Merge pull request #116 from raphaelreinauer/master

Updated outdated docstring of FFNet and fixed types

README.md

@@ -20,13 +20,13 @@ hyperparameter optimization in a few lines of code.
 
 You can find the documentation of this repository here: https://giotto-ai.github.io/giotto-deep/
 
-## Run tensorboard for visualisation
+## Run tensorboard for visualization
 
 In order to analyse the results of your models, you need to start **tensorboard**. On the terminal, move inside the `/examples` folder. There, run the following command:
 ```
 tensorboard --logdir=runs
 ```
-Afterwards go [here](http://localhost:6006/) and, after running the notebooks of interest, you will see all the visualisation results that you stored in the `writer = SummaryWriter()`.
+Afterwards go [here](http://localhost:6006/) and, after running the notebooks of interest, you will see all the visualization results that you stored in the `writer = SummaryWriter()`.
 
 ## Install user version
 

docs/source/modules/index.rst

@@ -20,7 +20,7 @@ This pages contains a list of available features in the library.
 
    utility
 
-   visualisation
+   visualization
 
 References
 ----------

docs/source/modules/visualisation.rst

@@ -1,5 +1,5 @@
-Visualisation
+visualization
 ============
 
-.. automodule:: gdeep.visualisation
+.. automodule:: gdeep.visualization
    :members:

examples/basic_tutorial_ensemble_learning.ipynb

@@ -40,7 +40,7 @@
     "from gdeep.utility.optimization import SAMOptimizer\n",
     "from gdeep.models import FFNet\n",
     "from gdeep.utility import ensemble_wrapper\n",
-    "from gdeep.visualisation import Visualiser\n",
+    "from gdeep.visualization import Visualiser\n",
     "from gdeep.search import GiottoSummaryWriter\n"
    ]
   },
@@ -58,7 +58,7 @@
     "tensorboard --logdir=runs\n",
     "```\n",
     "\n",
-    "Then go [here](http://localhost:6006/) after the training to see all the visualisation results."
+    "Then go [here](http://localhost:6006/) after the training to see all the visualization results."
    ]
   },
   {

examples/basic_tutorial_hpo_and_benchmarking.ipynb

@@ -54,7 +54,7 @@
     "from gdeep.search import Benchmark\n",
     "from gdeep.search import HyperParameterOptimization, GiottoSummaryWriter\n",
     "from gdeep.models import FFNet\n",
-    "from gdeep.visualisation import persistence_diagrams_of_activations\n"
+    "from gdeep.visualization import persistence_diagrams_of_activations\n"
    ]
   },
   {
@@ -70,7 +70,7 @@
     "tensorboard --logdir=runs\n",
     "```\n",
     "\n",
-    "Then go [here](http://localhost:6006/) after the training to see all the visualisation results.\n",
+    "Then go [here](http://localhost:6006/) after the training to see all the visualization results.\n",
     "\n",
     "In this example, we use our modified version of the writer, as we believe it displays better results in the `hparams` dashboard."
    ]

examples/basic_tutorial_image.ipynb

@@ -45,12 +45,12 @@
     "\n",
     "from gdeep.data.datasets import DatasetBuilder, DataLoaderBuilder\n",
     "from gdeep.models import FFNet\n",
-    "from gdeep.visualisation import persistence_diagrams_of_activations\n",
+    "from gdeep.visualization import persistence_diagrams_of_activations\n",
     "from gdeep.data.preprocessors import ToTensorImage\n",
     "from gdeep.trainer import Trainer\n",
     "from gdeep.models import ModelExtractor\n",
     "from gdeep.analysis.interpretability import Interpreter\n",
-    "from gdeep.visualisation import Visualiser\n",
+    "from gdeep.visualization import Visualiser\n",
     "from gdeep.search import GiottoSummaryWriter"
    ]
   },
@@ -67,7 +67,7 @@
     "tensorboard --logdir=runs\n",
     "```\n",
     "\n",
-    "Then go [here](http://localhost:6006/) after the training of your model to see all the visualisation results."
+    "Then go [here](http://localhost:6006/) after the training of your model to see all the visualization results."
    ]
   },
   {
@@ -309,7 +309,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Interactive 3d visualisation\n",
+    "## Interactive 3d visualization\n",
     "\n",
     "You can visualise the dataset in 3D (choosing dynamically the dimensionality reduction algorithm) the dataset on tehsnorboard. In order to do so, just run teh next cell!"
    ]

