Some more mock-ups for ODE-GNN demo.

examples/ODE-GNN

@@ -77,20 +77,6 @@
       "target": "Concatenate 1",
       "targetHandle": "b"
     },
-    {
-      "id": "Concatenate 1 Neural ODE 1",
-      "source": "Concatenate 1",
-      "sourceHandle": "x",
-      "target": "Neural ODE 1",
-      "targetHandle": "x"
-    },
-    {
-      "id": "Neural ODE 1 MSE loss 1",
-      "source": "Neural ODE 1",
-      "sourceHandle": "x",
-      "target": "MSE loss 1",
-      "targetHandle": "x"
-    },
     {
       "id": "Input: label 1 MSE loss 1",
       "source": "Input: label 1",
@@ -104,6 +90,20 @@
       "sourceHandle": "loss",
       "target": "Optimizer 1",
       "targetHandle": "loss"
+    },
+    {
+      "id": "Concatenate 1 Neural ODE 2",
+      "source": "Concatenate 1",
+      "sourceHandle": "x",
+      "target": "Neural ODE 2",
+      "targetHandle": "x"
+    },
+    {
+      "id": "Neural ODE 2 MSE loss 1",
+      "source": "Neural ODE 2",
+      "sourceHandle": "x",
+      "target": "MSE loss 1",
+      "targetHandle": "x"
     }
   ],
   "env": "PyTorch model",
@@ -165,7 +165,7 @@
       "height": 200.0,
       "id": "Graph conv 1",
       "position": {
-        "x": 360.0,
+        "x": 350.98078368755864,
         "y": 195.0
       },
       "type": "basic",
@@ -173,6 +173,8 @@
     },
     {
       "data": {
+        "__execution_delay": 0.0,
+        "collapsed": null,
         "display": null,
         "error": null,
         "meta": {
@@ -207,7 +209,7 @@
           "type": "basic"
         },
         "params": {
-          "times": 1.0
+          "times": "5"
         },
         "status": "planned",
         "title": "Repeat"
@@ -568,49 +570,6 @@
       "type": "basic",
       "width": 200.0
     },
-    {
-      "data": {
-        "__execution_delay": null,
-        "collapsed": true,
-        "display": null,
-        "error": null,
-        "meta": {
-          "inputs": {
-            "x": {
-              "name": "x",
-              "position": "bottom",
-              "type": {
-                "type": "tensor"
-              }
-            }
-          },
-          "name": "Neural ODE",
-          "outputs": {
-            "x": {
-              "name": "x",
-              "position": "top",
-              "type": {
-                "type": "tensor"
-              }
-            }
-          },
-          "params": {},
-          "type": "basic"
-        },
-        "params": {},
-        "status": "planned",
-        "title": "Neural ODE"
-      },
-      "dragHandle": ".bg-primary",
-      "height": 200.0,
-      "id": "Neural ODE 1",
-      "position": {
-        "x": 475.11029083619064,
-        "y": -633.1862788850791
-      },
-      "type": "basic",
-      "width": 200.0
-    },
     {
       "data": {
         "__execution_delay": null,
@@ -645,10 +604,6 @@
             }
           },
           "params": {},
-          "position": {
-            "x": 783.0,
-            "y": 101.0
-          },
           "type": "basic"
         },
         "params": {},
@@ -684,10 +639,6 @@
             }
           },
           "params": {},
-          "position": {
-            "x": 893.0,
-            "y": 369.0
-          },
           "type": "basic"
         },
         "params": {},
@@ -729,7 +680,7 @@
               }
             },
             "type": {
-              "default": 1.0,
+              "default": "1",
               "name": "type",
               "type": {
                 "enum": [
@@ -744,10 +695,6 @@
               }
             }
           },
-          "position": {
-            "x": 986.0,
-            "y": 165.0
-          },
           "type": "basic"
         },
         "params": {
@@ -766,6 +713,84 @@
       },
       "type": "basic",
       "width": 190.0
+    },
+    {
+      "data": {
+        "display": null,
+        "error": null,
+        "meta": {
+          "inputs": {
+            "x": {
+              "name": "x",
+              "position": "bottom",
+              "type": {
+                "type": "tensor"
+              }
+            }
+          },
+          "name": "Neural ODE",
+          "outputs": {
+            "x": {
+              "name": "x",
+              "position": "top",
+              "type": {
+                "type": "tensor"
+              }
+            }
+          },
+          "params": {
+            "absolute_tolerance": {
+              "default": null,
+              "name": "absolute_tolerance",
+              "type": {
+                "type": "None"
+              }
+            },
+            "method": {
+              "default": "1",
+              "name": "method",
+              "type": {
+                "enum": [
+                  "dopri8",
+                  "dopri5",
+                  "bosh3",
+                  "fehlberg2",
+                  "adaptive_heun",
+                  "euler",
+                  "midpoint",
+                  "rk4",
+                  "explicit_adams",
+                  "implicit_adams"
+                ]
+              }
+            },
+            "relative_tolerance": {
+              "default": null,
+              "name": "relative_tolerance",
+              "type": {
+                "type": "None"
+              }
+            }
+          },
+          "type": "basic"
+        },
+        "params": {
+          "absolute_tolerance": null,
+          "method": 1.0,
+          "relative_tolerance": null
+        },
+        "status": "planned",
+        "title": "Neural ODE"
+      },
+      "dragHandle": ".bg-primary",
+      "height": 200.0,
+      "id": "Neural ODE 2",
+      "position": {
+        "x": 342.3226409443945,
+        "y": -687.1882072175634
+      },
+      "type": "basic",
+      "width": 200.0
     }
   ]
 }

