process function needs 2 dimension for y

graph_dit/datasets/dataset.py

@@ -674,7 +674,7 @@ class Dataset(InMemoryDataset):
             edge_index = torch.tensor(edges_list, dtype=torch.long).t()
             edge_type = torch.tensor(edge_type, dtype=torch.long)
             edge_attr = edge_type
-            y = torch.tensor([0], dtype=torch.float).view(1, -1)
+            y = torch.tensor([0, 0], dtype=torch.float).view(1, -1)
             data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr, y=y, idx=i)
             return data
         graph_list = []
@@ -898,7 +898,7 @@ class Dataset_origin(InMemoryDataset):
         torch.save(self.collate(data_list), self.processed_paths[0])
 
 def parse_architecture_string(arch_str):
-    print(arch_str)
+    # print(arch_str)
     steps = arch_str.split('+')
     nodes = ['input']  # Start with input node
     edges = []

graph_dit/diffusion/diffusion_utils.py

@@ -65,10 +65,11 @@ def reverse_tensor(x):
 
 def sample_discrete_features(probX, probE, node_mask, step=None, add_nose=True):
     ''' Sample features from multinomial distribution with given probabilities (probX, probE, proby)
-        :param probX: bs, n, dx_out        node features
-        :param probE: bs, n, n, de_out     edge features
-        :param proby: bs, dy_out           global features.
+        :param probX: bs, n, dx_out        node features        1200 8 7
+        :param probE: bs, n, n, de_out     edge features        1200 8 8 2
+        :param proby: bs, dy_out           global features.     1200 8
     '''
+    # print(f"sample_discrete_features in: probX: {probX.shape}, probE: {probE.shape}, node_mask: {node_mask.shape}")
     bs, n, _ = probX.shape
 
     # Noise X
@@ -97,8 +98,11 @@ def sample_discrete_features(probX, probE, node_mask, step=None, add_nose=True):
 
     # Sample E
     E_t = probE.multinomial(1).reshape(bs, n, n)    # (bs, n, n)
+    # print(f"sample_discrete_features out: X_t: {X_t.shape}, E_t: {E_t.shape}")
     E_t = torch.triu(E_t, diagonal=1)
+    # print(f"sample_discrete_features out: X_t: {X_t.shape}, E_t: {E_t.shape}")
     E_t = (E_t + torch.transpose(E_t, 1, 2))
+    # print(f"sample_discrete_features out: X_t: {X_t.shape}, E_t: {E_t.shape}")
 
     return PlaceHolder(X=X_t, E=E_t, y=torch.zeros(bs, 0).type_as(X_t))
 

graph_dit/diffusion/noise_schedule.py

@@ -103,16 +103,25 @@ class MarginalTransition:
         self.e_marginals = e_marginals # Dx, De
         self.xe_conditions = xe_conditions
 
-        self.u_x = x_marginals.unsqueeze(0).expand(self.X_classes, -1).unsqueeze(0) # 1, Dx, Dx
-        self.u_e = e_marginals.unsqueeze(0).expand(self.E_classes, -1).unsqueeze(0) # 1, De, De
-        self.u_xe = xe_conditions.unsqueeze(0) # 1, Dx, De
-        self.u_ex = ex_conditions.unsqueeze(0) # 1, De, Dx
+        self.u_x = x_marginals.unsqueeze(0).expand(self.X_classes, -1).unsqueeze(0) # 1, Dx, Dx 1 7 7
+        self.u_e = e_marginals.unsqueeze(0).expand(self.E_classes, -1).unsqueeze(0) # 1, De, De 1 2 2
+        self.u_xe = xe_conditions.unsqueeze(0) # 1, Dx, De 1 7 2
+        self.u_ex = ex_conditions.unsqueeze(0) # 1, De, Dx 1 2 7
         self.u = self.get_union_transition(self.u_x, self.u_e, self.u_xe, self.u_ex, n_nodes) # 1, Dx + n*De, Dx + n*De
+        # print(f"Shape of u_x: {self.u_x.shape}")
+        # print(f"Shape of u_e: {self.u_e.shape}")
+        # print(f"Shape of u_xe: {self.u_xe.shape}")
+        # print(f"Shape of u_ex: {self.u_ex.shape}")
+        # print(f"Shape of u: {self.u.shape}")
 
     def get_union_transition(self, u_x, u_e, u_xe, u_ex, n_nodes):
+        # print(f"before processing Shape of u_e: {u_e.shape}")
+        # print(f"before processing Shape of u_ex: {u_ex.shape}")
         u_e = u_e.repeat(1, n_nodes, n_nodes) # (1, n*de, n*de)
         u_xe = u_xe.repeat(1, 1, n_nodes) # (1, dx, n*de)
         u_ex = u_ex.repeat(1, n_nodes, 1) # (1, n*de, dx)
+        # print(f"After processing Shape of u_ex: {u_ex.shape}")
+        # print(f"After processing Shape of u_e: {u_e.shape}")
         u0 = torch.cat([u_x, u_xe], dim=2) # (1, dx, dx + n*de)
         u1 = torch.cat([u_ex, u_e], dim=2) # (1, n*de, dx + n*de)
         u = torch.cat([u0, u1], dim=1) # (1, dx + n*de, dx + n*de)

