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app.py

@@ -5,375 +5,22 @@ import torch.nn as nn
 import random
 from rdkit import Chem
 from rdkit.Chem import Draw
+from graph_decoder.diffusion_model import GraphDiT
 
-#####
-
-import os 
-import yaml
-import json
-
-import torch.nn.functional as F
-from graph_decoder import diffusion_utils as utils
-from graph_decoder.molecule_utils import graph_to_smiles, check_valid
-from graph_decoder.transformer import Transformer
-from graph_decoder.visualize_utils import MolecularVisualization
-
-class GraphDiT(nn.Module):
-    def __init__(
-        self,
-        model_config_path,
-        data_info_path,
-        model_dtype,
-    ):
+class RandomPolymerGenerator(nn.Module):
+    def __init__(self):
         super().__init__()
-        pass
-
-        # dm_cfg, data_info = utils.load_config(model_config_path, data_info_path)
-
-        # input_dims = data_info.input_dims
-        # output_dims = data_info.output_dims
-        # nodes_dist = data_info.nodes_dist
-        # active_index = data_info.active_index
-
-        # self.model_config = dm_cfg
-        # self.data_info = data_info
-        # self.T = dm_cfg.diffusion_steps
-        # self.Xdim = input_dims["X"]
-        # self.Edim = input_dims["E"]
-        # self.ydim = input_dims["y"]
-        # self.Xdim_output = output_dims["X"]
-        # self.Edim_output = output_dims["E"]
-        # self.ydim_output = output_dims["y"]
-        # self.node_dist = nodes_dist
-        # self.active_index = active_index
-        # self.max_n_nodes = data_info.max_n_nodes
-        # self.atom_decoder = data_info.atom_decoder
-        # self.hidden_size = dm_cfg.hidden_size
-        # self.mol_visualizer = MolecularVisualization(self.atom_decoder)
-
-        # self.denoiser = Transformer(
-        #     max_n_nodes=self.max_n_nodes,
-        #     hidden_size=dm_cfg.hidden_size,
-        #     depth=dm_cfg.depth,
-        #     num_heads=dm_cfg.num_heads,
-        #     mlp_ratio=dm_cfg.mlp_ratio,
-        #     drop_condition=dm_cfg.drop_condition,
-        #     Xdim=self.Xdim,
-        #     Edim=self.Edim,
-        #     ydim=self.ydim,
-        # )
-
-        # self.model_dtype = model_dtype
-        # self.noise_schedule = utils.PredefinedNoiseScheduleDiscrete(
-        #     dm_cfg.diffusion_noise_schedule, timesteps=dm_cfg.diffusion_steps
-        # )
-        # x_marginals = data_info.node_types.to(self.model_dtype) / torch.sum(
-        #     data_info.node_types.to(self.model_dtype)
-        # )
-        # e_marginals = data_info.edge_types.to(self.model_dtype) / torch.sum(
-        #     data_info.edge_types.to(self.model_dtype)
-        # )
-        # x_marginals = x_marginals / x_marginals.sum()
-        # e_marginals = e_marginals / e_marginals.sum()
-
-        # xe_conditions = data_info.transition_E.to(self.model_dtype)
-        # xe_conditions = xe_conditions[self.active_index][:, self.active_index]
-
-        # xe_conditions = xe_conditions.sum(dim=1)
-        # ex_conditions = xe_conditions.t()
-        # xe_conditions = xe_conditions / xe_conditions.sum(dim=-1, keepdim=True)
-        # ex_conditions = ex_conditions / ex_conditions.sum(dim=-1, keepdim=True)
-
-        # self.transition_model = utils.MarginalTransition(
-        #     x_marginals=x_marginals,
-        #     e_marginals=e_marginals,
-        #     xe_conditions=xe_conditions,
-        #     ex_conditions=ex_conditions,
-        #     y_classes=self.ydim_output,
-        #     n_nodes=self.max_n_nodes,
-        # )
-        # self.limit_dist = utils.PlaceHolder(X=x_marginals, E=e_marginals, y=None)
-
-    def init_model(self, model_dir):
-        model_file = os.path.join(model_dir, 'model.pt')
-        if os.path.exists(model_file):
-            self.denoiser.load_state_dict(torch.load(model_file, map_location='cpu', weights_only=True))
-        else:
-            raise FileNotFoundError(f"Model file not found: {model_file}")
-
-    def disable_grads(self):
-        self.denoiser.disable_grads()
-    
-    def forward(
-        self, x, edge_index, edge_attr, graph_batch, properties, no_label_index
-    ):
-        raise ValueError('Not Implement')
-
-    def _forward(self, noisy_data, unconditioned=False):
-        noisy_x, noisy_e, properties = (
-            noisy_data["X_t"].to(self.model_dtype),
-            noisy_data["E_t"].to(self.model_dtype),
-            noisy_data["y_t"].to(self.model_dtype).clone(),
-        )
-        node_mask, timestep = (
-            noisy_data["node_mask"],
-            noisy_data["t"],
-        )
-        
-        pred = self.denoiser(
-            noisy_x,
-            noisy_e,
-            node_mask,
-            properties,
-            timestep,
-            unconditioned=unconditioned,
-        )
-        return pred
-
-    def apply_noise(self, X, E, y, node_mask):
-        """Sample noise and apply it to the data."""
