harmonised notebooks

MARBLE/default_params.yaml

@@ -14,7 +14,7 @@ include_self: True # include vector at the center of feature
 
 # network parameters
 dropout: 0. # dropout in the MLP
-hidden_channels: [16] # number of hidden channels
+hidden_channels: [32] # number of hidden channels
 out_channels: 3 # number of output channels (if null, then =hidden_channels)
 vec_norm: False # normalise features at each order of derivatives
 bias: True # learn bias parameters in MLP

MARBLE/main.py

@@ -151,6 +151,7 @@ def check_parameters(self, data):
             "n_sampled_nb",
             "include_positions",
             "include_self",
+            "processes",
         ]
 
         for p in self.params.keys():
@@ -279,7 +280,7 @@ def forward(self, data, n_id, adjs=None):
     def evaluate(self, data):
         """Evaluate."""
         warnings.warn("MARBLE.evaluate() is deprecated. Use MARBLE.transform() instead.")
-        self.transform(data)
+        return self.transform(data)
 
     def transform(self, data):
         """Forward pass @ evaluation (no minibatches)"""

MARBLE/plotting.py

@@ -8,6 +8,7 @@
 import torch
 from matplotlib import gridspec
 from matplotlib.colors import LinearSegmentedColormap
+from matplotlib.patches import FancyArrowPatch
 from mpl_toolkits.mplot3d import proj3d
 from scipy.spatial import Voronoi
 from scipy.spatial import voronoi_plot_2d
@@ -216,7 +217,7 @@ def embedding(
             plot_trajectories = False
 
         if plot_trajectories:
-            l_ = data.l[mask * (labels == typ)]
+            l_ = data.label[mask * (labels == typ)]
             if len(l_) == 0:
                 continue
             end = np.where(np.diff(l_) < 0)[0] + 1
@@ -680,6 +681,8 @@ def create_axis(*args, fig=None):
         ax = fig.add_subplot(*args)
     elif dim == 3:
         ax = fig.add_subplot(*args, projection="3d")
+    else:
+        raise Exception('Data dimension is {}. We can only plot 2D or 3D data.'.format(dim))
 
     return fig, ax