config.yml

# Params
# Experimental Params
run_params:
  fresh_posterior: True    # Create new posterior using SBI
  fresh_trial_data: True   # Create new trial dataset
  fresh_fitting: True      # Perform inference on all trials in dataset
  fresh_validation: True    # Perform validation on samples drawn from prior
  saving: True              # Save output to unique folder
  note: "First Run"         # Add a note to be used as a note for save folder

# SBI Parameters
sbi_params:
  sbi_seed: 11
  prior_bounds_std: [0, 40.0] # Bounds I_sigma for prior
  prior_bounds_mu: [-2, 2]    # Bounds I_mu for prior
  prior_nr_rounds: 3          # Number of iterations for prior restriction
  prior_nr_sims: 5_000        # Number of simulations per round
  nr_train_sims: 150_000      # Number of simulations for training data generation
  nr_workers: -1              # Number of cores used (-1 for max)
  validation_samples: 30_000   # Number of samples drawn from prior for validation
  nr_posterior_samples: 1000  # Number of posterior samples drawn for each inference

# Simulation Parameters
sim_params:
  mu_I: None                  # Don't touch
  std_I: None                 # Don't touch
  dt_noise: 0.1               # Noise timescale
  sim_res: 0.1                # Temporal resolution of simulation
  simtime: 1500               # Simulation time (also impacts length of trials from data)
  dry_simtime: 700            # Simulation time before recording (for convergence)
  numpy_seed: 70

# Real Data Parameters
data_params:
  area: None                         # Don't touch
  dataset: 'ChangeDetectionConflict' # Don't touch
  skip_transient: 200                # Length of transient period (excluded)
  min_fr_in_trial: 5                 # Minimum number of spikes to be included in dataset
  max_fr_in_trial: 50                # Maximum number of spikes to be included in dataset
  areas_to_fit: ['PPC']              # Don't touch

# Neuron Parameter
neuron_params:
  C_m: 1.0          # Membrane capacity [pF]
  t_ref: 0.1        # Duration of refractory period [ms]
  V_reset: -70.0    # Reset value for membrane potential (V_m) after spike
  tau_m: 20.0       # Membrane timeconstant (ms)
  V_th: -55.0       # Membrane threshold (mV)
  E_L: -70.0        # Leak potential (mV, should be same as V_reset)

# Plotting parameters
plot_params:
  show_figures: True          # plt.show() figures after plotting
  trial_to_plot: 8            # Trial to plot for Fig2
  analysis_min_spikes: 15     # Minimum number of spikes for trial inclusion
  analysis_max_spikes: 75     # Maximum number of spikes for trial inclusion
  analysis_burst_cutoff: 0.5  # Upper bound for burstiness ratio
  dpi: 100                    # Resolution of figures
  fig_format: '.pdf'          # Figure file type (.svg/.pdf/.png)