examples/Using a model

@@ -0,0 +1,466 @@
+{
+  "edges": [
+    {
+      "id": "Import CSV 1 Train/test split 1",
+      "source": "Import CSV 1",
+      "sourceHandle": "output",
+      "target": "Train/test split 1",
+      "targetHandle": "bundle"
+    },
+    {
+      "id": "Train/test split 1 Create graph 1",
+      "source": "Train/test split 1",
+      "sourceHandle": "output",
+      "target": "Create graph 1",
+      "targetHandle": "bundle"
+    },
+    {
+      "id": "Biomedical foundation graph (PLACEHOLDER) 1 Create graph 1",
+      "source": "Biomedical foundation graph (PLACEHOLDER) 1",
+      "sourceHandle": "output",
+      "target": "Create graph 1",
+      "targetHandle": "bundle"
+    },
+    {
+      "id": "Define model 1 Create graph 1",
+      "source": "Define model 1",
+      "sourceHandle": "output",
+      "target": "Create graph 1",
+      "targetHandle": "bundle"
+    },
+    {
+      "id": "Create graph 1 Train model 1",
+      "source": "Create graph 1",
+      "sourceHandle": "output",
+      "target": "Train model 1",
+      "targetHandle": "bundle"
+    },
+    {
+      "id": "Train model 1 Model inference 1",
+      "source": "Train model 1",
+      "sourceHandle": "output",
+      "target": "Model inference 1",
+      "targetHandle": "bundle"
+    }
+  ],
+  "env": "LynxKite Graph Analytics",
+  "nodes": [
+    {
+      "data": {
+        "__execution_delay": 0.0,
+        "collapsed": null,
+        "display": null,
+        "error": null,
+        "meta": {
+          "inputs": {},
+          "name": "Biomedical foundation graph (PLACEHOLDER)",
+          "outputs": {
+            "output": {
+              "name": "output",
+              "position": "right",
+              "type": {
+                "type": "None"
+              }
+            }
+          },
+          "params": {
+            "filter_nodes": {
+              "default": null,
+              "name": "filter_nodes",
+              "type": {
+                "type": "<class 'str'>"
+              }
+            }
+          },
+          "type": "basic"
+        },
+        "params": {
+          "filter_nodes": "drug,gene,disease"
+        },
+        "status": "done",
+        "title": "Biomedical foundation graph (PLACEHOLDER)"
+      },
+      "dragHandle": ".bg-primary",
+      "height": 200.0,
+      "id": "Biomedical foundation graph (PLACEHOLDER) 1",
+      "position": {
+        "x": 230.1082040835347,
+        "y": 643.2454063689602
+      },
+      "type": "basic",
+      "width": 200.0
+    },
+    {
+      "data": {
+        "__execution_delay": null,
+        "collapsed": true,
+        "display": null,
+        "error": "Missing input: bundle",
+        "meta": {
+          "inputs": {
+            "bundle": {
+              "name": "bundle",
+              "position": "left",
+              "type": {
+                "type": "<class 'lynxkite_graph_analytics.core.Bundle'>"
+              }
+            }
+          },
+          "name": "Train/test split",
+          "outputs": {
+            "output": {
+              "name": "output",
+              "position": "right",
+              "type": {
+                "type": "None"
+              }
+            }
+          },
+          "params": {
+            "table_name": {
+              "default": null,
+              "name": "table_name",
+              "type": {
+                "type": "<class 'str'>"
+              }
+            },
+            "test_ratio": {
+              "default": 0.1,
+              "name": "test_ratio",
+              "type": {
+                "type": "<class 'float'>"
+              }
+            }
+          },
+          "type": "basic"
+        },
+        "params": {
+          "table_name": null,
+          "test_ratio": 0.1
+        },
+        "status": "planned",
+        "title": "Train/test split"
+      },
+      "dragHandle": ".bg-primary",
+      "height": 200.0,
+      "id": "Train/test split 1",
+      "position": {
+        "x": 313.3745540124723,
+        "y": 412.5466021460861
