Morgan dev

acegen/data/__init__.py

@@ -1,2 +1,2 @@
 from acegen.data.smiles_dataset import load_dataset, MolBloomDataset, SMILESDataset
-from acegen.data.utils import smiles_to_tensordict
+from acegen.data.utils import collate_smiles_to_tensordict, smiles_to_tensordict

acegen/data/utils.py

@@ -67,3 +67,18 @@ def smiles_to_tensordict(
     smiles_tensordict.set(("next", "is_init"), next_is_init)
 
     return smiles_tensordict
+
+
+def collate_smiles_to_tensordict(
+    arr, max_length: int, reward: torch.Tensor = None, device: str = "cpu"
+):
+    """Function to take a list of encoded sequences and turn them into a tensordict."""
+    collated_arr = torch.ones(len(arr), max_length) * -1
+    for i, seq in enumerate(arr):
+        collated_arr[i, : seq.size(0)] = seq
+    data = smiles_to_tensordict(
+        collated_arr, reward=reward, replace_mask_value=0, device=device
+    )
+    data.set("sequence", data.get("observation"))
+    data.set("sequence_mask", data.get("mask"))
+    return data

scripts/augmented_memory/augmem.py

@@ -0,0 +1,373 @@
+#! /usr/bin/python3
+import datetime
+import os
+import random
+from copy import deepcopy
+from pathlib import Path
+
+import hydra
+import numpy as np
+
+import torch
+import tqdm
+import yaml
+from acegen.data import collate_smiles_to_tensordict
+
+from acegen.models import adapt_state_dict, models, register_model
+from acegen.rl_env import generate_complete_smiles, TokenEnv
+from acegen.scoring_functions import (
+    custom_scoring_functions,
+    register_custom_scoring_function,
+    Task,
+)
+from acegen.vocabulary import Vocabulary
+from omegaconf import OmegaConf, open_dict
+from tensordict.utils import isin
+
+from torchrl.data import (
+    LazyTensorStorage,
+    PrioritizedSampler,
+    TensorDictMaxValueWriter,
+    TensorDictReplayBuffer,
+)
+from torchrl.envs import InitTracker, TransformedEnv
+from torchrl.modules.utils import get_primers_from_module
+from torchrl.record.loggers import get_logger
+
+try:
+    import molscore
+    from molscore import MolScoreBenchmark, MolScoreCurriculum
+    from molscore.manager import MolScore
+    from molscore.utils import augment_smiles
+
+    _has_molscore = True
+except ImportError as err:
+    _has_molscore = False
+    MOLSCORE_ERR = err
+
+# hydra outputs saved in /tmp
+os.chdir("/tmp")
+
+
+@hydra.main(
+    config_path=".",
+    config_name="config_denovo",
+    version_base="1.2",
+)
+def main(cfg: "DictConfig"):
+
+    if isinstance(cfg.seed, int):
+        cfg.seed = [cfg.seed]
+
+    for seed in cfg.seed:
+
+        # Set seed
+        random.seed(int(seed))
+        np.random.seed(int(seed))
+        torch.manual_seed(int(seed))
+
+        # Define save_dir and save config
+        current_time = datetime.datetime.now()
+        timestamp_str = current_time.strftime("%Y_%m_%d_%H%M%S")
+        os.chdir(os.path.dirname(__file__))
+        save_dir = (
+            f"{cfg.log_dir}/{cfg.experiment_name}_{cfg.agent_name}_{timestamp_str}"
+        )
+        with open_dict(cfg):
+            cfg.save_dir = save_dir
+        os.makedirs(save_dir, exist_ok=True)
+        with open(Path(save_dir) / "config.yaml", "w") as yaml_file:
+            cfg_dict = OmegaConf.to_container(cfg, resolve=True)
+            yaml.dump(cfg_dict, yaml_file, default_flow_style=False)
+
+        # Define training task and run
+        if cfg.get("molscore_task", None):
+
+            if not _has_molscore:
+                raise RuntimeError(
+                    "MolScore library not found. Unable to create a scoring function. "
+                    "To install MolScore, use: `pip install MolScore`"
+                ) from MOLSCORE_ERR
+
+            if cfg.molscore_mode == "single":
+                task = MolScore(
+                    model_name=cfg.agent_name,
+                    task_config=cfg.molscore_task,
+                    budget=cfg.total_smiles,
+                    replay_size=cfg.replay_buffer_size,
+                    replay_purge=True,
+                    output_dir=os.path.abspath(save_dir),
+                    add_run_dir=True,
+                    **cfg.get("molscore_kwargs", {}),
+                )
+                run_reinvent(cfg, task)
+
+            if cfg.molscore_mode == "benchmark":
+                MSB = MolScoreBenchmark(
+                    model_name=cfg.agent_name,
+                    model_parameters=dict(cfg),
+                    benchmark=cfg.molscore_task,
+                    budget=cfg.total_smiles,
+                    replay_size=cfg.replay_buffer_size,
+                    replay_purge=True,
+                    output_dir=os.path.abspath(save_dir),
+                    add_benchmark_dir=False,
+                    **cfg.get("molscore_kwargs", {}),
+                )
