427 research outputs found
Statistical Physics and Representations in Real and Artificial Neural Networks
This document presents the material of two lectures on statistical physics
and neural representations, delivered by one of us (R.M.) at the Fundamental
Problems in Statistical Physics XIV summer school in July 2017. In a first
part, we consider the neural representations of space (maps) in the
hippocampus. We introduce an extension of the Hopfield model, able to store
multiple spatial maps as continuous, finite-dimensional attractors. The phase
diagram and dynamical properties of the model are analyzed. We then show how
spatial representations can be dynamically decoded using an effective Ising
model capturing the correlation structure in the neural data, and compare
applications to data obtained from hippocampal multi-electrode recordings and
by (sub)sampling our attractor model. In a second part, we focus on the problem
of learning data representations in machine learning, in particular with
artificial neural networks. We start by introducing data representations
through some illustrations. We then analyze two important algorithms, Principal
Component Analysis and Restricted Boltzmann Machines, with tools from
statistical physics
Uncovering representations of sleep-associated hippocampal ensemble spike activity
Pyramidal neurons in the rodent hippocampus exhibit spatial tuning during spatial navigation, and they are reactivated in specific temporal order during sharp-wave ripples observed in quiet wakefulness or slow wave sleep. However, analyzing representations of sleep-associated hippocampal ensemble spike activity remains a great challenge. In contrast to wake, during sleep there is a complete absence of animal behavior, and the ensemble spike activity is sparse (low occurrence) and fragmental in time. To examine important issues encountered in sleep data analysis, we constructed synthetic sleep-like hippocampal spike data (short epochs, sparse and sporadic firing, compressed timescale) for detailed investigations. Based upon two Bayesian population-decoding methods (one receptive field-based, and the other not), we systematically investigated their representation power and detection reliability. Notably, the receptive-field-free decoding method was found to be well-tuned for hippocampal ensemble spike data in slow wave sleep (SWS), even in the absence of prior behavioral measure or ground truth. Our results showed that in addition to the sample length, bin size, and firing rate, number of active hippocampal pyramidal neurons are critical for reliable representation of the space as well as for detection of spatiotemporal reactivated patterns in SWS or quiet wakefulness.Collaborative Research in Computational Neuroscience (Award IIS-1307645)United States. Office of Naval Research. Multidisciplinary University Research Initiative (Grant N00014-10-1-0936)National Institutes of Health (U.S.) (Grant TR01-GM10498
Slow Inhibition and Inhibitory Recruitment in the Hippocampal Dentate Gyrus
Lâhippocampe joue un rĂŽle central dans la navigation spatiale, la mĂ©moire et lâorganisation spatio-temporelle des souvenirs. Ces fonctions sont maintenues par la capacitĂ© du gyrus dentĂ© (GD) de sĂ©paration des patrons d'activitĂ© neuronales. Le GD est situĂ© Ă lâentrĂ©e de la formation hippocampique oĂč il reconnaĂźt la prĂ©sence de nouveaux motifs parmi la densitĂ© de signaux affĂ©rant arrivant par la voie entorhinale (voie perforante). Le codage parcimonieux est la marque distinctive du GD. Ce type de codage est le rĂ©sultat de la faible excitabilitĂ© intrinsĂšque des cellules granulaires (CGs) en combinaison avec une inhibition locale prĂ©dominante. En particulier, lâinhibition de type « feedforward » ou circuit inhibiteur antĂ©rograde, est engagĂ©e par la voie perforante en mĂȘme temps que les CGs. Ainsi les interneurones du circuit antĂ©rograde fournissent des signaux GABAergique aux CGs de maniĂšre presque simultanĂ©e quâelles reçoivent les signaux glutamatergiques. Cette thĂšse est centrĂ©e sur lâĂ©tude des interactions entre ces signaux excitateurs de la voie entorhinale et les signaux inhibiteurs provenant des interneurones rĂ©sidant dans le GD et ceci dans le contexte du codage parcimonieux et le patron de dĂ©charge en rafale caractĂ©ristique des cellules granulaires. Nous avons adressĂ© les relations entre les projections entorhinales et le rĂ©seau inhibitoire antĂ©rograde du GD en faisant des enregistrements Ă©lectrophysiologiques des CG pendant que la voie perforante est stimulĂ©e de maniĂšre Ă©lectrique ou optogĂ©nĂ©tique. Nous avons dĂ©couvert un nouvel mĂ©canisme dâinhibition qui apparait Ă dĂ©lais dans les CGs suite Ă une stimulation