VMO Feedback Model on ModelDB

Sensory feedback in a multiple oscillator model of place cell activity

Authors: Joseph D. Monaco [1]
James J. Knierim [1]
Kechen Zhang [2]
Contact: jmonaco@jhu.edu
Organization: [1] Zanvyl Krieger Mind/Brain Institute, Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA; [2] Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA

Abstract

Mammals navigate by integrating self-motion signals ('path integration') and occasionally fixing on familiar environmental landmarks. The rat hippocampus is a model system of spatial representation in which place cells are thought to integrate both sensory and spatial information from entorhinal cortex. The localized firing fields of hippocampal place cells and entorhinal grid cells demonstrate a phase relationship with the local theta (6-10 Hz) rhythm that may be a temporal signature of path integration. However, encoding self-motion in the phase of theta oscillations requires high temporal precision and is susceptible to idiothetic noise, neuronal variability, and a changing environment. We present a model based on oscillatory interference theory, previously studied in the context of grid cells, in which transient temporal synchronization among a pool of path-integrating theta oscillators produces hippocampal-like place fields. We hypothesize that a spatiotemporally extended sensory interaction with external cues modulates feedback to the theta oscillators. We implement a form of this cue-driven feedback and show that it can restore learned fixed-points in the phase code of position. A single cue can smoothly reset oscillator phases to correct for both systematic errors and continuous noise in path integration. Further, simulations in which local and global cues are rotated against each other reveal a phase-code mechanism in which conflicting cue arrangements can reproduce experimentally observed distributions of 'partial remapping' responses. This abstract model demonstrates that phase-code feedback can provide stability to the temporal coding of position during navigation and may contribute to the context-dependence of hippocampal spatial representations. While the anatomical substrates of these processes have not been fully characterized, our findings suggest several signatures that can be evaluated in future experiments.

Installation

Please see the INSTALL file for details, but you essentially need to have the Enthought EPD python distribution installed. Then you unzip this archive, go into the new directory and run sudo python setup.py install. The model can then be run interactively in an IPython session.

Libraries

Here is a brief description of the main modules and classes:

Top-level Modules

vmo
VMOModel: main model simulation class
double_rotation
VMODoubleRotation: subclass that performs double rotation
session
VMOSession: container that computes and stores simulation results
compare
Functions for comparing remapping responses
placemap
CirclePlaceMap: class that computes place fields
error
Function definitions for solutions to the phase error integral

Subpackages

core
  • Base classes for models, analyses, and time-series data
figures
  • PathIntFigure: basis for Figure 2

  • RemappingFigure: basis for Figure 3

  • FeedbackFigure: basis for Figure 5
    • VMOTrackModel: model subclass that tracks phase information
    • VMOToyModel: implements idealized linear trajectory
  • PhaseNoiseFigure: basis for Figure 6

  • MismatchFigure [1]: basis for Figures 7 and 8

remapping
  • VMOExperiment [1]: parallelized double rotation simulations
  • MismatchAnalysis: comprehensive remapping comparisons
  • MismatchTrends: remapping trends across mismatch angles
tools
  • A collection of supporting utility functions
trajectory
  • CircleTrackData: loads trajectory data, computes laps, etc.
[1](1, 2)

These classes farm simulations out to IPython ipengine instances running on your machine. You must first start them in another terminal:

$ ipcluster local -n C

Set C to the number of cores available on your machine.

Example Usage

You can run the model itself, specifying various parameters, or you can run pre-cooked analyses that were used as the basis of figures in the paper.

Running the model

Start IPython in -pylab mode:

$ ipython -pylab

Then, import the libraries and create a model instance:

In [0]: from vmo_feedback import *
In [1]: model = VMOModel()

It will automatically load the trajectory data. To see all the user-settable parameters, you can print the model:

In [2]: print model
VMOModel(Model) object
--------------------------------
Parameters:
        C_W : 0.050000000000000003
        N_cues : 3
        N_cues_distal : 3
        N_cues_local : 3
        N_outputs : 500
        N_theta : 1000
        cue_offset : 0.0
        cue_std : 0.15707963267948966
        distal_cue_std : 0.15707963267948966
        distal_offset : 0.0
        done : False
        epsilon : 0.050000000000000003
        gamma_distal : 0.46101227797811462
        gamma_local : 0.46101227797811462
        init_random : True
        lambda_range : (100, 200)
        local_cue_std : 0.15707963267948966
        local_offset : 0.0
        monitoring : True
        omega : 7
        pause : False
        refresh_fixed_points : True
Tracking:
        C_distal, C_local, I, active_distal_cue, x, y, alpha,
        active_local_cue, vel