-
-        # Sample a timestep t.
-        # When evaluating, the loss for t=0 is computed separately
-        lowest_t = 0 if self.training else 1
-        t_int = torch.randint(
-            lowest_t, self.T + 1, size=(X.size(0), 1), device=X.device
-        ).to(
-            self.model_dtype
-        )  # (bs, 1)
-        s_int = t_int - 1
-
-        t_float = t_int / self.T
-        s_float = s_int / self.T
-
-        # beta_t and alpha_s_bar are used for denoising/loss computation
-        beta_t = self.noise_schedule(t_normalized=t_float)  # (bs, 1)
-        alpha_s_bar = self.noise_schedule.get_alpha_bar(t_normalized=s_float)  # (bs, 1)
-        alpha_t_bar = self.noise_schedule.get_alpha_bar(t_normalized=t_float)  # (bs, 1)
-
-        Qtb = self.transition_model.get_Qt_bar(
-            alpha_t_bar, X.device
-        )  # (bs, dx_in, dx_out), (bs, de_in, de_out)
-
-        bs, n, d = X.shape
-        X_all = torch.cat([X, E.reshape(bs, n, -1)], dim=-1)
-        prob_all = X_all @ Qtb.X
-        probX = prob_all[:, :, : self.Xdim_output]
-        probE = prob_all[:, :, self.Xdim_output :].reshape(bs, n, n, -1)
-
-        sampled_t = utils.sample_discrete_features(
-            probX=probX, probE=probE, node_mask=node_mask
-        )
-
-        X_t = F.one_hot(sampled_t.X, num_classes=self.Xdim_output)
-        E_t = F.one_hot(sampled_t.E, num_classes=self.Edim_output)
-        assert (X.shape == X_t.shape) and (E.shape == E_t.shape)
-
-        y_t = y
-        z_t = utils.PlaceHolder(X=X_t, E=E_t, y=y_t).type_as(X_t).mask(node_mask)
-
-        noisy_data = {
-            "t_int": t_int,
-            "t": t_float,
-            "beta_t": beta_t,
-            "alpha_s_bar": alpha_s_bar,
-            "alpha_t_bar": alpha_t_bar,
-            "X_t": z_t.X,
-            "E_t": z_t.E,
-            "y_t": z_t.y,
-            "node_mask": node_mask,
-        }
-        return noisy_data
-
-    @torch.no_grad()
-    def generate(
-        self,
-        properties,
-        device,
-        guide_scale=1.,
-        num_nodes=None,
-        number_chain_steps=50,
-    ):
-        properties = [float('nan') if x is None else x for x in properties]
-        properties = torch.tensor(properties, dtype=torch.float).reshape(1, -1).to(device)
-        batch_size = properties.size(0)
-        assert batch_size == 1
-        if num_nodes is None:
-            num_nodes = self.node_dist.sample_n(batch_size, device)
-        else:
-            num_nodes = torch.LongTensor([num_nodes]).to(device)
-
-        arange = (
-            torch.arange(self.max_n_nodes, device=device)
-            .unsqueeze(0)
-            .expand(batch_size, -1)
-        )
-        node_mask = arange < num_nodes.unsqueeze(1)
-
-        z_T = utils.sample_discrete_feature_noise(
-            limit_dist=self.limit_dist, node_mask=node_mask
-        )
-        X, E = z_T.X, z_T.E
-
-        assert (E == torch.transpose(E, 1, 2)).all()
-
-        if number_chain_steps > 0:
-            chain_X_size = torch.Size((number_chain_steps, X.size(1)))
-            chain_E_size = torch.Size((number_chain_steps, E.size(1), E.size(2)))
-            chain_X = torch.zeros(chain_X_size)
-            chain_E = torch.zeros(chain_E_size)
+        self.fc1 = nn.Linear(5, 64)
+        self.fc2 = nn.Linear(64, 128)
+        self.fc3 = nn.Linear(128, 256)
+        self.fc4 = nn.Linear(256, 100)  # Output size set to 100 for simplicity
 
-        # Iteratively sample p(z_s | z_t) for t = 1, ..., T, with s = t - 1.