dans les frĂ©quences gamma. Ce mĂ©canisme induit une hyperpolarisation de longue durĂ©e (HLD) et dâune amplitude prononce. Cette longue hyperpolarisation est particuliĂšrement prolongĂ©e et dĂ©passe la durĂ©e dâautres types dâinhibition transitoire lente dĂ©crits chez les CGs. Lâinduction de HLD crĂ©e une fenĂȘtre temporaire de faible excitabilitĂ© suite Ă laquelle le patron de dĂ©charge des CGs et lâintĂ©gration dâautres signaux excitateurs sont altĂ©rĂ©s de maniĂšre transitoire. Nous avons donc conclu que lâactivitĂ© inhibitrice antĂ©rograde joue un rĂŽle central dans les processus de codage dans le GD. Cependant, alors quâil existe une multitude dâĂ©tudes dĂ©crivant les interneurones qui font partie de ce circuit inhibiteur, la question de comment ces cellules sont recrutĂ©es par la voie entorhinale reste quelque peu explorĂ©e. Pour apprendre plus Ă ce sujet, nous avons enregistrĂ© des interneurones rĂ©sidant iii dans la couche molĂ©culaire du GD tout en stimulant la voie perforante de maniĂšre optogĂ©nĂ©tique. Cette mĂ©thode de stimulation nous a permis dâinduire la libĂ©ration de glutamate endogĂšne des terminales entorhinales et ainsi dâobserver le recrutement purement synaptique dâinterneurones. De maniĂšre surprenante, les rĂ©sultats de cette expĂ©rience dĂ©montrent un faible taux dâactivation des interneurones, accompagnĂ© dâun tout aussi faible nombre total de potentiels dâaction Ă©mis en rĂ©ponse Ă la stimulation mĂȘme Ă haute frĂ©quence. Ce constat semble contre-intuitif Ă©tant donnĂ© quâen gĂ©nĂ©rale on assume quâune forte activitĂ© inhibitrice est requise pour le maintien du codage parcimonieux. Tout de mĂȘme, lâanalyse des patrons de dĂ©charge des interneurones qui ont Ă©tĂ© activĂ©s a fait ressortir la prĂ©Ă©minence de trois grands types: dĂ©charge prĂ©coce, retardĂ©e ou rĂ©guliĂšre par rapport le dĂ©but des pulses lumineux. Les rĂ©sultats obtenus durant cette thĂšse mettent la lumiĂšre sur lâimportant consĂ©quences fonctionnelles des interactions synaptique et polysynaptique de nature transitoire dans les rĂ©seaux neuronaux. Nous aimerions aussi souligner lâeffet prononcĂ© de lâinhibition Ă court terme du type prolongĂ©e sur lâexcitabilitĂ© des neurones et leurs capacitĂ©s dâĂ©mettre des potentiels dâaction. De plus que cet effet est encore plus prononcĂ© dans le cas de HLD dont la durĂ©e dĂ©passe souvent la seconde et altĂšre lâintĂ©gration dâautres signaux arrivants simultanĂ©ment. Donc on croit que les effets de HLD se traduisent au niveau du rĂ©seaux neuronal du GD comme une composante cruciale pour le codage parcimonieux. En effet, ce type de codage semble ĂȘtre la marque distinctive de cette rĂ©gion Ă©tant donnĂ© que nous avons aussi observĂ© un faible niveau dâactivation chez les interneurones. Cependant, le manque dâactivitĂ© accrue du rĂ©seau inhibiteur antĂ©rograde peut ĂȘtre compensĂ© par le maintien dâun gradient GABAergique constant Ă travers le GD via lâalternance des trois modes de dĂ©charges des interneurones. En conclusion, il semble que le codage parcimonieux dans le GD peut ĂȘtre prĂ©servĂ© mĂȘme en absence dâactivitĂ© soutenue du rĂ©seau inhibiteur antĂ©rograde et ceci grĂące Ă des mĂ©canismes alternatives dâinhibition prolongĂ©e Ă court terme.The hippocampus is implicated in spatial navigation, the generation and recall of memories, as well as their spatio-temporal organization. These functions are supported by the processes of pattern separation that occurs in the dentate gyrus (DG). Situated at the entry of the hippocampal formation, the DG is well placed to detect and sort novelty patterns amongst the high-density excitatory signals that arrive via the entorhinal cortex (EC). A hallmark of the DG is sparse encoding that is enabled by a combination of low intrinsic excitability of the principal cells and local inhibition. Feedforward inhibition (FFI) is recruited directly by the EC and simultaneously with the granule cells (GCs). Therefore, FFI provides fast GABA release and shapes input integration at the millisecond time scale. This thesis aimed to investigate the interplay of entorhinal excitatory signals with GCs and interneurons, from the FFI in the DG, in the framework of sparse encoding and GCâs characteristic burst firing. We addressed the long-range excitation â local inhibitory network interactions using electrophysiological recordings of GCs â while applying an electrical or optogenetic stimulation of the perforant path (PP) in the DG. We discovered and described a novel delayed-onset inhibitory post synaptic potential (IPSP) in GCs, following PP stimulation in the gamma frequency range. Most importantly, the IPSP was characterized by a large amplitude and prolonged decay, outlasting