examples/basic_tutorial_question_answering.ipynb

@@ -46,7 +46,7 @@
     "from torch.utils.data.sampler import SubsetRandomSampler\n",
     "\n",
     "from gdeep.models import FFNet\n",
-    "from gdeep.visualisation import persistence_diagrams_of_activations\n",
+    "from gdeep.visualization import persistence_diagrams_of_activations\n",
     "from gdeep.data.datasets import DatasetBuilder\n",
     "from gdeep.trainer import Trainer\n",
     "from gdeep.models import ModelExtractor\n",
@@ -55,7 +55,7 @@
     "from gdeep.data import TransformingDataset\n",
     "from gdeep.data.preprocessors import Normalization, TokenizerQA\n",
     "from gdeep.data.datasets import DataLoaderBuilder\n",
-    "from gdeep.visualisation import Visualiser\n",
+    "from gdeep.visualization import Visualiser\n",
     "from gdeep.search import GiottoSummaryWriter\n"
    ]
   },
@@ -72,7 +72,7 @@
     "tensorboard --logdir=runs\n",
     "```\n",
     "\n",
-    "Then go [here](http://localhost:6006/) after the training to see all the visualisation results."
+    "Then go [here](http://localhost:6006/) after the training to see all the visualization results."
    ]
   },
   {
@@ -464,7 +464,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from gdeep.visualisation import Visualiser\n",
+    "from gdeep.visualization import Visualiser\n",
     "\n",
     "vs = Visualiser(pipe)\n",
     "\n",

examples/basic_tutorial_regression.ipynb

@@ -50,7 +50,7 @@
     "\n",
     "from gdeep.search import GiottoSummaryWriter\n",
     "from gdeep.models import FFNet\n",
-    "from gdeep.visualisation import persistence_diagrams_of_activations\n",
+    "from gdeep.visualization import persistence_diagrams_of_activations\n",
     "from gdeep.trainer import Trainer\n",
     "from gdeep.data.datasets import DatasetBuilder, FromArray, DataLoaderBuilder\n",
     "from gdeep.utility import DEVICE\n"
@@ -69,7 +69,7 @@
     "tensorboard --logdir=runs\n",
     "```\n",
     "\n",
-    "Then go [here](http://localhost:6006/), after the training phase, to see all the visualisation results."
+    "Then go [here](http://localhost:6006/), after the training phase, to see all the visualization results."
    ]
   },
   {

examples/basic_tutorial_tabular.ipynb

@@ -49,10 +49,10 @@
     "from gdeep.models import ModelExtractor\n",
     "from gdeep.analysis.interpretability import Interpreter\n",
     "from gdeep.utility.optimization import SAMOptimizer\n",
-    "from gdeep.visualisation import persistence_diagrams_of_activations\n",
+    "from gdeep.visualization import persistence_diagrams_of_activations\n",
     "from gdeep.trainer import Trainer\n",
     "from gdeep.data.datasets import DatasetBuilder, DataLoaderBuilder\n",
-    "from gdeep.visualisation import Visualiser\n",
+    "from gdeep.visualization import Visualiser\n",
     "from gdeep.utility import DEVICE\n",
     "from gdeep.search import GiottoSummaryWriter"
    ]
@@ -70,7 +70,7 @@
     "tensorboard --logdir=runs\n",
     "```\n",
     "\n",
-    "Then go [here](http://localhost:6006/) after the training pahse to see all the visualisation results."
+    "Then go [here](http://localhost:6006/) after the training pahse to see all the visualization results."
    ]
   },
   {

