Post process + classification bug

modnet/__init__.py

@@ -1 +1 @@
-__version__ = "0.1.9"
+__version__ = "0.1.10"

modnet/matbench/benchmark.py

@@ -167,8 +167,6 @@ def train_fold(
     fold_ind, (train_data, test_data) = fold
 
     results = {}
-    if classification:
-        fit_settings["num_classes"] = {t: 2 for t in target_weights}
 
     multi_target = bool(len(target) - 1)
 
@@ -185,6 +183,9 @@ def train_fold(
 
     model_settings.update(model_kwargs)
 
+    if classification:
+        model_settings["num_classes"] = {t: 2 for t in target_weights}
+
     model = model_type(target, target_weights, **model_settings)
 
     if hp_optimization:

modnet/models/ensemble.py

@@ -365,21 +365,24 @@ def fit_preset(
         )
 
         if refit:
-            LOG.info("Refitting with all data and parameters: {}".format(best_preset))
+            LOG.info(
+                "Refitting with all data and parameters: {} models, {}".format(
+                    100, best_preset
+                )
+            )
             # Building final model
 
             n_feat = min(len(data.get_optimal_descriptors()), best_preset["n_feat"])
-            self.model = EnsembleMODNetModel(
+            self.__init__(
                 self.targets,
                 self.weights,
-                n_models=self.n_models,
+                n_models=100,
                 num_neurons=best_preset["num_neurons"],
                 n_feat=n_feat,
                 act=best_preset["act"],
                 out_act=self.out_act,
                 num_classes=self.num_classes,
-            ).model
-            self.n_feat = n_feat
+            )
             self.fit(
                 data,
                 val_fraction=0,

modnet/models/vanilla.py

@@ -286,22 +286,27 @@ def fit(
             ].values
             val_x = self._scaler.transform(val_x)
             val_x = np.nan_to_num(val_x, nan=-1)
-            try:
-                val_y = list(
-                    val_data.get_target_df()[self.targets_flatten]
-                    .values.astype(np.float, copy=False)
-                    .transpose()
-                )
-            except Exception:
-                val_y = list(
-                    val_data.get_target_df()
-                    .values.astype(np.float, copy=False)
-                    .transpose()
-                )
+            val_y = []
+            for targ in self.targets_flatten:
+                if self.num_classes[targ] >= 2:  # Classification
+                    y_inner = tf.keras.utils.to_categorical(
+                        val_data.df_targets[targ].values,
+                        num_classes=self.num_classes[targ],
+                    )
+                    loss = "categorical_crossentropy"
+                else:
+                    y_inner = val_data.df_targets[targ].values.astype(
+                        np.float, copy=False
+                    )
+                val_y.append(y_inner)
             validation_data = (val_x, val_y)
         else:
             validation_data = None
 
+        # set up bounds for postprocessing
+        self.min_y = training_data.df_targets.values.min(axis=0)
+        self.max_y = training_data.df_targets.values.max(axis=0)
+
         # Optionally set up print callback
         if verbose:
             if val_fraction > 0 or validation_data:
@@ -585,8 +590,24 @@ class OR only return the most probable class.
             x = np.nan_to_num(x, nan=-1)
 
         p = np.array(self.model.predict(x))
+
         if len(p.shape) == 2:
             p = np.array([p])
+
+        # post-process based on training data
+        yrange = self.max_y - self.min_y
+        upper_bound = self.max_y + 0.25 * yrange
+        lower_bound = self.min_y - 0.25 * yrange
+        for i, vals in enumerate(p):
+            out_of_range_idxs = np.where(
+                (vals < lower_bound[i]) | (vals > upper_bound[i])
+            )
+            vals[out_of_range_idxs] = (
+                np.random.uniform(0, 1, size=len(out_of_range_idxs[0]))
+                * (self.max_y[i] - self.min_y[i])
+                + self.min_y[i]
+            )
+
         p_dic = {}
         for i, name in enumerate(self.targets_flatten):
             if self.num_classes[name] >= 2: