Remove node_type_row/node_type_column as redundant in add_relation_type().

src/icosagon/data.py

@@ -80,22 +80,12 @@ class RelationFamily(RelationFamilyBase):
         self.relation_types = []
 
     def add_relation_type(self,
-        name: str, node_type_row: int, node_type_column: int,
-        adjacency_matrix: torch.Tensor,
+        name: str, adjacency_matrix: torch.Tensor,
         adjacency_matrix_backward: torch.Tensor = None) -> None:
 
         name = str(name)
-        node_type_row = int(node_type_row)
-        node_type_column = int(node_type_column)
-
-        if (node_type_row, node_type_column) != (self.node_type_row, self.node_type_column):
-            raise ValueError('Specified node_type_row/node_type_column tuple does not belong to this family')
-
-        if node_type_row < 0 or node_type_row >= len(self.data.node_types):
-            raise ValueError('node_type_row outside of the valid range of node types')
-
-        if node_type_column < 0 or node_type_column >= len(self.data.node_types):
-            raise ValueError('node_type_column outside of the valid range of node types')
+        node_type_row = self.node_type_row
+        node_type_column = self.node_type_column
 
         if adjacency_matrix is None and adjacency_matrix_backward is None:
             raise ValueError('adjacency_matrix and adjacency_matrix_backward cannot both be None')
@@ -104,13 +94,6 @@ class RelationFamily(RelationFamilyBase):
             not isinstance(adjacency_matrix, torch.Tensor):
             raise ValueError('adjacency_matrix must be a torch.Tensor')
 
-        # if isinstance(adjacency_matrix_backward, str) and \
-        #     adjacency_matrix_backward == 'symmetric':
-        #     if self.is_symmetric:
-        #         adjacency_matrix_backward = None
-        #     else:
-        #         adjacency_matrix_backward = adjacency_matrix.transpose(0, 1)
-
         if adjacency_matrix_backward is not None \
             and not isinstance(adjacency_matrix_backward, torch.Tensor):
             raise ValueError('adjacency_matrix_backward must be a torch.Tensor')
@@ -154,7 +137,7 @@ class RelationFamily(RelationFamilyBase):
             s += '\n  - %s%s' % (r.name, ' (two-way)' \
                 if (r.adjacency_matrix is not None \
                     and r.adjacency_matrix_backward is not None) \
-                        or self.is_symmetric \
+                        or self.node_type_row == self.node_type_column \
                             else '%s <- %s' % (self.node_name(self.node_type_row),
                                 self.node_name(self.node_type_column)))
 
@@ -167,7 +150,7 @@ class RelationFamily(RelationFamilyBase):
             s += '\n    - %s%s' % (r.name, ' (two-way)' \
                 if (r.adjacency_matrix is not None \
                     and r.adjacency_matrix_backward is not None) \
-                        or self.is_symmetric \
+                        or self.node_type_row == self.node_type_column \
                             else '%s <- %s' % (self.node_name(self.node_type_row),
                                 self.node_name(self.node_type_column)))
 
@@ -195,6 +178,17 @@ class Data(object):
         node_type_column: int, is_symmetric: bool,
         decoder_class: Type = DEDICOMDecoder):
 
+        name = str(name)
+        node_type_row = int(node_type_row)
+        node_type_column = int(node_type_column)
+        is_symmetric = bool(is_symmetric)
+
+        if node_type_row < 0 or node_type_row >= len(self.node_types):
+            raise ValueError('node_type_row outside of the valid range of node types')
+
+        if node_type_column < 0 or node_type_column >= len(self.node_types):
+            raise ValueError('node_type_column outside of the valid range of node types')
+
         fam = RelationFamily(self, name, node_type_row, node_type_column,
             is_symmetric, decoder_class)
         self.relation_families.append(fam)

tests/icosagon/test_convlayer.py

@@ -26,19 +26,19 @@ def _some_data_with_interactions():
     d.add_node_type('Drug', 100)
 
     fam = d.add_relation_family('Drug-Gene', 1, 0, True)
-    fam.add_relation_type('Target', 1, 0,
+    fam.add_relation_type('Target',
         torch.rand((100, 1000), dtype=torch.float32).round())
 
     fam = d.add_relation_family('Gene-Gene', 0, 0, True)
-    fam.add_relation_type('Interaction', 0, 0,
+    fam.add_relation_type('Interaction',
         _symmetric_random(1000, 1000))
 
     fam = d.add_relation_family('Drug-Drug', 1, 1, True)
-    fam.add_relation_type('Side Effect: Nausea', 1, 1,
+    fam.add_relation_type('Side Effect: Nausea',
         _symmetric_random(100, 100))
-    fam.add_relation_type('Side Effect: Infertility', 1, 1,
+    fam.add_relation_type('Side Effect: Infertility',
         _symmetric_random(100, 100))
-    fam.add_relation_type('Side Effect: Death', 1, 1,
+    fam.add_relation_type('Side Effect: Death',
         _symmetric_random(100, 100))
     return d
 