graph_dit/main.py

@@ -11,9 +11,13 @@ import utils
 from datasets import dataset
 from diffusion_model import Graph_DiT
 from metrics.molecular_metrics_train import TrainMolecularMetricsDiscrete
+from metrics.molecular_metrics_train import TrainGraphMetricsDiscrete
 from metrics.molecular_metrics_sampling import SamplingMolecularMetrics
+from metrics.molecular_metrics_sampling import SamplingGraphMetrics
+
 
 from analysis.visualization import MolecularVisualization
+from analysis.visualization import GraphVisualization
 
 warnings.filterwarnings("ignore", category=UserWarning)
 torch.set_float32_matmul_precision("medium")
@@ -79,19 +83,20 @@ def main(cfg: DictConfig):
     datamodule = dataset.DataModule(cfg)
     datamodule.prepare_data()
     dataset_infos = dataset.DataInfos(datamodule=datamodule, cfg=cfg, dataset=datamodule.dataset)
-    # train_smiles, reference_smiles = datamodule.get_train_smiles()
-    train_graphs, reference_graphs = datamodule.get_train_graphs()
+    train_smiles, reference_smiles = datamodule.get_train_smiles()
+    # train_graphs, reference_graphs = datamodule.get_train_graphs()
 
     # get input output dimensions
     dataset_infos.compute_input_output_dims(datamodule=datamodule)
     train_metrics = TrainMolecularMetricsDiscrete(dataset_infos)
+    # train_metrics = TrainGraphMetricsDiscrete(dataset_infos)
 
-    # sampling_metrics = SamplingMolecularMetrics(
-    #     dataset_infos, train_smiles, reference_smiles
-    # )
-    sampling_metrics = SamplingGraphMetrics(
-        dataset_infos, train_graphs, reference_graphs
+    sampling_metrics = SamplingMolecularMetrics(
+        dataset_infos, train_smiles, reference_smiles
     )
+    # sampling_metrics = SamplingGraphMetrics(
+    #     dataset_infos, train_graphs, reference_graphs
+    # )
     visualization_tools = MolecularVisualization(dataset_infos)
 
     model_kwargs = {
@@ -149,6 +154,54 @@ def test(cfg: DictConfig):
     train_graphs, reference_graphs = datamodule.get_train_graphs()
 
     dataset_infos.compute_input_output_dims(datamodule=datamodule)
+    train_metrics = TrainGraphMetricsDiscrete(dataset_infos)
+
+    sampling_metrics = SamplingGraphMetrics(
+        dataset_infos, train_graphs, reference_graphs
+    )
+
+    visulization_tools = GraphVisualization(dataset_infos)
+
+    model_kwargs = {
+        "dataset_infos": dataset_infos,
+        "train_metrics": train_metrics,
+        "sampling_metrics": sampling_metrics,
+        "visualization_tools": visulization_tools,
+    }
+
+    if cfg.general.test_only:
+        cfg, _ = get_resume(cfg, model_kwargs)
+        os.chdir(cfg.general.test_only.split("checkpoints")[0])
+    elif cfg.general.resume is not None:
+        cfg, _ = get_resume_adaptive(cfg, model_kwargs)
+        os.chdir(cfg.general.resume.split("checkpoints")[0])
+    model = Graph_DiT(cfg=cfg, **model_kwargs)
+    trainer = Trainer(
+        gradient_clip_val=cfg.train.clip_grad,
+        # accelerator="cpu",
+        accelerator="gpu"
+        if torch.cuda.is_available() and cfg.general.gpus > 0
+        else "cpu",
+        devices=cfg.general.gpus
+        if torch.cuda.is_available() and cfg.general.gpus > 0
+        else None,
+        max_epochs=cfg.train.n_epochs,
+        enable_checkpointing=False,
+        check_val_every_n_epoch=cfg.train.check_val_every_n_epoch,
+        val_check_interval=cfg.train.val_check_interval,
+        strategy="ddp" if cfg.general.gpus > 1 else "auto",
+        enable_progress_bar=cfg.general.enable_progress_bar,
+        callbacks=[],
+        reload_dataloaders_every_n_epochs=0,
+        logger=[],
+    )
+
+    if not cfg.general.test_only:
+        print("start testing fit method")
+        trainer.fit(model, datamodule=datamodule, ckpt_path=cfg.general.resume)
+        if cfg.general.save_model:
+            trainer.save_checkpoint(f"checkpoints/{cfg.general.name}/last.ckpt")
+        trainer.test(model, datamodule=datamodule)
 
 if __name__ == "__main__":
     test()

graph_dit/metrics/molecular_metrics_train.py

@@ -85,7 +85,7 @@ class EdgeMetricsCE(MetricCollection):
         ce_SI = SingleCE(1)
         ce_DO = DoubleCE(2)
         ce_TR = TripleCE(3)
-        super().__init__([ce_no_bond, ce_SI, ce_DO, ce_TR])
+        super().__init__([ce_no_bond, ce_SI])
 