previously described slow inhibitory events in GCs. The long-lasting hyperpolarization (LLH) caused by the slow IPSPs generates a low excitability time window, alters the GCs firing pattern, and interferes with other stimuli that arrive simultaneously. FFI is therefore a key player in the computational processes that occurs in the DG. However, while many studies have been dedicated to the description of the various types of the interneurons from the FFI, the question of how these cells are synaptically recruited by the EC remains not entirely elucidated. We tackled this problem by recording from interneurons in the DG molecular layer during PP-specific optogenetic stimulation. Light-driven activation of the EC terminals enabled a purely synaptic recruitment of interneurons via endogenous glutamate release. We found that this method of stimulation recruits only a subset of interneurons. In addition, the total number of action potentials (AP) was surprisingly low even at high frequency stimulation. This result is counterintuitive, as strong and persistent inhibitory signals are assumed to restrict GC v activation and maintain sparseness. However, amongst the early firing interneurons, late and regular spiking patterns were clearly distinguishable. Interestingly, some interneurons expressed LLH similar to the GCs, arguing that it could be a commonly used mechanism for regulation of excitability across the hippocampal network. In summary, we show that slow inhibition can result in a prolonged hyperpolarization that significantly alters concurrent inputâs integration. We believe that these interactions contribute to important computational processes such as sparse encoding. Interestingly, sparseness seems to be the hallmark of the DG, as we observed a rather low activation of the interneuron network as well. However, the alternating firing of ML-INs could compensate the lack of persistent activity by the continuous GABA release across the DG. Taken together these results offer an insight into a mechanism of feedforward inhibition serving as a sparse neural code generator in the DG
Deciphering the Firing Patterns of Hippocampal Neurons During Sharp-Wave Ripples
The hippocampus is essential for learning and memory. Neurons in the rat hippocampus selectively fire when the animal is at specific locations - place fields - within an environment. Place fields corresponding to such place cells tile the entire environment, forming a stable spatial map supporting navigation and planning. Remarkably, the same place cells reactivate together outside of their place fields and in coincidence with sharp-wave ripples (SWRs) - dominant electrical field oscillations (150-250 Hz) in the hippocampus. These offline SWR events frequently occur during quiet wake periods in the middle of exploration and the follow-up slow-wave sleep and are associated with spatial memory performance and stabilization of spatial maps. Therefore, deciphering the firing patterns during these events is essential to understanding offline memory processing.I provide two novel methods to analyze the SWRs firing patterns in this dissertation project. The first method uses hidden Markov models (HMM), in which I model the dynamics of neural activity during SWRs in terms of transitions between distinct states of neuronal ensemble activity. This method detects consistent temporal structures over many instances of SWRs and, in contrast to standard approaches, relaxes the dependence on positional data during the behavior to interpret temporal patterns during SWRs. To validate this method, I applied the method to quiet wake SWRs. In a simple spatial memory task in which the animal ran on a linear track or in an open arena, the individual states corresponded to the activation of distinct group of neurons with inter-state transitions that resembled the animalâs trajectories during the exploration. In other words, this method enabled us to identify the topology and spatial map of the explored environment by dissecting the firings occurring during the quiescence periodsâ SWRs. This result indicated that downstream brain regions may rely only on SWRs to uncover hippocampal code as a substrate for memory processing. I developed a second analysis method based on the principles of Bayesian learning. This method enabled us to track the spatial tunings over the sleep following exploration of an environment by taking neuronsâ place fields in the environment as the prior belief and updating it using dynamic ensemble firing patterns unfolding over time. This method introduces a neuronal-ensemble-based approach that calculates tunings to the position encoded by ensemble firings during sleep rather than the