Neuroscience
Study of the nervous system and brain, often involving computational models to understand neural processes and cognitive functions.
On sparsity and overcompleteness in image models
Pietro Berkes, Richard E. Turner, Maneesh Sahani, 2008. (In nips20). Edited by J. C. Platt, D. Koller, Y. Singer, S. Roweis. mit.
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Computational models of visual cortex, and in particular those based on sparse coding, have enjoyed much recent attention. Despite this currency, the question of how sparse or how over-complete a sparse representation should be, has gone without principled answer. Here, we use Bayesian model-selection methods to address these questions for a sparse-coding model based on a Student-t prior. Having validated our methods on toy data, we find that natural images are indeed best modelled by extremely sparse distributions; although for the Student-t prior, the associated optimal basis size is only modestly over-complete.
A Structured Model of Video Reproduces Primary Visual Cortical Organisation
Pietro Berkes, Richard E. Turner, Maneesh Sahani, 09 2009. (PLoS Computational Biology). Public Library of Science. DOI: 10.1371/journal.pcbi.1000495.
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The visual system must learn to infer the presence of objects and features in the world from the images it encounters, and as such it must, either implicitly or explicitly, model the way these elements interact to create the image. Do the response properties of cells in the mammalian visual system reflect this constraint? To address this question, we constructed a probabilistic model in which the identity and attributes of simple visual elements were represented explicitly and learnt the parameters of this model from unparsed, natural video sequences. After learning, the behaviour and grouping of variables in the probabilistic model corresponded closely to functional and anatomical properties of simple and complex cells in the primary visual cortex (V1). In particular, feature identity variables were activated in a way that resembled the activity of complex cells, while feature attribute variables responded much like simple cells. Furthermore, the grouping of the attributes within the model closely parallelled the reported anatomical grouping of simple cells in cat V1. Thus, this generative model makes explicit an interpretation of complex and simple cells as elements in the segmentation of a visual scene into basic independent features, along with a parametrisation of their moment-by-moment appearances. We speculate that such a segmentation may form the initial stage of a hierarchical system that progressively separates the identity and appearance of more articulated visual elements, culminating in view-invariant object recognition.
Influence of heart rate on the BOLD signal: the cardiac response function
C. Chang, J. P. Cunningham, G. Glover, 2009. (NeuroImage).
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It has previously been shown that low-frequency fluctuations in both respiratory volume and cardiac rate can induce changes in the blood-oxygen level dependent (BOLD) signal. Such physiological noise can obscure the detection of neural activation using fMRI, and it is therefore important to model and remove the effects of this noise. While a hemodynamic response function relating respiratory variation (RV) and the BOLD signal has been described, no such mapping for heart rate (HR) has been proposed. In the current study, the effects of RV and HR are simultaneously deconvolved from resting state fMRI. It is demonstrated that a convolution model including RV and HR can explain significantly more variance in gray matter BOLD signal than a model that includes RV alone, and an average HR response function is proposed that well characterizes our subject population. It is observed that the voxel-wise morphology of the deconvolved RV responses is preserved when HR is included in the model, and that its form is adequately modeled by Birn et al.’s previously described respiration response function. Furthermore, it is shown that modeling out RV and HR can significantly alter functional connectivity maps of the default-mode network.
Cortical preparatory activity: Representation of movement or first cog in a dynamical machine?
M. M. Churchland, J. P. Cunningham, M. T. Kaufman, S. I. Ryu, K. V. Shenoy., 2010. (Neuron).
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The motor cortices are active during both movement and movement preparation. A common assumption is that preparatory activity constitutes a subthreshold form of movement activity: a neuron active during rightward movements becomes modestly active during preparation of a rightward movement. We asked whether this pattern of activity is, in fact, observed. We found that it was not: at the level of a single neuron, preparatory tuning was weakly correlated with movement-period tuning. Yet, somewhat paradoxically, preparatory tuning could be captured by a preferred direction in an abstract “space” that described the population-level pattern of movement activity. In fact, this relationship accounted for preparatory responses better than did traditional tuning models. These results are expected if preparatory activity provides the initial state of a dynamical system whose evolution produces movement activity. Our results thus suggest that preparatory activity may not represent specific factors, and may instead play a more mechanistic role.
