Migrate from sklearn.manifold TSNE to openTSNE for visualizing node embeddings

.gitignore

@@ -91,4 +91,7 @@ coverage/
 
 # Jupyter Notebook
 .ipynb_checkpoints
-*.nbconvert*
+*.nbconvert*
+
+# Python environments
+.conda

README.md

@@ -120,7 +120,7 @@ The [Code Structure Analysis Pipeline](./.github/workflows/java-code-analysis.ym
   - [pip](https://pip.pypa.io/en/stable)
   - [monotonic](https://github.com/atdt/monotonic)
   - [Neo4j Python Driver](https://neo4j.com/docs/api/python-driver)
-  - [sklearn](https://scikit-learn.org)
+  - [openTSNE](https://github.com/pavlin-policar/openTSNE)
   - [wordcloud](https://github.com/amueller/word_cloud)
 - [Graph Visualization](./graph-visualization/README.md) uses [node.js](https://nodejs.org/de) and the dependencies listed in [package.json](./graph-visualization/package.json).
 

jupyter/NodeEmbeddingsJava.ipynb

@@ -58,7 +58,7 @@
     "import matplotlib.pyplot as plot\n",
     "import typing as typ\n",
     "import numpy as np\n",
-    "from sklearn.manifold import TSNE\n",
+    "from openTSNE.sklearn import TSNE\n",
     "from neo4j import GraphDatabase"
    ]
   },
@@ -69,9 +69,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import sklearn\n",
-    "print('The scikit-learn version is {}.'.format(sklearn.__version__))\n",
-    "print('The pandas version is {}.'.format(pd.__version__))\n"
+    "from openTSNE import __version__ as openTSNE_version\n",
+    "print('The openTSNE version is: {}'.format(openTSNE_version))\n",
+    "print('The pandas version is: {}'.format(pd.__version__))\n"
    ]
   },
   {
@@ -231,7 +231,7 @@
     "\n",
     "> It converts similarities between data points to joint probabilities and tries to minimize the Kullback-Leibler divergence between the joint probabilities of the low-dimensional embedding and the high-dimensional data.\n",
     "\n",
-    "(see https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html#sklearn.manifold.TSNE)"
+    "(see https://opentsne.readthedocs.io)"
    ]
   },
   {
@@ -245,7 +245,7 @@
     "    \"\"\"\n",
     "    Reduces the dimensionality of the node embeddings (e.g. 64 floating point numbers in an array)\n",
     "    to two dimensions for 2D visualization.\n",
-    "    see https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html#sklearn.manifold.TSNE\n",
+    "    see https://opentsne.readthedocs.io\n",
     "    \"\"\"\n",
     "\n",
     "    if embeddings.empty: \n",
@@ -258,16 +258,9 @@
     "    # See https://bobbyhadz.com/blog/python-attributeerror-list-object-has-no-attribute-shape\n",
     "    embeddings_as_numpy_array = np.array(embeddings.embedding.to_list())\n",
     "\n",
-    "    # The parameter \"perplexity\" needs to be smaller than the sample size\n",
-    "    # See https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html\n",
-    "    number_of_nodes=embeddings.shape[0]\n",
-    "    perplexity = min(number_of_nodes - 1.0, 30.0)\n",
-    "    print(\"t-SNE: Sample size (Number of nodes)={size}\".format(size = number_of_nodes))\n",
-    "    print(\"t-SNE: perplexity={perplexity}\".format(perplexity=perplexity))\n",
-    "\n",
     "    # Use t-distributed stochastic neighbor embedding (t-SNE) to reduce the dimensionality \n",
     "    # of the previously calculated node embeddings to 2 dimensions for visualization\n",
-    "    t_distributed_stochastic_neighbor_embedding = TSNE(n_components=2, perplexity=perplexity, verbose=1, random_state=50)\n",
+    "    t_distributed_stochastic_neighbor_embedding = TSNE(n_components=2, verbose=1, random_state=47)\n",
     "    two_dimension_node_embeddings = t_distributed_stochastic_neighbor_embedding.fit_transform(embeddings_as_numpy_array)\n",
     "    display(two_dimension_node_embeddings.shape) # Display the shape of the t-SNE result\n",
     "\n",
@@ -365,7 +358,9 @@
    "source": [
     "### 1.1 Generate Node Embeddings using Fast Random Projection (Fast RP) for Java Packages\n",
     "\n",
-    "[Fast Random Projection](https://neo4j.com/docs/graph-data-science/current/machine-learning/node-embeddings/fastrp) is used to reduce the dimensionality of the node feature space while preserving most of the distance information. Nodes with similar neighborhood result in node embedding with similar vectors."
+    "[Fast Random Projection](https://neo4j.com/docs/graph-data-science/current/machine-learning/node-embeddings/fastrp) is used to reduce the dimensionality of the node feature space while preserving most of the distance information. Nodes with similar neighborhood result in node embedding with similar vectors.\n",
+    "\n",
+    "**👉Hint:** To skip existing node embeddings and always calculate them based on the parameters below edit `Node_Embeddings_0a_Query_Calculated` so that it won't return any results."
    ]
   },
   {
@@ -511,7 +506,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.11.9"
   },
   "title": "Object Oriented Design Quality Metrics for Java with Neo4j"
  },

