Added settings for models in test in readable fashion, removed unnece…

…ssary model templates, organizer tests/ect (untested acutally, thinking of this, the setup scripts should be tested as well). Added micro an macro metrics for torch now going for tensorflow
tensor-works · Jul 2, 2024 · 1c3d1e4 · 1c3d1e4
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Showing 76 changed files with 547 additions and 820 deletions.
diff --git a/condensator.py b/condensator.py
diff --git a/datalab/read_dataset.ipynb b/datalab/read_dataset.ipynb
@@ -37,7 +37,7 @@
    "source": [
     "proc_reader = datasets.load_data(chunksize=75835,\n",
     "                                 source_path=TEST_DATA_DIR,\n",
-    "                                 storage_path=\"./tmp\",\n",
+    "                                 storage_path=\"./temp\",\n",
     "                                 discretize=True,\n",
     "                                 deep_supervision=True,\n",
     "                                 task=\"DECOMP\")"

diff --git a/model_templates/__init__.py b/model_templates/__init__.py
diff --git a/model_templates/mimic/.gitignore b/model_templates/mimic/.gitignore
diff --git a/model_templates/mimic/logistic_default/decompensation/data_config.json b/model_templates/mimic/logistic_default/decompensation/data_config.json
diff --git a/model_templates/mimic/logistic_default/decompensation/model_config.json b/model_templates/mimic/logistic_default/decompensation/model_config.json
diff --git a/model_templates/mimic/logistic_default/decompensation/pipeline_config.json b/model_templates/mimic/logistic_default/decompensation/pipeline_config.json
diff --git a/model_templates/mimic/logistic_default/in_hospital_mortality/data_config.json b/model_templates/mimic/logistic_default/in_hospital_mortality/data_config.json
diff --git a/model_templates/mimic/logistic_default/in_hospital_mortality/model_config.json b/model_templates/mimic/logistic_default/in_hospital_mortality/model_config.json
diff --git a/model_templates/mimic/logistic_default/in_hospital_mortality/pipeline_config.json b/model_templates/mimic/logistic_default/in_hospital_mortality/pipeline_config.json
diff --git a/model_templates/mimic/logistic_default/length_of_stay/data_config.json b/model_templates/mimic/logistic_default/length_of_stay/data_config.json
diff --git a/model_templates/mimic/logistic_default/length_of_stay/model_config.json b/model_templates/mimic/logistic_default/length_of_stay/model_config.json
diff --git a/model_templates/mimic/logistic_default/length_of_stay/pipeline_config.json b/model_templates/mimic/logistic_default/length_of_stay/pipeline_config.json
diff --git a/model_templates/mimic/logistic_default/phenotyping/data_config.json b/model_templates/mimic/logistic_default/phenotyping/data_config.json
diff --git a/model_templates/mimic/logistic_default/phenotyping/model_config.json b/model_templates/mimic/logistic_default/phenotyping/model_config.json
diff --git a/model_templates/mimic/logistic_default/phenotyping/pipeline_config.json b/model_templates/mimic/logistic_default/phenotyping/pipeline_config.json
diff --git a/model_templates/mimic/lstm_concept_drift_ehr/decompensation/history.json b/model_templates/mimic/lstm_concept_drift_ehr/decompensation/history.json
diff --git a/model_templates/mimic/lstm_concept_drift_ehr/decompensation/loss.png b/model_templates/mimic/lstm_concept_drift_ehr/decompensation/loss.png
diff --git a/model_templates/mimic/lstm_concept_drit_bm/decompensation/history.json b/model_templates/mimic/lstm_concept_drit_bm/decompensation/history.json
diff --git a/model_templates/mimic/lstm_concept_drit_bm/decompensation/loss.png b/model_templates/mimic/lstm_concept_drit_bm/decompensation/loss.png
diff --git a/model_templates/mimic/lstm_debug/decompensation/data_config.json b/model_templates/mimic/lstm_debug/decompensation/data_config.json
diff --git a/model_templates/mimic/lstm_debug/decompensation/history.json b/model_templates/mimic/lstm_debug/decompensation/history.json
diff --git a/model_templates/mimic/lstm_debug/decompensation/loss.png b/model_templates/mimic/lstm_debug/decompensation/loss.png
diff --git a/model_templates/mimic/lstm_debug/decompensation/model_config.json b/model_templates/mimic/lstm_debug/decompensation/model_config.json
diff --git a/model_templates/mimic/lstm_debug/decompensation/pipeline_config.json b/model_templates/mimic/lstm_debug/decompensation/pipeline_config.json
diff --git a/model_templates/mimic/lstm_debug/in_hospital_mortality/data_config.json b/model_templates/mimic/lstm_debug/in_hospital_mortality/data_config.json
diff --git a/model_templates/mimic/lstm_debug/in_hospital_mortality/model_config.json b/model_templates/mimic/lstm_debug/in_hospital_mortality/model_config.json
diff --git a/model_templates/mimic/lstm_debug/in_hospital_mortality/pipeline_config.json b/model_templates/mimic/lstm_debug/in_hospital_mortality/pipeline_config.json
diff --git a/model_templates/mimic/lstm_debug/length_of_stay/data_config.json b/model_templates/mimic/lstm_debug/length_of_stay/data_config.json
diff --git a/model_templates/mimic/lstm_debug/length_of_stay/model_config.json b/model_templates/mimic/lstm_debug/length_of_stay/model_config.json
diff --git a/model_templates/mimic/lstm_debug/length_of_stay/pipeline_config.json b/model_templates/mimic/lstm_debug/length_of_stay/pipeline_config.json
diff --git a/model_templates/mimic/lstm_debug/phenotyping/data_config.json b/model_templates/mimic/lstm_debug/phenotyping/data_config.json