Stimulus onset quashes neural variability: a widespread cortical phenomenon
M. M. Churchland, B. M. Yu, J. P. Cunningham, L. P. Sugrue, M. R. Cohen, G. S. Corrado, W. T. Newsome, A. M. Clark, P. Hosseini, B. B. Scott, D. C. Bradley, M. A. Smith, A. Kohn, J. A. Movshon, K. M. Armstrong, T. Moore, S. W. Chang, L. H. Snyder, S. G. Lisberger, N. J. Priebe, I. M. Finn, D. Ferster, S. I. Ryu, G. Santhanam, M. Sahani, K. V. Shenoy., 2010. (Nature Neuro).
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Neural responses are typically characterized by computing the mean firing rate, but response variability can exist across trials. Many studies have examined the effect of a stimulus on the mean response, but few have examined the effect on response variability. We measured neural variability in 13 extracellularly recorded datasets and one intracellularly recorded dataset from seven areas spanning the four cortical lobes in monkeys and cats. In every case, stimulus onset caused a decline in neural variability. This occurred even when the stimulus produced little change in mean firing rate. The variability decline was observed in membrane potential recordings, in the spiking of individual neurons and in correlated spiking variability measured with implanted 96-electrode arrays. The variability decline was observed for all stimuli tested, regardless of whether the animal was awake, behaving or anaesthetized. This widespread variability decline suggests a rather general property of cortex, that its state is stabilized by an input.
Derivation of Expectation Propagation for "Fast Gaussian process methods for point process intensity estimation"
J. P. Cunningham, 2008. Stanford University,
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We derive the Expectation Propagation algorithm updates for approximating the posterior distribution on intensity in a conditionally inhomogeneous gamma interval process with a Gaussian Process prior (GP IGIP), a model which appeared in Cunningham, Shenoy, Sahani (2008) ICML.
A closed-loop human simulator for investigating the role of feedback-control in brain-machine interfaces
J. P. Cunningham, P. Nuyujukian, V. Gilja, C. A. Chestek, S. I. Ryu, K. V. Shenoy., 2011. (Journal of Neurophysiology).
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Neural prosthetic systems seek to improve the lives of severely disabled people by decoding neural activity into useful behavioral commands. These systems and their decoding algorithms are typically developed “offline”, using neural activity previously gathered from a healthy animal, and the decoded movement is then compared with the true movement that accompanied the recorded neural activity. However, this offline design and testing may neglect important features of a real prosthesis, most notably the critical role of feedback control, which enables the user to adjust neural activity while using the prosthesis. We hypothesize that under- standing and optimally designing high-performance decoders require an experimental platform where humans are in closed-loop with the various candidate decode systems and algorithms. It remains unexplored the extent to which the subject can, for a particular decode system, algorithm, or parameter, engage feedback and other strategies to improve decode performance. Closed-loop testing may suggest different choices than offline analyses. Here we ask if a healthy human subject, using a closed-loop neural prosthesis driven by synthetic neural activity, can inform system design. We use this online pros- thesis simulator (OPS) to optimize “online” decode performance based on a key parameter of a current state-of-the-art decode algorithm, the bin width of a Kalman filter. First, we show that offline and online analyses indeed suggest different parameter choices. Previous literature and our offline analyses agree that neural activity should be analyzed in bins of 100- to 300-ms width. OPS analysis, which incorporates feedback control, suggests that much shorter bin widths (25-50 ms) yield higher decode performance. Second, we confirm this surprising finding using a closed-loop rhesus monkey prosthetic system. These findings illustrate the type of discovery made possible by the OPS, and so we hypothesize that this novel testing approach will help in the design of prosthetic systems that will translate well to human patients.
Fast Gaussian process methods for point process intensity estimation
J. P. Cunningham, K. V. Shenoy, M. Sahani, June 2008. (In 25th International Conference on Machine Learning). Helsinki, Finland.
