diff --git a/configs/data/mnist.yaml b/configs/data/mnist.yaml deleted file mode 100644 index 51bfaff0..00000000 --- a/configs/data/mnist.yaml +++ /dev/null @@ -1,6 +0,0 @@ -_target_: src.data.mnist_datamodule.MNISTDataModule -data_dir: ${paths.data_dir} -batch_size: 128 # Needs to be divisible by the number of devices (e.g., if in a distributed setup) -train_val_test_split: [55_000, 5_000, 10_000] -num_workers: 0 -pin_memory: False diff --git a/configs/data/molbind.yaml b/configs/data/molbind.yaml new file mode 100644 index 00000000..c507dc3a --- /dev/null +++ b/configs/data/molbind.yaml @@ -0,0 +1,10 @@ +_target_: molbind.data.dataloaders.load_combined_loader +central_modality: "smiles" +modalities: + - "selfies" +train_frac : 0.8 +val_frac : 0.2 +seed: 42 +fraction_data: 1.0 +dataset_path: "subset.csv" +batch_size: 64 \ No newline at end of file diff --git a/configs/logger/wandb.yaml b/configs/logger/wandb.yaml index ece16588..2af3344f 100644 --- a/configs/logger/wandb.yaml +++ b/configs/logger/wandb.yaml @@ -2,15 +2,6 @@ wandb: _target_: lightning.pytorch.loggers.wandb.WandbLogger - # name: "" # name of the run (normally generated by wandb) - save_dir: "${paths.output_dir}" offline: False - id: null # pass correct id to resume experiment! - anonymous: null # enable anonymous logging - project: "lightning-hydra-template" - log_model: False # upload lightning ckpts - prefix: "" # a string to put at the beginning of metric keys - # entity: "" # set to name of your wandb team - group: "" - tags: [] - job_type: "" + project: "molbind" + entity: "adrianmirza" diff --git a/configs/model/mnist.yaml b/configs/model/mnist.yaml deleted file mode 100644 index 6f9c2fa1..00000000 --- a/configs/model/mnist.yaml +++ /dev/null @@ -1,25 +0,0 @@ -_target_: src.models.mnist_module.MNISTLitModule - -optimizer: - _target_: torch.optim.Adam - _partial_: true - lr: 0.001 - weight_decay: 0.0 - -scheduler: - _target_: torch.optim.lr_scheduler.ReduceLROnPlateau - _partial_: true - mode: min - factor: 0.1 - patience: 10 - -net: - _target_: src.models.components.simple_dense_net.SimpleDenseNet - input_size: 784 - lin1_size: 64 - lin2_size: 128 - lin3_size: 64 - output_size: 10 - -# compile model for faster training with pytorch 2.0 -compile: false diff --git a/configs/paths/default.yaml b/configs/paths/default.yaml index ec81db2d..7855a3d9 100644 --- a/configs/paths/default.yaml +++ b/configs/paths/default.yaml @@ -15,4 +15,4 @@ log_dir: ${paths.root_dir}/logs/ output_dir: ${hydra:runtime.output_dir} # path to working directory -work_dir: ${hydra:runtime.cwd} +work_dir: ${hydra:runtime.cwd} \ No newline at end of file diff --git a/configs/train.yaml b/configs/train.yaml index ef7bdab6..f71d7cc7 100644 --- a/configs/train.yaml +++ b/configs/train.yaml @@ -4,14 +4,15 @@ # order of defaults determines the order in which configs override each other defaults: - _self_ - - data: mnist - - model: mnist - - callbacks: default - - logger: null # set logger here or use command line (e.g. `python train.py logger=tensorboard`) - - trainer: default - - paths: default - - extras: default - - hydra: default + - data: molbind + - model: molbind + - logger: wandb + # - callbacks: default + # - logger: null # set logger here or use command line (e.g. `python train.py logger=tensorboard`) + # - trainer: default + # - paths: default + # - extras: default + # - hydra: default # experiment configs allow for version control of specific hyperparameters # e.g. best hyperparameters for given model and datamodule @@ -46,4 +47,4 @@ test: True ckpt_path: null # seed for random number generators in pytorch, numpy and python.random -seed: null +seed: 42 diff --git a/environment.yaml b/environment.yaml index f74ee8c7..5d69835f 100644 --- a/environment.yaml +++ b/environment.yaml @@ -5,7 +5,7 @@ # - conda allows for installing packages without requiring certain compilers or # libraries to be available in the system, since it installs precompiled binaries -name: myenv 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"selfies": {"dims": [256, 128], "activation": "leakyrelu", "batch_norm": False}, + "smiles": {"dims": [256, 128], "activation": "leakyrelu", "batch_norm": False}, + }, + "encoders": { + "smiles": {"pretrained": True, "freeze_encoder": False}, + "selfies": {"pretrained": True, "freeze_encoder": False}, + }, + "optimizer": {"lr": 