to the description of natural situations. Second, biologically plausible models of reward-modulated spike-timing-dependent plasticity require precise calculation of the reward prediction error, yet it remains to be shown how this can be computed by neurons. Here we propose a solution to these problems by extending the continuous temporal difference (TD) learning of Doya (2000) to the case of spiking neurons in an actor-critic network operating in continuous time, and with continuous state and action representations. In our model, the critic learns to predict expected future rewards in real time. Its activity, together with actual rewards, conditions the delivery of a neuromodulatory TD signal to itself and to the actor, which is responsible for action choice. In simulations, we show that such an architecture can solve a Morris water-maze-like navigation task, in a number of trials consistent with reported animal performance. We also use our model to solve the acrobot and the cartpole problems, two complex motor control tasks. Our model provides a plausible way of computing reward prediction error in the brain. Moreover, the analytically derived learning rule is consistent with experimental evidence for dopamine-modulated spike-timing-dependent plasticity.

Viruses' complete genomes classification based on geometrical learning

In this paper, we proposed a method of classification for viruses' complete genomes based on graph geometrical theory in order to viruses classification. Firstly, a model of triangular geometrical graph was put forward, and then constructed feature-space-samples-graphs for classes of viruses' complete genomes in feature space after feature extraction and normalization. Finally, we studied an algorithm for classification of viruses' complete genomes based on feature-space-samples-graphs. Compared with the BLAST algorithm, experiments prove its efficiency.

Opening doors as well as banging on tables. An assessment of UNISON/employer partnerships on learning in the UK public sector.

The academic debate on partnerships has so far mainly focused on whether there are mutual gains for both unions and employers and whether they support or undermine branch organisation. This debate is here assessed in relation to learning partnerships, which are considered to be a distinctive form of partnership and represent a process of institution-building.

Reconceptualising moderation in asynchronous online discussions using grounded theory.

This paper reports a grounded theory study of e-moderation of asynchronous online discussions, to explore the processes by which tutors in higher education decide when and how to e-moderate. It aims to construct a theory of e-moderation based on some key factors which appear to influence e-moderation. It discusses previous research on the definition and practice of e-moderation, and then describes the study, which involved four e-moderators working in two different university contexts. Key themes on e-moderation, which emerged using a grounded theory approach, are discussed. It proposes a paradigm framework for e-moderation and suggests that as a facilitative activity, it should be sufficiently contained within ‘a ring-fenced learning arena’. Factors outwith and inside the ring-fence which appear to influence e-moderation and their implications for future theory development and validation are discussed. Keywords: e-moderation; grounded theory; online learning; asynchronous discussions; ring-fence

Choices of approaches in e-moderation: conclusions from a grounded theory study

Much has been published in recent years about the desirable nature of facilitated interactions in on-line discussions with educational purposes. However little has been reported about the roles which tutors actually adopt in real life learning contexts, how these range between ‘tutoring, ‘managing’ and ‘facilitating’, and what the distinctions between these three roles may be. In this paper choices of priorities in e-moderation, which were made in three naturalistic (real life) case studies by three higher education practitioners, are identified and discussed. These contrasting approaches were captured and analysed using grounded theory principles. The paper also discusses these occasions when the facilitation was less effective than might have been desired. It finally summarises the potential of various approaches within e-moderation – and some of the attendant risks. The finding is that principles and practices developed for face-to-face support of student-directed learning were found equally applicable in e-moderated online group work, despite several significant differences between the two types of setting. Keywords: higher education, e-learning, e-moderation, asynchronous discussions, learning outcomes, grounded theory

Learning and Production of Movement Sequences: Behavioral, Neurophysiological, and Modeling Perspectives

A growing wave of behavioral studies, using a wide variety of paradigms that were introduced or greatly refined in recent years, has generated a new wealth of parametric observations about serial order behavior. What was a mere trickle of neurophysiological studies has grown to a more steady stream of probes of neural sites and mechanisms underlying sequential behavior. Moreover, simulation models of serial behavior generation have begun to open a channel to link cellular dynamics with cognitive and behavioral dynamics. Here we summarize the major results from prominent sequence learning and performance tasks, namely immediate serial recall, typing, 2XN, discrete sequence production, and serial reaction time. These populate a continuum from higher to lower degrees of internal control of sequential organization. The main movement classes covered are speech and keypressing, both involving small amplitude movements that are very amenable to parametric study. A brief synopsis of classes of serial order models, vis-à-vis the detailing of major effects found in the behavioral data, leads to a focus on competitive queuing (CQ) models. Recently, the many behavioral predictive successes of CQ models have been joined by successful prediction of distinctively patterend electrophysiological recordings in prefrontal cortex, wherein parallel activation dynamics of multiple neural ensembles strikingly matches the parallel dynamics predicted by CQ theory. An extended CQ simulation model-the N-STREAMS neural network model-is then examined to highlight issues in ongoing attemptes to accomodate a broader range of behavioral and neurophysiological data within a CQ-consistent theory. Important contemporary issues such as the nature of working memory representations for sequential behavior, and the development and role of chunks in hierarchial control are prominent throughout.