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Point processes are difficult to analyze because they provide only a sparse and noisy observation of the intensity function driving the process. Gaussian Processes offer an attractive framework within which to infer underlying intensity functions. The result of this inference is a continuous function defined across time that is typically more amenable to analytical efforts. However, a naive implementation will become computationally infeasible in any problem of reasonable size, both in memory and run time requirements. We demonstrate problem specific methods for a class of renewal processes that eliminate the memory burden and reduce the solve time by orders of magnitude.
Inferring neural firing rates from spike trains using Gaussian processes
J. P. Cunningham, B. M. Yu, K. V. Shenoy, M. Sahani, December 2008. (In Advances in Neural Information Processing Systems 20). Vancouver, BC.
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Neural spike trains present challenges to analytical efforts due to their noisy, spiking nature. Many studies of neuroscientific and neural prosthetic importance rely on a smoothed, denoised estimate of the spike train’s underlying firing rate. Current techniques to find time-varying firing rates require ad hoc choices of parameters, offer no confidence intervals on their estimates, and can obscure potentially important single trial variability. We present a new method, based on a Gaussian Process prior, for inferring probabilistically optimal estimates of firing rate functions underlying single or multiple neural spike trains. We test the performance of the method on simulated data and experimentally gathered neural spike trains, and we demonstrate improvements over conventional estimators.
Comment: Spotlight Presentation
Computational Structure of coordinate transformations: A generalization study
Zoubin Ghahramani, Daniel M. Wolpert, Michael I. Jordan, 1994. (In Advances in Neural Information Processing Systems 7). Edited by Gerald Tesauro, David S. Touretzky, Todd K. Leen. MIT Press.
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One of the fundamental properties that both neural networks and the central nervous system share is the ability to learn and generalize from examples. While this property has been studied extensively in the neural network literature it has not been thoroughly explored in human perceptual and motor learning. We have chosen a coordinate transformation system—the visuomotor map which transforms visual coordinates into motor coordinates—to study the generalization effects of learning new input–output pairs. Using a paradigm of computer controlled altered visual feedback, we have studied the generalization of the visuomotor map subsequent to both local and context-dependent remappings. A local remapping of one or two input-output pairs induced a significant global, yet decaying, change in the visuomotor map, suggesting a representation for the map composed of units with large functional receptive fields. Our study of context-dependent remappings indicated that a single point in visual space can be mapped to two different finger locations depending on a context variable—the starting point of the movement. Furthermore, as the context is varied there is a gradual shift between the two remappings, consistent with two visuomotor modules being learned and gated smoothly with the context.
Cognitive tomography reveals complex task-independent mental representations
Neil Houlsby, Ferenc Huszár, Mohammad M Ghassemi, Gergő Orbán, Daniel M Wolpert, Máté Lengyel, 2013. (Current Biology). DOI: 10.1016/j.cub.2013.09.012.
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Humans develop rich mental representations that guide their behavior in a variety of every-day tasks. However, it is unknown whether these representations, often formalized as priors in Bayesian inference, are specific for each task or subserve multiple tasks. Current approaches cannot distinguish between these two possibilities because they cannot extract comparable representations across different tasks. Here, we develop a novel method, termed cognitive tomography, that can extract complex, multi-dimensional priors across tasks. We apply this method to human judgments in two qualitatively different tasks, familiarity and odd-one-out, involving an ecologically relevant set of stimuli, human faces. We show that priors over faces are structurally complex and vary dramatically across subjects, but are invariant across the tasks within each subject. The priors we extract from each task allow us to predict with high precision the behavior of subjects for novel stimuli both in the same task as well as in the other task. Our results provide the first evidence for a single high-dimensional structured representation of a naturalistic stimulus set that guides behavior in multiple tasks. Moreover, the representations estimated by cognitive tomography can provide independent, behavior-based regressors for elucidating the neural correlates of complex naturalistic priors.
A role for amplitude modulation phase relationships in speech rhythm perception
Victoria Leong, Michael A Stone, Richard E Turner, Usha Goswami, 2014. (Journal of the Acoustical Society of America). Acoustical Society of America.