examples/basic_tutorial_text_classification.ipynb

@@ -47,15 +47,15 @@
     "from torchvision import transforms\n",
     "\n",
     "from gdeep.models import FFNet\n",
-    "from gdeep.visualisation import persistence_diagrams_of_activations\n",
+    "from gdeep.visualization import persistence_diagrams_of_activations\n",
     "from gdeep.data.datasets import DatasetBuilder\n",
     "from gdeep.data import PreprocessingPipeline\n",
     "from gdeep.data import TransformingDataset\n",
     "from gdeep.data.preprocessors import Normalization, TokenizerTextClassification\n",
     "from gdeep.data.datasets import DataLoaderBuilder\n",
     "from gdeep.trainer import Trainer\n",
     "from gdeep.analysis.interpretability import Interpreter\n",
-    "from gdeep.visualisation import Visualiser\n",
+    "from gdeep.visualization import Visualiser\n",
     "from gdeep.models import ModelExtractor\n",
     "from gdeep.search import GiottoSummaryWriter\n"
    ]
@@ -73,7 +73,7 @@
     "tensorboard --logdir=runs\n",
     "```\n",
     "\n",
-    "Then go [here](http://localhost:6006/) after the training to see all the visualisation results."
+    "Then go [here](http://localhost:6006/) after the training to see all the visualization results."
    ]
   },
   {

examples/basic_tutorial_translation.ipynb

@@ -70,15 +70,15 @@
     "\n",
     "# our special guests!\n",
     "from gdeep.models import FFNet\n",
-    "from gdeep.visualisation import persistence_diagrams_of_activations\n",
+    "from gdeep.visualization import persistence_diagrams_of_activations\n",
     "from gdeep.data.datasets import DatasetBuilder\n",
     "from gdeep.trainer import Trainer\n",
     "from gdeep.data import TransformingDataset\n",
     "from gdeep.data.preprocessors import TokenizerTranslation\n",
     "from gdeep.data.datasets import DataLoaderBuilder\n",
     "from gdeep.models import ModelExtractor\n",
     "from gdeep.analysis.interpretability import Interpreter\n",
-    "from gdeep.visualisation import Visualiser\n",
+    "from gdeep.visualization import Visualiser\n",
     "from gdeep.search import GiottoSummaryWriter\n"
    ]
   },

examples/compactification.ipynb

@@ -68,7 +68,7 @@
     "tensorboard --logdir=runs\n",
     "```\n",
     "\n",
-    "Then go [here](http://localhost:6006/) after the training of your model to see all the visualisation results."
+    "Then go [here](http://localhost:6006/) after the training of your model to see all the visualization results."
    ]
   },
   {
@@ -153,7 +153,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from gdeep.visualisation import Visualiser\n",
+    "from gdeep.visualization import Visualiser\n",
     "\n",
     "vs = Visualiser(pipe)\n",
     "vs.plot_interactive_model()  # send to tensorboard the interactive model of FFNet\n",

examples/decision_boundary_tori.ipynb

@@ -72,7 +72,7 @@
     "tensorboard --logdir=runs\n",
     "```\n",
     "\n",
-    "Then go [here](http://localhost:6006/) after the training of your model to see all the visualisation results."
+    "Then go [here](http://localhost:6006/) after the training of your model to see all the visualization results."
    ]
   },
   {
@@ -134,7 +134,7 @@
    "source": [
     "## Visualising the decision boundary\n",
     "\n",
-    "We are sending to the tensorboard the visualisation data: hence, you can explore the different sections to find the different plots there. Note that the interactive 3D decison boundary can be found in the **projector** section."
+    "We are sending to the tensorboard the visualization data: hence, you can explore the different sections to find the different plots there. Note that the interactive 3D decison boundary can be found in the **projector** section."
    ]
   },
   {
@@ -143,7 +143,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from gdeep.visualisation import Visualiser\n",
+    "from gdeep.visualization import Visualiser\n",
     "\n",
     "vs = Visualiser(pipe)\n",
     "vs.plot_interactive_model()\n",

examples/orbit_5k_pipeline.ipynb

@@ -73,7 +73,7 @@
     "from sklearn.model_selection import train_test_split\n",
     "from torch.optim import Adam\n",
     "from torch.utils.data import Subset\n",
-    "from gdeep.visualisation import Visualiser\n",
+    "from gdeep.visualization import Visualiser\n",
     "from gdeep.data.datasets import OrbitsGenerator, DataLoaderKwargs\n",
     "\n",
     "\n",
@@ -221,7 +221,7 @@
     "tensorboard --logdir=runs\n",
     "```\n",
     "\n",
-    "Then go [here](http://localhost:6006/) after the training to see all the visualisation results.\n"
+    "Then go [here](http://localhost:6006/) after the training to see all the visualization results.\n"
    ]
   },
   {