+      },
+      "type": "basic",
+      "width": 200.0
+    },
+    {
+      "data": {
+        "display": null,
+        "error": "[Errno 2] No such file or directory: ''",
+        "meta": {
+          "inputs": {},
+          "name": "Import CSV",
+          "outputs": {
+            "output": {
+              "name": "output",
+              "position": "right",
+              "type": {
+                "type": "None"
+              }
+            }
+          },
+          "params": {
+            "columns": {
+              "default": "<from file>",
+              "name": "columns",
+              "type": {
+                "type": "<class 'str'>"
+              }
+            },
+            "filename": {
+              "default": null,
+              "name": "filename",
+              "type": {
+                "type": "<class 'str'>"
+              }
+            },
+            "separator": {
+              "default": "<auto>",
+              "name": "separator",
+              "type": {
+                "type": "<class 'str'>"
+              }
+            }
+          },
+          "type": "basic"
+        },
+        "params": {
+          "columns": "<from file>",
+          "filename": null,
+          "separator": "<auto>"
+        },
+        "status": "done",
+        "title": "Import CSV"
+      },
+      "dragHandle": ".bg-primary",
+      "height": 200.0,
+      "id": "Import CSV 1",
+      "position": {
+        "x": -2.1743215714344757,
+        "y": 346.06014722935214
+      },
+      "type": "basic",
+      "width": 200.0
+    },
+    {
+      "data": {
+        "__execution_delay": 0.0,
+        "collapsed": null,
+        "display": null,
+        "error": "Missing input: bundle",
+        "meta": {
+          "inputs": {
+            "bundle": {
+              "name": "bundle",
+              "position": "left",
+              "type": {
+                "type": "<class 'lynxkite_graph_analytics.core.Bundle'>"
+              }
+            }
+          },
+          "name": "Model inference",
+          "outputs": {
+            "output": {
+              "name": "output",
+              "position": "right",
+              "type": {
+                "type": "None"
+              }
+            }
+          },
+          "params": {
+            "model_mapping": {
+              "default": null,
+              "name": "model_mapping",
+              "type": {
+                "type": "<class 'str'>"
+              }
+            },
+            "model_name": {
+              "default": null,
+              "name": "model_name",
+              "type": {
+                "type": "<class 'str'>"
+              }
+            },
+            "save_output_as": {
+              "default": "prediction",
+              "name": "save_output_as",
+              "type": {
+                "type": "<class 'str'>"
+              }
+            }
+          },
+          "type": "basic"
+        },
+        "params": {
+          "model_mapping": "input: data_test",
+          "model_name": "model",
+          "save_output_as": "prediction"
+        },
+        "status": "done",
+        "title": "Model inference"
+      },
+      "dragHandle": ".bg-primary",
+      "height": 339.0,
+      "id": "Model inference 1",
+      "position": {
+        "x": 1736.5697434242886,
+        "y": 357.0743204289906
+      },
+      "type": "basic",
+      "width": 281.0
+    },
+    {
+      "data": {
+        "__execution_delay": null,
+        "collapsed": true,
+        "display": null,
+        "error": "Missing input: bundle",
+        "meta": {
+          "inputs": {
+            "bundle": {
+              "name": "bundle",
+              "position": "left",
+              "type": {
+                "type": "list[lynxkite_graph_analytics.core.Bundle]"
+              }
+            }
+          },
+          "name": "Create graph",
+          "outputs": {
+            "output": {
+              "name": "output",
+              "position": "right",
+              "type": {