1e-4, "weight_decay": 1e-4}, + }, + "loss": {"temperature": 0.1}, + "data": { + "central_modality": "smiles", + "modalities": ["selfies"], + "dataset_path": "subset.csv", + "train_frac": 0.8, + "valid_frac": 0.2, + "seed": 42, + "fraction_data": 1, + "batch_size": 64, + }, + } + + config = DictConfig(config) + train_molbind(config) diff --git a/pyproject.toml b/pyproject.toml index 1e02601d..22ad907b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,7 +25,7 @@ classifiers = [ "Operating System :: MacOS", ] requires-python = ">=3.9, <3.13" -dependencies = ["numpy"] +dependencies = ["numpy", "transformers", "pandas", "polars"] [project.optional-dependencies] dev = ["codecov-cli>=0.4.1", "pytest>=7.4.0", "pytest-cov>=3.0.0", "ruff>=0.0.285"] diff --git a/requirements.txt b/requirements.txt index d837268c..981451a8 100644 --- a/requirements.txt +++ b/requirements.txt @@ -3,6 +3,7 @@ torch>=2.0.0 torchvision>=0.15.0 lightning>=2.0.0 torchmetrics>=0.11.4 +info-nce-pytorch # --------- hydra --------- # hydra-core==1.3.2 @@ -10,7 +11,7 @@ hydra-colorlog==1.2.0 hydra-optuna-sweeper==1.2.0 # --------- loggers --------- # -# wandb +wandb # neptune-client # mlflow # comet-ml @@ -21,4 +22,4 @@ rootutils # standardizing the project root setup pre-commit # hooks for applying linters on commit rich # beautiful text formatting in terminal pytest # tests -# sh # for running bash commands in some tests (linux/macos only) +# sh # for running bash commands in some tests (linux/macos only) \ No newline at end of file diff --git a/setup.py b/setup.py deleted file mode 100644 index f1826cc5..00000000 --- a/setup.py +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env python - -from setuptools import find_packages, setup - -setup( - name="src", - version="0.0.1", - description="Describe Your Cool Project", - author="", - author_email="", - url="https://github.com/user/project", - install_requires=["lightning", "hydra-core"], - packages=find_packages(), - # use this to customize global commands available in the terminal after installing the package - entry_points={ - "console_scripts": [ - "train_command = src.train:main", - "eval_command = src.eval:main", - ] - }, -) diff --git a/src/molbind/data/components/tokenizers.py b/src/molbind/data/components/tokenizers.py new file mode 100644 index 00000000..092c35f8 --- /dev/null +++ b/src/molbind/data/components/tokenizers.py @@ -0,0 +1,4 @@ +from transformers import AutoTokenizer + +SMILES_TOKENIZER = AutoTokenizer.from_pretrained("seyonec/ChemBERTa-zinc-base-v1") +SELFIES_TOKENIZER = AutoTokenizer.from_pretrained("HUBioDataLab/SELFormer") \ No newline at end of file diff --git a/src/molbind/data/dataloaders.py b/src/molbind/data/dataloaders.py index 58b749c5..de2bbd13 100644 --- a/src/molbind/data/dataloaders.py +++ b/src/molbind/data/dataloaders.py @@ -1,63 +1,113 @@ -from torch.utils.data import DataLoader -from pytorch_lightning import LightningDataModule +from torch.utils.data import DataLoader, Dataset from lightning.pytorch.utilities.combined_loader import CombinedLoader from molbind.data.components.tokenizers import SMILES_TOKENIZER, SELFIES_TOKENIZER -import networkx as nx from networkx import Graph -from typing import List, Dict +from typing import Tuple +from torch import Tensor MODALITY_DATA_TYPES = { - "smiles" : str, - "selfies" : str, - "graph" : Graph, - "nmr" : str, - "ir" : str + "smiles": str, + "selfies": str, + "graph": Graph, + "nmr": str, + "ir": str, } +STRING_TOKENIZERS = { + "smiles": SMILES_TOKENIZER, + "selfies": SELFIES_TOKENIZER, + "iupac_name": "iupac_name_tokenizer", +} + + +class StringDataset(Dataset): + def __init__( + self, dataset: Tuple[Tensor, Tensor], modality: str, context_length=256 + ): + """_summary_ -class StringDataLoader(DataLoader): - def __init__(self, dataset, batch_size, shuffle, num_workers, modality="smiles"): - super(StringDataLoader, self).__init__(dataset, batch_size=batch_size, shuffle=shuffle, num_workers=num_workers) + Args: + dataset (Tuple[Tensor, Tensor]): pair of SMILES and data for the modality (smiles always index 0, modality index 1) + modality (str): name of data modality as found in MODALITY_DATA_TYPES + context_length (int, optional): _description_. Defaults to 256. + """ + assert len(dataset) == 2 + assert len(dataset[0]) == len(dataset[1]) self.modality = modality + self.tokenized_smiles = STRING_TOKENIZERS["smiles"]( + dataset[0], + padding="max_length", + truncation=True, + return_tensors="pt", + max_length=context_length, + ) + self.tokenized_string = STRING_TOKENIZERS[modality]( + dataset[1], + padding="max_length", + truncation=True, + return_tensors="pt", + max_length=context_length, + ) + def __len__(self): - return len(self.dataset) - - def __iter__(self): - for batch in super(StringDataLoader, self).