@@ -97,7 +97,7 @@ def test_decagon_layer_04():
     d = Data()
     d.add_node_type('Dummy', 100)
     fam = d.add_relation_family('Dummy-Dummy', 0, 0, True)
-    fam.add_relation_type('Dummy Relation', 0, 0,
+    fam.add_relation_type('Dummy Relation',
         _symmetric_random(100, 100).to_sparse())
 
     in_layer = OneHotInputLayer(d)
@@ -139,9 +139,9 @@ def test_decagon_layer_05():
     d = Data()
     d.add_node_type('Dummy', 100)
     fam = d.add_relation_family('Dummy-Dummy', 0, 0, True)
-    fam.add_relation_type('Dummy Relation 1', 0, 0,
+    fam.add_relation_type('Dummy Relation 1',
         _symmetric_random(100, 100).to_sparse())
-    fam.add_relation_type('Dummy Relation 2', 0, 0,
+    fam.add_relation_type('Dummy Relation 2',
         _symmetric_random(100, 100).to_sparse())
 
     in_layer = OneHotInputLayer(d)

tests/icosagon/test_data.py

@@ -4,11 +4,80 @@
 #
 
 
-from icosagon import Data
+from icosagon.data import Data, \
+    _equal, \
+    RelationFamily
+from icosagon.decode import DEDICOMDecoder
 import torch
 import pytest
 
 
+def test_equal_01():
+    x = torch.rand((10, 10))
+    y = torch.rand((10, 10)).round().to_sparse()
+
+    assert torch.all(_equal(x, x))
+    assert torch.all(_equal(y, y))
+    with pytest.raises(ValueError):
+        _equal(x, y)
+
+    z = torch.rand((10, 10)).round().to_sparse()
+    assert not torch.all(_equal(y, z))
+
+
+def test_relation_family_01():
+    d = Data()
+    d.add_node_type('Whatever', 10)
+
+    fam = RelationFamily(d, 'Dummy-Dummy', 0, 0, True, DEDICOMDecoder)
+
+    with pytest.raises(ValueError):
+        fam.add_relation_type('Dummy-Dummy', None, None)
+
+    with pytest.raises(ValueError):
+        fam.add_relation_type('Dummy-Dummy', 'bad-value', None)
+
+    with pytest.raises(ValueError):
+        fam.add_relation_type('Dummy-Dummy', None, 'bad-value')
+
+    with pytest.raises(ValueError):
+        fam.add_relation_type('Dummy-Dummy', torch.rand((5, 5)), None)
+
+    with pytest.raises(ValueError):
+        fam.add_relation_type('Dummy-Dummy', None, torch.rand((5, 5)))
+
+    with pytest.raises(ValueError):
+        fam.add_relation_type('Dummy-Dummy', torch.rand((10, 10)), torch.rand((10, 10)))
+
+    with pytest.raises(ValueError):
+        fam.add_relation_type('Dummy-Dummy', torch.rand((10, 10)), None)
+
+
+def test_relation_family_02():
+    d = Data()
+    d.add_node_type('A', 10)
+    d.add_node_type('B', 5)
+
+    fam = RelationFamily(d, 'A-B', 0, 1, True, DEDICOMDecoder)
+
+    with pytest.raises(ValueError):
+        fam.add_relation_type('A-B', torch.rand((10, 5)).round(),
+            torch.rand((5, 10)).round())
+
+
+def test_relation_family_03():
+    d = Data()
+    d.add_node_type('A', 10)
+    d.add_node_type('B', 5)
+
+    fam = RelationFamily(d, 'A-B', 0, 1, True, DEDICOMDecoder)
+    
+    fam.add_relation_type('A-B', torch.rand((10, 5)).round())
+
+    assert torch.all(fam.relation_types[0].adjacency_matrix.transpose(0, 1) == \
+        fam.relation_types[0].adjacency_matrix_backward)
+
+
 def test_data_01():
     d = Data()
     d.add_node_type('Gene', 1000)
@@ -17,14 +86,18 @@ def test_data_01():
     dummy_1 = torch.zeros((1000, 100))
     dummy_2 = torch.zeros((100, 100))
     dummy_3 = torch.zeros((1000, 1000))
+
     fam = d.add_relation_family('Drug-Gene', 1, 0, True)
-    fam.add_relation_type('Target', 1, 0, dummy_0)
+    fam.add_relation_type('Target', dummy_0)
+
     fam = d.add_relation_family('Gene-Gene', 0, 0, True)
-    fam.add_relation_type('Interaction', 0, 0, dummy_3)
+    fam.add_relation_type('Interaction', dummy_3)
+
     fam = d.add_relation_family('Drug-Drug', 1, 1, True)
-    fam.add_relation_type('Side Effect: Nausea', 1, 1, dummy_2)
-    fam.add_relation_type('Side Effect: Infertility', 1, 1, dummy_2)
-    fam.add_relation_type('Side Effect: Death', 1, 1, dummy_2)
+    fam.add_relation_type('Side Effect: Nausea', dummy_2)
+    fam.add_relation_type('Side Effect: Infertility', dummy_2)
+    fam.add_relation_type('Side Effect: Death', dummy_2)
+
     print(d)
 
