Generating functionals for autonomous latching dynamics in attractor relict networks.
Ontology highlight
ABSTRACT:
SUBMITTER: Linkerhand M
PROVIDER: S-EPMC3687227 | biostudies-other | 2013
REPOSITORIES: biostudies-other
Similar Datasets
Project description:BackgroundThe experimental observations and numerical studies with dissipative metabolic networks have shown that cellular enzymatic activity self-organizes spontaneously leading to the emergence of a Systemic Metabolic Structure in the cell, characterized by a set of different enzymatic reactions always locked into active states (metabolic core) while the rest of the catalytic processes are only intermittently active. This global metabolic structure was verified for Escherichia coli, Helicobacter pylori and Saccharomyces cerevisiae, and it seems to be a common key feature to all cellular organisms. In concordance with these observations, the cell can be considered a complex metabolic network which mainly integrates a large ensemble of self-organized multienzymatic complexes interconnected by substrate fluxes and regulatory signals, where multiple autonomous oscillatory and quasi-stationary catalytic patterns simultaneously emerge. The network adjusts the internal metabolic activities to the external change by means of flux plasticity and structural plasticity.Methodology/principal findingsIn order to research the systemic mechanisms involved in the regulation of the cellular enzymatic activity we have studied different catalytic activities of a dissipative metabolic network under different external stimuli. The emergent biochemical data have been analysed using statistical mechanic tools, studying some macroscopic properties such as the global information and the energy of the system. We have also obtained an equivalent Hopfield network using a Boltzmann machine. Our main result shows that the dissipative metabolic network can behave as an attractor metabolic network.Conclusions/significanceWe have found that the systemic enzymatic activities are governed by attractors with capacity to store functional metabolic patterns which can be correctly recovered from specific input stimuli. The network attractors regulate the catalytic patterns, modify the efficiency in the connection between the multienzymatic complexes, and stably retain these modifications. Here for the first time, we have introduced the general concept of attractor metabolic network, in which this dynamic behavior is observed.
| S-EPMC3598861 | biostudies-literature
Project description:Recurrent neural networks (RNNs) are a widely used tool for modeling sequential data, yet they are often treated as inscrutable black boxes. Given a trained recurrent network, we would like to reverse engineer it-to obtain a quantitative, interpretable description of how it solves a particular task. Even for simple tasks, a detailed understanding of how recurrent networks work, or a prescription for how to develop such an understanding, remains elusive. In this work, we use tools from dynamical systems analysis to reverse engineer recurrent networks trained to perform sentiment classification, a foundational natural language processing task. Given a trained network, we find fixed points of the recurrent dynamics and linearize the nonlinear system around these fixed points. Despite their theoretical capacity to implement complex, high-dimensional computations, we find that trained networks converge to highly interpretable, low-dimensional representations. In particular, the topological structure of the fixed points and corresponding linearized dynamics reveal an approximate line attractor within the RNN, which we can use to quantitatively understand how the RNN solves the sentiment analysis task. Finally, we find this mechanism present across RNN architectures (including LSTMs, GRUs, and vanilla RNNs) trained on multiple datasets, suggesting that our findings are not unique to a particular architecture or dataset. Overall, these results demonstrate that surprisingly universal and human interpretable computations can arise across a range of recurrent networks.
| S-EPMC7416638 | biostudies-literature
Project description:The attractor neural network scenario is a popular scenario for memory storage in the association cortex, but there is still a large gap between models based on this scenario and experimental data. We study a recurrent network model in which both learning rules and distribution of stored patterns are inferred from distributions of visual responses for novel and familiar images in the inferior temporal cortex (ITC). Unlike classical attractor neural network models, our model exhibits graded activity in retrieval states, with distributions of firing rates that are close to lognormal. Inferred learning rules are close to maximizing the number of stored patterns within a family of unsupervised Hebbian learning rules, suggesting that learning rules in ITC are optimized to store a large number of attractor states. Finally, we show that there exist two types of retrieval states: one in which firing rates are constant in time and another in which firing rates fluctuate chaotically.
