From 4068d67caaac1e28d56964da68e0214817e38428 Mon Sep 17 00:00:00 2001 From: haotian Date: Wed, 9 Aug 2023 14:30:54 -0400 Subject: [PATCH] :bento: add and update files --- examples/pretrain.py | 1167 + examples/sbatch_census.sh | 70 + scgpt/data_collator.py | 317 +- scgpt/model/flash_layers.py | 427 + scgpt/model/layers.py | 165 + scgpt/model/model.py | 396 +- scgpt/preprocess.py | 69 +- scgpt/tokenizer/default_census_vocab.json | 60696 ++++++++++++++++++++ scgpt/tokenizer/gene_tokenizer.py | 2 +- 9 files changed, 63193 insertions(+), 116 deletions(-) create mode 100644 examples/pretrain.py create mode 100644 examples/sbatch_census.sh create mode 100644 scgpt/model/flash_layers.py create mode 100644 scgpt/model/layers.py create mode 100644 scgpt/tokenizer/default_census_vocab.json diff --git a/examples/pretrain.py b/examples/pretrain.py new file mode 100644 index 00000000..61b2fb79 --- /dev/null +++ b/examples/pretrain.py @@ -0,0 +1,1167 @@ +""" Example call for running evaluation +DATASET="path_to/datasets/3faad104-2ab8-4434-816d-474d8d2641db.scb" +DATASET=test +JOB_NAME="cellxgene_3faad1" +LOG_INTERVAL=100 +VALID_SIZE_OR_RATIO=0.1 +MAX_LENGTH=600 +per_proc_batch_size=64 +LAYERS=4 +MODEL_SCALE=1 +python pretrain.py --data-source $DATASET --save-dir ./save/eval-$(date +%b%d-%H-%M-%Y) --max-seq-len $MAX_LENGTH --batch-size $per_proc_batch_size --eval-batch-size $(($per_proc_batch_size * 2)) --epochs 3 --lr 0.0001 --warmup-ratio-or-step 0.1 --log-interval $LOG_INTERVAL --trunc-by-sample --no-cls --no-cce --fp16 + +python pretrain.py \ + --data-source $DATASET \ + --save-dir ./save/eval-$(date +%b%d-%H-%M-%Y) \ + --load-model $CHECKPOINT \ + --max-seq-len $MAX_LENGTH \ + --batch-size $per_proc_batch_size \ + --eval-batch-size $(($per_proc_batch_size * 2)) \ + --epochs 0 \ + --log-interval $LOG_INTERVAL \ + --trunc-by-sample \ + --no-cls \ + --no-cce \ + --fp16 + +Example call for running fine-tuning +python pretrain.py \ + --data-source $DATASET \ + --save-dir ./save/eval-$(date +%b%d-%H-%M-%Y) \ + --load-model $CHECKPOINT \ + --max-seq-len $MAX_LENGTH \ + --batch-size $per_proc_batch_size \ + --eval-batch-size $(($per_proc_batch_size * 2)) \ + --epochs 3 \ + --lr 0.0001 \ + --warmup-ratio-or-step 0.1 \ + --log-interval $LOG_INTERVAL \ + --trunc-by-sample \ + --no-cls \ + --no-cce \ + --fp16 +""" +# %% +import os +import sys +import argparse +import json +import time +from datetime import timedelta +from pathlib import Path +from typing import List, Tuple, Dict, Union, Optional + +import scanpy as sc +import numpy as np +import torch +import transformers +from torch import nn +from torch.nn import functional as F +from torch.utils.tensorboard import SummaryWriter +from torch.utils.data.distributed import DistributedSampler +from torch.utils.data import DataLoader, BatchSampler, RandomSampler, SequentialSampler +from datasets import Dataset, load_dataset, concatenate_datasets + + +sys.path.insert(0, "../") +import scgpt as scg +from scgpt.model import TransformerModel +from scgpt.loss import masked_mse_loss, masked_relative_error +from scgpt.tokenizer import GeneVocab, random_mask_value +from scgpt.scbank import DataBank +from scgpt.utils import MainProcessOnly +from scgpt import logger + + +# torch.autograd.set_detect_anomaly(True) + +sc.set_figure_params(figsize=(4, 4)) +sc.settings.verbosity = "debug" +scg.utils.set_seed(42) + +# %% +# argparse +parser = argparse.ArgumentParser() +parser.add_argument( + "-d", + "--data-source", + type=str, + required=True, + help='The name of the data source (currently support "scvi" datasets), or the ' + "path to the data file.", +) +parser.add_argument( + "-s", + "--save-dir", + type=str, + required=True, + help="The directory to save the trained model and the results.", +) +parser.add_argument( + "--load-model", + type=str, + default=None, + help="The directory containing the model and configs to load and continue training.", +) + +# settings for data +parser.add_argument( + "--n-hvg", + type=int, + default=None, + help="The number of highly variable genes. If set to 0, will use all genes. " + "Default is None, which will determine the n_hvg automatically.", +) +parser.add_argument( + "--valid-size-or-ratio", + type=float, + default=0.1, + help="The ratio or size of the validation set size if split the dataset. " + "If value is between 0 and 1, will be parsed as the ratio. If value is " + "greater than 1 and be an integer, will be parsed as the size. If value " + "is 0, will not split the dataset.", +) + +parser.add_argument( + "--grad-accu-steps", + type=int, + default=1, + help="The number of gradient accumulation steps. Default is 1.", +) + +# settings for tokenizer +parser.add_argument( + "--pad-token", + type=str, + default="", + help="The