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Path from torchvision.datasets import Caltech256 from torchvision.transforms import ToTensor -from torch.utils.data import random_split -from torch.utils.data import BatchSampler +from torch.utils.data import DataLoader, random_split PROJECT_ROOT = Path(__file__).parent.parent +DATASET_DIR = PROJECT_ROOT / "datasets/" -def get_dataset( +def create_dataset( split: (float, float, float) = (0.7, 0.1, 0.2), dataset=Caltech256, - batch_size: int = 128, - drop_last: bool = False, **kwargs, ): - _kwargs = { - "transform": ToTensor(), - } - _kwargs.update(kwargs) - ds = dataset(PROJECT_ROOT / "datasets/", download=True, **_kwargs) - train, val, test = ( - BatchSampler(i, batch_size, drop_last) for i in random_split(ds, split) - ) + ds = dataset(DATASET_DIR, download=True, transform=ToTensor()) + train, val, test = (DataLoader(i, **kwargs) for i in random_split(ds, split)) return train, val, test diff --git a/symbolic_nn_tests/experiment1/model.py b/symbolic_nn_tests/experiment1/model.py index b164471..a3bfa11 100644 --- a/symbolic_nn_tests/experiment1/model.py +++ b/symbolic_nn_tests/experiment1/model.py @@ -1,4 +1,5 @@ from functools import lru_cache +import torch from torch import nn @@ -9,17 +10,35 @@ model = nn.Sequential( ) +def collate(batch): + x, y = zip(*batch) + x = [i[0] for i in x] + y = [torch.tensor(i) for i in y] + x = torch.stack(x).to("cuda") + y = torch.tensor(y).to("cuda") + return x, y + + # This is just a quick, lazy way to ensure all models are trained on the same dataset @lru_cache(maxsize=1) def get_singleton_dataset(): from torchvision.datasets import QMNIST - from symbolic_nn_tests.dataloader import get_dataset + from symbolic_nn_tests.dataloader import create_dataset - return get_dataset(dataset=QMNIST) + return create_dataset( + dataset=QMNIST, collate_fn=collate, batch_size=128, shuffle=True + ) -def main(loss_func=nn.functional.cross_entropy, logger=None, **kwargs): +def oh_vs_cat_cross_entropy(y_bin, y_cat): + return nn.functional.cross_entropy( + y_bin, + nn.functional.one_hot(y_cat), + ) + + +def main(loss_func=oh_vs_cat_cross_entropy, logger=None, **kwargs): import lightning as L from symbolic_nn_tests.train import TrainingWrapper diff --git a/symbolic_nn_tests/experiment1/semantic_loss.py b/symbolic_nn_tests/experiment1/semantic_loss.py index ade67ed..5c4a633 100644 --- a/symbolic_nn_tests/experiment1/semantic_loss.py +++ b/symbolic_nn_tests/experiment1/semantic_loss.py @@ -10,7 +10,10 @@ def create_semantic_cross_entropy(semantic_matrix): semantic_penalty = (abs_diff * penalty_tensor).sum() return ce_loss * semantic_penalty - return semantic_cross_entropy + def oh_vs_cat_semantic_cross_entropy(input_oh, target_cat): + return semantic_cross_entropy(input_oh, torch.nn.functional.one_hot(target_cat)) + + return oh_vs_cat_semantic_cross_entropy # NOTE: This similarity matrix defines loss scaling factors for misclassification diff --git a/symbolic_nn_tests/experiment2/__init__.py b/symbolic_nn_tests/experiment2/__init__.py new file mode 100644 index 0000000..e845b79 --- /dev/null +++ b/symbolic_nn_tests/experiment2/__init__.py @@ -0,0 +1,75 @@ +LEARNING_RATE = 10e-5 + + +def test(loss_func, version, tensorboard=True, wandb=True): + from .model import main as test_model + + logger = [] + + if tensorboard: + from lightning.pytorch.loggers import TensorBoardLogger + + tb_logger = TensorBoardLogger( + save_dir=".", + name="logs/comparison", + version=version, + ) + logger.append(tb_logger) + + if wandb: + import wandb as _wandb + from lightning.pytorch.loggers import WandbLogger + + wandb_logger = WandbLogger( + project="Symbolic_NN_Tests", + name=version, + dir="wandb", + ) + logger.append(wandb_logger) + + test_model(logger=logger, loss_func=loss_func, lr=LEARNING_RATE) + + if wandb: + _wandb.finish() + + +def run(tensorboard: bool = True, wandb: bool = True): + from . import semantic_loss + from torch import nn + + test( + nn.functional.cross_entropy, + "cross_entropy", + tensorboard=tensorboard, + wandb=wandb, + ) + test( + semantic_loss.similarity_cross_entropy, + "similarity_cross_entropy", + tensorboard=tensorboard, + wandb=wandb, + ) + test( + semantic_loss.hasline_cross_entropy, + "hasline_cross_entropy", + tensorboard=tensorboard, + wandb=wandb, + ) + test( + semantic_loss.hasloop_cross_entropy, + "hasloop_cross_entropy", + tensorboard=tensorboard, + wandb=wandb, + ) + test( + semantic_loss.multisemantic_cross_entropy, + "multisemantic_cross_entropy", + tensorboard=tensorboard, + wandb=wandb, + ) + test( + semantic_loss.garbage_cross_entropy, + "garbage_cross_entropy", + tensorboard=tensorboard, + wandb=wandb, + ) diff --git a/symbolic_nn_tests/experiment2/dataset.py b/symbolic_nn_tests/experiment2/dataset.py new file mode 100644 index 0000000..4b91a12 --- /dev/null +++ b/symbolic_nn_tests/experiment2/dataset.py @@ -0,0 +1,244 @@ +import kaggle +import polars as pl +import shutil +from functools import lru_cache +from periodic_table import PeriodicTable +import numpy as np +import torch +from torch.utils.data import TensorDataset +import pickle +from multiprocessing import Pool +from symbolic_nn_tests.dataloader import DATASET_DIR +import warnings +from tqdm.auto import tqdm + + +warnings.filterwarnings(action="ignore", category=UserWarning) + + +PUBCHEM_DIR = DATASET_DIR / "PubChem" + +ORBITALS = { + "s": (0, 2), + "p": (1, 6), + "d": (2, 10), + "f": (3, 14), +} + + +def collate(batch): + x0_in, x1_in, y_in = list(zip(*batch)) + x0_out = torch.nested.as_nested_tensor(list(x0_in)) + x1_out = torch.nested.as_nested_tensor(list(x1_in)) + y_out = torch.as_tensor(y_in) + return (x0_out, x1_out), y_out + + +def pubchem(*args, **kwargs): + PUBCHEM_DIR.mkdir(exist_ok=True, parents=True) + return get_dataset() + + +def get_dataset(): + if not ( + "pubchem_x0.pickle" + and "pubchem_x1.pickle" + and "pubchem_y.pickle" in (x.name for x in PUBCHEM_DIR.iterdir()) + ): + construct_dataset("pubchem") + else: + print("Pre-existing dataset detected!") + print("Dataset loaded!") + return TensorDataset(*load_dataset("pubchem")) + + +def construct_dataset(filename): + print("Constructing dataset...") + df = construct_ds_dataframe(filename) + save_dataframe_to_dataset(df, PUBCHEM_DIR / f"{filename}.pickle") + print("Dataset constructed!") + + +def construct_ds_dataframe(filename): + print("Constructing dataset dataframe...") + df = add_molecule_encodings(construct_raw_dataset(filename)) + # NOTE: This kind of checkpointing will be used throughout the construction process It doesn't + # take much disk space, it lets the GC collect out-of-scope data from the construction process + # and it makes it easier to debug if construction fails + parquet_file = PUBCHEM_DIR / f"{filename}.parquet" + df.write_parquet(parquet_file) + print("Dataset dataframe constructed!") + return pl.read_parquet(parquet_file) + + +def construct_raw_dataset(filename): + print("Constructing raw dataset...") + df = collate_dataset() + parquet_file = PUBCHEM_DIR / f"{filename}_raw.parquet" + df.write_parquet(parquet_file) + print("Raw dataset constructed!") + return pl.read_parquet(parquet_file) + + +def collate_dataset(): + print("Collating dataset...") + if not (PUBCHEM_DIR.exists() and len(tuple(PUBCHEM_DIR.glob("*.json")))): + fetch_dataset() + + df = pl.concat( + map(pl.read_json, PUBCHEM_DIR.glob("*.json")), + ).drop("id") + print("dataset collated!") + return df + + +def fetch_dataset(): + print("Fetching dataset...") + kaggle.api.dataset_download_files( + "burakhmmtgl/predict-molecular-properties", quiet=False, path=DATASET_DIR + ) + shutil.unpack_archive(DATASET_DIR / "predict-molecular-properties.zip", PUBCHEM_DIR) + print("Dataset fetched!") + + +@lru_cache(maxsize=1) +def get_periodic_table(): + return PeriodicTable() + + +def add_molecule_encodings(df): + atom_properties, atom_electrons = encode_molecules(df["atoms"]) + return df.with_columns( + atom_properties=atom_properties, atom_electrons=atom_electrons + ) + + +def encode_molecules(series): + # Yes, it is gross and RAM inefficient to do it this way but i dont have all day... + with Pool() as p: + molecules = p.map(encode_molecule, series) + properties, electrons = zip(*molecules) + return pl.Series(properties), pl.Series(electrons) + + +def encode_molecule(molecule): + properties, electrons = zip(*_encode_molecule(molecule)) + properties = pl.Series(properties) + return properties, electrons + + +def _encode_molecule(molecule): + for atom in molecule: + properties, electrons = encode_atom(atom["type"]) + yield np.array([*properties, *atom["xyz"]]), pl.Series(electrons) + + +def encode_atom(atom): + element = get_periodic_table().search_symbol(atom) + return ( + np.array( + [ + # n and z need to be scaled somehow to normalize to approximately 1 + # Because this is kind arbitrary i've decided to scale relative to + # Fermium (n = 100) + element.atomic / 100.0, + element.atomic_mass / 257.0, + element.electron_affinity / 350.0, # Highest known is just below 350 + element.electronegativity_pauling + / 4.0, # Max theoretical val is 4.0 here + ], + ), + encode_electron_config(element.electron_configuration), + ) + + +def encode_electron_config(config): + return np.array([encode_orbital(x) for x in config.split()]) + + +def encode_orbital(orbital): + shell, subshell, *n = orbital + shell = int(shell) + n = int("".join(n)) + azimuthal, capacity = ORBITALS[subshell] + return np.array( + [ + 1.0 + / shell, # This is the simplest way to normalize shell, as shells become less distinct as n increases + azimuthal / 4.0, # This is simply normalizing the azimuthal quantum number + n / capacity, # Basically encoding this as a proportion of "fullness" + ], + ) + + +def save_dataframe_to_dataset(df, filename): + print("Saving dataset to tensors...") + with (filename.parent / f"{filename.stem}_x0{filename.suffix}").open("wb") as f: + pickle.dump(properties_to_tensor(df).float(), f) + with (filename.parent / f"{filename.stem}_x1{filename.suffix}").open("wb") as f: + pickle.dump(electrons_to_tensor(df).float(), f) + with (filename.parent / f"{filename.stem}_y{filename.suffix}").open("wb") as f: + pickle.dump(df["En"].to_torch().float(), f) + del df + print("Tensors saved!") + + +def chunked_df(df, n): + chunk_size = (len(df) // n) + 1 + chunk_boundaries = [*range(0, len(df), chunk_size), len(df)] + chunk_ranges = list(zip(chunk_boundaries[:-1], chunk_boundaries[1:])) + yield from (df[i:j] for i, j in chunk_ranges) + + +def properties_to_tensor(df): + with Pool() as p: + out = torch.cat( + p.map( + property_chunk_to_torch, chunked_df(df["atom_properties"], p._processes) + ) + ) + return out + + +def property_chunk_to_torch(chunk): + return torch.nested.nested_tensor([properties_to_torch(x) for x in chunk]) + + +def properties_to_torch(p): + return torch.stack(tuple(map(pl.Series.to_torch, p))) + + +def electrons_to_tensor(df): + return torch.nested.nested_tensor( + [ + molecule_electrons_to_torch(e) + for e in tqdm(df["atom_electrons"], desc="Converting molecules to orbitals") + ] + ) + + +def molecule_electrons_to_torch(e): + return torch.stack([atom_electrons_to_torch(x) for x in e]) + + +def atom_electrons_to_torch(e): + # pytorch doesn't like doubly nested tensors, and the unnocupied orbitals still exist here even if + # they're empty, so it makes sense to pad here instead. No elements in the dataset exceed an + # azimuthal of 3, so we only need to pad to length 10. Also: i'm realising here that the orbital + # info will be unecessary if we have to pad here anyway + return pad_tensor_to(torch.tensor(tuple(x[-1] for x in e)), 10) + + +def pad_tensor_to(t, length): + return torch.nn.functional.pad(t, (0, length - t.shape[0])) + + +def load_dataset(filename): + filepath = PUBCHEM_DIR / f"{filename}.pickle" + with (filepath.parent / f"{filepath.stem}_x0{filepath.suffix}").open("rb") as f: + x0 = pickle.load(f) + with (filepath.parent / f"{filepath.stem}_x1{filepath.suffix}").open("rb") as f: + x1 = pickle.load(f) + with (filepath.parent / f"{filepath.stem}_y{filepath.suffix}").open("rb") as f: + y = pickle.load(f) + return x0, x1, y diff --git a/symbolic_nn_tests/experiment2/model.py b/symbolic_nn_tests/experiment2/model.py new file mode 100644 index 0000000..a436e8f --- /dev/null +++ b/symbolic_nn_tests/experiment2/model.py @@ -0,0 +1,76 @@ +from functools import lru_cache +import torch +from torch import nn + + +class Model(nn.Module): + def __init__(self): + super().