| | Models | Description |
| 1. |
A computational model of action selection in the basal ganglia (Suryanarayana et al 2019)
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" ... Here, we incorporate newly revealed subgroups of neurons
within the GPe into an existing computational model of the basal
ganglia, and investigate their role in action selection. Three
main results ensued. First, using previously used metrics for
selection, the new extended connectivity improved the action
selection performance of the model. Second, low frequency theta
oscillations were observed in the subpopulation of the GPe (the
TA or ‘arkypallidal’ neurons) which project exclusively to the
striatum. These oscillations were suppressed by increased
dopamine activity — revealing a possible link with symptoms of
Parkinson’s disease. Third, a new phenomenon was observed in
which the usual monotonic relationship between input to the basal
ganglia and its output within an action ‘channel’ was, under some
circumstances, reversed.
..." |
| 2. |
A contracting model of the basal ganglia (Girard et al. 2008)
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Basal ganglia model : selection processes between channels, dynamics controlled by contraction analysis, rate-coding model of neurons based on locally projected dynamical systems (lPDS). |
| 3. |
A dendritic disinhibitory circuit mechanism for pathway-specific gating (Yang et al. 2016)
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"While reading a book in a noisy café, how does your brain ‘gate in’ visual information while filtering out auditory stimuli? Here we propose a mechanism for such flexible routing of information flow in a complex brain network (pathway-specific gating), tested using a network model of pyramidal neurons and three classes of interneurons with connection probabilities constrained by data. We find that if inputs from different pathways cluster on a pyramidal neuron dendrite, a pathway can be gated-on by a disinhibitory circuit motif. ..." |
| 4. |
A microcircuit model of the frontal eye fields (Heinzle et al. 2007)
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" ... we show that the canonical circuit (Douglas et al. 1989, Douglas and Martin 1991) can,
with a few modifications, model the primate FEF. The spike-based network of integrate-and-fire neurons was tested in tasks that were
used in electrophysiological experiments in behaving macaque monkeys. The dynamics of the model matched those of neurons observed
in the FEF, and the behavioral results matched those observed in psychophysical experiments. The close relationship between the model
and the cortical architecture allows a detailed comparison of the simulation results with physiological data and predicts details of the
anatomical circuit of the FEF." |
| 5. |
A spatial model of the intermediate superior colliculus (Moren et. al. 2013)
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A spatial model of the intermediate superior colliculus. It reproduces the collicular saccade-generating output profile from NMDA receptor-driven burst neurons, shaped by integrative inhibitory feedback from spreading buildup neuron activity. The model is consistent with the view that collicular activity directly shapes the temporal profile of saccadic eye movements.
We use the Adaptive exponential integrate and fire neuron model, augmented with an NMDA-like membrane potential-dependent receptor. In addition, we use a synthetic spike integrator model as a stand-in for a spike-integrator circuit in the reticular formation.
NOTE: We use a couple of custom neuron models, so the supplied model file includes an entire version of NEST. I also include a patch that applies to a clean version of the simulator (see the doc/README). |
| 6. |
Basal ganglia-thalamocortical loop model of action selection (Humphries and Gurney 2002)
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We embed our basal ganglia model into a wider circuit containing the motor thalamocortical loop and thalamic reticular nucleus (TRN). Simulation of this extended model showed that the additions gave five main results which are desirable in a selection/switching mechanism. First, low salience actions (i.e. those with low urgency) could be selected. Second, the range of salience values over which actions could be switched between was increased. Third, the contrast between the selected and non-selected actions was enhanced via improved differentiation of outputs from the BG. Fourth, transient increases in the salience of a non-selected action were prevented from interrupting the ongoing action, unless the transient was of sufficient magnitude. Finally, the selection of the ongoing action persisted when a new closely matched salience action became active. The first result was facilitated by the thalamocortical loop; the rest were dependent on the presence of the TRN. Thus, we conclude that the results are consistent with these structures having clearly defined functions in action selection. |
| 7. |
Biologically Constrained Basal Ganglia model (BCBG model) (Lienard, Girard 2014)
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We studied the physiology and function of the basal ganglia through the design of mean-field models of the whole basal ganglia. The parameterizations are optimized with multi-objective evolutionary algorithm to respect best a collection of numerous anatomical data and electrophysiological data. The main outcomes of our study are: • The strength of the GPe to GPi/SNr connection does not support opposed activities in the GPe and GPi/SNr. • STN and MSN target more the GPe than the GPi/SNr. • Selection arises from the structure of the basal ganglia, without properly segregated direct and indirect pathways and without specific inputs from pyramidal tract neurons of the cortex. Selection is enhanced when the projection from GPe to GPi/SNr has a diffuse pattern. |
| 8. |
Coding explains development of binocular vision and its failure in Amblyopia (Eckmann et al 2020)
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This is the MATLAB code for the Active Efficient Coding model introduced in Eckmann et al 2020.