 class AtomMetricsCE(MetricCollection):
     def __init__(self, active_atoms):

graph_dit/models/transformer.py

@@ -87,7 +87,7 @@ class Denoiser(nn.Module):
     def forward(self, x, e, node_mask, y, t, unconditioned):
         
         print("Denoiser Forward")
-        print(x.shape, e.shape, y.shape, t.shape, unconditioned)
+        # print(x.shape, e.shape, y.shape, t.shape, unconditioned)
         force_drop_id = torch.zeros_like(y.sum(-1))
         # drop the nan values
         force_drop_id[torch.isnan(y.sum(-1))] = 1
@@ -98,32 +98,32 @@ class Denoiser(nn.Module):
         # bs = batch size, n = number of nodes
         bs, n, _ = x.size()
         x = torch.cat([x, e.reshape(bs, n, -1)], dim=-1)
-        print("X after concat with E")
-        print(x.shape)
+        # print("X after concat with E")
+        # print(x.shape)
         # self.x_embedder = nn.Linear(Xdim + max_n_nodes * Edim, hidden_size, bias=False)
         x = self.x_embedder(x)
-        print("X after x_embedder")
-        print(x.shape)
+        # print("X after x_embedder")
+        # print(x.shape)
 
         # self.t_embedder = TimestepEmbedder(hidden_size)
         c1 = self.t_embedder(t)
-        print("C1 after t_embedder")
-        print(c1.shape)
+        # print("C1 after t_embedder")
+        # print(c1.shape)
         for i in range(1, self.ydim):
             if i == 1:
                 c2 = self.y_embedding_list[i-1](y[:, :2], self.training, force_drop_id, t)
             else:
                 c2 = c2 + self.y_embedding_list[i-1](y[:, i:i+1], self.training, force_drop_id, t)
-        print("C2 after y_embedding_list")
-        print(c2.shape)
-        print("C1 + C2")
+        # print("C2 after y_embedding_list")
+        # print(c2.shape)
+        # print("C1 + C2")
         c = c1 + c2
-        print(c.shape)
+        # print(c.shape)
         
         for i, block in enumerate(self.encoders):
             x = block(x, c, node_mask)
-        print("X after block")
-        print(x.shape)
+        # print("X after block")
+        # print(x.shape)
 
         # X: B * N * dx, E: B * N * N * de
         X, E, y = self.out_layer(x, x_in, e_in, c, t, node_mask)

graph_dit/utils.py

@@ -46,13 +46,17 @@ def unnormalize(X, E, y, norm_values, norm_biases, node_mask, collapse=False):
 
 
 def to_dense(x, edge_index, edge_attr, batch, max_num_nodes=None):
+    # print(f"to dense X: {x.shape}, edge_index: {edge_index.shape}, edge_attr: {edge_attr.shape}, batch: {batch}, max_num_nodes: {max_num_nodes}")
     X, node_mask = to_dense_batch(x=x, batch=batch, max_num_nodes=max_num_nodes)
     # node_mask = node_mask.float()
     edge_index, edge_attr = torch_geometric.utils.remove_self_loops(edge_index, edge_attr)
     if max_num_nodes is None:
         max_num_nodes = X.size(1)
+    # print(f"to dense X: {X.shape}, edge_index: {edge_index.shape}, edge_attr: {edge_attr.shape}, batch: {batch}, max_num_nodes: {max_num_nodes}")
     E = to_dense_adj(edge_index=edge_index, batch=batch, edge_attr=edge_attr, max_num_nodes=max_num_nodes)
     E = encode_no_edge(E)
+    # print(f"to dense X: {X.shape}, edge_index: {edge_index.shape}, edge_attr: {edge_attr.shape}, batch: {batch}, max_num_nodes: {max_num_nodes}")
+    # print(f"to dense X: {X.shape}, E: {E.shape}, batch: {batch}, lenE: {len(E)}")
     return PlaceHolder(X=X, E=E, y=None), node_mask
 
 
@@ -119,6 +123,7 @@ class PlaceHolder:
         x_mask = node_mask.unsqueeze(-1)          # bs, n, 1
         e_mask1 = x_mask.unsqueeze(2)             # bs, n, 1, 1
         e_mask2 = x_mask.unsqueeze(1)             # bs, 1, n, 1
+        # print(f"mask X: {self.X.shape}, E: {self.E.shape}, node_mask: {node_mask.shape}, x_mask: {x_mask.shape}, e_mask1: {e_mask1.shape}, e_mask2: {e_mask2.shape}")
 
         if collapse:
             self.X = torch.argmax(self.X, dim=-1)
@@ -127,8 +132,13 @@ class PlaceHolder:
             self.X[node_mask == 0] = - 1
             self.E[(e_mask1 * e_mask2).squeeze(-1) == 0] = - 1
         else:
+            # print(f"X: {self.X.shape}, E: {self.E.shape}")
+            # print(f"X: {self.X}, E: {self.E}")
+            # print(f"x_mask: {x_mask}, e_mask1: {e_mask1}, e_mask2: {e_mask2}")
             self.X = self.X * x_mask
             self.E = self.E * e_mask1 * e_mask2
+            # print(f"X: {self.X.shape}, E: {self.E.shape}")
+            # print(f"X: {self.X}, E: {self.E}")
             assert torch.allclose(self.E, torch.transpose(self.E, 1, 2))
         return self
 

graph_dit/workingdoc.md

@@ -0,0 +1,374 @@
+0626
+**dataset.py**
+## class DataModule:
+
+### def prepare_data(self) -> None:
+
+    dataset = Dataset(source=source, root=root_path, target_prop=target, transform=None)
+
+## class Dataset:
+
+Dataset is the subclass of `InMemoryDataset` from `torch_geometric.data` module.
+
+
+```python
+super().__init__(root, transform, pre_transform)
+```
+
+
+### def __init__(self, source, root, target_prop=None, transform=None, pre_transform=None, pre_filter=None):
+
+initiliaze the nasbench api and load the dataset.
+
+`self.data` and `self.slices` are loaded from the nasbench api.
+
+try to print the data of `self.data` and `self.slices`
+get
+
+```text
+self.data=Data(x=[125000], edge_index=[2, 93750], edge_attr=[93750, 1], y=[15625, 5]), 
+self.slices=defaultdict(<class 'dict'>, {'x': tensor([     0,      8,     16,  ..., 124984, 124992, 125000]), 
+'edge_index': tensor([    0,     6,    12,  ..., 93738, 93744, 93750]), 
+'edge_attr': tensor([    0,     6,    12,  ..., 93738, 93744, 93750]), 
+'y': tensor([    0,     1,     2,  ..., 15623, 15624, 15625])})
+```
+
+The original get :
+
+<details>
+<summary>click to expand</summary>
+
+```text
+self.data: Data(x=[16599], edge_index=[2, 36132], edge_attr=[36132], y=[553, 5], idx=[553]),
+self.slices: defaultdict(<class 'dict'>, {'x': tensor([    0,     9,    32,    56,    78,   113,   138,   157,   173,   203,
+          219,   262,   299,   326,   350,   391,   432,   466,   502,   528,
+          547,   583,   589,   599,   609,   622,   637,   652,   664,   675,
+          687,   703,   715,   719,   729,   735,   742,   749,   754,   770,
+          799,   836,   840,   846,   878,   917,   954,   991,  1022,  1065,
+         1096,  1127,  1158,  1197,  1228,  1259,  1298,  1343,  1381,  1412,
+         1457,  1500,  1539,  1583,  1601,  1640,  1679,  1688,  1733,  1768,
+         1797,  1830,  1870,  1901,  1926,  1950,  1971,  2000,  2043,  2090,
+         2137,  2176,  2220,  2261,  2301,  2337,  2378,  2420,  2460,  2508,
+         2549,  2580,  2615,  2644,  2673,  2717,  2748,  2780,  2809,  2833,
+         2865,  2875,  2884,  2923,  2966,  3006,  3017,  3028,  3048,  3079,
+         3090,  3101,  3110,  3115,  3129,  3155,  3173,  3194,  3224,  3256,
+         3299,  3336,  3379,  3426,  3470,  3514,  3542,  3566,  3587,  3615,
+         3636,  3664,  3684,  3698,  3728,  3754,  3780,  3796,  3808,  3825,
+         3853,  3881,  3906,  3924,  3949,  3982,  4007,  4044,  4092,  4128,
+         4174,  4209,  4244,  4292,  4339,  4372,  4419,  4468,  4502,  4545,
+         4588,  4609,  4638,  4688,  4717,  4767,  4814,  4861,  4894,  4935,
+         4985,  5023,  5057,  5080,  5114,  5148,  5156,  5202,  5251,  5299,
+         5348,  5367,  5376,  5386,  5400,  5413,  5429,  5448,  5474,  5485,
+         5497,  5513,  5519,  5558,  5592,  5631,  5656,  5679,  5705,  5734,
+         5763,  5788,  5813,  5838,  5863,  5887,  5911,  5935,  5959,  5982,
+         6027,  6072,  6097,  6133,  6179,  6211,  6250,  6297,  6338,  6370,
+         6411,  6458,  6493,  6528,  6576,  6615,  6654,  6694,  6733,  6760,
+         6784,  6816,  6861,  6907,  6944,  6982,  7027,  7073,  7117,  7160,
+         7203,  7243,  7283,  7323,  7360,  7407,  7421,  7457,  7502,  7543,
+         7563,  7585,  7605,  7624,  7665,  7706,  7717,  7754,  7791,  7815,
+         7839,  7863,  7908,  7952,  7984,  8010,  8035,  8073,  8117,  8143,
+         8189,  8223,  8271,  8306,  8353,  8378,  8415,  8449,  8483,  8520,
+         8558,  8605,  8636,  8680,  8727,  8762,  8809,  8823,  8854,  8879,
+         8915,  8954,  8997,  9039,  9078,  9120,  9153,  9195,  9237,  9272,
+         9314,  9356,  9389,  9400,  9449,  9497,  9536,  9571,  9621,  9662,
+         9698,  9740,  9783,  9825,  9871,  9915,  9965, 10006, 10050, 10097,
+        10138, 10188, 10232, 10256, 10267, 10287, 10301, 10344, 10358, 10373,
+        10387, 10429, 10441, 10472, 10480, 10500, 10510, 10521, 10533, 10552,
