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add sample phase and try to get log prob

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mhz
2024-09-08 23:26:49 +02:00
parent 0c4b597dd2
commit 5dccf590e7
2 changed files with 76 additions and 26 deletions
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31
graph_dit/diffusion_model.py
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@@ -286,7 +286,7 @@ class Graph_DiT(pl.LightningModule):
samples.extend(self.sample_batch(batch_id=ident, batch_size=to_generate, y=batch_y, samples.extend(self.sample_batch(batch_id=ident, batch_size=to_generate, y=batch_y,
save_final=to_save, save_final=to_save,
keep_chain=chains_save, keep_chain=chains_save,
number_chain_steps=self.number_chain_steps)) number_chain_steps=self.number_chain_steps)[0])
ident += to_generate ident += to_generate
start_index += to_generate start_index += to_generate
@@ -360,7 +360,7 @@ class Graph_DiT(pl.LightningModule):
batch_y = torch.ones(to_generate, self.ydim_output, device=self.device) batch_y = torch.ones(to_generate, self.ydim_output, device=self.device)
cur_sample = self.sample_batch(batch_id, to_generate, batch_y, save_final=to_save, cur_sample = self.sample_batch(batch_id, to_generate, batch_y, save_final=to_save,
keep_chain=chains_save, number_chain_steps=self.number_chain_steps) keep_chain=chains_save, number_chain_steps=self.number_chain_steps)[0]
samples = samples + cur_sample samples = samples + cur_sample
all_ys.append(batch_y) all_ys.append(batch_y)
@@ -601,6 +601,8 @@ class Graph_DiT(pl.LightningModule):
assert (E == torch.transpose(E, 1, 2)).all() assert (E == torch.transpose(E, 1, 2)).all()
total_log_probs = torch.zeros(batch_size, device=self.device)
# Iteratively sample p(z_s | z_t) for t = 1, ..., T, with s = t - 1. # Iteratively sample p(z_s | z_t) for t = 1, ..., T, with s = t - 1.
for s_int in reversed(range(0, self.T)): for s_int in reversed(range(0, self.T)):
s_array = s_int * torch.ones((batch_size, 1)).type_as(y) s_array = s_int * torch.ones((batch_size, 1)).type_as(y)
@@ -609,21 +611,22 @@ class Graph_DiT(pl.LightningModule):
t_norm = t_array / self.T t_norm = t_array / self.T
# Sample z_s # Sample z_s
sampled_s, discrete_sampled_s = self.sample_p_zs_given_zt(s_norm, t_norm, X, E, y, node_mask) sampled_s, discrete_sampled_s, log_probs= self.sample_p_zs_given_zt(s_norm, t_norm, X, E, y, node_mask)
X, E, y = sampled_s.X, sampled_s.E, sampled_s.y X, E, y = sampled_s.X, sampled_s.E, sampled_s.y
total_log_probs += log_probs
# Sample # Sample
sampled_s = sampled_s.mask(node_mask, collapse=True) sampled_s = sampled_s.mask(node_mask, collapse=True)
X, E, y = sampled_s.X, sampled_s.E, sampled_s.y X, E, y = sampled_s.X, sampled_s.E, sampled_s.y
molecule_list = [] graph_list = []
for i in range(batch_size): for i in range(batch_size):
n = n_nodes[i] n = n_nodes[i]
atom_types = X[i, :n].cpu() node_types = X[i, :n].cpu()
edge_types = E[i, :n, :n].cpu() edge_types = E[i, :n, :n].cpu()
molecule_list.append([atom_types, edge_types]) graph_list.append([node_types, edge_types])
return molecule_list return graph_list, total_log_probs
def sample_p_zs_given_zt(self, s, t, X_t, E_t, y_t, node_mask): def sample_p_zs_given_zt(self, s, t, X_t, E_t, y_t, node_mask):
"""Samples from zs ~ p(zs | zt). Only used during sampling. """Samples from zs ~ p(zs | zt). Only used during sampling.
@@ -635,6 +638,7 @@ class Graph_DiT(pl.LightningModule):
# Neural net predictions # Neural net predictions
noisy_data = {'X_t': X_t, 'E_t': E_t, 'y_t': y_t, 't': t, 'node_mask': node_mask} noisy_data = {'X_t': X_t, 'E_t': E_t, 'y_t': y_t, 't': t, 'node_mask': node_mask}
print(f"sample p zs given zt X_t shape: {X_t.shape}, E_t shape: {E_t.shape}, y_t shape: {y_t.shape}, node_mask shape: {node_mask.shape}")
def get_prob(noisy_data, unconditioned=False): def get_prob(noisy_data, unconditioned=False):
pred = self.forward(noisy_data, unconditioned=unconditioned) pred = self.forward(noisy_data, unconditioned=unconditioned)
@@ -674,6 +678,17 @@ class Graph_DiT(pl.LightningModule):
# with condition = P_t(G_{t-1} |G_t, C) # with condition = P_t(G_{t-1} |G_t, C)
# with condition = P_t(A_{t-1} |A_t, y) # with condition = P_t(A_{t-1} |A_t, y)
prob_X, prob_E, pred = get_prob(noisy_data) prob_X, prob_E, pred = get_prob(noisy_data)
print(f'prob_X shape: {prob_X.shape}, prob_E shape: {prob_E.shape}')
print(f'X_t shape: {X_t.shape}, E_t shape: {E_t.shape}, y_t shape: {y_t.shape}')
print(f'X_t: {X_t}')
log_prob_X = torch.log(torch.gather(prob_X, -1, X_t.long()).squeeze(-1)) # bs, n
log_prob_E = torch.log(torch.gather(prob_E, -1, E_t.long()).squeeze(-1)) # bs, n, n
# Sum the log_prob across dimensions for total log_prob
log_prob_X = log_prob_X.sum(dim=-1)
log_prob_E = log_prob_E.sum(dim=(1, 2))
print(f'log_prob_X shape: {log_prob_X.shape}, log_prob_E shape: {log_prob_E.shape}')
log_probs = log_prob_E + log_prob_X
### Guidance ### Guidance
if self.guidance_target is not None and self.guide_scale is not None and self.guide_scale != 1: if self.guidance_target is not None and self.guide_scale is not None and self.guide_scale != 1:
@@ -810,4 +825,4 @@ class Graph_DiT(pl.LightningModule):
out_one_hot = utils.PlaceHolder(X=X_s, E=E_s, y=y_t) out_one_hot = utils.PlaceHolder(X=X_s, E=E_s, y=y_t)
out_discrete = utils.PlaceHolder(X=X_s, E=E_s, y=y_t) out_discrete = utils.PlaceHolder(X=X_s, E=E_s, y=y_t)
return out_one_hot.mask(node_mask).type_as(y_t), out_discrete.mask(node_mask, collapse=True).type_as(y_t) return out_one_hot.mask(node_mask).type_as(y_t), out_discrete.mask(node_mask, collapse=True).type_as(y_t), log_probs

