Upload models.

mimic_iv_ecg_physionet_pretrained.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4d0142bcb485eb9f0c7845e0c19ff3463f6ae9d0e458eab69136efe90ceb9b7e
+size 1090825421

mimic_iv_ecg_physionet_pretrained.yaml

@@ -0,0 +1,153 @@
+_name: null
+common:
+  _name: null
+  no_progress_bar: false
+  log_interval: 10
+  log_format: csv
+  log_file: null
+  wandb_project: null
+  wandb_entity: null
+  seed: 1
+  fp16: false
+  memory_efficient_fp16: false
+  fp16_no_flatten_grads: false
+  fp16_init_scale: 128
+  fp16_scale_window: null
+  fp16_scale_tolerance: 0.0
+  on_cpu_convert_precision: false
+  min_loss_scale: 0.0001
+  threshold_loss_scale: null
+  empty_cache_freq: 0
+  all_gather_list_size: 16384
+  model_parallel_size: 1
+  profile: false
+  reset_logging: false
+  suppress_crashes: false
+common_eval:
+  _name: null
+  path: null
+  quiet: false
+  model_overrides: '{}'
+  save_outputs: false
+  results_path: null
+distributed_training:
+  _name: null
+  distributed_world_size: 4
+  distributed_rank: 0
+  distributed_backend: nccl
+  distributed_init_method: null
+  distributed_port: 12355
+  device_id: 0
+  ddp_comm_hook: none
+  bucket_cap_mb: 25
+  fix_batches_to_gpus: false
+  find_unused_parameters: false
+  heartbeat_timeout: -1
+  broadcast_buffers: false
+  fp16: ${common.fp16}
+  memory_efficient_fp16: ${common.memory_efficient_fp16}
+dataset:
+  _name: null
+  num_workers: 10
+  skip_invalid_size_inputs_valid_test: false
+  max_tokens: null
+  batch_size: 64
+  required_batch_size_multiple: 8
+  data_buffer_size: 10
+  train_subset: train
+  valid_subset: valid
+  combine_valid_subsets: null
+  ignore_unused_valid_subsets: false
+  validate_interval: 1
+  validate_interval_updates: 0
+  validate_after_updates: 0
+  fixed_validation_seed: null
+  disable_validation: false
+  max_tokens_valid: ${dataset.max_tokens}
+  batch_size_valid: ${dataset.batch_size}
+  max_valid_steps: null
+  curriculum: 0
+  num_shards: 1
+  shard_id: 0
+optimization:
+  _name: null
+  max_epoch: 200
+  max_update: 0
+  lr:
+  - 5.0e-05
+  stop_time_hours: 0.0
+  clip_norm: 0.0
+  update_freq:
+  - 2
+  stop_min_lr: -1.0
+checkpoint:
+  _name: null
+  save_dir: <REDACTED>
+  restore_file: checkpoint_last.pt
+  finetune_from_model: null
+  reset_dataloader: false
+  reset_lr_scheduler: false
+  reset_meters: false
+  reset_optimizer: false
+  optimizer_overrides: '{}'
+  save_interval: 10
+  save_interval_updates: 0
+  keep_interval_updates: -1
+  keep_interval_updates_pattern: -1
+  keep_last_epochs: 0
+  keep_best_checkpoints: -1
+  no_save: false
+  no_epoch_checkpoints: false
+  no_last_checkpoints: false
+  no_save_optimizer_state: false
+  best_checkpoint_metric: loss
+  maximize_best_checkpoint_metric: false
+  patience: -1
+  checkpoint_suffix: ''
+  checkpoint_shard_count: 1
+  load_checkpoint_on_all_dp_ranks: false
+model:
+  _name: wav2vec2_cmsc
+  apply_mask: true
+  mask_prob: 0.65
+  encoder_layers: 24
+  encoder_embed_dim: 1024
+  encoder_ffn_embed_dim: 4096
+  encoder_attention_heads: 16
+  quantize_targets: true
+  final_dim: 256
+  dropout_input: 0.1
+  dropout_features: 0.1
+  feature_grad_mult: 0.1
+  in_d: 12
+task:
+  _name: ecg_pretraining
+  data: <REDACTED>/cmsc
+  perturbation_mode:
+  - random_leads_masking
+  p:
+  - 1.0
+  mask_leads_selection: random
+  mask_leads_prob: 0.5
+  normalize: false
+  enable_padding: true
+  enable_padding_leads: false
+  leads_to_load: null
+criterion:
+  _name: wav2vec2_with_cmsc
+  infonce: true
+  log_keys:
+  - prob_perplexity
+  - code_perplexity
+  - temp
+  loss_weights:
+  - 0.1
+  - 10
+lr_scheduler:
+  _name: fixed
+  warmup_updates: 0
+optimizer:
+  _name: adam
+  adam_betas: (0.9, 0.98)
+  adam_eps: 1.0e-06
+  weight_decay: 0.01

physionet_finetuned.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:96ecf96d044e735f6477a022d36d5a00f714693ee5e563faf19e47e9d319f28e
+size 1081741532