+        10583, 10604, 10621, 10635, 10647, 10660, 10676, 10697, 10728, 10758,
+        10789, 10799, 10813, 10821, 10833, 10850, 10858, 10869, 10917, 10926,
+        10936, 10948, 10972, 10992, 11011, 11024, 11040, 11059, 11065, 11072,
+        11082, 11099, 11107, 11115, 11124, 11135, 11147, 11167, 11178, 11184,
+        11198, 11209, 11220, 11226, 11242, 11248, 11261, 11269, 11288, 11308,
+        11335, 11363, 11392, 11415, 11435, 11449, 11475, 11518, 11537, 11550,
+        11565, 11578, 11599, 11614, 11631, 11674, 11717, 11738, 11771, 11811,
+        11831, 11846, 11855, 11869, 11877, 11884, 11889, 11895, 11917, 11956,
+        11968, 11979, 12018, 12029, 12036, 12041, 12051, 12061, 12067, 12086,
+        12109, 12134, 12165, 12191, 12232, 12273, 12307, 12354, 12385, 12433,
+        12472, 12518, 12565, 12611, 12657, 12703, 12742, 12788, 12836, 12882,
+        12928, 12967, 13013, 13052, 13091, 13130, 13173, 13214, 13264, 13314,
+        13364, 13403, 13450, 13497, 13544, 13589, 13634, 13677, 13717, 13752,
+        13793, 13828, 13855, 13890, 13925, 13965, 14011, 14057, 14105, 14151,
+        14190, 14238, 14285, 14313, 14343, 14362, 14405, 14443, 14475, 14509,
+        14537, 14553, 14597, 14636, 14647, 14658, 14705, 14736, 14786, 14810,
+        14830, 14849, 14869, 14910, 14950, 14956, 14994, 15042, 15077, 15125,
+        15172, 15196, 15204, 15236, 15268, 15311, 15350, 15393, 15433, 15466,
+        15499, 15530, 15565, 15600, 15639, 15675, 15711, 15750, 15782, 15814,
+        15849, 15882, 15921, 15956, 15999, 16038, 16078, 16118, 16155, 16182,
+        16209, 16235, 16261, 16290, 16319, 16345, 16370, 16415, 16460, 16503,
+        16530, 16539, 16585, 16599]), 
+        'edge_index': tensor([    0,    18,    70,   124,   172,   250,   308,   350,   384,   454,
+          488,   590,   674,   736,   790,   882,   976,  1050,  1134,  1194,
+         1236,  1318,  1328,  1348,  1368,  1394,  1428,  1462,  1488,  1510,
+         1534,  1570,  1594,  1600,  1620,  1630,  1642,  1654,  1662,  1694,
+         1762,  1850,  1856,  1866,  1938,  2026,  2110,  2194,  2264,  2362,
+         2432,  2502,  2572,  2662,  2732,  2802,  2890,  2992,  3078,  3148,
+         3250,  3348,  3436,  3536,  3574,  3662,  3750,  3768,  3870,  3946,
+         4008,  4080,  4168,  4238,  4294,  4346,  4392,  4456,  4556,  4664,
+         4768,  4856,  4956,  5050,  5140,  5220,  5312,  5406,  5496,  5604,
+         5698,  5766,  5844,  5908,  5972,  6072,  6140,  6210,  6274,  6326,
+         6396,  6414,  6432,  6520,  6616,  6704,  6726,  6748,  6790,  6850,
+         6872,  6894,  6910,  6918,  6946,  6998,  7034,  7076,  7144,  7212,
+         7308,  7386,  7476,  7580,  7676,  7772,  7832,  7882,  7926,  7984,
+         8028,  8086,  8128,  8156,  8220,  8276,  8330,  8360,  8382,  8416,
+         8474,  8532,  8584,  8620,  8672,  8742,  8794,  8878,  8984,  9062,
+         9164,  9240,  9320,  9426,  9532,  9606,  9710,  9818,  9892,  9986,
+        10080, 10124, 10186, 10298, 10360, 10472, 10578, 10684, 10756, 10846,
+        10956, 11040, 11114, 11162, 11236, 11310, 11324, 11424, 11532, 11638,
+        11744, 11784, 11800, 11818, 11844, 11868, 11898, 11934, 11988, 12008,
+        12030, 12060, 12070, 12156, 12230, 12316, 12370, 12416, 12474, 12538,
+        12602, 12658, 12712, 12766, 12820, 12872, 12924, 12976, 13028, 13078,
+        13180, 13282, 13338, 13418, 13518, 13588, 13674, 13776, 13866, 13936,
+        14028, 14136, 14214, 14292, 14400, 14488, 14576, 14666, 14754, 14814,
+        14866, 14940, 15038, 15140, 15224, 15310, 15410, 15512, 15610, 15708,
+        15802, 15890, 15978, 16066, 16144, 16248, 16276, 16354, 16454, 16548,
+        16590, 16636, 16678, 16718, 16808, 16898, 16920, 17000, 17080, 17132,
+        17184, 17236, 17336, 17434, 17504, 17560, 17612, 17694, 17788, 17844,
+        17948, 18022, 18128, 18204, 18306, 18358, 18436, 18508, 18580, 18660,
+        18742, 18844, 18908, 19002, 19106, 19182, 19286, 19314, 19382, 19436,
+        19514, 19600, 19696, 19790, 19876, 19968, 20042, 20134, 20226, 20304,
+        20396, 20488, 20562, 20584, 20696, 20802, 20890, 20968, 21078, 21170,
+        21248, 21342, 21438, 21536, 21644, 21748, 21860, 21954, 22054, 22162,
+        22254, 22366, 22464, 22516, 22538, 22580, 22608, 22704, 22732, 22762,
+        22788, 22882, 22906, 22976, 22990, 23032, 23050, 23070, 23092, 23130,
+        23192, 23232, 23264, 23290, 23312, 23336, 23366, 23408, 23472, 23534,
+        23598, 23616, 23642, 23656, 23678, 23712, 23726, 23746, 23854, 23870,
+        23888, 23912, 23960, 24000, 24038, 24062, 24092, 24128, 24138, 24150,
+        24168, 24202, 24218, 24232, 24248, 24270, 24294, 24332, 24354, 24364,