__iter__(): - - if self.modality == "smiles": - tokenized_batch = SMILES_TOKENIZER(batch, padding="max_length", truncation=True, return_tensors="pt") - elif self.modality == "selfies": - tokenized_batch = SELFIES_TOKENIZER(batch, padding="max_length", truncation=True, return_tensors="pt") - yield tokenized_batch["input_ids"], tokenized_batch["attention_mask"] - - -def load_combined_loader(data_modalities : Dict, batch_size : int, shuffle : bool, num_workers : int) -> CombinedLoader: + return len(self.tokenized_smiles.input_ids) + + def __getitem__(self, idx): + return { + "smiles": ( + self.tokenized_smiles.input_ids[idx], + self.tokenized_smiles.attention_mask[idx], + ), + self.modality: ( + self.tokenized_string.input_ids[idx], + self.tokenized_string.attention_mask[idx], + ), + } + + +class GraphDataset(Dataset): + pass + + +def load_combined_loader( + data_modalities: dict, + batch_size: int, + shuffle: bool, + num_workers: int, + drop_last: bool = True, +) -> CombinedLoader: + """Combine multiple dataloaders for different modalities into a single dataloader. + + Args: + data_modalities (dict): data inputs for each modality as pairs of (SMILES, modality) + batch_size (int): batch size for the dataloader + shuffle (bool): shuffle the dataset + num_workers (int): number of workers for the dataloader + drop_last (bool, optional): whether to drop the last batch; defaults to True. + + Returns: + CombinedLoader: a combined dataloader for all the modalities + """ loaders = {} - - for modality in data_modalities.keys(): - # import pdb; pdb.set_trace() + + for modality in [*data_modalities]: if MODALITY_DATA_TYPES[modality] == str: - loaders[modality] = StringDataLoader(data_modalities[modality], batch_size, shuffle, num_workers, modality) + dataset_instance = StringDataset(data_modalities[modality], modality) + loaders[modality] = DataLoader( + dataset_instance, + batch_size=batch_size, + shuffle=shuffle, + num_workers=num_workers, + drop_last=drop_last, + ) elif MODALITY_DATA_TYPES[modality] == Graph: - loaders[modality] = DataLoader(data_modalities[modality], batch_size=batch_size, shuffle=shuffle, num_workers=num_workers) - return CombinedLoader(loaders, "min_size") - - -smiles = ["CCO", "CCN", "CCO", "CCN"] -selfies = ["[C][C][O]", "[C][C][N]", "[C][C][O]", "[C][C][N]"] -dummy_graphs = ["dummy_graph", "dummy_graph", "dummy_graph", "dummy_graph"] - -combined_loader = load_combined_loader( - data_modalities = { - "smiles" : smiles, - "selfies" : selfies, - "graph" : dummy_graphs - }, - batch_size=2, - shuffle=True, - num_workers=1) - -for batch, batch_idx, dataloader_idx in combined_loader: - print(f"{batch}, {batch_idx=}, {dataloader_idx=}") \ No newline at end of file + graph_dataset_instance = GraphDataset(data_modalities[modality]) + loaders[modality] = DataLoader( + graph_dataset_instance, + batch_size=batch_size, + shuffle=shuffle, + num_workers=num_workers, + drop_last=drop_last, + ) + return CombinedLoader(loaders, mode="sequential") diff --git a/src/molbind/models/components/base_encoder.py b/src/molbind/models/components/base_encoder.py index 891f27ed..a1770e16 100644 --- a/src/molbind/models/components/base_encoder.py +++ b/src/molbind/models/components/base_encoder.py @@ -1,22 +1,56 @@ -from typing import Dict, Literal +from typing import Tuple from transformers import AutoModelForCausalLM import torch.nn as nn - - +from torch import Tensor + + +def xavier_init(model: nn.Module): + for param in model.parameters(): + if len(param.shape) > 1: + nn.init.xavier_uniform_(param) + return model + + class BaseModalityEncoder(nn.Module): - def __init__(self, - projection_head_type : Literal["linear", "non-linear"] = "non-linear", - pretrained=True, - **kwargs): - self.pretrained = pretrained - self.encoder = self.build_encoder() - - - def build_encoder(self): - pass - - def forward(self, x): - x = self.encoder(x) - x = self.projection_head(x) - # pooling - return x \ No newline at end of file + def __init__( + self, + model_name: str, + freeze_encoder: bool = False, + pretrained: bool = True, + **kwargs, + ): + super(BaseModalityEncoder, self).