token to use for padding. Default is .", +) +parser.add_argument( + "--input-style", + type=str, + choices=["normed_raw", "log1p", "binned"], + default="binned", + help="The style of the input data. Default is binned.", +) +parser.add_argument( + "--input-emb-style", + type=str, + choices=["category", "continuous", "scaling"], + default="continuous", + help="The style of the input embedding. Default is continuous.", +) +parser.add_argument( + "--n-bins", + type=int, + default=51, + help="The number of bins to use for the binned input style. Default is 51.", +) +parser.add_argument( + "--max-seq-len", + type=int, + default=1536, + help="The maximum length of the sequence. Default is 1000. The actual used " + "max length would be the minimum of this value and the length of the longest " + "sequence in the data.", +) +# omit the args for MLM and MVC, will always use them by default +parser.add_argument( + "--training-tasks", # choices of "mlm", "gen", "both" + type=str, + default="both", + choices=["pcpt", "gen", "both"], + help="The tasks to use for training. pcpt: perception training with maked token " + "learning. gen: generation. Default is both.", +) +parser.add_argument( + "--mask-ratio", + type=float, + default=0.40, + help="The ratio of masked values in the training data. Default is 0.40. This" + "value will be ignored if --training-tasks is set to gen or both.", +) +parser.add_argument( + "--trunc-by-sample", + action="store_true", + help="Whether to truncate the input by sampling rather than cutting off if " + "sequence length > max_seq_length. Default is False.", +) +parser.add_argument( + "--vocab-path", + type=str, + help="Path to the vocabulary file.", +) +# settings for training +parser.add_argument( + "--local-rank", + type=int, + default=-1, + help="The local rank of the process for using the torch.distributed.launch " + "utility. Will be -1 if not running in distributed model.", +) +parser.add_argument( + "--batch-size", + type=int, + default=32, + help="The batch size for training. Default is 32.", +) +parser.add_argument( + "--eval-batch-size", + type=int, + default=32, + help="The batch size for evaluation. Default is 32.", +) +parser.add_argument( + "--epochs", + type=int, + default=10, + help="The number of epochs for training.", +) +parser.add_argument( + "--lr", + type=float, + default=1e-3, + help="The learning rate for training. Default is 1e-3.", +) +parser.add_argument( + "--scheduler-interval", + type=int, + default=100, + help="The interval iterations for updating the learning rate. Default is 100. " + "This will only be used when warmup-ratio is 0.", +) +parser.add_argument( + "--scheduler-factor", + type=float, + default=0.99, + help="The factor for updating the learning rate. Default is 0.99. " + "This will only be used when warmup-ratio is 0.", +) +parser.add_argument( + "--warmup-ratio-or-step", + type=float, + default=0.1, + help="The ratio of warmup steps out of the total training steps. Default is 0.1. " + "If warmup-ratio is above 0, will use a cosine scheduler with warmup. If " + "the value is above 1, will use it as the number of warmup steps.", +) +parser.add_argument( + "--no-cls", + action="store_true", + help="Whether to deactivate the classification loss. Default is False.", +) +parser.add_argument( + "--no-cce", + action="store_true", + help="Whether to deactivate the contrastive cell embedding objective. " + "Default is False.", +) +parser.add_argument( + "--fp16", + action="store_true", + help="Whether to train in automatic mixed precision. Default is False.", +) +parser.add_argument( + "--fast-transformer", + type=bool, + default=True, + help="Whether to use the fast transformer. Default is True.", +) + +# settings for model +parser.add_argument( + "--nlayers", + type=int, + default=4, + help="The number of layers for the transformer. Default is 4.", +) +parser.add_argument( + "--nheads", + type=int, + default=4, + help="The number of heads for the transformer. Default is 4.", +) +parser.add_argument( + "--embsize", + type=int, + default=64, + help="The embedding size for the transformer. Default is 64.", +) +parser.add_argument( + "--d-hid", + type=int, + default=64, + help="dimension of the feedforward network model in the transformer. " + "Default is 64.", +) +parser.add_argument( + "--dropout", + type=float, + default=0.2, + help="The dropout rate. Default is 0.2.", +) +parser.add_argument( + "--n-layers-cls", + type=int, + default=3, + help="The number of layers for the classification network, including the " + "output layer. Default is 3.", +) + +# settings for logging +parser.add_argument( + "--log-interval", + type=int, + default=100, + help="The interval for logging. Default is 