-        y = properties
-        for s_int in reversed(range(0, self.T)):
-            s_array = s_int * torch.ones((batch_size, 1)).type_as(y)
-            t_array = s_array + 1
-            s_norm = s_array / self.T
-            t_norm = t_array / self.T
+    def forward(self, x):
+        x = torch.relu(self.fc1(x))
+        x = torch.relu(self.fc2(x))
+        x = torch.relu(self.fc3(x))
+        return torch.sigmoid(self.fc4(x))
 
-            # Sample z_s
-            sampled_s, discrete_sampled_s = self.sample_p_zs_given_zt(
-                s_norm, t_norm, X, E, y, node_mask, guide_scale, device
-            )
-            X, E, y = sampled_s.X, sampled_s.E, sampled_s.y
-            
-            if number_chain_steps > 0:
-                # Save the first keep_chain graphs
-                write_index = (s_int * number_chain_steps) // self.T
-                chain_X[write_index] = discrete_sampled_s.X[:1]
-                chain_E[write_index] = discrete_sampled_s.E[:1]
-
-        # Sample
-        sampled_s = sampled_s.mask(node_mask, collapse=True)
-        X, E, y = sampled_s.X, sampled_s.E, sampled_s.y
-
-        molecule_list = []
-        n = num_nodes[0]
-        atom_types = X[0, :n].cpu()
-        edge_types = E[0, :n, :n].cpu()
-        molecule_list.append([atom_types, edge_types])
-        smiles = graph_to_smiles(molecule_list, self.atom_decoder)[0]
-
-        # Visualize Chains
-        if number_chain_steps > 0:
-            final_X_chain = X[:1]
-            final_E_chain = E[:1]
-
-            chain_X[0] = final_X_chain                  # Overwrite last frame with the resulting X, E
-            chain_E[0] = final_E_chain
-
-            chain_X = utils.reverse_tensor(chain_X)
-            chain_E = utils.reverse_tensor(chain_E)
-
-            # Repeat last frame to see final sample better
-            chain_X = torch.cat([chain_X, chain_X[-1:].repeat(10, 1)], dim=0)
-            chain_E = torch.cat([chain_E, chain_E[-1:].repeat(10, 1, 1)], dim=0)
-            mol_img_list = self.mol_visualizer.visualize_chain(chain_X.numpy(), chain_E.numpy())
-        else:
-            mol_img_list = []
-
-        return smiles, mol_img_list
-
-    def check_valid(self, smiles):
-        return check_valid(smiles)
-    
-    def sample_p_zs_given_zt(
-        self, s, t, X_t, E_t, properties, node_mask, guide_scale, device
-    ):
-        """Samples from zs ~ p(zs | zt). Only used during sampling.
