Merge pull request #213 from biggraph/darabos-ode-groups

examples/ODE-GNN.lynxkite.json

@@ -119,13 +119,6 @@
       "target": "Graph conv 2",
       "targetHandle": "edges"
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-      "source": "Graph conv 2",
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       "id": "Input: tensor 3 output Embedding 1 x",
       "source": "Input: tensor 3",
@@ -255,6 +248,119 @@
   ],
   "env": "PyTorch model",
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+        "error": "Unknown operation.",
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@@ -313,13 +419,16 @@
         "status": "done",
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@@ -376,13 +485,16 @@
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@@ -429,7 +541,7 @@
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@@ -477,18 +589,23 @@
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@@ -536,13 +653,16 @@
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@@ -651,18 +774,21 @@
           "type": "basic"
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         "params": {
-          "name": "future volumes"
+          "name": "future volumes                                                                                                           "
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@@ -709,13 +835,16 @@
         "status": "done",
         "title": "MSE loss"
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@@ -773,13 +902,16 @@
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@@ -821,13 +953,16 @@
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@@ -989,12 +1124,12 @@
           "mlp_activation": "ReLU",
           "mlp_hidden_size": "64",
           "mlp_layers": "3",
-          "relative_tolerance": "0.001"
+          "relative_tolerance": "                                         0.001                                           "
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@@ -1085,17 +1223,17 @@
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+          "name": "current volume                                                              "
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@@ -1146,7 +1284,7 @@
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@@ -1202,13 +1340,16 @@
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@@ -1255,13 +1396,16 @@
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@@ -1472,13 +1625,16 @@
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@@ -1541,18 +1697,21 @@
           "edge_modules_order": "disease-assoc-gene, drug-targets-gene",
           "node_embedding_order": "gene, disease, drug",
           "node_embeddings": "gene, disease, drug",
-          "node_embeddings_order": "gene, disease, drug"
+          "node_embeddings_order": "gene, disease, drug                                       "
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@@ -1614,13 +1773,16 @@
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-          "embedding_dim": "64",
+          "embedding_dim": "64                                                                                                                                    ",
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+          "index": "disease                                                                                                                                                                                                                                                                                                                                 "
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+      "dragHandle": ".drag-handle",
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       "height": 200.0,
       "id": "Mean pool 2",
+      "parentId": "Group 3",
       "position": {
-        "x": -82.8001236321482,
-        "y": 319.6613707505728
+        "x": 500.14194620596317,
+        "y": 301.77073327896215
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+      "selected": false,
       "type": "basic",
       "width": 200.0
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         "error": null,
         "input_metadata": null,
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@@ -2144,15 +2333,231 @@
         "status": "done",
         "title": "Mean pool"
       },
-      "dragHandle": ".bg-primary",
+      "dragHandle": ".drag-handle",
+      "extent": "parent",
       "height": 200.0,
       "id": "Mean pool 3",
+      "parentId": "Group 3",
       "position": {
-        "x": 201.4812200884588,
-        "y": 314.0505547560871
+        "x": 785.4145357661607,
+        "y": 300.1249006428384
       },
+      "selected": false,
       "type": "basic",
       "width": 200.0
+    },
+    {
+      "data": {
+        "__execution_delay": 0.0,
+        "collapsed": null,
+        "display": null,
+        "error": "Unknown operation.",
+        "input_metadata": null,
+        "meta": {},
+        "params": {
+          "text": "# Past tumor volume embedding with LSTM"
+        },
+        "status": "done",
+        "title": "Comment"
+      },
+      "dragHandle": ".drag-handle",
+      "extent": "parent",
+      "height": 130.0,
+      "id": "Comment 1",
+      "parentId": "Group 1",
+      "position": {
+        "x": 10.0,
+        "y": 406.3216561052855
+      },
+      "selected": false,
+      "type": "comment",
+      "width": 400.0
+    },
+    {
+      "data": {
+        "__execution_delay": 0.0,
+        "collapsed": null,
+        "display": null,
+        "error": "Unknown operation.",
+        "input_metadata": null,
+        "meta": {},
+        "params": {
+          "text": "# Gene-gene graph embedding"
+        },
+        "status": "done",
+        "title": "Comment"
+      },
+      "dragHandle": ".drag-handle",
+      "extent": "parent",
+      "height": 90.0,
+      "id": "Comment 2",
+      "parentId": "Group 2",
+      "position": {
+        "x": 10.0,
+        "y": 214.69868480627042
+      },
+      "selected": false,
+      "type": "comment",
+      "width": 400.0
+    },
+    {
+      "data": {
+        "__execution_delay": 0.0,
+        "collapsed": null,
+        "display": null,
+        "error": "Unknown operation.",
+        "input_metadata": null,
+        "meta": {},
+        "params": {
+          "text": "# Learned initial drug & disease embeddings"
+        },
+        "status": "done",
+        "title": "Comment"
+      },
+      "dragHandle": ".drag-handle",
+      "extent": "parent",
+      "height": 90.0,
+      "id": "Comment 3",
+      "parentId": "Group 4",
+      "position": {
+        "x": 886.9430712292642,
+        "y": 1852.533426575776
+      },
+      "selected": false,
+      "type": "comment",
+      "width": 400.0
+    },
+    {
+      "data": {
+        "__execution_delay": 0.0,
+        "collapsed": null,
+        "display": null,
+        "error": "Unknown operation.",
+        "input_metadata": null,
+        "meta": {},
+        "params": {
+          "text": "# Extracting the graph embedding\n\nWe mean-pool the node embeddings of each node type, then concatenate these vectors."