Spikes, Synchrony, and Attentive Learning by Laminar Thalamocortical Circuits

This article develops the Synchronous Matching Adaptive Resonance Theory (SMART) neural model to explain how the brain may coordinate multiple levels of thalamocortical and corticocortical processing to rapidly learn, and stably remember, important information about a changing world. The model clarifies how bottom-up and top-down processes work together to realize this goal, notably how processes of learning, expectation, attention, resonance, and synchrony are coordinated. The model hereby clarifies, for the first time, how the following levels of brain organization coexist to realize cognitive processing properties that regulate fast learning and stable memory of brain representations: single cell properties, such as spiking dynamics, spike-timing-dependent plasticity (STDP), and acetylcholine modulation; detailed laminar thalamic and cortical circuit designs and their interactions; aggregate cell recordings, such as current-source densities and local field potentials; and single cell and large-scale inter-areal oscillations in the gamma and beta frequency domains. In particular, the model predicts how laminar circuits of multiple cortical areas interact with primary and higher-order specific thalamic nuclei and nonspecific thalamic nuclei to carry out attentive visual learning and information processing. The model simulates how synchronization of neuronal spiking occurs within and across brain regions, and triggers STDP. Matches between bottom-up adaptively filtered input patterns and learned top-down expectations cause gamma oscillations that support attention, resonance, and learning. Mismatches inhibit learning while causing beta oscillations during reset and hypothesis testing operations that are initiated in the deeper cortical layers. The generality of learned recognition codes is controlled by a vigilance process mediated by acetylcholine.

Cortical Learning of Recognition Categories: A Resolution of the Exemplar Vs. Prototype Debate

Do humans and animals learn exemplars or prototypes when they categorize objects and events in the world? How are different degrees of abstraction realized through learning by neurons in inferotemporal and prefrontal cortex? How do top-down expectations influence the course of learning? Thirty related human cognitive experiments (the 5-4 category structure) have been used to test competing views in the prototype-exemplar debate. In these experiments, during the test phase, subjects unlearn in a characteristic way items that they had learned to categorize perfectly in the training phase. Many cognitive models do not describe how an individual learns or forgets such categories through time. Adaptive Resonance Theory (ART) neural models provide such a description, and also clarify both psychological and neurobiological data. Matching of bottom-up signals with learned top-down expectations plays a key role in ART model learning. Here, an ART model is used to learn incrementally in response to 5-4 category structure stimuli. Simulation results agree with experimental data, achieving perfect categorization in training and a good match to the pattern of errors exhibited by human subjects in the testing phase. These results show how the model learns both prototypes and certain exemplars in the training phase. ART prototypes are, however, unlike the ones posited in the traditional prototype-exemplar debate. Rather, they are critical patterns of features to which a subject learns to pay attention based on past predictive success and the order in which exemplars are experienced. Perturbations of old memories by newly arriving test items generate a performance curve that closely matches the performance pattern of human subjects. The model also clarifies exemplar-based accounts of data concerning amnesia.

Adaptive Resonance Theory

SyNAPSE program of the Defense Advanced Projects Research Agency (Hewlett-Packard Company, subcontract under DARPA prime contract HR0011-09-3-0001, and HRL Laboratories LLC, subcontract #801881-BS under DARPA prime contract HR0011-09-C-0001); CELEST, an NSF Science of Learning Center (SBE-0354378)

Sequential Memory with ART: A Self-Organizing Network Capable of Learning Sequences of Patterns

A model which extends the adaptive resonance theory model to sequential memory is presented. This new model learns sequences of events and recalls a sequence when presented with parts of the sequence. A sequence can have repeated events and different sequences can share events. The ART model is modified by creating interconnected sublayers within ART's F2 layer. Nodes within F2 learn temporal patterns by forming recency gradients within LTM. Versions of the ART model like ART I, ART 2, and fuzzy ART can be used.