animalâs actual position during exploration. When I applied this method to several datasets, I found that during the early slow-wave sleep after an experience, but not during late hours of sleep or sleep before the exploration, the spatial tunings highly resembled the place fields on the track. Furthermore, the fidelity of the spatial tunings to the place fields predicted the place fieldsâ stability when the animal was re-exposed to the same environment after ~ 9h. Moreover, even for neurons with shifted place fields during re-exposure, the spatial tunings during early sleep were predictive of the place fields during the re-exposure. These results indicated that early sleep actively maintains or retunes the place fields of neurons, explaining the representational drift of place fields across multiple exposures
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A Neural Signal Processor for Low-Latency Spike Inference
This thesis describes the development of a system that can assign identities to a population of single-units, in multi-electrode recordings, at single-spike resolution with low-latency. The system has two parts. The first is a Field-Programmable Gate Array (FPGA)-based Neural Signal Processor (NSP) that receives raw input and generates labelled spikes as output, a process referred to as real-time spike inference. The second is a piece of software (Spiketag) that runs on a PC, communicates with the NSP, and generates a spike-sorted model to guide the real-time spike inference. The NSP provides clocks and control signals to five 32-channel INTAN RHD2132 chips to manage the acquisition of 160 channels of raw neural data. In parallel, the NSP further filters, detects and extracts extracellular spike waveforms from the raw neural data recorded by tetrodes or silicon probes and assigns single-unit identity to each detected spike. A set of Python application programming interfaces (APIs) was developed in Spiketag to enable the communication between the NSP and the PC. These APIs allow the NSP to obtain a model from the PC, which holds parameters such as reference channels, spike detection thresholds, spike feature transformation matrix and vector quantized clusters generated by spike sorting a short recording session. Using the spike-sorted model, the NSP performs data acquisition and real-time spike inference simultaneously. Algorithmic modules were implemented in the FPGA and pipelined to compute during 40 ms acquisition intervals. At the output end of the FPGA NSP, the real-time assigned single-unit identity (spike-id) is packaged with the timestamp, the electrode group, and the spike features as a spike-id packet. Spike-id packets are asynchronously transmitted through a low-latency Peripheral Component Interconnect Express (PCIe) interface to the PC, producing the real-time spike trains. The real-time spike trains can be used for further processing, such as real-time decoding. Several types of ground-truth data, including intracellular/extracellular paired recordings, synthesized
tetrode extracellular waveforms with ground-truth spike timing and high-channel-count silicon probe recordings with ground-truth animal positions during navigation were used to validate the low-latency (1 ms) and high-accuracy (as high as state-of-the-art offline sorting and decoding algorithms) of the NSPâs real-time spike inference and the NSP-based
real-time population decoding performance
Micro-, Meso- and Macro-Dynamics of the Brain
Neurosciences, Neurology, Psychiatr
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On memories, neural ensembles and mental flexibility
Memories are assumed to be represented by groups of co-activated neurons, called neural ensembles. Describing ensembles is a challenge: complexity of the underlying micro-circuitry is immense. Current approaches use a piecemeal fashion, focusing on single neurons and employing local measures like pairwise correlations. We introduce an alternative approach that identifies ensembles and describes the effective connectivity between them in a holistic fashion. It also links the oscillatory frequencies observed in ensembles with the spatial scales at which activity is expressed. Using unsupervised learning, biophysical modeling and graph theory, we analyze multi-electrode LFPs from frontal cortex during a spatial delayed response task. We find distinct ensembles for different cues and more parsimonious connectivity for cues on the horizontal axis, which may explain the oblique effect in psychophysics. Our approach paves the way for biophysical models with learned parameters that can guide future Brain Computer Interface development
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