In parameter names above, parameters with local and distal control one of the two cue sets (local rotate CCW, distal CW) to allow for independent manipulation:

C_W            feedforward connectivity and
N_theta        number of theta oscillators
N_outputs      the number of output units; each receives input from
                   C_W*N_theta oscillators
N_cues         number of cues per cue set
cue_offset     starting point on the track for laying out cues
cue_std        cue size (s.d.) in radians
epsilon        error tolerance
lambda_range   the range of spatial scales (multiplied by 2PI)
gamma          peak cue gains; if not specified, these gains are set
                   automatically based on epsilon
init_random    whether each trial gets randomized initial phases
omega          frequency of the carrier signal.

The values shown are the defaults used for the paper (aside from cue manipulations, etc.). The tracked variables are time-series data that are saved from the simulation:

C_*            cue interaction coefficients
I              summed oscillatory inputs for each output
x, y           trajectory position
vel            instantaneous velocity vector
alpha          track angle
active_*_cue   index number of the currently active cue

Parameters can be changed by passing them as keyword arguments to the constructor. To simulate only 200 oscillators, you would call VMOModel(N_theta=200).

Run the simulation:

In [3]: model.advance()

Look at the tracked data:

In [4]: data = model.post_mortem()
In [5]: print data.tracking
In [6]: subplot(221)
In [7]: plot(data.x, data.y, 'k-')

Plot cue coefficients for the local and distal cue sets:

In [8]: subplot(222)
In [9]: scatter(x=data.x, y=data.y, c=data.C_local, s=1, linewidths=0)
In [10]: subplot(224)
In [11]: scatter(x=data.x, y=data.y, c=data.C_distal, s=1, linewidths=0)

Now compute the output responses based on the amplitude envelope of excitation. These are computed and stored in VMOSession objects based on the simulation results:

In [12]: session = VMOSession(model)

Get the population response matrix and plot the place fields:

In [13]: subplot(223)
In [14]: R = session.get_population_matrix()
In [15]: plot(R.T, 'k-')
In [16]: xlim(0, 360)

The VMODoubleRotation is a subclass that automatically performs double rotations across a series of mismatch angles. Running double rotation and computing the responses is as easy as:

In [17]: drmodel = VMODoubleRotation()
In [18]: drmodel.advance_all()
In [19]: drsessions = VMOSession.get_session_list(drmodel)

The analysis subclasses in the remapping subpackage encapsulate double rotation experiment simulations and various remapping analyses.

Running figure analyses

To run the figure analyses, you simply create an analysis object and run it by calling it with analysis parameters. The single-cue feedback analysis is performed by the FeedbackFigure analysis class:

In [20]: fig = FeedbackFigure(desc='test')
In [21]: fig.collect_data?

The first command creates an analysis object with the description 'test'. The second command (with the ?) tells IPython to print out meta-data about the collect_data method. This is the method that actually performs the analysis when you call the object, so this tells you the available parameters along with their descriptions. We could run the analysis with different cue sizes:

In [22]: fig(cue_sizes=[5, 25])

This performs the simulations, collects data for the figures, and stores data, statistics, and an analysis.log file in the analysis directory. When that completes, you can bring up the resulting figure and save it:

In [23]: fig.view()
In [24]: fig.save_plots()

Running the view method renders the figures, outputs RGB image files, and saves a figure.log file in the analysis directory. Some of the figures have parameter arguments to change the figure. You will have to use the create_plots method, as this is what the view method actually calls. To see the figure parameters and make changes:

In [25]: fig.create_plots?
In [26]: fig.create_plots(...)

The same process can be used for the other figure analysis classes. You can create your own analyses by subclassing from core.analysis.BaseAnalysis and implementing the collect_data and create_plots methods.


Please explore the code, and let me know at jmonaco@jhu.edu if there are any major issues. There are no guaranteesthat this code will work perfectly everywhere.

Enjoy.