__init__() + + self.x0_encoder = nn.TransformerEncoderLayer(7, 7) + self.x1_encoder = nn.TransformerEncoderLayer(10, 10) + self.encode_x0 = self.create_xval_encoding_fn(self.x0_encoder) + self.encode_x1 = self.create_xval_encoding_fn(self.x1_encoder) + self.ff = nn.Sequential( + nn.Linear(17, 256), + nn.ReLU(), + nn.Linear(256, 128), + nn.ReLU(), + nn.Linear(128, 64), + nn.ReLU(), + nn.Linear(64, 32), + nn.ReLU(), + nn.Linear(32, 16), + nn.ReLU(), + nn.Linear(16, 8), + nn.ReLU(), + nn.Linear(8, 1), + ) + + @staticmethod + def create_xval_encoding_fn(layer): + def encoding_fn(xbatch): + return torch.stack([layer(x)[-1] for x in xbatch]) + + return encoding_fn + + def forward(self, x): + x0, x1 = x + x0 = self.encode_x0(x0) + x1 = self.encode_x1(x1) + x = torch.cat([x0, x1], dim=1) + y = self.ff(x) + return y + + +# This is just a quick, lazy way to ensure all models are trained on the same dataset +@lru_cache(maxsize=1) +def get_singleton_dataset(): + from symbolic_nn_tests.dataloader import create_dataset + from symbolic_nn_tests.experiment2.dataset import collate, pubchem + + return create_dataset( + dataset=pubchem, collate_fn=collate, batch_size=128, shuffle=True + ) + + +def main(loss_func=nn.functional.smooth_l1_loss, logger=None, **kwargs): + import lightning as L + + from symbolic_nn_tests.train import TrainingWrapper + + if logger is None: + from lightning.pytorch.loggers import TensorBoardLogger + + logger = TensorBoardLogger(save_dir=".", name="logs/ffnn") + + train, val, test = get_singleton_dataset() + lmodel = TrainingWrapper(Model(), loss_func=loss_func) + lmodel.configure_optimizers(optimizer=torch.optim.NAdam, **kwargs) + trainer = L.Trainer(max_epochs=20, logger=logger) + trainer.fit(model=lmodel, train_dataloaders=train, val_dataloaders=val) + trainer.test(dataloaders=test) + + +if __name__ == "__main__": + main() diff --git a/symbolic_nn_tests/experiment2/semantic_loss.py b/symbolic_nn_tests/experiment2/semantic_loss.py new file mode 100644 index 0000000..aaa3285 --- /dev/null +++ b/symbolic_nn_tests/experiment2/semantic_loss.py @@ -0,0 +1 @@ +import torch diff --git a/symbolic_nn_tests/train.py b/symbolic_nn_tests/train.py index fe76f02..a82969f 100644 --- a/symbolic_nn_tests/train.py +++ b/symbolic_nn_tests/train.py @@ -1,37 +1,26 @@ -import torch from torch import nn, optim import lightning as L -def collate_batch(batch): - x, y = zip(*batch) - x = [i[0] for i in x] - y = [torch.tensor(i) for i in y] - x = torch.stack(x).to("cuda") - y = torch.tensor(y).to("cuda") - return x, y - - class TrainingWrapper(L.LightningModule): - def __init__(self, model, loss_func=nn.functional.cross_entropy): + def __init__(self, model, loss_func=nn.functional.mse_loss, accuracy=None): super().__init__() self.model = model self.loss_func = loss_func + self.accuracy = accuracy def _forward_step(self, batch, batch_idx, label=""): - x, y = collate_batch(batch) + x, y = batch y_pred = self.model(x) - batch_size = x.shape[0] - one_hot_y = nn.functional.one_hot(y).type(torch.float64) - loss = self.loss_func(y_pred, one_hot_y) - acc = torch.sum(y_pred.argmax(dim=1) == y) / batch_size - self.log(f"{label}{'_' if label else ''}loss", loss, batch_size=batch_size) - self.log(f"{label}{'_' if label else ''}acc", acc, batch_size=batch_size) - return loss, acc + loss = self.loss_func(y_pred, y) + self.log(f"{label}{'_' if label else ''}loss", loss) + if self.accuracy is not None: + acc = self.accuracy(y_pred, y) + self.log(f"{label}{'_' if label else ''}acc", acc) + return loss def training_step(self, batch, batch_idx): - loss, _ = self._forward_step(batch, batch_idx, label="train") - return loss + return self._forward_step(batch, batch_idx, label="train") def validation_step(self, batch, batch_idx): self._forward_step(batch, batch_idx, label="val")