__init__() + self.model_name = model_name + self.freeze_encoder = freeze_encoder + self.pretrained = pretrained + self.encoder = None + self._initialize_encoder() + + def _initialize_encoder(self): + if self.pretrained: + self.encoder = AutoModelForCausalLM.from_pretrained(self.model_name) + if self.freeze_encoder: + for param in self.encoder.parameters(): + param.requires_grad = False + else: + self.encoder = AutoModelForCausalLM.from_pretrained(self.model_name) + self.encoder = xavier_init(self.encoder) + + def forward(self, x: Tuple[Tensor, Tensor]) -> Tensor: + token_ids, attention_mask = x + output = self.encoder( + input_ids=token_ids, + attention_mask=attention_mask, + output_hidden_states=True, + ) + last_hidden_state = output.hidden_states[-1] + + return self._non_pad_token_embed_averaging(last_hidden_state, attention_mask) + + def _non_pad_token_embed_averaging( + self, last_hidden_state: Tensor, attention_mask: Tensor + ) -> Tensor: + attention_mask = attention_mask.float().unsqueeze(-1) + sum_ = (last_hidden_state * attention_mask).sum(dim=1) + norm = attention_mask.squeeze(-1).sum(dim=1).unsqueeze(1) + return sum_ / norm diff --git a/src/molbind/models/components/custom_encoders.py b/src/molbind/models/components/custom_encoders.py index 030a9753..c81cbaa1 100644 --- a/src/molbind/models/components/custom_encoders.py +++ b/src/molbind/models/components/custom_encoders.py @@ -1,44 +1,29 @@ -import torch.nn as nn -from typing import Dict, Literal -from molbind.models.components.head import ProjectionHead from molbind.models.components.base_encoder import BaseModalityEncoder -from transformers import AutoModelForCausalLM class SmilesEncoder(BaseModalityEncoder): - def __init__(self, - projection_head_type=Literal["linear", "non-linear"], - pretrained=True, - **kwargs): - super().__init__(projection_head_type, pretrained, **kwargs) - self.encoder = self.build_encoder() - - def build_encoder(self): - return AutoModelForCausalLM.from_pretrained("seyonec/ChemBERTa-zinc-base-v1") - - def forward(self, x): - x = self.encoder(x) - return x - - + def __init__(self, freeze_encoder: bool = False, pretrained: bool = True, **kwargs): + super().__init__( + "seyonec/ChemBERTa-zinc-base-v1", freeze_encoder, pretrained, **kwargs + ) + + class SelfiesEncoder(BaseModalityEncoder): - def __init__(self, - freeze_encoder: bool = False, - pretrained=True, - **kwargs): - super().__init__(projection_head_type, pretrained, **kwargs) - self.encoder = self.build_encoder() - - def build_encoder(self): - if self.pretrained: - return AutoModelForCausalLM.from_pretrained("seyonec/ChemBERTa-zinc-base-v1") - else: - return AutoModelForCausalLM.from_config(self.config) - - def forward(self, x): - x = self.encoder(x) - # pool embeddings - - x = self.projection_head(x) - # pooling - return x \ No newline at end of file + def __init__(self, freeze_encoder: bool = False, pretrained: bool = True, **kwargs): + super().__init__("HUBioDataLab/SELFormer", freeze_encoder, pretrained, **kwargs) + + +class IUPACNameEncoder(BaseModalityEncoder): + pass + + +class IREncoder(BaseModalityEncoder): + pass + + +class GraphEncoder(BaseModalityEncoder): + pass + + +class NMREncoder(BaseModalityEncoder): + pass diff --git a/src/molbind/models/components/head.py b/src/molbind/models/components/head.py index 1ffee63b..fcfb49d1 100644 --- a/src/molbind/models/components/head.py +++ b/src/molbind/models/components/head.py @@ -1,38 +1,51 @@ from torch import nn from typing import Union, List +from class_resolver import ClassResolver + +ACTIVATION_RESOLVER = ClassResolver( + [nn.ReLU, nn.LeakyReLU, nn.Sigmoid, nn.Tanh], base=nn.Module, default=nn.ReLU +) class ProjectionHead(nn.Module): - def __init__(self, dims, activation : Union[str, List[str]] = "leakyrelu"): + def __init__( + self, + dims, + activation: Union[str, List[str]] = "leakyrelu", + batch_norm: bool = False, + ): super(ProjectionHead, self).