+                "type": "None"
+              }
+            }
+          },
+          "params": {
+            "relations": {
+              "default": null,
+              "name": "relations",
+              "type": {
+                "type": "<class 'str'>"
+              }
+            }
+          },
+          "type": "graph_creation_view"
+        },
+        "params": {
+          "relations": null
+        },
+        "status": "planned",
+        "title": "Create graph"
+      },
+      "dragHandle": ".bg-primary",
+      "height": 322.0,
+      "id": "Create graph 1",
+      "position": {
+        "x": 846.6882598271658,
+        "y": 480.6258932907771
+      },
+      "type": "graph_creation_view",
+      "width": 313.0
+    },
+    {
+      "data": {
+        "__execution_delay": 0.0,
+        "collapsed": null,
+        "display": null,
+        "error": null,
+        "meta": {
+          "inputs": {},
+          "name": "Define model",
+          "outputs": {
+            "output": {
+              "name": "output",
+              "position": "right",
+              "type": {
+                "type": "None"
+              }
+            }
+          },
+          "params": {
+            "model_workspace": {
+              "default": null,
+              "name": "model_workspace",
+              "type": {
+                "type": "<class 'str'>"
+              }
+            },
+            "save_as": {
+              "default": "model",
+              "name": "save_as",
+              "type": {
+                "type": "<class 'str'>"
+              }
+            }
+          },
+          "position": {
+            "x": 286.0,
+            "y": 208.0
+          },
+          "type": "basic"
+        },
+        "params": {
+          "model_workspace": "ODE-GNN",
+          "save_as": "model"
+        },
+        "status": "done",
+        "title": "Define model"
+      },
+      "dragHandle": ".bg-primary",
+      "height": 200.0,
+      "id": "Define model 1",
+      "position": {
+        "x": 311.976524267066,
+        "y": 146.99006795914332
+      },
+      "type": "basic",
+      "width": 200.0
+    },
+    {
+      "data": {
+        "__execution_delay": 0.0,
+        "collapsed": null,
+        "display": null,
+        "error": "Missing input: bundle",
+        "meta": {
+          "inputs": {
+            "bundle": {
+              "name": "bundle",
+              "position": "left",
+              "type": {
+                "type": "<class 'lynxkite_graph_analytics.core.Bundle'>"
+              }
+            }
+          },
+          "name": "Train model",
+          "outputs": {
+            "output": {
+              "name": "output",
+              "position": "right",
+              "type": {
+                "type": "None"
+              }
+            }
+          },
+          "params": {
+            "epochs": {
+              "default": 1.0,
+              "name": "epochs",
+              "type": {
+                "type": "<class 'int'>"
+              }
+            },
+            "model_mapping": {
+              "default": null,
+              "name": "model_mapping",
+              "type": {
+                "type": "<class 'str'>"
+              }
+            },
+            "model_name": {
+              "default": null,
+              "name": "model_name",
+              "type": {
+                "type": "<class 'str'>"
+              }
+            }
+          },
+          "position": {
+            "x": 995.0,
+            "y": 350.0
+          },
+          "type": "basic"
+        },
+        "params": {
+          "epochs": 1.0,
+          "model_mapping": "input: data_train",
+          "model_name": "model"
+        },
+        "status": "planned",
+        "title": "Train model"
+      },
+      "dragHandle": ".bg-primary",
+      "height": 342.0,
+      "id": "Train model 1",
+      "position": {
+        "x": 1358.7213662492159,
+        "y": 352.03096133771896
+      },
+      "type": "basic",
+      "width": 296.0
+    }
+  ]
+}

