def process(self):
data_list = []
for y, raw_path in enumerate(self.raw_paths):
raw_path = osp.join(raw_path, os.listdir(raw_path)[0])
filenames = glob.glob(osp.join(raw_path, '*.edgelist'))
for filename in filenames:
with open(filename, 'r') as f:
edges = f.read().split('\n')[5:-1]
edge_index = [[int(s) for s in edge.split()] for edge in edges]
edge_index = torch.tensor(edge_index).t().contiguous()
# Remove isolated nodes, including those with only a self-loop
edge_index = remove_isolated_nodes(edge_index)[0]
num_nodes = int(edge_index.max()) + 1
data = Data(edge_index=edge_index, y=y, num_nodes=num_nodes)
data_list.append(data)
if self.pre_filter is not None:
data_list = [data for data in data_list if self.pre_filter(data)]
if self.pre_transform is not None:
data_list = [self.pre_transform(data) for data in data_list]
torch.save(self.collate(data_list), self.processed_paths[0])
def test_remove_isolated_nodes():
edge_index = torch.tensor([[0, 1, 0], [1, 0, 0]])
out, _, mask = remove_isolated_nodes(edge_index)
assert out.tolist() == [[0, 1, 0], [1, 0, 0]]
assert mask.tolist() == [1, 1]
out, _, mask = remove_isolated_nodes(edge_index, num_nodes=3)
assert out.tolist() == [[0, 1, 0], [1, 0, 0]]
assert mask.tolist() == [1, 1, 0]
edge_index = torch.tensor([[0, 2, 1, 0, 2], [2, 0, 1, 0, 2]])
edge_attr = torch.tensor([1, 2, 3, 4, 5])
out1, out2, mask = remove_isolated_nodes(edge_index, edge_attr)
assert out1.tolist() == [[0, 1, 0, 1], [1, 0, 0, 1]]
assert out2.tolist() == [1, 2, 4, 5]
assert mask.tolist() == [1, 0, 1]
def __call__(self, data):
num_nodes = data.num_nodes
out = remove_isolated_nodes(data.edge_index, data.edge_attr, num_nodes)
data.edge_index, data.edge_attr, mask = out
for key, item in data:
if torch.is_tensor(item) and item.size(
0) == num_nodes and "edge" not in key:
data[key] = item[mask]
return data
def __call__(self, data):
num_nodes = data.num_nodes
out = remove_isolated_nodes(data.edge_index, data.edge_attr, num_nodes)
data.edge_index, data.edge_attr, mask = out
for key, item in data:
if bool(re.search('edge', key)):
continue
if torch.is_tensor(item) and item.size(0) == num_nodes:
data[key] = item[mask]
return data
def __call__(cls, state_pixels):
"""Convert raw pixels to a graph
Args:
- state_pixels: (W, H, 3) np.uint8
- embedding: function taking a (W, H, 3) and returning (W, H, N) Tensor
N>= 4 and always include the embedding_minimal
- linker: function taking a (W, H, 3) state and returning edges_index
Return:
- torch_geometric Data instance
"""
# Pixel state
state = torch.tensor(state_pixels, dtype=torch.uint8)
# Nodes (original) coordinates (num_nodes, 2)
num_nodes = state.size(0) * state.size(1)
pos = np.stack(np.unravel_index(np.arange(num_nodes), state.shape[:2]),
axis=1)
# Nodes embedding (num_nodes, n_features)
x = cls.embedding(state).float().reshape(num_nodes, -1)
# Edges
edges_index = cls.linker(state)
# Remove isolated nodes
edges_index, _, nodes_mask = remove_isolated_nodes(edges_index,
num_nodes=num_nodes)
x = x[nodes_mask]
pos = torch.tensor(pos[nodes_mask], dtype=torch.long)
# Action mask
player_idx = utils.find_player_idx(x) # (1,)
# (num_nodes, 1) bool
mask = cls.get_node_neighbors_mask(player_idx, edges_index, x)
# Edge features, None or (num_edges_features)
edge_attr = cls.get_edge_attr(edges_index, x, pos)
# Apply mask
graph = Data(
x=x,
pos=pos,
edge_index=edges_index.contiguous(),
edge_attr=edge_attr,
mask=mask,
player_idx=player_idx,
)
return graph
def save_attention(edge_index, att, labels, genes):
# ------------------- Saving attention network ----------------------------------- #
att = att.max(1).reshape((-1, 1))
print(edge_index.shape, labels.shape, att.shape)
t = lambda t: torch.tensor(t)
edge_index, att = remove_self_loops(t(edge_index.T), t(att))
edge_index, att, _ = remove_isolated_nodes(edge_index, att)
edge_index = edge_index.numpy().T
att = att.numpy()
print(edge_index.shape, labels.shape, att.shape)
nodes_edges = np.unique(edge_index.reshape((-1)))
nodes_idx = np.intersect1d(np.arange(len(labels)), nodes_edges)
labels = labels[nodes_idx]
genes = genes[nodes_idx]
meta_edges = pd.DataFrame(np.concatenate([edge_index.astype(int), att], 1))
meta_edges.to_csv(f'../data/essential_genes/gat_attention/{organism}_edges.csv', index=False)
meta_nodes = pd.DataFrame(np.stack([nodes_idx, genes, labels], 1))
path = f'../data/essential_genes/gat_attention/{organism}_nodes.csv'
meta_nodes.to_csv(path, index=False)
print(meta_edges.shape, meta_nodes.shape)
print('Saved edges and nodes to ', path)