__init__() # build projection head - self.projection_head = self.build_projection_head(dims, activation) + self.projection_head = self._build_projection_head(dims, activation, batch_norm) - - def build_projection_head(self, dims, activation): + def _build_projection_head( + self, + dims: List[int], + activation: Union[str, List[str]], + batch_norm: bool = False, + ) -> nn.Sequential: # Build projection head dynamically based on the length of dims layers = [] for i in range(len(dims) - 1): layers.append(nn.Linear(dims[i], dims[i + 1])) - layers.append(nn.BatchNorm1d(dims[i + 1])) # Optional: add batch normalization - layers.append(self._get_activation(activation)) # Apply activation function - - self.projection = nn.Sequential(*layers) + # Optional: add batch normalization + if batch_norm: + layers.append(nn.BatchNorm1d(dims[i + 1])) + # Apply activation function + layers.append(self._get_activation(activation)) + + return nn.Sequential(*layers) + + def _get_activation(self, activation: Union[str, List[str]]): + if isinstance(activation, str): + return ACTIVATION_RESOLVER.make(activation) + elif isinstance(activation, list): + # In case you want multiple activation functions in sequence + return nn.Sequential(*[self._get_activation(act) for act in activation]) + else: + raise ValueError( + "Activation should be either a string or a list of strings." + ) - def _get_activation(self, activation): - if isinstance(activation, str): - if activation.lower() == 'relu': - return nn.ReLU(inplace=True) - elif activation.lower() == 'leakyrelu': - return nn.LeakyReLU(inplace=True) - elif activation.lower() == 'sigmoid': - return nn.Sigmoid() - elif activation.lower() == 'tanh': - return nn.Tanh() - else: - raise NotImplementedError(f"Activation {activation} is not implemented.") - elif isinstance(activation, list): - # In case you want multiple activation functions in sequence - return nn.Sequential(*[self._get_activation(act) for act in activation]) - else: - raise ValueError("Activation should be either a string or a list of strings.") \ No newline at end of file + def forward(self, x): + return self.projection_head(x) diff --git a/src/molbind/models/lightning_module.py b/src/molbind/models/lightning_module.py index 35283f40..b2d6a8c3 100644 --- a/src/molbind/models/lightning_module.py +++ b/src/molbind/models/lightning_module.py @@ -2,43 +2,119 @@ from pytorch_lightning import LightningModule from molbind.models.model import MolBind import torch -from torch.nn.functional import cosine_similarity +import pytorch_lightning as L +from molbind.data.dataloaders import load_combined_loader +from typing import Dict +import polars as pl class MolBindModule(LightningModule): - def __init__(self, cfg) - + def __init__(self, cfg): super().__init__() self.model = MolBind(cfg=cfg) self.config = cfg - + self.loss = InfoNCE(temperature=cfg.loss.temperature, negative_mode="unpaired") + def forward(self, input): - embedding_dict = self.model(input) - return embedding_dict + return self.model(input) + + def _info_nce_loss(self, z1, z2): + return self.loss(z1, z2) - def _info_nce_loss(self, z1, z2, temperature, prefix): - loss = InfoNCE(temperature=temperature, negative_mode="unpaired") - loss = loss(z1, z2) - print(f"{prefix}_loss", loss) + def _multimodal_loss(self, embeddings_dict, prefix): + modality_pair = [*embeddings_dict.keys()] + loss = self._info_nce_loss( + embeddings_dict[modality_pair[0]], embeddings_dict[modality_pair[1]] + ) self.log(f"{prefix}_loss", loss) - self.log(f"{prefix}_cosine_similarity", cosine_similarity(z1, z2, dim=1).mean()) - return loss - - def _multimodal_loss(embeddings_dict): - loss = 0 - for modality_embedding in embeddings_dict.keys(): - # loss as sum of pairs of embeddings (smiles-modality_1, smiles-modality_2) - if modality_embedding != "smiles": - loss += self._info_nce_loss(embeddings_dict["smiles"], embeddings_dict[modality_embedding], temperature=0.1, prefix=modality_embedding) return loss - + def training_step(self, input): embeddings_dict = self.forward(input) - return self._multimodal_loss(embeddings_dict) - + return self._multimodal_loss(embeddings_dict, "train") + def validation_step(self, input): embeddings_dict = self.forward(input) - return self._multimodal_loss(embeddings_dict) - + return self._multimodal_loss(embeddings_dict, "val") + def configure_optimizers(self): - return torch.optim.AdamW(self.parameters(), lr=self.config.optimizer.lr, weight_decay=self.config.optimizer.weight_decay) \ No newline at end of file + return torch.optim.AdamW( + self.model.parameters(), + lr=self.config.model.optimizer.lr, + weight_decay=self.config.model.optimizer.weight_decay, + ) + + +# def