+        24392, 24412, 24434, 24444, 24476, 24486, 24512, 24526, 24564, 24606,
+        24666, 24728, 24794, 24844, 24886, 24914, 24970, 25062, 25104, 25130,
+        25164, 25192, 25236, 25266, 25300, 25388, 25476, 25520, 25594, 25684,
+        25724, 25754, 25770, 25798, 25812, 25824, 25832, 25842, 25888, 25976,
+        26000, 26022, 26110, 26132, 26144, 26152, 26170, 26188, 26198, 26236,
+        26284, 26338, 26406, 26462, 26552, 26644, 26718, 26822, 26886, 26992,
+        27078, 27182, 27288, 27390, 27492, 27594, 27680, 27782, 27890, 27992,
+        28094, 28180, 28282, 28368, 28454, 28542, 28638, 28730, 28840, 28950,
+        29060, 29146, 29250, 29354, 29458, 29558, 29658, 29752, 29838, 29912,
+        30000, 30074, 30130, 30204, 30278, 30364, 30468, 30570, 30676, 30778,
+        30864, 30972, 31076, 31136, 31194, 31232, 31326, 31408, 31476, 31550,
+        31610, 31640, 31736, 31824, 31846, 31870, 31974, 32042, 32148, 32204,
+        32248, 32290, 32334, 32424, 32512, 32522, 32608, 32714, 32790, 32900,
+        33008, 33058, 33072, 33142, 33212, 33312, 33394, 33490, 33578, 33648,
+        33718, 33784, 33858, 33932, 34020, 34100, 34180, 34262, 34330, 34398,
+        34472, 34542, 34624, 34698, 34794, 34882, 34970, 35058, 35140, 35200,
+        35260, 35318, 35376, 35440, 35504, 35562, 35618, 35722, 35826, 35926,
+        35982, 36000, 36104, 36132]), 
+        'edge_attr': tensor([    0,    18,    70,   124,   172,   250,   308,   350,   384,   454,
+          488,   590,   674,   736,   790,   882,   976,  1050,  1134,  1194,
+         1236,  1318,  1328,  1348,  1368,  1394,  1428,  1462,  1488,  1510,
+         1534,  1570,  1594,  1600,  1620,  1630,  1642,  1654,  1662,  1694,
+         1762,  1850,  1856,  1866,  1938,  2026,  2110,  2194,  2264,  2362,
+         2432,  2502,  2572,  2662,  2732,  2802,  2890,  2992,  3078,  3148,
+         3250,  3348,  3436,  3536,  3574,  3662,  3750,  3768,  3870,  3946,
+         4008,  4080,  4168,  4238,  4294,  4346,  4392,  4456,  4556,  4664,
+         4768,  4856,  4956,  5050,  5140,  5220,  5312,  5406,  5496,  5604,
+         5698,  5766,  5844,  5908,  5972,  6072,  6140,  6210,  6274,  6326,
+         6396,  6414,  6432,  6520,  6616,  6704,  6726,  6748,  6790,  6850,
+         6872,  6894,  6910,  6918,  6946,  6998,  7034,  7076,  7144,  7212,
+         7308,  7386,  7476,  7580,  7676,  7772,  7832,  7882,  7926,  7984,
+         8028,  8086,  8128,  8156,  8220,  8276,  8330,  8360,  8382,  8416,
+         8474,  8532,  8584,  8620,  8672,  8742,  8794,  8878,  8984,  9062,
+         9164,  9240,  9320,  9426,  9532,  9606,  9710,  9818,  9892,  9986,
+        10080, 10124, 10186, 10298, 10360, 10472, 10578, 10684, 10756, 10846,
+        10956, 11040, 11114, 11162, 11236, 11310, 11324, 11424, 11532, 11638,
+        11744, 11784, 11800, 11818, 11844, 11868, 11898, 11934, 11988, 12008,
+        12030, 12060, 12070, 12156, 12230, 12316, 12370, 12416, 12474, 12538,
+        12602, 12658, 12712, 12766, 12820, 12872, 12924, 12976, 13028, 13078,
+        13180, 13282, 13338, 13418, 13518, 13588, 13674, 13776, 13866, 13936,
+        14028, 14136, 14214, 14292, 14400, 14488, 14576, 14666, 14754, 14814,
+        14866, 14940, 15038, 15140, 15224, 15310, 15410, 15512, 15610, 15708,
+        15802, 15890, 15978, 16066, 16144, 16248, 16276, 16354, 16454, 16548,
+        16590, 16636, 16678, 16718, 16808, 16898, 16920, 17000, 17080, 17132,
+        17184, 17236, 17336, 17434, 17504, 17560, 17612, 17694, 17788, 17844,
+        17948, 18022, 18128, 18204, 18306, 18358, 18436, 18508, 18580, 18660,
+        18742, 18844, 18908, 19002, 19106, 19182, 19286, 19314, 19382, 19436,
+        19514, 19600, 19696, 19790, 19876, 19968, 20042, 20134, 20226, 20304,
+        20396, 20488, 20562, 20584, 20696, 20802, 20890, 20968, 21078, 21170,
+        21248, 21342, 21438, 21536, 21644, 21748, 21860, 21954, 22054, 22162,
+        22254, 22366, 22464, 22516, 22538, 22580, 22608, 22704, 22732, 22762,
+        22788, 22882, 22906, 22976, 22990, 23032, 23050, 23070, 23092, 23130,
+        23192, 23232, 23264, 23290, 23312, 23336, 23366, 23408, 23472, 23534,
+        23598, 23616, 23642, 23656, 23678, 23712, 23726, 23746, 23854, 23870,
+        23888, 23912, 23960, 24000, 24038, 24062, 24092, 24128, 24138, 24150,
+        24168, 24202, 24218, 24232, 24248, 24270, 24294, 24332, 24354, 24364,
+        24392, 24412, 24434, 24444, 24476, 24486, 24512, 24526, 24564, 24606,
+        24666, 24728, 24794, 24844, 24886, 24914, 24970, 25062, 25104, 25130,
+        25164, 25192, 25236, 25266, 25300, 25388, 25476, 25520, 25594, 25684,
+        25724, 25754, 25770, 25798, 25812, 25824, 25832, 25842, 25888, 25976,
+        26000, 26022, 26110, 26132, 26144, 26152, 26170, 26188, 26198, 26236,
