Skip to content

change graph to undirected, improve cco calculation #41

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
pegerto merged 1 commit into from
Mar 5, 2025
Merged

change graph to undirected, improve cco calculation #41

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 6 additions & 4 deletions src/graphpro/graph.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -65,9 +65,11 @@ def to_networkx(self) -> nx.Graph:

def to_data(self, node_encoders = [], target: Target = None) -> Data:
""" Return a PyG object from this existing graph"""
directed = torch.tensor([[edge[0],edge[1]] for edge in self.to_networkx().edges], dtype=torch.long)
inversed = torch.tensor([[edge[1],edge[0]] for edge in self.to_networkx().edges], dtype=torch.long)
cco = torch.cat((directed, inversed), 0).t().contiguous()
row, col = np.nonzero(self.adjacency)
values = self.adjacency[row, col]
indices = torch.tensor(np.array([row,col], dtype=int), dtype=torch.long)
values = torch.tensor(values, dtype=torch.float)
cco = torch.sparse_coo_tensor(indices, values, self.adjacency.shape).coalesce()

x = None
y = None
Expand All @@ -82,7 +84,7 @@ def to_data(self, node_encoders = [], target: Target = None) -> Data:
if target:
y = target.encode(self)

return Data(x=x, edge_index=cco, y=y)
return Data(x=x, edge_index=cco.indices(), y=y)

def nodes(self) -> list[int]:
""" Return node list """
Expand Down
4 changes: 2 additions & 2 deletions test/graphpro/graph_test.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -47,9 +47,9 @@ def test_graph_plot():
SIMPLE_G.plot(show=False)

def test_to_data_index():
edge_index = torch.tensor([[0, 0, 1, 0, 1, 1],
[0, 1, 1, 0, 0, 1]], dtype=torch.long)
edge_index = torch.tensor([[0, 0, 1, 1],[0, 1, 0, 1]])
assert(torch.allclose(SIMPLE_G.to_data().edge_index, edge_index))
assert(SIMPLE_G.to_data().is_directed() == False)

def test_to_data_x_transformer():
assert SIMPLE_G_ATTR.to_data(node_encoders=[ResidueType()]).x.size() == (2,22)
Expand Down