Delete configs/model/metrics

configs/model/metrics/accuracy.yaml

@@ -1,4 +0,0 @@
-Accuracy:
-  _target_: torchmetrics.Accuracy
-  task: ${task.task}
-  num_classes: ${task.num_classes}

configs/model/metrics/auprc.yaml

@@ -1,4 +0,0 @@
-AUPRC:
-  _target_: torchmetrics.AveragePrecision
-  task: ${task.task}
-  num_classes: ${task.num_classes}

configs/model/metrics/auroc.yaml

@@ -1,4 +0,0 @@
-AUROC:
-  _target_: torchmetrics.AUROC
-  task: ${task.task}
-  num_classes: ${task.num_classes}

configs/model/metrics/bedroc.yaml

@@ -1,3 +0,0 @@
-BEDROC:
-  _target_: deepscreen.models.metrics.bedroc.BEDROC
-  alpha: 80.5

configs/model/metrics/ci.yaml

@@ -1,2 +0,0 @@
-CI:
-  _target_: deepscreen.models.metrics.ci.ConcordanceIndex

configs/model/metrics/concordance_index.yaml

@@ -1,2 +0,0 @@
-# FIXME: implement concordance index
-_target_:

configs/model/metrics/confusion_matrix.yaml

@@ -1 +0,0 @@
-_target_: torchmetrics.ConfusionMatrix

configs/model/metrics/dta_metrics.yaml

@@ -1,4 +0,0 @@
-defaults:
-  - mse
-  - pearson
-  - ci

configs/model/metrics/dti_case_study.yaml

@@ -1,18 +0,0 @@
-# train/test with many metrics at once
-
-defaults:
-  - auroc
-  - auprc
-  - specificity
-  - sensitivity
-  - precision
-  - recall
-  - f1_score
-  - ef
-  - bedroc
-  - hit_rate
-
-# Common virtual screening metrics:
-#  - ef
-#  - bedroc
-#  - hit_rate

configs/model/metrics/dti_metrics.yaml

@@ -1,15 +0,0 @@
-# train/test with many metrics at once
-
-defaults:
-  - auroc
-  - auprc
-  - specificity
-  - sensitivity
-  - precision
-  - recall
-  - f1_score
-
-# Common virtual screening metrics:
-#  - ef
-#  - bedroc
-#  - hit_rate

configs/model/metrics/ef.yaml

@@ -1,23 +0,0 @@
-EF1:
-  _target_: deepscreen.models.metrics.ef.EnrichmentFactor
-  alpha: 0.01
-
-EF2:
-  _target_: deepscreen.models.metrics.ef.EnrichmentFactor
-  alpha: 0.02
-
-EF5:
-  _target_: deepscreen.models.metrics.ef.EnrichmentFactor
-  alpha: 0.05
-
-EF10:
-  _target_: deepscreen.models.metrics.ef.EnrichmentFactor
-  alpha: 0.10
-
-EF15:
-  _target_: deepscreen.models.metrics.ef.EnrichmentFactor
-  alpha: 0.15
-
-EF20:
-  _target_: deepscreen.models.metrics.ef.EnrichmentFactor
-  alpha: 0.20

configs/model/metrics/f1_score.yaml

@@ -1,4 +0,0 @@
-F1:
-  _target_: torchmetrics.F1Score
-  task: ${task.task}
-  num_classes: ${task.num_classes}

configs/model/metrics/hit_rate.yaml

@@ -1,24 +0,0 @@
-HR0_01:
-  _target_: deepscreen.models.metrics.hit_rate.HitRate
-  alpha: 0.01
-
-HR0_02:
-  _target_: deepscreen.models.metrics.hit_rate.HitRate
-  alpha: 0.02
-
-HR0_05:
-  _target_: deepscreen.models.metrics.hit_rate.HitRate
-  alpha: 0.05
-
-HR0_10:
-  _target_: deepscreen.models.metrics.hit_rate.HitRate
-  alpha: 0.10
-
-HR0_15:
-  _target_: deepscreen.models.metrics.hit_rate.HitRate
-  alpha: 0.15
-
-HR0_20:
-  _target_: deepscreen.models.metrics.hit_rate.HitRate
-  alpha: 0.20
-

configs/model/metrics/ir_hit_rate.yaml

@@ -1,3 +0,0 @@
-RetrievalHitRate:
-  _target_: torchmetrics.retrieval.RetrievalHitRate
-  top_k: 100

configs/model/metrics/mean_squared_error.yaml

@@ -1,2 +0,0 @@
-mean_squared_error:
-  _target_: torchmetrics.MeanSquaredError

configs/model/metrics/mse.yaml

@@ -1,2 +0,0 @@
-Mean squared error:
-  _target_: torchmetrics.MeanSquaredError

configs/model/metrics/pearson.yaml

@@ -1,2 +0,0 @@
-Pearson:
-  _target_: torchmetrics.PearsonCorrCoef

configs/model/metrics/prc.yaml

@@ -1,4 +0,0 @@
-PR curve:
-  _target_: torchmetrics.PrecisionRecallCurve
-  task: ${task.task}
-  num_classes: ${task.num_classes}

