rmse score fix (#372)

* rmse score fix * .. * bump python version --------- Co-authored-by: Moshe Raboh [email protected] <[email protected]>
BiomedSciAI · Oct 6, 2024 · 1626ae1 · 1626ae1
1 parent e0c7b73
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diff --git a/README.md b/README.md
@@ -178,7 +178,7 @@ Note - in general, we find it helpful to follow the same directory structure sho
 
 # Installation
 
-FuseMedML is tested on Python >= 3.7 and PyTorch >= 1.5
+FuseMedML is tested on Python >= 3.9 and PyTorch >= 2.0
 
 ## We recommend using a Conda environment
 

diff --git a/fuse/eval/metrics/regression/metrics.py b/fuse/eval/metrics/regression/metrics.py
@@ -2,7 +2,12 @@
 from fuse.eval.metrics.libs.stat import Stat
 from fuse.eval.metrics.metrics_common import MetricDefault
 import numpy as np
-from sklearn.metrics import mean_absolute_error, mean_squared_error, r2_score
+from sklearn.metrics import (
+    mean_absolute_error,
+    mean_squared_error,
+    r2_score,
+    root_mean_squared_error,
+)
 
 
 class MetricPearsonCorrelation(MetricDefault):
@@ -107,26 +112,23 @@ def __init__(
         super().__init__(
             pred=pred,
             target=target,
-            metric_func=self.mse,
+            metric_func=self.rmse,
             **kwargs,
         )
 
-    def mse(
+    def rmse(
         self,
         pred: Union[List, np.ndarray],
         target: Union[List, np.ndarray],
         **kwargs: dict,
     ) -> float:
-
         pred = np.array(pred).flatten()
         target = np.array(target).flatten()
-
         assert len(pred) == len(
             target
         ), f"Expected pred and target to have the dimensions but found: {len(pred)} elements in pred and {len(target)} in target"
 
-        squared_diff = (pred - target) ** 2
-        return squared_diff.mean()
+        return root_mean_squared_error(y_true=target, y_pred=pred)
 
 
 class MetricR2(MetricDefault):

diff --git a/fuse/requirements.txt b/fuse/requirements.txt
@@ -5,7 +5,7 @@ pandas>=1.2
 tqdm>=4.52.0
 scipy>=1.5.4
 matplotlib>=3.3.3
-scikit-learn>=0.23.2
+scikit-learn>=1.4
 termcolor>=1.1.0
 pycocotools>=2.0.1
 pytorch_lightning>=1.6

diff --git a/run_all_unit_tests.sh b/run_all_unit_tests.sh
@@ -32,7 +32,7 @@ create_env() {
     fi
 
     # Python version
-    PYTHON_VER=3.8
+    PYTHON_VER=3.9
     ENV_NAME="fuse_$PYTHON_VER-CUDA-$force_cuda_version-$(echo -n $requirements | sha256sum | awk '{print $1;}')"
     echo $ENV_NAME