This repository contains data and code that accompany the manuscript entitled "Explaining the effectiveness of fear extinction through latent-cause inference".

Table of Contents

• handscores/ contains the data reported in Gershman et al. (2013)
  • gershman2013_experiment1.xlsx: Experiment 1 (spontaneous recovery)
  • gershman2013_experiment2.xlsx: Experiment 2 (reinstatement)
• *.m files: code for model simulation and plotting figures (see details below)
• results/ contains the model simulation results; can be reproduced with simu_particle_filter.m; used for generating figures in the manuscript.
• stats.ipynb: statistical test results

Model simulation:

simu_particle_filter.m contains the model simulation code. You can run the scripts below to simulate the main model and alternative models; alternatively, you can directly access the simulation results saved in results/.

Main model:

simu_particle_filter([1,2],'RL',[0.2,1,0.1,0.1,0.2,0.2,0.2,0.4,0.5,0.05,0.7],1,10000,1);

Alternative models:

% Standard CRP prior
simu_particle_filter([1,2],'RL',[0.2,1,0,0.1,0.2,0.2,0.2,0.4,0.5,0.05,0.7],1,10000,1);

% Learning through inference
simu_particle_filter([1,2],'inference',[0.2,1,0.1,0.1,0.5,0.5,0.95,0.05,0.7],1,10000,1);

% Full posterior
simu_particle_filter([1,2],'RL',[0.2,1,0.1,0.1,0.2,0.2,0.2,0.4,0.5,0.05,0.7],0,10000,1);

% No perseveration
simu_particle_filter([1,2],'RL',[0.2,1,0.1,0.1,0.2,0.2,0.2,0.4,0.5,0.05,0],1,10000,1);

% No perseveration + low learning rate
simu_particle_filter([1,2],'RL',[0.2,1,0.1,0.1,0.1,0.1,0.1,0.2,0.5,0.05,0],1,10000,1,0);

Other experiments:

% spaced vs massed extinction
simu_particle_filter_other_exps('multiple_sessions',[1,2],'RL',[0.05,1,0.1,0.1,0.2,0.2,0.2,0.4,0.5,0.05,0.7],1,10000,1);
	
% occasional reinforcement experiments
simu_particle_filter_other_exps('occasional_reinforcement',3,'RL',[0.2,1,0.1,0.1,0.2,0.2,0.2,0.4,0.5,0.05,0.7],1,10000,1);

% low intensity shock during reinforcement experiment
simu_particle_filter_other_exps('low_intensity',2,'RL',[0.2,1,0.1,0.1,0.2,0.2,0.2,0.4,0.5,0.05,0.7],1,10000,1);

Shock with continuous intensity:

simu_particle_filter_continuous([1,2],'RL',[0.2,1,0.1,0.1,0.2,0.2,0.2,0.4,0.5,0.05,0.7,0.4],1,10000,1);

Simulation with varying parameter values:

newp('simulation');

To reproduce figures in the manuscript

• plot_cause_probability.m: Figure 3
• plot_freeze_rate('main'): Figure 4
• plot_summary.m: Figure 5, Supplemenary Figure 2
• plot_freeze_rate('alternative'): Figure 6
• plot_multiple_sessions.m: Figure 7A
• plot_low_intensity.m: Figure 7B
• plot_occasional_reinforcement.m: Figure 7C
• plot_continuous.m: Figure 7D
• newp('plot'): Supplementary Figure 1

Helper functions

• func_pshock2freeze.m: the mapping from p(shock) to freezing rate.
• my_xticklabels.m: helper function to format xticklabels in figures (by Pekka Kumpulainen)