Upload config.yaml

config.yaml

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+model_class: NDT1
+
+
+encoder:
+
+  from_pt: null
+  stitching: false
+
+  masker:
+    force_active: true         
+    mode: temporal             
+    ratio: 0.3                 # ratio of data to predict
+    zero_ratio: 1.0            # of the data to predict, ratio of zeroed out
+    random_ratio: 1.0          # of the not zeroed, ratio of randomly replaced
+    expand_prob: 0.0           # probability of expanding the mask in ``temporal`` mode
+    max_timespan: 1            # max span of mask if expanded
+    channels: null             # neurons to mask in "co-smoothing" mode
+    timesteps: null            # time steps to mask in ``forward-pred`` mode
+    mask_regions: ['all']      # brain regions to mask in ``inter-region`` mode
+    target_regions: ['all']    # brain regions to predict in ``intra-region`` mode
+    n_mask_regions: 1          # num of regions to choose from the list of mask_regions or target_regions
+    
+  # context available for each timestep
+  context:
+    forward: -1
+    backward: -1
+
+  norm_and_noise:
+    active: false
+    smooth_sd: 2                # gaussian smoohing  
+    norm: "zscore"              # which normalization layer to use (null/layernorm/scalenorm/zscore)
+    eps: 1.e-7                  # avoid dividing by zero when normalizing padded spikes     
+    white_noise_sd: 1.0         # gaussian noise added to the inputs  1.0 originally
+    constant_offset_sd: 0.2     # gaussian noise added to the inputs but contsnat in the time dimension 0.2 originally
+    
+  embedder:
+    n_channels: 668       # number of neurons recorded 
+    n_blocks: 24          # number of blocks of experiments
+    n_dates: 24           # number of days of experiments
+    max_F: 100            # max feature len in timesteps
+
+    mode: linear          # linear/embed/identity
+    mult: 2               # embedding multiplier. hiddden_sizd = n_channels * mult
+    adapt: false          # adapt the embedding layer for each day
+    pos: true             # embed position 
+    act: softsign         # activation for the embedding layers
+    scale: 1              # scale the embedding multiplying by this number
+    bias: true            # use bias in the embedding layer
+    dropout: 0.2          # dropout in embedding layer
+    
+    fixup_init: false     # modify weight initialization
+    init_range: 0.1       # initialization range for embeddings
+    spike_log_init: false # special initialization 
+    max_spikes: 0         # max number of spikes in a single time bin
+
+    tokenize_binary_mask: false
+    use_prompt: false
+    use_session: false
+
+    stack:
+      active: false       # wether to stack consecutive timesteps
+      size: 32            # number of consecutive timesteps to stack
+      stride: 4           # stacking stride
+
+
+  transformer:
+    n_layers: 5           # number of transformer layers
+    hidden_size: 512      # hidden space of the transformer
+    use_scalenorm: false  # use scalenorm  instead of layernorm
+    use_rope: false       # use rotary postional encoding
+    rope_theta: 10000.0   # rope angle of rotation
+
+
+    n_heads: 8            # number of attentiomn heads
+    attention_bias: true  # learn bias in the attention layers
+
+    act: gelu             # activiation function in mlp layers
+    inter_size: 1024      # intermediate dimension in the mlp layers
+    mlp_bias: true        # learn bias in the mlp layers
+    
+    dropout: 0.4          # dropout in transformer layers
+    fixup_init: true      # modify weight initialization
+
+
+  factors:  
+    active: false             # project from hidden_size to factors
+    size: 8                   # factors size  
+    act: relu                 # activation function after projecting to factors
+    bias: true                # use bias in projection to factors
+    dropout: 0.0              # dropout in projection to factors
+    fixup_init: false         # modify weight initialization
+    init_range: 0.1           # initialization range for factors projetion
+    
+decoder:
+  from_pt: null
+
+