It simulates an agent that self-calibrates vergence and accommodation eye movements in a simple visual environment. All algorithms are explained in detail in the main manuscript and the supplementary material of the paper. |
| 9. |
Cognitive and motor cortico-basal ganglia interactions during decision making (Guthrie et al 2013)
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This is a re-implementation of Guthrie et al 2013 by Topalidou and Rougier 2015. The original study investigated how multiple level action selection
could be performed by the basal ganglia. |
| 10. |
Continuous lateral oscillations as a mechanism for taxis in Drosophila larvae (Wystrach et al 2016)
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" ...Our analysis of larvae motion reveals a rhythmic, continuous lateral oscillation of the anterior body, encompassing all head-sweeps, small or large, without breaking the oscillatory rhythm. Further, we show that an agent-model that embeds this hypothesis reproduces a surprising number of taxis signatures observed in larvae. Also, by coupling the sensory input to a neural oscillator in continuous time, we show that the mechanism is robust and biologically plausible. ..." |
| 11. |
Cortico - Basal Ganglia Loop (Mulcahy et al 2020)
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The model represents learning and reversal tasks and shows performance in control, Parkinsonian and Huntington disease conditions |
| 12. |
Dynamic dopamine modulation in the basal ganglia: Learning in Parkinson (Frank et al 2004,2005)
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See README file for all info on how to run models under different tasks and simulated Parkinson's and medication conditions. |
| 13. |
Human Attentional Networks: A Connectionist Model (Wang and Fan 2007)
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"... We describe a connectionist model of human attentional networks to explore the
possible interplays among the networks from a computational
perspective. This model is developed in the framework of
leabra (local, error-driven, and associative, biologically realistic
algorithm) and simultaneously involves these attentional networks
connected in a biologically inspired way. ...
We evaluate the model by simulating the empirical data collected on normal human
subjects using the Attentional Network Test (ANT).
The simulation results fit the experimental data well.
In addition, we show that the same model, with a single parameter change that
affects executive control, is able to simulate the empirical data collected
from patients with schizophrenia.
This model represents a plausible connectionist explanation for the functional structure
and interaction of human attentional networks."
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| 14. |
Inhibitory control by an integral feedback signal in prefrontal cortex (Miller and Wang 2006)
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The prefrontal cortex (PFC) is known to be critical for inhibitory
control of behavior, but the underlying mechanisms are unclear.
Here, we propose that inhibitory control can be instantiated by an
integral signal derived from working memory, another key function of the PFC. Specifically, we assume that an integrator converts
excitatory input into a graded mnemonic activity that provides an
inhibitory signal (integral feedback control) to upstream afferent
neurons. We demonstrate this scenario in a neuronal-network
model for a temporal discrimination task... See paper for details
and more.