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Prosodic rhythm in speech [the alternation of “Strong” (S) and “weak” (w) syllables] is cued, among others, by slow rates of amplitude modulation (AM) within the speech envelope. However, it is unclear exactly which envelope modulation rates and statistics are the most important for the rhythm percept. Here, the hypothesis that the phase relationship between “Stress” rate ( 2 Hz) and “Syllable” rate ( 4 Hz) AMs provides a perceptual cue for speech rhythm is tested. In a rhythm judgment task, adult listeners identified AM tone-vocoded nursery rhyme sentences that carried either trochaic (S-w) or iambic patterning (w-S). Manipulation of listeners’ rhythm perception was attempted by parametrically phase-shifting the Stress AM and Syllable AM in the vocoder. It was expected that a 1π radian phase-shift (half a cycle) would reverse the perceived rhythm pattern (i.e., trochaic -> iambic) whereas a 2πradian shift (full cycle) would retain the perceived rhythm pattern (i.e., trochaic -> trochaic). The results confirmed these predictions. Listeners judgments of rhythm systematically followed Stress-Syllable AM phase-shifts, but were unaffected by phase-shifts between the Syllable AM and the Sub-beat AM ( 14 Hz) in a control condition. It is concluded that the Stress-Syllable AM phase relationship is an envelope-based modulation statistic that supports speech rhythm perception.
Occlusive Components Analysis
Jörg Lücke, Richard E. Turner, Maneesh Sahani, Marc Henniges, 2009. (In Advances in Neural Information Processing Systems 22). Edited by Y Bengio, D Schuurmans, J Lafferty, C K I Williams, A Culotta. mit.
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We study unsupervised learning in a probabilistic generative model for occlusion. The model uses two types of latent variables: one indicates which objects are present in the image, and the other how they are ordered in depth. This depth order then determines how the positions and appearances of the objects present, specified in the model parameters, combine to form the image. We show that the object parameters can be learnt from an unlabelled set of images in which objects occlude one another. Exact maximum-likelihood learning is intractable. However, we show that tractable approximations to Expectation Maximization (EM) can be found if the training images each contain only a small number of objects on average. In numerical experiments it is shown that these approximations recover the correct set of object parameters. Experiments on a novel version of the bars test using colored bars, and experiments on more realistic data, show that the algorithm performs well in extracting the generating causes. Experiments based on the standard bars benchmark test for object learning show that the algorithm performs well in comparison to other recent component extraction approaches. The model and the learning algorithm thus connect research on occlusion with the research field of multiple-causes component extraction methods.
Empirical models of spiking in neural populations
J. H. Macke, L. Busing, J. P. Cunningham, B. M. Yu, K. V. Shenoy, M. Sahani, December 2011. (In Advances in Neural Information Processing Systems 25). Granada, Spain.
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Neurons in the neocortex code and compute as part of a locally interconnected population. Large-scale multi-electrode recording makes it possible to access these population processes empirically by fitting statistical models to unaveraged data. What statistical structure best describes the concurrent spiking of cells within a local network? We argue that in the cortex, where firing exhibits extensive correlations in both time and space and where a typical sample of neurons still reflects only a very small fraction of the local population, the most appropriate model captures shared variability by a low-dimensional latent process evolving with smooth dynamics, rather than by putative direct coupling. We test this claim by comparing a latent dynamical model with realistic spiking observations to coupled generalised linear spike-response models (GLMs) using cortical recordings. We find that the latent dynamical approach outperforms the GLM in terms of goodness-of- fit, and reproduces the temporal correlations in the data more accurately. We also compare models whose observations models are either derived from a Gaussian or point-process models, finding that the non-Gaussian model provides slightly better goodness-of-fit and more realistic population spike counts.
Dynamical Segmentation of single trials from population neural data
B. Petreska, B. M. Yu, J. P. Cunningham, G. Santhanam, S. I. Ryu, K. V. Shenoy, M. Sahani, December 2011. (In Advances in Neural Information Processing Systems 25). Granada, Spain.