| S-EPMC6091895 | biostudies-literature
Project description:Predicting motions of vessels in extreme sea states represents one of the most challenging problems in naval hydrodynamics. It involves computing complex nonlinear wave-body interactions, hence taxing heavily computational resources. Here, we put forward a new simulation paradigm by training recurrent type neural networks (RNNs) that take as input the stochastic wave elevation at a certain sea state and output the main vessel motions, e.g. pitch, heave and roll. We first compare the performance of standard RNNs versus GRU and LSTM neural networks (NNs) and show that LSTM NNs lead to the best performance. We then examine the testing error of two representative vessels, a catamaran in sea state 1 and a battleship in sea state 8. We demonstrate that good accuracy is achieved for both cases in predicting the vessel motions for unseen wave elevations. We train the NNs with expensive CFD simulations offline, but upon training, the prediction of the vessel dynamics online can be obtained at a fraction of a second. This work is motivated by the universal approximation theorem for functionals (Chen & Chen, 1993. IEEE Trans. Neural Netw. 4, 910-918 (doi:10.1109/72.286886)), and it is the first implementation of such theory to realistic engineering problems.
| S-EPMC7897645 | biostudies-literature
Project description:BackgroundBoolean networks (BNs) provide an effective modelling formalism for various complex biochemical phenomena. Their long term behaviour is represented by attractors-subsets of the state space towards which the BN eventually converges. These are then typically linked to different biological phenotypes. Depending on various logical parameters, the structure and quality of attractors can undergo a significant change, known as a bifurcation. We present a methodology for analysing bifurcations in asynchronous parametrised Boolean networks.ResultsIn this paper, we propose a computational framework employing advanced symbolic graph algorithms that enable the analysis of large networks with hundreds of Boolean variables. To visualise the results of this analysis, we developed a novel interactive presentation technique based on decision trees, allowing us to quickly uncover parameters crucial to the changes in the attractor landscape. As a whole, the methodology is implemented in our tool AEON. We evaluate the method's applicability on a complex human cell signalling network describing the activity of type-1 interferons and related molecules interacting with SARS-COV-2 virion. In particular, the analysis focuses on explaining the potential suppressive role of the recently proposed drug molecule GRL0617 on replication of the virus.ConclusionsThe proposed method creates a working analogy to the concept of bifurcation analysis widely used in kinetic modelling to reveal the impact of parameters on the system's stability. The important feature of our tool is its unique capability to work fast with large-scale networks with a relatively large extent of unknown information. The results obtained in the case study are in agreement with the recent biological findings.
| S-EPMC9092939 | biostudies-literature
Project description:The autoassociative memory model of hippocampal field CA3 postulates that Hebbian associations among external input features produce attractor states embedded in a recurrent synaptic matrix. In contrast, the attractor-map model postulates that a two-dimensional continuum of attractor states is preconfigured in the network during development and that transitions among these states are governed primarily by self-motion information ("path-integration"), giving rise to the strong spatial characteristic of hippocampal activity. In this model, learned associations between "coordinates" on the attractor map and external cues can result in abrupt jumps between states, in the case of mismatches between the current input and previous associations between internal coordinates and external landmarks. Both models predict attractor dynamics, but for fundamentally different reasons; however, the two models are not a priori mutually exclusive. We contrasted these two models by comparing the dynamics of state transitions when two previously learned environmental shapes were morphed between their endpoints, in animals that had first experienced the environments either at the same location, or at two different locations, connected by a passageway through which they walked. As predicted from attractor-map theory, the latter animals expressed abrupt transitions between representations at the midpoint of the morph series. Contrary to the predictions of autoassociation theory, the former group expressed no evidence of attractor dynamics during the morph series; there was only a gradual transition between endpoints. The results of this critical test thus cast the autoassociator theory for CA3 into doubt and indicate the need for a new theory for this structure.