examples/time_series_persformer.ipynb

@@ -68,7 +68,7 @@
     "from gdeep.trainer.trainer import Trainer\n",
     "from gdeep.utility.utils import autoreload_if_notebook\n",
     "from gdeep.analysis.interpretability import Interpreter\n",
-    "from gdeep.visualisation import Visualiser\n",
+    "from gdeep.visualization import Visualiser\n",
     "\n",
     "\n",
     "autoreload_if_notebook()\n"

examples/topo_deep_neural_networks.ipynb

@@ -52,7 +52,7 @@
     "# gdeep\n",
     "from gdeep.data.datasets import DatasetBuilder, DataLoaderBuilder\n",
     "from gdeep.models import FFNet\n",
-    "from gdeep.visualisation import persistence_diagrams_of_activations\n",
+    "from gdeep.visualization import persistence_diagrams_of_activations\n",
     "from gdeep.data.preprocessors import ToTensorImage\n",
     "from gdeep.trainer import Trainer\n",
     "from gdeep.search import Benchmark\n",
@@ -85,7 +85,7 @@
     "tensorboard --logdir=runs\n",
     "```\n",
     "\n",
-    "Then go [here](http://localhost:6006/) after the training to see all the visualisation results.\n"
+    "Then go [here](http://localhost:6006/) after the training to see all the visualization results.\n"
    ]
   },
   {
@@ -204,7 +204,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from gdeep.visualisation import Visualiser\n",
+    "from gdeep.visualization import Visualiser\n",
     "\n",
     "# Choose the size of the subset of the dataset\n",
     "batch_size = 500\n",

gdeep/__init__.py

@@ -9,7 +9,7 @@
     search,
     topology_layers,
     utility,
-    visualisation,
+    visualization,
 )
 
 __all__ = [
@@ -20,5 +20,5 @@
     "search",
     "topology_layers",
     "utility",
-    "visualisation",
+    "visualization",
 ]

gdeep/analysis/decision_boundary/tests/test_decision_boundary_calculator.py

@@ -10,7 +10,7 @@
 
 def test_gfdbc_2_dim():
 
-    circle_detect_nn = FFNet([2, 2]).to(DEVICE)
+    circle_detect_nn = FFNet((2, 2)).to(DEVICE)
 
     g = GradientFlowDecisionBoundaryCalculator(
         model=circle_detect_nn,
@@ -24,7 +24,7 @@ def test_gfdbc_2_dim():
 
 def test_gfdbc_multiclass():
 
-    circle_nn_3d = FFNet([3, 3]).to(DEVICE)
+    circle_nn_3d = FFNet((3, 3)).to(DEVICE)
 
     g = GradientFlowDecisionBoundaryCalculator(
         model=circle_nn_3d,

gdeep/analysis/interpretability/captum.py

@@ -9,7 +9,7 @@
 
 from gdeep.utility import DEVICE
 
-from gdeep.utility.custome_types import Tensor
+from gdeep.utility.custom_types import Tensor
 
 
 class Interpreter:
@@ -38,7 +38,7 @@ def __init__(self, model: nn.Module, method: str = "IntegratedGradients"):
         # self.model = model
         self.model = model.to(DEVICE)
         self.method = method
-        self.stored_visualisations: List = []
+        self.stored_visualizations: List = []
 
     def interpret(
         self,
@@ -209,7 +209,7 @@ def interpret_text(
             pred_ind,
             label,
             delta.item(),
-            self.stored_visualisations,
+            self.stored_visualizations,
         )
         return sentence, self.attribution
 

gdeep/analysis/interpretability/tests/test_captum.py

@@ -4,7 +4,7 @@
 
 from gdeep.data.datasets import DatasetBuilder
 from gdeep.analysis.interpretability import Interpreter
-from gdeep.visualisation import Visualiser
+from gdeep.visualization import Visualiser
 from gdeep.data import PreprocessingPipeline
 from gdeep.data import TransformingDataset
 from gdeep.data.preprocessors import Normalization, TokenizerTextClassification