+        26284, 26338, 26406, 26462, 26552, 26644, 26718, 26822, 26886, 26992,
+        27078, 27182, 27288, 27390, 27492, 27594, 27680, 27782, 27890, 27992,
+        28094, 28180, 28282, 28368, 28454, 28542, 28638, 28730, 28840, 28950,
+        29060, 29146, 29250, 29354, 29458, 29558, 29658, 29752, 29838, 29912,
+        30000, 30074, 30130, 30204, 30278, 30364, 30468, 30570, 30676, 30778,
+        30864, 30972, 31076, 31136, 31194, 31232, 31326, 31408, 31476, 31550,
+        31610, 31640, 31736, 31824, 31846, 31870, 31974, 32042, 32148, 32204,
+        32248, 32290, 32334, 32424, 32512, 32522, 32608, 32714, 32790, 32900,
+        33008, 33058, 33072, 33142, 33212, 33312, 33394, 33490, 33578, 33648,
+        33718, 33784, 33858, 33932, 34020, 34100, 34180, 34262, 34330, 34398,
+        34472, 34542, 34624, 34698, 34794, 34882, 34970, 35058, 35140, 35200,
+        35260, 35318, 35376, 35440, 35504, 35562, 35618, 35722, 35826, 35926,
+        35982, 36000, 36104, 36132]), 
+        'y': tensor([  0,   1,   2,   3,   4,   5,   6,   7,   8,   9,  10,  11,  12,  13,
+         14,  15,  16,  17,  18,  19,  20,  21,  22,  23,  24,  25,  26,  27,
+         28,  29,  30,  31,  32,  33,  34,  35,  36,  37,  38,  39,  40,  41,
+         42,  43,  44,  45,  46,  47,  48,  49,  50,  51,  52,  53,  54,  55,
+         56,  57,  58,  59,  60,  61,  62,  63,  64,  65,  66,  67,  68,  69,
+         70,  71,  72,  73,  74,  75,  76,  77,  78,  79,  80,  81,  82,  83,
+         84,  85,  86,  87,  88,  89,  90,  91,  92,  93,  94,  95,  96,  97,
+         98,  99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111,
+        112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125,
+        126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139,
+        140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153,
+        154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167,
+        168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181,
+        182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195,
+        196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209,
+        210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223,
+        224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237,
+        238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251,
+        252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265,
+        266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279,
+        280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293,
+        294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307,
+        308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321,
+        322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335,
+        336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349,
+        350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363,
+        364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377,
+        378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391,
+        392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405,
+        406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419,
+        420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433,
+        434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447,
+        448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461,
+        462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475,
+        476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489,
+        490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503,
+        504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517,
+        518, 519, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531,
+        532, 533, 534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545,
+        546, 547, 548, 549, 550, 551, 552, 553]), 
+        'idx': tensor([  0,   1,   2,   3,   4,   5,   6,   7,   8,   9,  10,  11,  12,  13,
+         14,  15,  16,  17,  18,  19,  20,  21,  22,  23,  24,  25,  26,  27,
+         28,  29,  30,  31,  32,  33,  34,  35,  36,  37,  38,  39,  40,  41,
+         42,  43,  44,  45,  46,  47,  48,  49,  50,  51,  52,  53,  54,  55,
+         56,  57,  58,  59,  60,  61,  62,  63,  64,  65,  66,  67,  68,  69,
+         70,  71,  72,  73,  74,  75,  76,  77,  78,  79,  80,  81,  82,  83,
+         84,  85,  86,  87,  88,  89,  90,  91,  92,  93,  94,  95,  96,  97,
+         98,  99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111,
+        112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125,
+        126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139,
+        140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153,