lynxkite-graph-analytics/src/lynxkite_graph_analytics/lynxkite_ops.py

@@ -342,3 +342,41 @@ def create_graph(bundle: core.Bundle, *, relations: str = None) -> core.Bundle:
             core.RelationDefinition(**r) for r in json.loads(relations).values()
         ]
     return ops.Result(output=bundle, display=bundle.to_dict(limit=100))
+
+
+@op("Define model")
+def define_model(*, model_workspace: str, save_as: str = "model"):
+    """Reads a PyTorch model workspace and returns it as a model in a bundle."""
+    return None
+
+
+@op("Biomedical foundation graph (PLACEHOLDER)")
+def biomedical_foundation_graph(*, filter_nodes: str):
+    """Loads the gigantic Lynx-maintained knowledge graph. Includes drugs, diseases, genes, proteins, etc."""
+    return None
+
+
+@op("Train model")
+def train_model(
+    bundle: core.Bundle, *, model_name: str, model_mapping: str, epochs: int = 1
+):
+    """Trains the selected model on the selected dataset. Most training parameters are set in the model definition."""
+    return None
+
+
+@op("Model inference")
+def model_inference(
+    bundle: core.Bundle,
+    *,
+    model_name: str,
+    model_mapping: str,
+    save_output_as: str = "prediction",
+):
+    """Executes a trained model."""
+    return None
+
+
+@op("Train/test split")
+def train_test_split(bundle: core.Bundle, *, table_name: str, test_ratio: float = 0.1):
+    """Splits a dataframe in the bundle into separate "_train" and "_test" dataframes."""
+    return None

lynxkite-graph-analytics/src/lynxkite_graph_analytics/pytorch_model_ops.py

@@ -33,7 +33,29 @@ reg("Input: sequential", outputs=["y"])
 reg("Input: zeros", outputs=["x"])
 
 reg("LSTM", inputs=["x", "h"], outputs=["x", "h"])
-reg("Neural ODE", inputs=["x"])
+reg(
+    "Neural ODE",
+    inputs=["x"],
+    params=[
+        P.basic("relative_tolerance"),
+        P.basic("absolute_tolerance"),
+        P.options(
+            "method",
+            [
+                "dopri8",
+                "dopri5",
+                "bosh3",
+                "fehlberg2",
+                "adaptive_heun",
+                "euler",
+                "midpoint",
+                "rk4",
+                "explicit_adams",
+                "implicit_adams",
+            ],
+        ),
+    ],
+)
 reg("Attention", inputs=["q", "k", "v"], outputs=["x", "weights"])
 reg("LayerNorm", inputs=["x"])
 reg("Dropout", inputs=["x"], params=[P.basic("p", 0.5)])