| S-EPMC2904215 | biostudies-literature
Project description:Rhythmic joint coordination is ubiquitous in daily-life human activities. In order to coordinate their actions towards shared goals, individuals need to co-regulate their timing and move together at the collective level of behavior. Remarkably, basic forms of coordinated behavior tend to emerge spontaneously as long as two individuals are exposed to each other's rhythmic movements. The present study investigated the dynamics of spontaneous dyadic entrainment, and more specifically how they depend on the sensory modalities mediating informational coupling. By means of a novel interactive paradigm, we showed that dyadic entrainment systematically takes place during a minimalistic rhythmic task despite explicit instructions to ignore the partner. Crucially, the interaction was organized by clear dynamics in a modality-dependent fashion. Our results showed highly consistent coordination patterns in visually-mediated entrainment, whereas we observed more chaotic and more variable profiles in the auditorily-mediated counterpart. The proposed experimental paradigm yields empirical evidence for the overwhelming tendency of dyads to behave as coupled rhythmic units. In the context of our experimental design, it showed that coordination dynamics differ according to availability and nature of perceptual information. Interventions aimed at rehabilitating, teaching or training sensorimotor functions can be ultimately informed and optimized by such fundamental knowledge.
| S-EPMC8443558 | biostudies-literature
Project description:Our cognition relies on the ability of the brain to segment hierarchically structured events on multiple scales. Recent evidence suggests that the brain performs this event segmentation based on the structure of state-transition graphs behind sequential experiences. However, the underlying circuit mechanisms are poorly understood. In this paper we propose an extended attractor network model for graph-based hierarchical computation which we call the Laplacian associative memory. This model generates multiscale representations for communities (clusters) of associative links between memory items, and the scale is regulated by the heterogenous modulation of inhibitory circuits. We analytically and numerically show that these representations correspond to graph Laplacian eigenvectors, a popular method for graph segmentation and dimensionality reduction. Finally, we demonstrate that our model exhibits chunked sequential activity patterns resembling hippocampal theta sequences. Our model connects graph theory and attractor dynamics to provide a biologically plausible mechanism for abstraction in the brain.
| S-EPMC8412329 | biostudies-literature
Project description:We demonstrate that a randomly connected attractor network with dynamic synapses can discriminate between similar sequences containing multiple stimuli suggesting such networks provide a general basis for neural computations in the brain. The network contains units representing assemblies of pools of neurons, with preferentially strong recurrent excitatory connections rendering each unit bi-stable. Weak interactions between units leads to a multiplicity of attractor states, within which information can persist beyond stimulus offset. When a new stimulus arrives, the prior state of the network impacts the encoding of the incoming information, with short-term synaptic depression ensuring an itinerancy between sets of active units. We assess the ability of such a network to encode the identity of sequences of stimuli, so as to provide a template for sequence recall, or decisions based on accumulation of evidence. Across a range of parameters, such networks produce the primacy (better final encoding of the earliest stimuli) and recency (better final encoding of the latest stimuli) observed in human recall data and can retain the information needed to make a binary choice based on total number of presentations of a specific stimulus. Similarities and differences in the final states of the network produced by different sequences lead to predictions of specific errors that could arise when an animal or human subject generalizes from training data, when the training data comprises a subset of the entire stimulus repertoire. We suggest that such networks can provide the general purpose computational engines needed for us to solve many cognitive tasks.
| S-EPMC6571095 | biostudies-literature
Project description:We provide a novel refined attractor-based complexity measurement for Boolean recurrent neural networks that represents an assessment of their computational power in terms of the significance of their attractor dynamics. This complexity measurement is achieved by first proving a computational equivalence between Boolean recurrent neural networks and some specific class of ?-automata, and then translating the most refined classification of ?-automata to the Boolean neural network context. As a result, a hierarchical classification of Boolean neural networks based on their attractive dynamics is obtained, thus providing a novel refined attractor-based complexity measurement for Boolean recurrent neural networks. These results provide new theoretical insights to the computational and dynamical capabilities of neural networks according to their attractive potentialities. An application of our findings is illustrated by the analysis of the dynamics of a simplified model of the basal ganglia-thalamocortical network simulated by a Boolean recurrent neural network. This example shows the significance of measuring network complexity, and how our results bear new founding elements for the understanding of the complexity of real brain circuits.
| S-EPMC3984152 | biostudies-literature