update the new graph to json function
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@@ -39,6 +39,16 @@ op_to_atom = {
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'none': 'S', # Sulfur for no operation
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'output': 'He' # Helium for output
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}
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op_type = {
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'nor_conv_1x1': 1,
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'nor_conv_3x3': 2,
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'avg_pool_3x3': 3,
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'skip_connect': 4,
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'output': 5,
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'none': 6,
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'input': 7
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}
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class DataModule(AbstractDataModule):
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def __init__(self, cfg):
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self.datadir = cfg.dataset.datadir
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@@ -343,6 +353,121 @@ class DataModule_original(AbstractDataModule):
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def test_dataloader(self):
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return self.test_loader
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def new_graphs_to_json(graphs, filename):
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source_name = "nasbench-201"
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num_graph = len(graphs)
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node_name_list = []
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node_count_list = []
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for op_name in op_type:
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node_name_list.append(op_name)
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node_count_list.append(0)
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node_name_list.append('*')
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node_count_list.append(0)
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n_nodes_per_graph = [0] * num_graph
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edge_count_list = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
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valencies = [0] * (len(op_type) + 1)
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transition_E = np.zeros((len(op_type) + 1, len(op_type) + 1, 2))
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n_node_list = []
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n_edge_list = []
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for graph in graphs:
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ops = graph[1]
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adj = graph[0]
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n_node = len(ops)
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n_edge = len(ops)
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n_node_list.append(n_node)
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n_edge_list.append(n_edge)
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n_nodes_per_graph[n_node] += 1
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cur_node_count_arr = np.zeros(len(op_type) + 1)
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for op in ops:
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node = op
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if node == '*':
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node_count_list[-1] += 1
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cur_node_count_arr[-1] += 1
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else:
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node_count_list[op_type[node]] += 1
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cur_node_count_arr[op_type[node]] += 1
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try:
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valencies[int(op_type[node])] += 1
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except:
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print('int(op_type[node])', int(op_type[node]))
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transition_E_temp = np.zeros((len(op_type) + 1, len(op_type) + 1, 2))
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for i in range(n_node):
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for j in range(n_node):
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if i == j or adj[i][j] == 0:
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continue
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start_node, end_node = i, j
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start_index = op_type[ops[start_node]]
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end_index = op_type[ops[end_node]]
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bond_index = 1
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edge_count_list[bond_index] += 2
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transition_E[start_index, end_index, bond_index] += 2
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transition_E[end_index, start_index, bond_index] += 2
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transition_E_temp[start_index, end_index, bond_index] += 2
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transition_E_temp[end_index, start_index, bond_index] += 2
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edge_count_list[0] += n_node * (n_node - 1) - n_edge * 2
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cur_tot_edge = cur_node_count_arr.reshape(-1,1) * cur_node_count_arr.reshape(1,-1) * 2
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print(f"cur_tot_edge={cur_tot_edge}, shape: {cur_tot_edge.shape}")
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cur_tot_edge = cur_tot_edge - np.diag(cur_node_count_arr) * 2
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transition_E[:, :, 0] += cur_tot_edge - transition_E_temp.sum(axis=-1)
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assert (cur_tot_edge > transition_E_temp.sum(axis=-1)).sum() >= 0
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n_nodes_per_graph = np.array(n_nodes_per_graph) / np.sum(n_nodes_per_graph)
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n_nodes_per_graph = n_nodes_per_graph.tolist()[:51]
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node_count_list = np.array(node_count_list) / np.sum(node_count_list)
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print('processed meta info: ------', filename, '------')
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print('len node_count_list', len(node_count_list))
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print('len node_name_list', len(node_name_list))
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active_nodes = np.array(node_name_list)[node_count_list > 0]
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active_nodes = active_nodes.tolist()
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node_count_list = node_count_list.tolist()
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edge_count_list = np.array(edge_count_list) / np.sum(edge_count_list)
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edge_count_list = edge_count_list.tolist()
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valencies = np.array(valencies) / np.sum(valencies)
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valencies = valencies.tolist()
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no_edge = np.sum(transition_E, axis=-1) == 0
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first_elt = transition_E[:, :, 0]
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first_elt[no_edge] = 1
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transition_E[:, :, 0] = first_elt
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transition_E = transition_E / np.sum(transition_E, axis=-1, keepdims=True)