train_molbind(config: Dict = None): +# wandb_logger = L.loggers.WandbLogger( +# project=config.wandb.project_name, entity=config.wandb.entity +# ) + +# device_count = torch.cuda.device_count() +# trainer = L.Trainer( +# max_epochs=100, +# accelerator="cuda", +# log_every_n_steps=10, +# logger=wandb_logger, +# devices=device_count if device_count > 1 else "auto", +# strategy="ddp" if device_count > 1 else "auto", +# ) + +# train_modality_data = {} +# valid_modality_data = {} + +# data = pl.read_csv(config.data.dataset_path) +# shuffled_data = data.sample( +# fraction=config.data.fraction_data, shuffle=True, seed=config.data.seed +# ) +# dataset_length = len(shuffled_data) +# valid_shuffled_data = shuffled_data.tail( +# int(config.data.valid_frac * dataset_length) +# ) +# train_shuffled_data = shuffled_data.head( +# int(config.data.train_frac * dataset_length) +# ) + +# columns = shuffled_data.columns +# # extract non-central modalities (i.e. not the central modality smiles) +# non_central_modalities = config.data.modalities +# central_modality = config.data.central_modality + +# for column in columns: +# if column in non_central_modalities: +# # drop nan for specific pair +# train_modality_pair = train_shuffled_data[ +# [central_modality, column] +# ].drop_nulls() +# valid_modality_pair = valid_shuffled_data[ +# [central_modality, column] +# ].drop_nulls() + +# train_modality_data[column] = [ +# train_modality_pair[central_modality].to_list(), +# train_modality_pair[column].to_list(), +# ] +# valid_modality_data[column] = [ +# valid_modality_pair[central_modality].to_list(), +# valid_modality_pair[column].to_list(), +# ] + +# combined_loader = load_combined_loader( +# data_modalities=train_modality_data, +# batch_size=config.data.batch_size, +# shuffle=True, +# num_workers=1, +# ) + +# valid_dataloader = load_combined_loader( +# data_modalities=valid_modality_data, +# batch_size=config.data.batch_size, +# shuffle=False, +# num_workers=1, +# ) + +# trainer.fit( +# MolBindModule(config), +# train_dataloaders=combined_loader, +# val_dataloaders=valid_dataloader, +# ) diff --git a/src/molbind/models/model.py b/src/molbind/models/model.py index ffae6e54..29fcaa73 100644 --- a/src/molbind/models/model.py +++ b/src/molbind/models/model.py @@ -1,43 +1,74 @@ -from molbind.models.components.custom_encoders import SmilesEncoder, SelfiesEncoder, GraphEncoder +from molbind.models.components.custom_encoders import ( + SmilesEncoder, + SelfiesEncoder, + GraphEncoder, +) from molbind.models.components.head import ProjectionHead -from molbind.models.component.pooler import EmbedPooler -from molbind.data.dataloaders import MolBindDataModule -import pytorch_lightning as pl from torch import Tensor +import torch.nn as nn +import torch +from typing import Dict, Union, Tuple + + +AVAILABLE_ENCODERS = { + "smiles": SmilesEncoder, + "selfies": SelfiesEncoder, + "graph": GraphEncoder, + "nmr": None, +} class MolBind(nn.Module): def __init__(self, cfg): super(MolBind, self).__init__() - # Instantiate all encoders - self.smiles_encoder = SmilesEncoder(cfg.model.smiles_encoder) - self.selfies_encoder = SelfiesEncoder(cfg.model.selfies_encoder) - self.graph_encoder = GraphEncoder(cfg.model.graph_encoder) - self.nmr_encoder = None - - self.dict_encoders = { - "smiles" : self.smiles_encoder, - "selfies" : self.selfies_encoder, - "graph" : self.graph_encoder, - "nmr" : self.nmr_encoder - } - - # Instantiate projection head and pooler - self.pooler = EmbedPooler(cfg.model.pooler) - + + modalities = cfg.data.modalities + central_modality = cfg.data.central_modality + self.central_modality = central_modality + + # Instantiate all encoders and projection heads + self.dict_encoders = {central_modality: SmilesEncoder(**cfg.model.encoders[central_modality])} self.dict_projection_heads = { - "smiles" : ProjectionHead(cfg.model.projection_head.smiles), - "selfies" : ProjectionHead(cfg.model.projection_head.selfies), - "graph" : ProjectionHead(cfg.model.projection_head.graph), - "nmr" : ProjectionHead(cfg.model.projection_head.nmr) + central_modality: ProjectionHead(**cfg.model.projection_heads[central_modality]) } - - def forward(self, input) -> Tensor: + # Add other modalities to `dict_encoders` and `dict_projection_heads + for modality in modalities: + if modality not