71
graph_dit/main.py
View File

@@ -1,5 +1,5 @@
# These imports are tricky because they use c++, do not move them # These imports are tricky because they use c++, do not move them
import tqdm from tqdm import tqdm
import os, shutil import os, shutil
import warnings import warnings
@@ -233,27 +233,62 @@ def test(cfg: DictConfig):
optimizer.zero_grad() optimizer.zero_grad()
# return {'loss': loss} # return {'loss': loss}
# start testing
print("start testing")
graph_dit_model.eval()
test_dataloader = accelerator.prepare(datamodule.test_dataloader())
for data in test_dataloader:
data_x = F.one_hot(data.x, num_classes=12).float()[:, graph_dit_model.active_index]
data_edge_attr = F.one_hot(data.edge_attr, num_classes=2).float()
dense_data, node_mask = utils.to_dense(data_x, data.edge_index, data_edge_attr, data.batch, graph_dit_model.max_n_nodes)
dense_data = dense_data.mask(node_mask)
noisy_data = graph_dit_model.apply_noise(dense_data.X, dense_data.E, data.y, node_mask)
pred = graph_dit_model.forward(noisy_data)
nll = graph_dit_model.compute_val_loss(pred, noisy_data, dense_data.X, dense_data.E, data.y, node_mask, test=True)
graph_dit_model.test_y_collection.append(data.y)
print(f'test loss: {nll}')
# start sampling # start sampling
samples = [] samples_left_to_generate = cfg.general.final_model_samples_to_generate
samples_left_to_save = cfg.general.final_model_samples_to_save
chains_left_to_save = cfg.general.final_model_chains_to_save
for i in tqdm( samples, all_ys, batch_id = [], [], 0
range(cfg.general.n_samples), desc="Sampling", disable=not cfg.general.enable_progress_bar test_y_collection = torch.cat(graph_dit_model.test_y_collection, dim=0)
): num_examples = test_y_collection.size(0)
batch_size = cfg.train.batch_size if cfg.general.final_model_samples_to_generate > num_examples:
num_steps = cfg.model.diffusion_steps ratio = cfg.general.final_model_samples_to_generate // num_examples
y = torch.ones(batch_size, num_steps, 1, 1, device=accelerator.device, dtype=inference_dtype) test_y_collection = test_y_collection.repeat(ratio+1, 1)
num_examples = test_y_collection.size(0)
# sample from the model while samples_left_to_generate > 0:
samples_batch = graph_dit_model.sample_batch( print(f'samples left to generate: {samples_left_to_generate}/'
batch_id=i, f'{cfg.general.final_model_samples_to_generate}', end='', flush=True)
batch_size=batch_size, bs = 1 * cfg.train.batch_size
y=y, to_generate = min(samples_left_to_generate, bs)
keep_chain=1, to_save = min(samples_left_to_save, bs)
number_chain_steps=num_steps, chains_save = min(chains_left_to_save, bs)
save_final=batch_size # batch_y = test_y_collection[batch_id : batch_id + to_generate]
) batch_y = torch.ones(to_generate, graph_dit_model.ydim_output, device=graph_dit_model.device)
samples.append(samples_batch)
cur_sample = graph_dit_model.sample_batch(batch_id, to_generate, batch_y, save_final=to_save,
keep_chain=chains_save, number_chain_steps=graph_dit_model.number_chain_steps)[0]
samples = samples + cur_sample
all_ys.append(batch_y)
batch_id += to_generate
samples_left_to_save -= to_save
samples_left_to_generate -= to_generate
chains_left_to_save -= chains_save
print(f"final Computing sampling metrics...")
graph_dit_model.sampling_metrics.reset()
graph_dit_model.sampling_metrics(samples, all_ys, graph_dit_model.name, graph_dit_model.current_epoch, graph_dit_model.val_counter, test=True)
graph_dit_model.sampling_metrics.reset()
print(f"Done.")
# save samples # save samples
print("Samples:") print("Samples:")