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meta_dict = {
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'source': source_name,
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'num_graph': num_graph,
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'n_nodes_per_graph': n_nodes_per_graph,
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'max_n_nodes': max(n_node_list),
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'max_n_edges': max(n_edge_list),
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'node_type_list': node_count_list,
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'edge_type_list': edge_count_list,
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'valencies': valencies,
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'active_nodes': active_nodes,
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'num_active_nodes': len(active_nodes),
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'transition_E': transition_E.tolist(),
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}
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with open(f'{filename}.meta.json', 'w') as f:
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json.dump(meta_dict, f)
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return meta_dict
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def graphs_to_json(graphs, filename):
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bonds = {
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'nor_conv_1x1': 1,
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@@ -490,7 +615,7 @@ def graphs_to_json(graphs, filename):
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'atom_type_dist': atom_count_list,
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'bond_type_dist': bond_count_list,
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'valencies': valencies,
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'active_atoms': [atom_name_list[i] for i in range(118) if atom_count_list[i] > 0],
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'active_nodes': [atom_name_list[i] for i in range(118) if atom_count_list[i] > 0],
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'num_atom_type': len([atom_name_list[i] for i in range(118) if atom_count_list[i] > 0]),
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'transition_E': transition_E.tolist(),
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}
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@@ -503,10 +628,10 @@ class Dataset(InMemoryDataset):
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self.target_prop = target_prop
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source = '/home/stud/hanzhang/nasbenchDiT/graph_dit/NAS-Bench-201-v1_1-096897.pth'
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self.source = source
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super().__init__(root, transform, pre_transform, pre_filter)
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print(self.processed_paths[0]) #/home/stud/hanzhang/Graph-DiT/graph_dit/NAS-Bench-201-v1_1-096897.pth.pt
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self.api = API(source) # Initialize NAS-Bench-201 API
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print('API loaded')
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super().__init__(root, transform, pre_transform, pre_filter)
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print(self.processed_paths[0]) #/home/stud/hanzhang/Graph-DiT/graph_dit/NAS-Bench-201-v1_1-096897.pth.pt
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print('Dataset initialized')
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self.data, self.slices = torch.load(self.processed_paths[0])
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self.data.edge_attr = self.data.edge_attr.squeeze()
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@@ -732,30 +857,35 @@ class DataInfos(AbstractDatasetInfos):
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arch_info = self.api.query_meta_info_by_index(i)
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nodes, edges = parse_architecture_string(arch_info.arch_str)
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adj_matrix, ops = create_adj_matrix_and_ops(nodes, edges)
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if i < 5:
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print("Adjacency Matrix:")
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print(adj_matrix)
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print("Operations List:")
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print(ops)
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# if i < 5:
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# print("Adjacency Matrix:")
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# print(adj_matrix)
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# print("Operations List:")
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# print(ops)
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for op in ops:
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if op not in ops_type:
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ops_type[op] = len(ops_type)
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len_ops.add(len(ops))
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graphs.append((adj_matrix, ops))
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meta_dict = graphs_to_json(graphs, 'nasbench-201')
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# check first five graphs
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for i in range(5):
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print(f'graph {i} : {graphs[i]}')
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print(f'ops_type: {ops_type}')
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meta_dict = new_graphs_to_json(graphs, 'nasbench-201')
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self.base_path = base_path
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self.active_atoms = meta_dict['active_atoms']
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self.max_n_nodes = meta_dict['max_node']
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self.original_max_n_nodes = meta_dict['max_node']
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self.n_nodes = torch.Tensor(meta_dict['n_atoms_per_mol_dist'])
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self.edge_types = torch.Tensor(meta_dict['bond_type_dist'])
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self.active_nodes = meta_dict['active_nodes']
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self.max_n_nodes = meta_dict['max_n_nodes']
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self.original_max_n_nodes = meta_dict['max_n_nodes']
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self.n_nodes = torch.Tensor(meta_dict['n_nodes_per_graph'])
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self.edge_types = torch.Tensor(meta_dict['edge_type_dist'])
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self.transition_E = torch.Tensor(meta_dict['transition_E'])
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self.atom_decoder = meta_dict['active_atoms']
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node_types = torch.Tensor(meta_dict['atom_type_dist'])
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self.node_decoder = meta_dict['active_nodes']
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node_types = torch.Tensor(meta_dict['node_type_dist'])
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active_index = (node_types > 0).nonzero().squeeze()
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self.node_types = torch.Tensor(meta_dict['atom_type_dist'])[active_index]
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self.node_types = torch.Tensor(meta_dict['node_type_dist'])[active_index]
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self.nodes_dist = DistributionNodes(self.n_nodes)
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self.active_index = active_index
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