configs/model/metrics/precision.yaml

@@ -1,4 +0,0 @@
-Precision:
-  _target_: torchmetrics.Precision
-  task: ${task.task}
-  num_classes: ${task.num_classes}

configs/model/metrics/recall.yaml

@@ -1,4 +0,0 @@
-Recall:
-  _target_: torchmetrics.Recall
-  task: ${task.task}
-  num_classes: ${task.num_classes}

configs/model/metrics/roc.yaml

@@ -1,4 +0,0 @@
-ROC curve:
-  _target_: torchmetrics.ROC
-  task: ${task.task}
-  num_classes: ${task.num_classes}

configs/model/metrics/sensitivity.yaml

@@ -1,4 +0,0 @@
-Sensitivity:
-  _target_: deepscreen.models.metrics.sensitivity.Sensitivity
-  task: ${task.task}
-  num_classes: ${task.num_classes}

configs/model/metrics/specificity.yaml

@@ -1,4 +0,0 @@
-Specificity:
-  _target_: torchmetrics.Specificity
-  task: ${task.task}
-  num_classes: ${task.num_classes}

configs/model/metrics/test_metrics.yaml

@@ -1,11 +0,0 @@
-# train with many loggers at once
-
-defaults:
-  - auroc
-  - auprc
-  - roc
-  - prc
-# Common virtual screening metrics:
-#  - ef
-#  - bedroc
-#  - hit_rate

configs/model/metrics/ww_dti_metrics.yaml

@@ -1,193 +0,0 @@
-defaults:
-  - auroc
-  - auprc
-
-Accuracy0_5:
-  _target_: torchmetrics.Accuracy
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.5
-
-Accuracy0_8:
-  _target_: torchmetrics.Accuracy
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.8
-
-Accuracy0_85:
-  _target_: torchmetrics.Accuracy
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.85
-
-Accuracy0_9:
-  _target_: torchmetrics.Accuracy
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.9
-
-Accuracy0_95:
-  _target_: torchmetrics.Accuracy
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.95
-
-
-
-Sensitivity0_5:
-  _target_: deepscreen.models.metrics.sensitivity.Sensitivity
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.5
-
-Sensitivity0_8:
-  _target_: deepscreen.models.metrics.sensitivity.Sensitivity
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.8
-
-Sensitivity0_85:
-  _target_: deepscreen.models.metrics.sensitivity.Sensitivity
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.85
-
-Sensitivity0_9:
-  _target_: deepscreen.models.metrics.sensitivity.Sensitivity
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.9
-
-Sensitivity0_95:
-  _target_: deepscreen.models.metrics.sensitivity.Sensitivity
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.95
-
-
-
-Specificity0_5:
-  _target_: torchmetrics.Specificity
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.5
-
-Specificity0_8:
-  _target_: torchmetrics.Specificity
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.8
-
-Specificity0_85:
-  _target_: torchmetrics.Specificity
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.85
-
-Specificity0_9:
-  _target_: torchmetrics.Specificity
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.9
-
-Specificity0_95:
-  _target_: torchmetrics.Specificity
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.95
-  
-
-
-Precision0_5:
-  _target_: torchmetrics.Precision
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.5
-
-Precision0_8:
-  _target_: torchmetrics.Precision
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.8
-
-Precision0_85:
-  _target_: torchmetrics.Precision
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.85
-
-Precision0_9:
-  _target_: torchmetrics.Precision
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.9
-
-Precision0_95:
-  _target_: torchmetrics.Precision
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.95
-  
-  
-
-Recall0_5:
-  _target_: torchmetrics.Recall
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.5
-
-Recall0_8:
-  _target_: torchmetrics.Recall
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.8
-
-Recall0_85:
-  _target_: torchmetrics.Recall
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.85
-
-Recall0_9:
-  _target_: torchmetrics.Recall
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.9
-
-Recall0_95:
-  _target_: torchmetrics.Recall
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.95
-  
-
-
-F1Score0_5:
-  _target_: torchmetrics.F1Score
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.5
-
-F1Score0_8:
-  _target_: torchmetrics.F1Score
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.8
-
-F1Score0_85:
-  _target_: torchmetrics.F1Score
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.85
-
-F1Score0_9:
-  _target_: torchmetrics.F1Score
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.9
-
-F1Score0_95:
-  _target_: torchmetrics.F1Score
-  task: ${task.task}
-  num_classes: ${task.num_classes}
-  threshold: 0.95