-        if last_step, return the graph prediction as well"""
-        bs, n, _ = X_t.shape
-        beta_t = self.noise_schedule(t_normalized=t)  # (bs, 1)
-        alpha_s_bar = self.noise_schedule.get_alpha_bar(t_normalized=s)
-        alpha_t_bar = self.noise_schedule.get_alpha_bar(t_normalized=t)
-
-        # Neural net predictions
-        noisy_data = {
-            "X_t": X_t,
-            "E_t": E_t,
-            "y_t": properties,
-            "t": t,
-            "node_mask": node_mask,
-        }
-
-        def get_prob(noisy_data, unconditioned=False):
-            pred = self._forward(noisy_data, unconditioned=unconditioned)
-
-            # Normalize predictions
-            pred_X = F.softmax(pred.X, dim=-1)  # bs, n, d0
-            pred_E = F.softmax(pred.E, dim=-1)  # bs, n, n, d0
-
-            # Retrieve transitions matrix
-            Qtb = self.transition_model.get_Qt_bar(alpha_t_bar, device)
-            Qsb = self.transition_model.get_Qt_bar(alpha_s_bar, device)
-            Qt = self.transition_model.get_Qt(beta_t, device)
-
-            Xt_all = torch.cat([X_t, E_t.reshape(bs, n, -1)], dim=-1)
-            predX_all = torch.cat([pred_X, pred_E.reshape(bs, n, -1)], dim=-1)
-
-            unnormalized_probX_all = utils.reverse_diffusion(
-                predX_0=predX_all, X_t=Xt_all, Qt=Qt.X, Qsb=Qsb.X, Qtb=Qtb.X
-            )
-
-            unnormalized_prob_X = unnormalized_probX_all[:, :, : self.Xdim_output]
-            unnormalized_prob_E = unnormalized_probX_all[
-                :, :, self.Xdim_output :
-            ].reshape(bs, n * n, -1)
-
-            unnormalized_prob_X[torch.sum(unnormalized_prob_X, dim=-1) == 0] = 1e-5
-            unnormalized_prob_E[torch.sum(unnormalized_prob_E, dim=-1) == 0] = 1e-5
-
-            prob_X = unnormalized_prob_X / torch.sum(
-                unnormalized_prob_X, dim=-1, keepdim=True
-            )  # bs, n, d_t-1
-            prob_E = unnormalized_prob_E / torch.sum(
-                unnormalized_prob_E, dim=-1, keepdim=True
-            )  # bs, n, d_t-1
-            prob_E = prob_E.reshape(bs, n, n, pred_E.shape[-1])
-
-            return prob_X, prob_E
-
-        prob_X, prob_E = get_prob(noisy_data)
-
-        ### Guidance
-        if guide_scale != 1:
-            uncon_prob_X, uncon_prob_E = get_prob(
-                noisy_data, unconditioned=True
-            )
-            prob_X = (
-                uncon_prob_X
-                * (prob_X / uncon_prob_X.clamp_min(1e-5)) ** guide_scale
-            )
-            prob_E = (
-                uncon_prob_E
-                * (prob_E / uncon_prob_E.clamp_min(1e-5)) ** guide_scale
-            )
-            prob_X = prob_X / prob_X.sum(dim=-1, keepdim=True).clamp_min(1e-5)
-            prob_E = prob_E / prob_E.sum(dim=-1, keepdim=True).clamp_min(1e-5)
-
-        # assert ((prob_X.sum(dim=-1) - 1).abs() < 1e-3).all()
-        # assert ((prob_E.sum(dim=-1) - 1).abs() < 1e-3).all()
-
-        sampled_s = utils.sample_discrete_features(
-            prob_X, prob_E, node_mask=node_mask, step=s[0, 0].item()
-        )
-
-        X_s = F.one_hot(sampled_s.X, num_classes=self.Xdim_output).to(self.model_dtype)
-        E_s = F.one_hot(sampled_s.E, num_classes=self.Edim_output).to(self.model_dtype)
-
-        assert (E_s == torch.transpose(E_s, 1, 2)).all()
-        assert (X_t.shape == X_s.shape) and (E_t.shape == E_s.shape)
-
-        out_one_hot = utils.PlaceHolder(X=X_s, E=E_s, y=properties)
-        out_discrete = utils.PlaceHolder(X=X_s, E=E_s, y=properties)
-
-        return out_one_hot.mask(node_mask).type_as(properties), out_discrete.mask(
-            node_mask, collapse=True
-        ).type_as(properties)
-    
-
-#####
-# from graph_decoder.diffusion_model import GraphDiT
 def load_graph_decoder(path='model_labeled'):
     model = GraphDiT(
         model_config_path=f"{path}/config.yaml",
@@ -384,7 +31,6 @@ def load_graph_decoder(path='model_labeled'):
     # model.disable_grads()
     return model
 
-
 ATOM_SYMBOLS = ['C', 'N', 'O', 'H']
 
 def generate_random_smiles(length=10):