cellclass train

Train a model using an ROI dataset or resume from saved state.

cellclass train [OPTIONS] DATASET.NPZ | STATE.JSON

Full --help output

Usage: cellclass train [OPTIONS] dataset.npz | state.json

  Train a model using an ROI dataset or resume from saved state.

Options:
  --size INTEGER                  Number of images to use.
  --data-seed INTEGER             [default: 42]
  -d, --device TEXT               [default: cuda]
  -s, --state TEXT                [default: training.json]
  --model [densenet121|densenet161|densenet169|densenet201|squeezenet1_0|shufflenet2x1_0|shufflenet2x1_5|shufflenet2x2_0|efficientnetb3|efficientnetb4|efficientnetb3s|efficientnetb4s|resenext50_32x4d|alexnet|alexnet_att|googlenet|googlenet_att|simplegooglenet|simplegooglenet_att|simplegooglenet_ch_att|simplegooglenet_ch_sp_att]
  -n, --name TEXT                 [default: model.pt]
  --existing [overwrite|load|error]
  --weights TEXT                  [default: DEFAULT]
  --freeze-weights / --no-freeze-weights
  --epochs INTEGER                [default: 2000]
  --batch-size INTEGER            [default: 32]
  --num-workers INTEGER           [default: 0]
  --seed INTEGER                  [default: 3735928559]
  --validation-size FLOAT         [default: 0.2]
  --lr FLOAT                      [default: 0.0001]
  --lr-scheduler [step|plateau]
  --lr-gamma FLOAT                [default: 0.1]
  --lr-step INTEGER               [default: 5]
  --lr-factor FLOAT               [default: 0.1]
  --lr-patience INTEGER           [default: 2]
  --patience INTEGER              [default: 10]
  --delta FLOAT                   [default: 0.0]
  --rel-delta FLOAT               [default: 0.0001]
  --weight-decay FLOAT            [default: 0.0001]
  --flip INTEGER                  [default: 1]
  --rotate INTEGER                [default: 180]
  --translate FLOAT               [default: 0.1]
  --loss-function [focal_loss|cross_entropy]
  --focal-gamma FLOAT             [default: 2.0]
  --loss-weights / --no-loss-weights
  --dropout FLOAT                 [default: 0.4]
  --testing-size FLOAT            [default: 0.2]
  --testing-interval INTEGER      [default: 5]
  --log-level INTEGER             [default: 20]
  --cudnn-benchmark / --no-cudnn-benchmark
  --pin-memory / --no-pin-memory
  --wandb / --no-wandb
  --entity TEXT                   Weights and Biases team/entity.
  --project TEXT                  [default: cellclass]
  --run-name TEXT                 Weights and Biases run display name.
  --tags TEXT                     Weights and Biases tags.
  --wandb-id TEXT                 Weights and Biases run ID.
  --help                          Show this message and exit.

Arguments

DATASET.NPZ | STATE.JSON: FILE

Required.

Options

--size: INTEGER = 0

Number of images to use.

--data-seed: INTEGER = 42

 

-d, --device: TEXT = cuda

 

-s, --state: TEXT = training.json

 

--model: CHOICE = densenet121

 

-n, --name: TEXT = model.pt

 

--existing: CHOICE = error

 

--weights: TEXT = DEFAULT

 

--freeze-weights, --no-freeze-weights

 

--epochs: INTEGER = 2000

 

--batch-size: INTEGER = 32

 

--num-workers: INTEGER = 0

 

--seed: INTEGER = 3735928559

 

--validation-size: FLOAT = 0.2

 

--lr: FLOAT = 0.0001

 

--lr-scheduler: CHOICE = step

 

--lr-gamma: FLOAT = 0.1

 

--lr-step: INTEGER = 5

 

--lr-factor: FLOAT = 0.1

 

--lr-patience: INTEGER = 2

 

--patience: INTEGER = 10

 

--delta: FLOAT = 0.0

 

--rel-delta: FLOAT = 0.0001

 

--weight-decay: FLOAT = 0.0001

 

--flip: INTEGER = 1

 

--rotate: INTEGER = 180

 

--translate: FLOAT = 0.1

 

--loss-function: CHOICE = focal_loss

 

--focal-gamma: FLOAT = 2.0

 

--loss-weights, --no-loss-weights

 

--dropout: FLOAT = 0.4

 

--testing-size: FLOAT = 0.2

 

--testing-interval: INTEGER = 5

 

--log-level: INTEGER = 20

 

--cudnn-benchmark, --no-cudnn-benchmark

 

--pin-memory, --no-pin-memory

 

--wandb, --no-wandb

 

--entity: TEXT

Weights and Biases team/entity.

--project: TEXT = cellclass

 

--run-name: TEXT

Weights and Biases run display name.

--tags: TEXT

Weights and Biases tags.

--wandb-id: TEXT

Weights and Biases run ID.