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Bayesian Visual Working Memory in Python.
Python

tweak

latest commit 494f57e453
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Data Data for abstract for cosyne 2012
Experiments tweak
README.md Markdown readme
cma.py Implement CMA-ES optimisation routine
computations_circular_precision_sensitivity.py Script checking precision dependence on randomness
computations_marginalfisherinfo_marginalposterior_1d.py Fisher information improvements
computations_marginalfisherinfo_marginalposterior_2d.py Refactor np.arange -> xrange
computations_marginalfisherinfo_marginalposterior_2d_nstim.py Tweaks and fixes
computations_misbinding_gaussian.py Misbinding analysis for Gaussians
data_analysis.py Refactor np.arange -> xrange
datagenerator.py Moved DataGeneratorRFN to a new file
datageneratorrfn.py Fix renormalized sigma_x bug
dataio.py DataIO Git fixed
datapbs.py Progress display for loading files
dirac_submission_slurm_unfilled.sh Added elapsed time for jobs
em_circularmixture.py Tweaks
em_circularmixture_allitems.py Optimisation tweak for EM fitting
em_circularmixture_allitems_kappafi.py Optimisation tweak for EM fitting
em_circularmixture_allitems_uniquekappa.py Refactored Experimental Data Loader
experimentalloader.py Reproduced Gorgo 11 plots
experimentalloaderbays09.py Refactored Experimental Data Loader
experimentalloaderdualrecall.py Refactored Experimental Data Loader
experimentalloadergorgo11.py Refactored Experimental Data Loader
experimentalloadergorgo11seq.py Reproduced Gorgo 11 plots
experimentalloadergorgo11sim.py Refactored Experimental Data Loader
experimentlauncher.py First tests of fits for Sequential
fisherinformation.py Added output noise after posterior sampling
fitexperiment.py Posterior convolved with noise output distribution
gibbs_sampler_continuous_fullcollapsed_randomfactorialnetwork.py First tests of fits for Sequential
hierarchicalrandomnetwork.py Launcher Fit Mixture models and Generators
highdimensionnetwork.py Support for Marginal FI computation
hinton_plot.py Added files. Version with R populations working for _discrete sampler…
jobwrapper.py Fixes and tweaks during paper revisions
keyboardthreadtest.py Testing keyboard listener in a thread
launchers.py First tests of fits for Sequential
launchers_bootstrap.py Fixed load_data_bays09 calls
launchers_errordistribution.py Launchers, Generators, Reloader for Error distributions
launchers_experimentalvolume.py Added output noise after posterior sampling
launchers_fisherinformation.py Added output noise after posterior sampling
launchers_fit_mixturemodels.py First tests of fits for Sequential
launchers_fitexperiment.py Posterior convolved with noise output distribution
launchers_hierarchicalnetwork.py Hierarchical plots all responses new EM plots
launchers_higher_dimensions.py Fisher information computation for R>2
launchers_memorycurves.py Added output noise after posterior sampling
launchers_memorycurves_marginal_fi.py tweaks
launchers_misbinding.py Housekeeping changes
launchers_mixed.py Housekeeping changes
launchers_multipleobjectchecker.py Added output noise after posterior sampling
launchers_noiseoutput.py Launcher to check effect of noise output on kappa and em mixture
launchers_parametersweeps.py Added output noise after posterior sampling
launchers_pbs.py Fixes and tweaks during paper revisions
launchers_profile.py Refactor Sampler initialisation
launchers_receptivesize.py Tweak
launchers_specificstimuli.py Bootstrap launcher for Misbinding runs, collect responses in Specific…
load_experimental_data.py Reproduced Gorgo 11 plots
pbs_parameters_creator.sh cleaned /home2 references
plots_cosyne12.py Refactor np.arange -> xrange
plots_cosyne13.py Plots Cosyne 2013
plots_experimental_data.py Plots sequential gorgo11
plots_paper_theo.py Plots to check experimental question from reviewers
plots_thesis.py Plot thesis, best bays09 fit
populationcode.py Refactor np.arange -> xrange
progress.py Cleaning, range to xrange
randomfactorialnetwork.py tweak
randomnetwork.py Refactor np.arange -> xrange
resultcomputation.py New ResultComputations, log kappa, summed
slicesampler.py Refactor Slicesampler
slicesampler_c.pyx Done some profiling, cython is ~2x faster. Big problem is dgesv for t…
slicesampler_numba.py Working numba version
smooth.py Plots and fixes, Smooth
statisticsmeasurer.py Various fixes, SLURM support
submitpbs.py SubmitPBS support for QOS slurm option
tests_randomfactorialnetwork.py Nose testing
utils.py Animation 3D Rotation function, allowing movie creation
utils_animation.py Animation 3D Rotation function, allowing movie creation
utils_directional_stats.py Fixed Wavelet population code
utils_fitting.py Fix for fit_beta_samples
utils_helper.py Reproduced Gorgo 11 plots
utils_interpolate.py Fix for plotting
utils_math.py Tweaks
utils_plot.py Plot mean std from samples, strict or moving average
utils_spherical.py Experimental bias, paper comment
vonmises_wrappedgaussian_comparison.py Added support for plots showing bias towards nontargets

README.md

DOI

code for Bayesian Visual Working Memory models.

Written by Loic Matthey Done at Gatsby Computational Neuroscience Unit.

Contact me for any informations or if you are interested by this project.

Entry point is in ExperimentLauncher (which is used to instantiate and run different experiments depending on input parameters).

Basic use-case is in launcher_do_simple_run()

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