in [*AVAILABLE_ENCODERS]: + raise ValueError(f"Modality {modality} not supported yet.") + self.dict_encoders[modality] = AVAILABLE_ENCODERS[modality]( + **cfg.model.encoders[modality] + ) + self.dict_projection_heads[modality] = ProjectionHead( + **cfg.model.projection_heads[modality] + ) + + # convert dicts to nn.ModuleDict + self.dict_encoders = nn.ModuleDict(self.dict_encoders) + self.dict_projection_heads = nn.ModuleDict(self.dict_projection_heads) + + def forward( + self, input_data: Dict[str, Union[Tuple[Tensor, Tensor], Tensor]] + ) -> Tensor: store_embeddings = {} - # dataloader keys are other modalities - for modality in input.keys(): - # forward through respective encoder - store_embeddings[modality] = self.dict_encoders[modality](input[modality]).last_hidden_state - # projection head - store_embeddings[modality] = self.dict_projection_heads[modality](store_embeddings[modality]) - return store_embeddings \ No newline at end of file + # input_data = [data, batch_index, dataloader_index] + input_data, _, _ = input_data + # input_data is a dictionary with (smiles, modality) pairs (where the central modality is at index 0) + central_modality = [*input_data][0] + modality = [*input_data][1] + # store embeddings as store_embeddings[modality] = (smiles_embedding, modality_embedding) + # forward through respective encoder + smiles_embedding = self.dict_encoders[central_modality].forward(input_data[central_modality]) + modality_embedding = self.dict_encoders[modality].forward(input_data[modality]) + central_modality_embedding_projected = self.dict_projection_heads[central_modality]( + smiles_embedding + ) + modality_embedding_projected = self.dict_projection_heads[modality]( + modality_embedding + ) + # projection heads + store_embeddings[central_modality] = central_modality_embedding_projected + store_embeddings[modality] = modality_embedding_projected + return store_embeddings + + def load_from_checkpoint(self, path: str): + return torch.load(path) diff --git a/src/molbind/models/moleculebind_module.py b/src/molbind/models/moleculebind_module.py deleted file mode 100644 index 40081a3f..00000000 --- a/src/molbind/models/moleculebind_module.py +++ /dev/null @@ -1,52 +0,0 @@ -from info_nce import InfoNCE -from pytorch_lightning import LightningModule -from molbind.models.components import MolBind -import torch -from torch.nn.functional import cosine_similarity - - -class MolBindModule(LightningModule): - def __init__(self, - model_opt_params = { - "modality_1": "smiles", - "modality_2": "selfies", - "learning_rate" : 1e-4, - "temperature" : 0.06, - "modality_1_fc" : [768, 512], - "modality_2_fc" : [768, 512] - }): - - super().__init__() - self.model = MolBind(model_opt_params) - - self.modality_1 = "smiles" - self.modality_2 = model_opt_params["modality_2"] - self.learning_rate = model_opt_params["learning_rate"] - self.temperature = model_opt_params["temperature"] - - - def forward(self, input_ids_modality_1, attention_mask_modality_1, input_ids_modality_2, attention_mask_modality_2): - joint_embedding = self.model(input_ids_modality_1, attention_mask_modality_1, input_ids_modality_2, attention_mask_modality_2) - return joint_embedding - - def _info_nce_loss(self, z1, z2, temperature, prefix): - loss = InfoNCE(temperature=temperature, negative_mode="unpaired") - loss = loss(z1, z2) - print(f"{prefix}_loss", loss) - self.log(f"{prefix}_loss", loss) - self.log(f"{prefix}_cosine_similarity", cosine_similarity(z1, z2, dim=1).mean()) - return loss - - def training_step(self, batch, batch_idx): - input_ids_modality_1, attention_mask_modality_1, input_ids_modality_2, attention_mask_modality_2 = batch - selfies_embedding, smiles_embedding = self.forward(input_ids_modality_1, attention_mask_modality_1, input_ids_modality_2, attention_mask_modality_2) - return self._info_nce_loss(smiles_embedding, selfies_embedding, self.temperature, prefix="train") - - def validation_step(self, batch, batch_idx): - input_ids_modality_1, attention_mask_modality_1, input_ids_modality_2, attention_mask_modality_2 = batch - - selfies_embedding, smiles_embedding = self.model(input_ids_modality_1, attention_mask_modality_1, input_ids_modality_2, attention_mask_modality_2) - return self._info_nce_loss(smiles_embedding, selfies_embedding, self.temperature, prefix="val") - - def configure_optimizers(self): - return