+                for task in MSB:
+                    run_reinvent(cfg, task)
+
+            if cfg.molscore_mode == "curriculum":
+                task = MolScoreCurriculum(
+                    model_name=cfg.agent_name,
+                    model_parameters=dict(cfg),
+                    benchmark=cfg.molscore_task,
+                    budget=cfg.total_smiles,
+                    replay_size=cfg.replay_buffer_size,
+                    replay_purge=True,
+                    output_dir=os.path.abspath(save_dir),
+                    **cfg.get("molscore_kwargs", {}),
+                )
+                run_reinvent(cfg, task)
+
+        elif cfg.get("custom_task", None):
+            if cfg.custom_task not in custom_scoring_functions:
+                register_custom_scoring_function(cfg.custom_task, cfg.custom_task)
+            task = Task(
+                name=cfg.custom_task,
+                scoring_function=custom_scoring_functions[cfg.custom_task],
+                budget=cfg.total_smiles,
+                output_dir=save_dir,
+            )
+            run_reinvent(cfg, task)
+
+        else:
+            raise ValueError("No scoring function specified.")
+
+
+def run_reinvent(cfg, task):
+
+    # Get available device
+    device = (
+        torch.device("cuda:0") if torch.cuda.device_count() > 0 else torch.device("cpu")
+    )
+
+    # If custom model, register it
+    if cfg.model not in models and cfg.get("custom_model_factory", None) is not None:
+        register_model(cfg.model, cfg.model_factory)
+
+    # Check if model is available
+    if cfg.model not in models:
+        raise ValueError(
+            f"Model {cfg.model} not found. For custom models, define a model factory as explain in the tutorials."
+        )
+
+    # Get model
+    (create_actor, _, _, voc_path, ckpt_path, tokenizer) = models[cfg.model]
+
+    # Create vocabulary
+    ####################################################################################################################
+
+    vocabulary = Vocabulary.load(voc_path, tokenizer=tokenizer)
+
+    # Create models
+    ####################################################################################################################
+
+    ckpt = torch.load(ckpt_path, map_location=device, weights_only=True)
+    actor_training, actor_inference = create_actor(vocabulary_size=len(vocabulary))
+    actor_inference.load_state_dict(
+        adapt_state_dict(deepcopy(ckpt), actor_inference.state_dict())
+    )
+    actor_inference = actor_inference.to(device)
+    actor_training = actor_training.to(device)
+
+    prior, _ = create_actor(vocabulary_size=len(vocabulary))
+    prior.load_state_dict(adapt_state_dict(deepcopy(ckpt), prior.state_dict()))
+    prior = prior.to(device)
+
+    # Create RL environment
+    ####################################################################################################################
+
+    env_kwargs = {
+        "start_token": vocabulary.start_token_index,
+        "end_token": vocabulary.end_token_index,
+        "length_vocabulary": len(vocabulary),
+        "max_length": cfg.get("max_length", 100),
+        "batch_size": cfg.num_envs,
+        "device": device,
+    }
+
+    def create_env_fn():
+        """Create a single RL rl_env."""
+        env = TokenEnv(**env_kwargs)
+        env = TransformedEnv(env)
+        env.append_transform(InitTracker())
+        if primers := get_primers_from_module(actor_inference):
+            env.append_transform(primers)
+        return env
+
+    env = create_env_fn()
+
+    # Create optimizer
+    ####################################################################################################################
+
+    optim = torch.optim.Adam(
+        actor_training.parameters(),
+        lr=cfg.lr,
+        eps=cfg.eps,
+        weight_decay=cfg.weight_decay,
+    )
+
+    # Create logger
+    ####################################################################################################################
+
+    logger = None
+    if cfg.logger_backend:
+        experiment_name = f"{cfg.agent_name}"
+        try:
+            experiment_name += f"_{task.cfg.get('task')}"
+        except AttributeError:
+            experiment_name += task.name
+        logger = get_logger(
+            cfg.logger_backend,
+            logger_name=cfg.save_dir,
+            experiment_name=experiment_name,
+            wandb_kwargs={
+                "config": dict(cfg),
+                "project": cfg.experiment_name,
+                "group": cfg.agent_name,
+                "reinit": True,
+            },
+        )
+
+    # Training loop
+    ####################################################################################################################
+
+    total_done = 0
+    sigma = cfg.sigma