physionet_finetuned.yaml

@@ -0,0 +1,166 @@
+_name: null
+common:
+  _name: null
+  no_progress_bar: false
+  log_interval: 10
+  log_format: csv
+  log_file: null
+  wandb_project: null
+  wandb_entity: null
+  seed: 1
+  fp16: false
+  memory_efficient_fp16: false
+  fp16_no_flatten_grads: false
+  fp16_init_scale: 128
+  fp16_scale_window: null
+  fp16_scale_tolerance: 0.0
+  on_cpu_convert_precision: false
+  min_loss_scale: 0.0001
+  threshold_loss_scale: null
+  empty_cache_freq: 0
+  all_gather_list_size: 2048000
+  model_parallel_size: 1
+  profile: false
+  reset_logging: false
+  suppress_crashes: false
+common_eval:
+  _name: null
+  path: null
+  quiet: false
+  model_overrides: '{}'
+  save_outputs: false
+  results_path: null
+distributed_training:
+  _name: null
+  distributed_world_size: 4
+  distributed_rank: 0
+  distributed_backend: nccl
+  distributed_init_method: null
+  distributed_port: 12355
+  device_id: 0
+  ddp_comm_hook: none
+  bucket_cap_mb: 25
+  fix_batches_to_gpus: false
+  find_unused_parameters: true
+  heartbeat_timeout: -1
+  broadcast_buffers: false
+  fp16: ${common.fp16}
+  memory_efficient_fp16: ${common.memory_efficient_fp16}
+dataset:
+  _name: null
+  num_workers: 3
+  skip_invalid_size_inputs_valid_test: false
+  max_tokens: null
+  batch_size: 64
+  required_batch_size_multiple: 8
+  data_buffer_size: 10
+  train_subset: train
+  valid_subset: valid
+  combine_valid_subsets: null
+  ignore_unused_valid_subsets: false
+  validate_interval: 1
+  validate_interval_updates: 0
+  validate_after_updates: 0
+  fixed_validation_seed: null
+  disable_validation: false
+  max_tokens_valid: ${dataset.max_tokens}
+  batch_size_valid: ${dataset.batch_size}
+  max_valid_steps: null
+  curriculum: 0
+  num_shards: 1
+  shard_id: 0
+optimization:
+  _name: null
+  max_epoch: 50
+  max_update: 320000
+  lr:
+  - 1.0e-06
+  stop_time_hours: 0.0
+  clip_norm: 0.0
+  update_freq:
+  - 1
+  stop_min_lr: -1.0
+checkpoint:
+  _name: null
+  save_dir: <REDACTED>
+  restore_file: checkpoint_last.pt
+  finetune_from_model: null
+  reset_dataloader: false
+  reset_lr_scheduler: false
+  reset_meters: false
+  reset_optimizer: false
+  optimizer_overrides: '{}'
+  save_interval: 1
+  save_interval_updates: 0
+  keep_interval_updates: -1
+  keep_interval_updates_pattern: -1
+  keep_last_epochs: 0
+  keep_best_checkpoints: -1
+  no_save: false
+  no_epoch_checkpoints: false
+  no_last_checkpoints: false
+  no_save_optimizer_state: false
+  best_checkpoint_metric: loss
+  maximize_best_checkpoint_metric: false
+  patience: -1
+  checkpoint_suffix: ''
+  checkpoint_shard_count: 1
+  load_checkpoint_on_all_dp_ranks: false
+model:
+  _name: ecg_transformer_classifier
+  model_path: <REDACTED>
+  num_labels: 26
+  no_pretrained_weights: false
+  dropout: 0.0
+  attention_dropout: 0.0
+  activation_dropout: 0.1
+  feature_grad_mult: 0.0
+  freeze_finetune_updates: 0
+  in_d: 12
+task:
+  _name: ecg_classification
+  data: <REDACTED>
+  normalize: false
+  enable_padding: true
+  enable_padding_leads: false
+  leads_to_load: null
+  label_file: <REDACTED>
+criterion:
+  _name: binary_cross_entropy_with_logits
+  report_auc: true
+  report_cinc_score: false
+  weights_file: ???
+  pos_weight:
+  - 15.390331
+  - 9.366471
+  - 178.694517
+  - 307.623318
+  - 58.330172
+  - 16.724182
+  - 23.509615
+  - 45.128016
+  - 10.223581
+  - 38.081772
+  - 223.179153
+  - 53.063629
+  - 43.894325
+  - 48.763557
+  - 1.994518
+  - 25.936595
+  - 58.587013
+  - 143.283019
+  - 44.729568
+  - 40.310324
+  - 68.729483
+  - 23.999274
+  - 3.564768
+  - 8.647183
+  - 6.384442
+  - 20.731291
+lr_scheduler:
+  _name: fixed
+  warmup_updates: 0
+optimizer:
+  _name: adam
+  adam_betas: (0.9, 0.98)
+  adam_eps: 1.0e-08