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Simultaneous recordings of many neurons embedded within a recurrently-connected cortical network may provide concurrent views into the dynamical processes of that network, and thus its computational function. In principle, these dynamics might be identified by purely unsupervised, statistical means. Here, we show that a Hidden Switching Linear Dynamical Systems (HSLDS) model - in which multiple linear dynamical laws approximate and nonlinear and potentially non-stationary dynamical process - is able to distinguish dynamical regimes within single-trial motor cortical activity associated with the preparation and initiation of hand movements. The regimes are identified without reference to behavioural or experimental epochs, but nonetheless transitions between them correlate strongly with external events whose timing may vary from trial to trial. The HSLDS model also performs better than recent comparable models in predicting the firing rate of an isolated neuron based on the firing rates of others, suggesting that it captures more of the “Shared variance” of the data. Thus, the method is able to trace the dynamical processes underlying the coordinated evolution of network activity in a way that appears to reflect its computational role.
Statistical Models for Natural Sounds
Richard E. Turner, 2010. Gatsby Computational Neuroscience Unit, UCL,
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It is important to understand the rich structure of natural sounds in order to solve important tasks, like automatic speech recognition, and to understand auditory processing in the brain. This thesis takes a step in this direction by characterising the statistics of simple natural sounds. We focus on the statistics because perception often appears to depend on them, rather than on the raw waveform. For example the perception of auditory textures, like running water, wind, fire and rain, depends on summary-statistics, like the rate of falling rain droplets, rather than on the exact details of the physical source. In order to analyse the statistics of sounds accurately it is necessary to improve a number of traditional signal processing methods, including those for amplitude demodulation, time-frequency analysis, and sub-band demodulation. These estimation tasks are ill-posed and therefore it is natural to treat them as Bayesian inference problems. The new probabilistic versions of these methods have several advantages. For example, they perform more accurately on natural signals and are more robust to noise, they can also fill-in missing sections of data, and provide error-bars. Furthermore, free-parameters can be learned from the signal. Using these new algorithms we demonstrate that the energy, sparsity, modulation depth and modulation time-scale in each sub-band of a signal are critical statistics, together with the dependencies between the sub-band modulators. In order to validate this claim, a model containing co-modulated coloured noise carriers is shown to be capable of generating a range of realistic sounding auditory textures. Finally, we explored the connection between the statistics of natural sounds and perception. We demonstrate that inference in the model for auditory textures qualitatively replicates the primitive grouping rules that listeners use to understand simple acoustic scenes. This suggests that the auditory system is optimised for the statistics of natural sounds.
A Maximum-Likelihood Interpretation for Slow Feature Analysis
Richard E. Turner, Maneesh Sahani, 2007. (Neural Computation). Cambridge, MA, USA. MIT Press. DOI: http://dx.doi.org/10.1162/neco.2007.19.4.1022. ISSN: 0899-7667.
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The brain extracts useful features from a maelstrom of sensory information, and a fundamental goal of theoretical neuroscience is to work out how it does so. One proposed feature extraction strategy is motivated by the observation that the meaning of sensory data, such as the identity of a moving visual object, is often more persistent than the activation of any single sensory receptor. This notion is embodied in the slow feature analysis (SFA) algorithm, which uses “slowness” as an heuristic by which to extract semantic information from multi-dimensional time-series. Here, we develop a probabilistic interpretation of this algorithm showing that inference and learning in the limiting case of a suitable probabilistic model yield exactly the results of SFA. Similar equivalences have proved useful in interpreting and extending comparable algorithms such as independent component analysis. For SFA, we use the equivalent probabilistic model as a conceptual spring-board, with which to motivate several novel extensions to the algorithm.
Forward dynamic models in human motor control: Psychophysical evidence
Daniel M. Wolpert, Zoubin Ghahramani, Michael I. Jordan, 1994. (In Advances in Neural Information Processing Systems 7). Edited by Gerald Tesauro, David S. Touretzky, Todd K. Leen. MIT Press.
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Based on computational principles, with as yet no direct experimental validation, it has been proposed that the central nervous system (CNS) uses an internal model to simulate the dynamic behavior of the motor system in planning, control and learning. We present experimental results and simulations based on a novel approach that investigates the temporal propagation of errors in the sensorimotor integration process. Our results provide direct support for the existence of an internal model.