+    pbar = tqdm.tqdm(total=cfg.total_smiles)
+
+    while not task.finished:
+
+        # Generate data
+        data = generate_complete_smiles(
+            policy_sample=actor_inference,
+            policy_evaluate=actor_training,
+            vocabulary=vocabulary,
+            scoring_function=task,
+            environment=env,
+            prompt=cfg.get("prompt", None),
+            promptsmiles=cfg.get("promptsmiles", None),
+            promptsmiles_optimize=cfg.get("promptsmiles_optimize", True),
+            promptsmiles_shuffle=cfg.get("promptsmiles_shuffle", True),
+            promptsmiles_multi=cfg.get("promptsmiles_multi", False),
+            promptsmiles_scan=cfg.get("promptsmiles_scan", False),
+            remove_duplicates=True,
+        )
+
+        log_info = {}
+        data_next = data.get("next")
+        done = data_next.get("done").squeeze(-1)
+        total_done += done.sum().item()
+        pbar.update(done.sum().item())
+
+        # Save info about smiles lengths and rewards
+        episode_rewards = data_next["reward"][done]
+        episode_length = (data_next["observation"] != 0.0).float().sum(-1).mean()
+        if len(episode_rewards) > 0:
+            log_info.update(
+                {
+                    "train/total_smiles": total_done,
+                    "train/reward": episode_rewards.mean().item(),
+                    "train/min_reward": episode_rewards.min().item(),
+                    "train/max_reward": episode_rewards.max().item(),
+                    "train/episode_length": episode_length.item(),
+                }
+            )
+
+        data, loss, agent_likelihood = compute_loss(data, actor_training, prior, sigma)
+
+        # Average loss over the batch
+        loss = loss.mean()
+
+        # Add regularizer that penalizes high likelihood for the entire sequence
+        loss_p = -(1 / agent_likelihood).mean()
+        loss += 5 * 1e3 * loss_p
+
+        # Calculate gradients and make an update to the network weights
+        optim.zero_grad()
+        loss.backward()
+        optim.step()
+
+        for _ in range(cfg.augmentation_rounds):
+            # Augment sampled SMILES
+            sampled_smiles = augment_smiles(data.get("SMILES").cpu().data)
+            sampled_reward = data.get(("next", "reward")).squeeze(-1).sum(-1)
+            # Sample replay buffer
+            replay_smiles, replay_reward = task.replay(
+                cfg.replay_batch_size, augment=True
+            )
+            replay_reward = torch.tensor(replay_reward, device=device).float()
+            # Concatenate and create tensor
+            aug_tokens = [
+                torch.tensor(vocabulary.encode(smi))
+                for smi in sampled_smiles + replay_smiles
+            ]
+            aug_reward = torch.cat([sampled_reward, replay_reward], dim=0)
+            aug_data = collate_smiles_to_tensordict(
+                arr=aug_tokens,
+                max_length=env.max_length,
+                reward=aug_reward,
+                device=device,
+            )
+            # Compute loss
+            aug_data, loss, agent_likelihood = compute_loss(
+                aug_data, actor_training, prior, sigma
+            )
+            # Average loss over the batch
+            loss = loss.mean()
+            # Add regularizer that penalizes high likelihood for the entire sequence
+            loss_p = -(1 / agent_likelihood).mean()
+            loss += 5 * 1e3 * loss_p
+            # Calculate gradients and make an update to the network weights
+            optim.zero_grad()
+            loss.backward()
+            optim.step()
+
+        # Log info
+        if logger:
+            for key, value in log_info.items():
+                logger.log_scalar(key, value, step=total_done)
+
+
+def get_log_prob(data, model):
+    actions = data.get("action")
+    model_in = data.select(*model.in_keys, strict=False)
+    log_prob = model.get_dist(model_in).log_prob(actions)
+    return log_prob
+
+
+def compute_loss(data, model, prior, sigma):
+
+    mask = data.get("mask").squeeze(-1)
+
+    if "prior_log_prob" not in data.keys():
+        with torch.no_grad():
+            prior_log_prob = get_log_prob(data, prior)
+            data.set("prior_log_prob", prior_log_prob)
+    else:
+        prior_log_prob = data.get("prior_log_prob")
+
+    agent_log_prob = get_log_prob(data, model)
+    agent_likelihood = (agent_log_prob * mask).sum(-1)
+    prior_likelihood = (prior_log_prob * mask).sum(-1)
+    score = data.get(("next", "reward")).squeeze(-1).sum(-1)
+
+    augmented_likelihood = prior_likelihood + sigma * score
+    loss = torch.pow((augmented_likelihood - agent_likelihood), 2)
+
+    return data, loss, agent_likelihood
+
+
+if __name__ == "__main__":
+    main()