+        },
+        "status": "done",
+        "title": "Comment"
+      },
+      "dragHandle": ".drag-handle",
+      "extent": "parent",
+      "height": 178.0,
+      "id": "Comment 4",
+      "parentId": "Group 3",
+      "position": {
+        "x": 10.0,
+        "y": 141.970585886959
+      },
+      "selected": false,
+      "type": "comment",
+      "width": 400.0
+    },
+    {
+      "data": {
+        "__execution_delay": 0.0,
+        "collapsed": null,
+        "display": null,
+        "error": "Unknown operation.",
+        "input_metadata": null,
+        "meta": {},
+        "params": {
+          "text": "# Knowledge graph embedding with GNN\n\nThis heterogeneous graph convolution creates node embeddings for all genes, diseases, and drugs in the graph."
+        },
+        "status": "done",
+        "title": "Comment"
+      },
+      "dragHandle": ".drag-handle",
+      "extent": "parent",
+      "height": 206.0,
+      "id": "Comment 5",
+      "parentId": "Group 4",
+      "position": {
+        "x": 686.3753672347915,
+        "y": 977.8926090141683
+      },
+      "selected": false,
+      "type": "comment",
+      "width": 400.0
+    },
+    {
+      "data": {
+        "__execution_delay": 0.0,
+        "collapsed": null,
+        "display": null,
+        "error": "Unknown operation.",
+        "input_metadata": null,
+        "meta": {},
+        "params": {
+          "text": "# Tumor volume trajectory predictions with ODE\n\nAn MLP is used to predict the derivative of the tumor volume at different stages, based on the knowledge graph embedding and the past tumor volume embeddings."
+        },
+        "status": "done",
+        "title": "Comment"
+      },
+      "dragHandle": ".drag-handle",
+      "height": 274.0,
+      "id": "Comment 6",
+      "position": {
+        "x": -0.7721924881518737,
+        "y": -865.6155529412208
+      },
+      "type": "comment",
+      "width": 400.0
+    },
+    {
+      "data": {
+        "__execution_delay": 0.0,
+        "collapsed": null,
+        "display": null,
+        "error": "Unknown operation.",
+        "input_metadata": null,
+        "meta": {},
+        "params": {
+          "text": "# Training configuration\n\nThe loss for the whole model is simply the MSE loss over the future volume measurements."
+        },
+        "status": "done",
+        "title": "Comment"
+      },
+      "dragHandle": ".drag-handle",
+      "extent": "parent",
+      "height": 138.0,
+      "id": "Comment 7",
+      "parentId": "Group 5",
+      "position": {
+        "x": 276.18914557042024,
+        "y": 267.8721350317928
+      },
+      "selected": false,
+      "type": "comment",
+      "width": 400.0
+    },
+    {
+      "data": {
+        "__execution_delay": 0.0,
+        "collapsed": null,
+        "display": null,
+        "error": "Unknown operation.",
+        "input_metadata": null,
+        "meta": {},
+        "params": {
+          "text": "## Disease-gene and drug-gene edges"
+        },
+        "status": "done",
+        "title": "Comment"
+      },
+      "dragHandle": ".drag-handle",
+      "extent": "parent",
+      "height": 74.0,
+      "id": "Comment 8",
+      "parentId": "Group 4",
+      "position": {
+        "x": 1615.9956563920114,
+        "y": 1872.1215872934476
+      },
+      "selected": false,
+      "type": "comment",
+      "width": 400.0
     }
   ]
 }