+        154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167,
+        168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181,
+        182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195,
+        196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209,
+        210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223,
+        224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237,
+        238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251,
+        252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265,
+        266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279,
+        280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293,
+        294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307,
+        308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321,
+        322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335,
+        336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349,
+        350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363,
+        364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377,
+        378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391,
+        392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405,
+        406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419,
+        420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433,
+        434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447,
+        448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461,
+        462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475,
+        476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489,
+        490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503,
+        504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517,
+        518, 519, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531,
+        532, 533, 534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545,
+        546, 547, 548, 549, 550, 551, 552, 553])})
+```
+</details>
+
+The different keys in the dictionary are:
+- `self.data`
+    - `edge_attr`: In nasbenchDiT, we get (edge_number, 1) size, but in DiT, we get (edge_number) dimension.
+    - `idx`: we do not have this key in nasbenchDiT.
+- `self.slices`: same with `self.data` 
+
+So I try to modify the self.data and self.slices to be compatible with the DiT dataset.
+
+## DataInfos
+
+now need a dataset to init the datainfo,
+because I need the nasbench api in the dataset
+```python
+        self.api = dataset.api
+```
+
+## get_train_smiles() vs. get_train_graphs()
+
+We want to remove molecules from the dataset, so we need to rerwrite the get_train_smiles() function to get_train_graphs() function.
+
+
+20240628
+
+## change the dataset ready for DiT
+
+Changed the process function in the dataset class to be compatible with the DiT dataset.
+
+<details>
+
+```python
+    def process(self):
+
+        data_list = []
+        len_data = len(self.api)
+
+        def graph_to_graph_data(graph):
+            ops = graph[1]
+            adj = graph[0]
+            nodes = []
+            for op in ops:
+                nodes.append(op_type[op])
+            x = torch.LongTensor(nodes)
+
+            edges_list = []
+            edge_type = []
+            for start in range(len(ops)):
+                for end in range(len(ops)):
+                    if adj[start][end] == 1:
+                        edges_list.append((start, end))
+                        edge_type.append(1)
+                        edges_list.append((end, start))
+                        edge_type.append(1)
+            
+            edge_index = torch.tensor(edges_list, dtype=torch.long).t()
+            edge_type = torch.tensor(edge_type, dtype=torch.long)
+            edge_attr = edge_type
+            y = torch.tensor([0], dtype=torch.float).view(1, -1)
+            data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr, y=y, idx=i)
+            return data
+        with tqdm(total = len_data) as pbar:
+            active_nodes = set()
+            for i in range(len_data):
+                arch_info = self.api.query_meta_info_by_index(i)
+                nodes, edges = parse_architecture_string(arch_info.arch_str)
+                adj_matrix, ops = create_adj_matrix_and_ops(nodes, edges)
+                for op in ops:
+                    if op not in active_nodes:
+                        active_nodes.add(op)
+                data = graph_to_graph_data((adj_matrix, ops)) 
+                data_list.append(data)
+                pbar.update(1)
+        
+        torch.save(self.collate(data_list), self.processed_paths[0])
+```
+</details>
+
+
+20240629
+
+## change to remove loading nasbench201 but read the data from the pt file
+