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| 15. |
Medial reticular formation of the brainstem: anatomy and dynamics (Humphries et al. 2006, 2007)
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A set of models to study the medial reticular formation (mRF) of the brainstem. We developed a collection of algorithms to derive the adult-state wiring of the model: one set a stochastic model; the other set mimicking the developmental process. We found that the anatomical models had small-world properties, irrespective of the choice of algorithm; and that the cluster-like organisation of the mRF may have arisen to minimise wiring costs. (The model code includes options to be run as dynamic models; papers examining these dynamics are included in the .zip file). |
| 16. |
Neural model of two-interval discrimination (Machens et al 2005)
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Two-interval discrimination involves comparison of two stimuli that are presented at different times. It has three phases: loading, in which the first stimulus is perceived and stored in working memory; maintenance of working memory; decision making, in which the second stimulus is perceived and compared with the first. In behaving monkeys, each phase is associated with characteristic firing activity of neurons in the prefrontal cortex. This model implements both working memory and decision making with a mutual inhibition network that reproduces all three phases of two-interval discrimination.
Machens, C.K., Romo, R., and Brody, C.D.
Flexible control of mutual inhibition: a neural model of two-interval discrimination.
Science 307:1121-1124, 2005. |
| 17. |
Population-level model of the basal ganglia and action selection (Gurney et al 2001, 2004)
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We proposed a new functional architecture for the basal ganglia (BG) based on the premise that these brain structures play a central role in behavioural action selection. The papers quantitatively describes the properties of the model using analysis and simulation. In the first paper, we show that the decomposition of the BG into selection and control pathways is supported in several ways. First, several elegant features are exposed--capacity scaling, enhanced selectivity and synergistic dopamine modulation--which might be expected to exist in a well designed action selection mechanism. Second, good matches between model GPe output and GPi and SNr output, and neurophysiological data, have been found. Third, the behaviour of the model as a signal selection mechanism has parallels with some kinds of action selection observed in animals under various levels of dopaminergic modulation.
In the second paper, we extend the BG model to include new connections, and show that action selection is maintained. In addition, we provide quantitative measures for defining different forms of selection, and methods for assessing performance changes in computational neuroscience models.
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| 18. |
Roles of subthalamic nucleus and DBS in reinforcement conflict-based decision making (Frank 2006)
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Deep brain stimulation (DBS) of the subthalamic nucleus dramatically improves the motor symptoms of Parkinson's disease, but causes cognitive side effects such as impulsivity. This model from Frank (2006) simulates the role of the subthalamic nucleus (STN) within the basal ganglia circuitry in decision making. The STN dynamically modulates network decision thresholds in proportion to decision conflict. The STN ``hold your horses'' signal adaptively allows the system more time to settle on the best choice when multiple options are valid. The model also replicates effects in Parkinson's patients on and off DBS in experiments designed to test the model (Frank et al, 2007). |
| 19. |
Spiking neuron model of the basal ganglia (Humphries et al 2006)
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A spiking neuron model of the basal ganglia (BG) circuit (striatum, STN, GP, SNr). Includes: parallel anatomical channels; tonic dopamine; dopamine receptors in striatum, STN, and GP; burst-firing in STN; GABAa, AMPA, and NMDA currents; effects of synaptic location. Model demonstrates selection and switching of input signals. Replicates experimental data on changes in slow-wave (<1 Hz) and gamma-band oscillations within BG nuclei following lesions and pharmacological manipulations. |
| 20. |
Striatal GABAergic microcircuit, dopamine-modulated cell assemblies (Humphries et al. 2009)
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To begin identifying potential dynamically-defined computational elements within the striatum, we constructed a new three-dimensional model of the striatal microcircuit's connectivity, and instantiated this with our dopamine-modulated neuron models of the MSNs and FSIs. A new model of gap junctions between the FSIs was introduced and tuned to experimental data. We introduced a novel multiple spike-train analysis method, and apply this to the outputs of the model to find groups of synchronised neurons at multiple time-scales. We found that, with realistic in vivo background input, small assemblies of synchronised MSNs spontaneously appeared, consistent with experimental observations, and that the number of assemblies and the time-scale of synchronisation was strongly dependent on the simulated concentration of dopamine. We also showed that feed-forward inhibition from the FSIs counter-intuitively increases the firing rate of the MSNs. |