A Neural Theory of Attentive Visual Search: Interactions of Boundary, Surface, Spatial, and Object Representations

Visual search data are given a unified quantitative explanation by a model of how spatial maps in the parietal cortex and object recognition categories in the inferotemporal cortex deploy attentional resources as they reciprocally interact with visual representations in the prestriate cortex. The model visual representations arc organized into multiple boundary and surface representations. Visual search in the model is initiated by organizing multiple items that lie within a given boundary or surface representation into a candidate search grouping. These items arc compared with object recognition categories to test for matches or mismatches. Mismatches can trigger deeper searches and recursive selection of new groupings until a target object io identified. This search model is algorithmically specified to quantitatively simulate search data using a single set of parameters, as well as to qualitatively explain a still larger data base, including data of Aks and Enns (1992), Bravo and Blake (1990), Chellazzi, Miller, Duncan, and Desimone (1993), Egeth, Viri, and Garbart (1984), Cohen and Ivry (1991), Enno and Rensink (1990), He and Nakayarna (1992), Humphreys, Quinlan, and Riddoch (1989), Mordkoff, Yantis, and Egeth (1990), Nakayama and Silverman (1986), Treisman and Gelade (1980), Treisman and Sato (1990), Wolfe, Cave, and Franzel (1989), and Wolfe and Friedman-Hill (1992). The model hereby provides an alternative to recent variations on the Feature Integration and Guided Search models, and grounds the analysis of visual search in neural models of preattentive vision, attentive object learning and categorization, and attentive spatial localization and orientation.

Texture Segregation By Visual Cortex: Perceptual Grouping, Attention, and Learning

A neural model is proposed of how laminar interactions in the visual cortex may learn and recognize object texture and form boundaries. The model brings together five interacting processes: region-based texture classification, contour-based boundary grouping, surface filling-in, spatial attention, and object attention. The model shows how form boundaries can determine regions in which surface filling-in occurs; how surface filling-in interacts with spatial attention to generate a form-fitting distribution of spatial attention, or attentional shroud; how the strongest shroud can inhibit weaker shrouds; and how the winning shroud regulates learning of texture categories, and thus the allocation of object attention. The model can discriminate abutted textures with blurred boundaries and is sensitive to texture boundary attributes like discontinuities in orientation and texture flow curvature as well as to relative orientations of texture elements. The model quantitatively fits a large set of human psychophysical data on orientation-based textures. Object boundar output of the model is compared to computer vision algorithms using a set of human segmented photographic images. The model classifies textures and suppresses noise using a multiple scale oriented filterbank and a distributed Adaptive Resonance Theory (dART) classifier. The matched signal between the bottom-up texture inputs and top-down learned texture categories is utilized by oriented competitive and cooperative grouping processes to generate texture boundaries that control surface filling-in and spatial attention. Topdown modulatory attentional feedback from boundary and surface representations to early filtering stages results in enhanced texture boundaries and more efficient learning of texture within attended surface regions. Surface-based attention also provides a self-supervising training signal for learning new textures. Importance of the surface-based attentional feedback in texture learning and classification is tested using a set of textured images from the Brodatz micro-texture album. Benchmark studies vary from 95.1% to 98.6% with attention, and from 90.6% to 93.2% without attention.

Towards a Unified Theory of Neocortex: Laminar Cortical Circuits for Vision and Cognition

A key goal of computational neuroscience is to link brain mechanisms to behavioral functions. The present article describes recent progress towards explaining how laminar neocortical circuits give rise to biological intelligence. These circuits embody two new and revolutionary computational paradigms: Complementary Computing and Laminar Computing. Circuit properties include a novel synthesis of feedforward and feedback processing, of digital and analog processing, and of pre-attentive and attentive processing. This synthesis clarifies the appeal of Bayesian approaches but has a far greater predictive range that naturally extends to self-organizing processes. Examples from vision and cognition are summarized. A LAMINART architecture unifies properties of visual development, learning, perceptual grouping, attention, and 3D vision. A key modeling theme is that the mechanisms which enable development and learning to occur in a stable way imply properties of adult behavior. It is noted how higher-order attentional constraints can influence multiple cortical regions, and how spatial and object attention work together to learn view-invariant object categories. In particular, a form-fitting spatial attentional shroud can allow an emerging view-invariant object category to remain active while multiple view categories are associated with it during sequences of saccadic eye movements. Finally, the chapter summarizes recent work on the LIST PARSE model of cognitive information processing by the laminar circuits of prefrontal cortex. LIST PARSE models the short-term storage of event sequences in working memory, their unitization through learning into sequence, or list, chunks, and their read-out in planned sequential performance that is under volitional control. LIST PARSE provides a laminar embodiment of Item and Order working memories, also called Competitive Queuing models, that have been supported by both psychophysical and neurobiological data. These examples show how variations of a common laminar cortical design can embody properties of visual and cognitive intelligence that seem, at least on the surface, to be mechanistically unrelated.