jupyter/NodeEmbeddingsTypescript.ipynb

@@ -58,7 +58,7 @@
     "import matplotlib.pyplot as plot\n",
     "import typing as typ\n",
     "import numpy as np\n",
-    "from sklearn.manifold import TSNE\n",
+    "from openTSNE.sklearn import TSNE\n",
     "from neo4j import GraphDatabase"
    ]
   },
@@ -69,8 +69,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import sklearn\n",
-    "print('The scikit-learn version is {}.'.format(sklearn.__version__))\n",
+    "from openTSNE import __version__ as openTSNE_version\n",
+    "print('The openTSNE version is: {}'.format(openTSNE_version))\n",
     "print('The pandas version is {}.'.format(pd.__version__))\n"
    ]
   },
@@ -231,7 +231,7 @@
     "\n",
     "> It converts similarities between data points to joint probabilities and tries to minimize the Kullback-Leibler divergence between the joint probabilities of the low-dimensional embedding and the high-dimensional data.\n",
     "\n",
-    "(see https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html#sklearn.manifold.TSNE)"
+    "(see https://opentsne.readthedocs.io)"
    ]
   },
   {
@@ -245,7 +245,7 @@
     "    \"\"\"\n",
     "    Reduces the dimensionality of the node embeddings (e.g. 32 floating point numbers in an array)\n",
     "    to two dimensions for 2D visualization.\n",
-    "    see https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html#sklearn.manifold.TSNE\n",
+    "    see https://opentsne.readthedocs.io\n",
     "    \"\"\"\n",
     "\n",
     "    if embeddings.empty: \n",
@@ -258,16 +258,9 @@
     "    # See https://bobbyhadz.com/blog/python-attributeerror-list-object-has-no-attribute-shape\n",
     "    embeddings_as_numpy_array = np.array(embeddings.embedding.to_list())\n",
     "\n",
-    "    # The parameter \"perplexity\" needs to be smaller than the sample size\n",
-    "    # See https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html\n",
-    "    number_of_nodes=embeddings.shape[0]\n",
-    "    perplexity = min(number_of_nodes - 1.0, 30.0)\n",
-    "    print(\"t-SNE: Sample size (Number of nodes)={size}\".format(size = number_of_nodes))\n",
-    "    print(\"t-SNE: perplexity={perplexity}\".format(perplexity=perplexity))\n",
-    "\n",
     "    # Use t-distributed stochastic neighbor embedding (t-SNE) to reduce the dimensionality \n",
     "    # of the previously calculated node embeddings to 2 dimensions for visualization\n",
-    "    t_distributed_stochastic_neighbor_embedding = TSNE(n_components=2, perplexity=perplexity, verbose=1, random_state=50)\n",
+    "    t_distributed_stochastic_neighbor_embedding = TSNE(n_components=2, verbose=1, random_state=47)\n",
     "    two_dimension_node_embeddings = t_distributed_stochastic_neighbor_embedding.fit_transform(embeddings_as_numpy_array)\n",
     "    display(two_dimension_node_embeddings.shape) # Display the shape of the t-SNE result\n",
     "\n",
@@ -365,7 +358,9 @@
    "source": [
     "### 1.1 Generate Node Embeddings for Typescript Modules using Fast Random Projection (Fast RP)\n",
     "\n",
-    "[Fast Random Projection](https://neo4j.com/docs/graph-data-science/current/machine-learning/node-embeddings/fastrp) is used to reduce the dimensionality of the node feature space while preserving most of the distance information. Nodes with similar neighborhood result in node embedding with similar vectors."
+    "[Fast Random Projection](https://neo4j.com/docs/graph-data-science/current/machine-learning/node-embeddings/fastrp) is used to reduce the dimensionality of the node feature space while preserving most of the distance information. Nodes with similar neighborhood result in node embedding with similar vectors.\n",
+    "\n",
+    "**👉 Hint:** To skip existing node embeddings and always calculate them based on the parameters below edit `Node_Embeddings_0a_Query_Calculated` so that it won't return any results."
    ]
   },
   {
@@ -514,7 +509,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.11.9"
   },
   "title": "Object Oriented Design Quality Metrics for Java with Neo4j"
  },

jupyter/environment.yml

@@ -10,7 +10,7 @@ dependencies:
   - numpy=1.23.*
   - pandas=1.5.*
   - pip=22.3.*
-  - scikit-learn=1.3.* # NodeEmbeddings.ipynb uses sklearn.manifold.TSNE 
+  - opentsne=1.0.* # to visualize node embeddings in 2D (t-SNE dimensionality reduction)
   - pip:
       - monotonic==1.*
       - wordcloud==1.9.*