 
@@ -40,19 +113,19 @@ def test_data_02():
 
     fam = d.add_relation_family('Drug-Gene', 1, 0, True)
     with pytest.raises(ValueError):
-        fam.add_relation_type('Target', 1, 0, dummy_1)
+        fam.add_relation_type('Target', dummy_1)
 
     fam = d.add_relation_family('Gene-Gene', 0, 0, True)
     with pytest.raises(ValueError):
-        fam.add_relation_type('Interaction', 0, 0, dummy_2)
+        fam.add_relation_type('Interaction', dummy_2)
 
     fam = d.add_relation_family('Drug-Drug', 1, 1, True)
     with pytest.raises(ValueError):
-        fam.add_relation_type('Side Effect: Nausea', 1, 1, dummy_3)
+        fam.add_relation_type('Side Effect: Nausea', dummy_3)
     with pytest.raises(ValueError):
-        fam.add_relation_type('Side Effect: Infertility', 1, 1, dummy_3)
+        fam.add_relation_type('Side Effect: Infertility', dummy_3)
     with pytest.raises(ValueError):
-        fam.add_relation_type('Side Effect: Death', 1, 1, dummy_3)
+        fam.add_relation_type('Side Effect: Death', dummy_3)
     print(d)
 
 
@@ -62,5 +135,5 @@ def test_data_03():
     d.add_node_type('Drug', 100)
     fam = d.add_relation_family('Drug-Gene', 1, 0, True)
     with pytest.raises(ValueError):
-        fam.add_relation_type('Target', 1, 0, None)
+        fam.add_relation_type('Target', None)
     print(d)

tests/icosagon/test_declayer.py

@@ -22,7 +22,7 @@ def test_decode_layer_01():
     d.add_node_type('Dummy', 100)
 
     fam = d.add_relation_family('Dummy-Dummy', 0, 0, False)
-    fam.add_relation_type('Dummy Relation 1', 0, 0,
+    fam.add_relation_type('Dummy Relation 1',
         torch.rand((100, 100), dtype=torch.float32).round().to_sparse())
 
     prep_d = prepare_training(d, TrainValTest(.8, .1, .1))

tests/icosagon/test_decode.py

@@ -151,7 +151,6 @@ def test_is_inner_product_symmetric_01():
     res_1 = [ dec(repr_1, repr_2, k) for k in range(7) ]
     res_2 = [ dec(repr_2, repr_1, k) for k in range(7) ]
 
-
     assert isinstance(res_1, list)
     assert isinstance(res_2, list)
 

tests/icosagon/test_input.py

@@ -11,15 +11,15 @@ def _some_data():
     d.add_node_type('Drug', 100)
 
     fam = d.add_relation_family('Drug-Gene', 1, 0, False)
-    fam.add_relation_type('Target', 1, 0, torch.rand(100, 1000))
+    fam.add_relation_type('Target', torch.rand(100, 1000))
 
     fam = d.add_relation_family('Gene-Gene', 0, 0, False)
-    fam.add_relation_type('Interaction', 0, 0, torch.rand(1000, 1000))
+    fam.add_relation_type('Interaction', torch.rand(1000, 1000))
 
     fam = d.add_relation_family('Drug-Drug', 1, 1, False)
-    fam.add_relation_type('Side Effect: Nausea', 1, 1, torch.rand(100, 100))
-    fam.add_relation_type('Side Effect: Infertility', 1, 1, torch.rand(100, 100))
-    fam.add_relation_type('Side Effect: Death', 1, 1, torch.rand(100, 100))
+    fam.add_relation_type('Side Effect: Nausea', torch.rand(100, 100))
+    fam.add_relation_type('Side Effect: Infertility', torch.rand(100, 100))
+    fam.add_relation_type('Side Effect: Death', torch.rand(100, 100))
     return d