Update models and README.

README.md

@@ -4,4 +4,4 @@ license: mit
    
 ECG-FM is a foundation model for electrocardogram (ECG) analysis. Please refer to our [GitHub](https://github.com/bowang-lab/ECG-FM) for more details.
 
-**Disclaimer: These models are different from those reported in our arXiv paper.** These BERT-Base sized models were trained purely on public data sources due to privacy concerns surrounding UHN-ECG data and patient identification. Validation for the final models will be available upon full publication.
+> ⚠️ **Note:** This repository is for hosting model weights only—the model **cannot** be loaded using `transformers`. Please download the weights and load them as per our [GitHub](https://github.com/bowang-lab/ECG-FM).

physionet_finetuned.pt → mimic_iv_ecg_finetuned.pt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:668c86ddc6a38ba138bd374c5bab388d839f5c36c807e28e97674de6dafae412
-size 1081734812
+oid sha256:f3e07588ee808d7e1e9e5608a997c9132883239518349f0565fd890590617b3d
+size 1081641499

physionet_finetuned.yaml → mimic_iv_ecg_finetuned.yaml

@@ -28,11 +28,11 @@ common_eval:
   path: null
   quiet: false
   model_overrides: '{}'
-  save_outputs: false
+  extract: null
   results_path: null
 distributed_training:
   _name: null
-  distributed_world_size: 4
+  distributed_world_size: 1
   distributed_rank: 0
   distributed_backend: nccl
   distributed_init_method: null
@@ -48,10 +48,10 @@ distributed_training:
   memory_efficient_fp16: ${common.memory_efficient_fp16}
 dataset:
   _name: null
-  num_workers: 3
+  num_workers: 7
   skip_invalid_size_inputs_valid_test: false
   max_tokens: null
-  batch_size: 64
+  batch_size: 256
   required_batch_size_multiple: 8
   data_buffer_size: 10
   train_subset: train
@@ -62,7 +62,7 @@ dataset:
   validate_interval_updates: 0
   validate_after_updates: 0
   fixed_validation_seed: null
-  disable_validation: false
+  disable_validation: true
   max_tokens_valid: ${dataset.max_tokens}
   batch_size_valid: ${dataset.batch_size}
   max_valid_steps: null
@@ -71,7 +71,7 @@ dataset:
   shard_id: 0
 optimization:
   _name: null
-  max_epoch: 50
+  max_epoch: 40
   max_update: 320000
   lr:
   - 1.0e-06
@@ -109,7 +109,7 @@ checkpoint:
 model:
   _name: ecg_transformer_classifier
   model_path: <REDACTED>
-  num_labels: 26
+  num_labels: 17
   no_pretrained_weights: false
   dropout: 0.0
   attention_dropout: 0.0
@@ -124,39 +124,30 @@ task:
   enable_padding: true
   enable_padding_leads: false
   leads_to_load: null
-  label_file: 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
+  - 36.796317
+  - 0.231449
+  - 14.49034
+  - 3.780268
+  - 1104.575439
+  - 23.01044
+  - 8.897255
+  - 54.976017
+  - 6.66556
+  - 7.404951
+  - 11.790818
+  - 12.727873
+  - 32.175994
+  - 11.188187
+  - 26.172215
+  - 3.464408
+  - 24.640965
 lr_scheduler:
   _name: fixed
   warmup_updates: 0