torch.optim.AdamW(self.parameters(), lr=self.learning_rate) \ No newline at end of file diff --git a/src/molbind/train.py b/src/molbind/train.py index 4adbcf44..6e0d3910 100644 --- a/src/molbind/train.py +++ b/src/molbind/train.py @@ -13,7 +13,7 @@ # the setup_root above is equivalent to: # - adding project root dir to PYTHONPATH # (so you don't need to force user to install project as a package) -# (necessary before importing any local modules e.g. `from src import utils`) +# (necessary before importing any local modules e.g. `from molbind import utils`) # - setting up PROJECT_ROOT environment variable # (which is used as a base for paths in "configs/paths/default.yaml") # (this way all filepaths are the same no matter where you run the code) @@ -26,7 +26,7 @@ # more info: https://github.com/ashleve/rootutils # ------------------------------------------------------------------------------------ # -from src.utils import ( +from molbind.utils import ( RankedLogger, extras, get_metric_value, @@ -67,7 +67,9 @@ def train(cfg: DictConfig) -> Tuple[Dict[str, Any], Dict[str, Any]]: logger: List[Logger] = instantiate_loggers(cfg.get("logger")) log.info(f"Instantiating trainer <{cfg.trainer._target_}>") - trainer: Trainer = hydra.utils.instantiate(cfg.trainer, callbacks=callbacks, logger=logger) + trainer: Trainer = hydra.utils.instantiate( + cfg.trainer, callbacks=callbacks, logger=logger + ) object_dict = { "cfg": cfg, diff --git a/src/molbind/utils/__init__.py b/src/molbind/utils/__init__.py index 5b0707ca..4d8d794f 100644 --- a/src/molbind/utils/__init__.py +++ b/src/molbind/utils/__init__.py @@ -1,5 +1,5 @@ -from src.utils.instantiators import instantiate_callbacks, instantiate_loggers -from src.utils.logging_utils import log_hyperparameters -from src.utils.pylogger import RankedLogger -from src.utils.rich_utils import enforce_tags, print_config_tree -from src.utils.utils import extras, get_metric_value, task_wrapper +from molbind.utils.instantiators import instantiate_callbacks, instantiate_loggers +from molbind.utils.logging_utils import log_hyperparameters +from molbind.utils.pylogger import RankedLogger +from molbind.utils.rich_utils import enforce_tags, print_config_tree +from molbind.utils.utils import extras, get_metric_value, task_wrapper \ No newline at end of file diff --git a/src/molbind/utils/instantiators.py b/src/molbind/utils/instantiators.py index 82b9278a..020b3362 100644 --- a/src/molbind/utils/instantiators.py +++ b/src/molbind/utils/instantiators.py @@ -5,7 +5,7 @@ from lightning.pytorch.loggers import Logger from omegaconf import DictConfig -from src.utils import pylogger +from molbind.utils import pylogger log = pylogger.RankedLogger(__name__, rank_zero_only=True) diff --git a/src/molbind/utils/logging_utils.py b/src/molbind/utils/logging_utils.py index 360abcdc..8fee17d7 100644 --- a/src/molbind/utils/logging_utils.py +++ b/src/molbind/utils/logging_utils.py @@ -3,7 +3,7 @@ from lightning_utilities.core.rank_zero import rank_zero_only from omegaconf import OmegaConf -from src.utils import pylogger +from molbind.utils import pylogger log = pylogger.RankedLogger(__name__, rank_zero_only=True) diff --git a/src/molbind/utils/rich_utils.py b/src/molbind/utils/rich_utils.py index aeec6806..43a321ca 100644 --- a/src/molbind/utils/rich_utils.py +++ b/src/molbind/utils/rich_utils.py @@ -9,7 +9,7 @@ from omegaconf import DictConfig, OmegaConf, open_dict from rich.prompt import Prompt -from src.utils import pylogger +from molbind.utils import pylogger log = pylogger.RankedLogger(__name__, rank_zero_only=True) diff --git a/src/molbind/utils/utils.py b/src/molbind/utils/utils.py index 02b55765..a7d3d2de 100644 --- a/src/molbind/utils/utils.py +++ b/src/molbind/utils/utils.py @@ -1,10 +1,10 @@ import warnings from importlib.util import find_spec from typing import Any, Callable, Dict, Optional, Tuple - from omegaconf import DictConfig +from molbind.utils import pylogger, rich_utils +import torch.nn as nn -from src.utils import pylogger, rich_utils log = pylogger.RankedLogger(__name__, rank_zero_only=True) @@ -116,4 +116,4 @@ def get_metric_value(metric_dict: Dict[str, Any], metric_name: Optional[str]) -> metric_value = metric_dict[metric_name].item() log.info(f"Retrieved metric value! <{metric_name}={metric_value}>") - return metric_value + return metric_value \ No newline at end of file