100.", +) +parser.add_argument( + "--save-interval", + type=int, + default=1000, + help="The interval for saving the model. Default is 1000.", +) + + +if scg.utils.isnotebook(): + args = parser.parse_args( + args=[ + "-d", + "/scratch/hdd001/home/haotian/datasets/cellxgene/3faad104-2ab8-4434-816d-474d8d2641db.scb", + "-s", + "./save/tmp", + "--batch-size", + "16", + "--max-seq-len", + "512", + "--trunc-by-sample", + "--no-cls", + "--no-cce", + ] + ) +else: + args = parser.parse_args() + + +# args.local_rank = os.environ['LOCAL_RANK'] +# validate settings +assert args.input_style in ["normed_raw", "log1p", "binned"] +assert args.input_emb_style in ["category", "continuous", "scaling"] +if args.input_style == "binned": + if args.input_emb_style == "scaling": + raise ValueError("input_emb_style `scaling` is not supported for binned input.") +elif args.input_style == "log1p" or args.input_style == "normed_raw": + if args.input_emb_style == "category": + raise ValueError( + "input_emb_style `category` is not supported for log1p or normed_raw input." + ) + +if args.input_emb_style == "category": + args.mask_value = args.n_bins + 1 + args.pad_value = args.n_bins # for padding gene expr values + n_input_bins = args.n_bins + 2 +else: + args.mask_value = -1 + args.pad_value = -2 + n_input_bins = args.n_bins + +if args.training_tasks in ["gen", "both"]: + args.mask_ratio = [0.25, 0.50, 0.75] + +# %% settings +print(args) + +special_tokens = [args.pad_token, "", ""] +USE_CLS = not args.no_cls +USE_CCE = not args.no_cce +MVC = True +USE_GENERATIVE_TRAINING = True if args.training_tasks in ["gen", "both"] else False + +IS_DATA_PARALLEL = args.local_rank != -1 +if IS_DATA_PARALLEL: + # These two lines is to solve issue #1 based on the suggestion from + # https://discuss.pytorch.org/t/94382 + os.environ["CUDA_VISIBLE_DEVICES"] = str(args.local_rank) + + torch.distributed.init_process_group( + backend="nccl", + rank=args.local_rank, + timeout=timedelta(hours=10), + ) + # specify device 0 since the CUDA_VISIBLE_DEVICES is set to one GPU + # https://discuss.pytorch.org/t/67488/4 + device = torch.device("cuda:0") + n_gpu = torch.cuda.device_count() + world_size = torch.distributed.get_world_size() + logger.info( + f"device: {device} in world size {world_size}, " + f"visible gpu(s): {os.environ['CUDA_VISIBLE_DEVICES']}/{n_gpu}" + ) +else: + device = torch.device("cuda" if torch.cuda.is_available() else "cpu") + +save_dir = Path(args.save_dir) +if args.local_rank in [0, -1]: + save_dir.mkdir(parents=True, exist_ok=True) + with open(save_dir / "args.json", "w") as f: + json.dump(vars(args), f, indent=2) + # copy all uncommitted changes to the save dir + os.system( + f"git diff > {str(save_dir / 'git_diff_')}{scg.utils.get_git_commit()}.diff" + ) +if IS_DATA_PARALLEL: + torch.distributed.barrier() + +scg.utils.add_file_handler(logger, save_dir / "run.log") +# log running date and current git commit +logger.info(f"Running on {time.strftime('%Y-%m-%d %H:%M:%S')}") +logger.info(f"Current git commit: {scg.utils.get_git_commit()}") + +writer = SummaryWriter(log_dir=save_dir / "tensorboard") +if IS_DATA_PARALLEL: + writer = MainProcessOnly(writer) + + +# %% [markdown] +# # Load and prepare data + + +# TODO: move this to the preprocessing in DataBank +def _map_append_cls(dataset: Dataset) -> Dataset: + logger.info(f"Rank {args.local_rank}: Appending to dataset") + dataset = dataset.map( + lambda example: { + "genes": [vocab[""]] + example["genes"], + "expressions": [args.pad_value] + example["expressions"], + }, + # batched=True, # not using since then the map func needs to loop + num_proc=len(os.sched_getaffinity(0)), + ) + + return dataset + + +# Load data +if args.data_source.endswith("human"): + TISSUE_LIST = [ + "heart", + "blood", + "brain", + "lung", + "kidney", + "intestine", + "pancreas", + "others", + ] + root_data_source = Path(args.data_source).parent + raw_dataset_list = [] + vocab = GeneVocab.from_file(Path(args.vocab_path)) + for tissue in TISSUE_LIST: + tissue_data_path = root_data_source / tissue + cls_prefix_datatable = ( + tissue_data_path / "all_counts" / "cls_prefix_data.parquet" + ) + cache_dir = tissue_data_path / "cache" + tissue_dataset = load_dataset( + "parquet", + data_files=str(cls_prefix_datatable), + split="train", + cache_dir=str(cache_dir), + ) + logger.info(f"Loaded {tissue} examples from {cls_prefix_datatable}") + raw_dataset_list.append(tissue_dataset) + print("merging dataset...") + raw_dataset = concatenate_datasets(raw_dataset_list) + print("done merging dataset") + for s in special_tokens: + if s not in vocab: + vocab.append_token(s) + +elif Path(args.data_source).is_dir() and args.data_source.endswith(".scb"): + # the large-scale data structure + db = DataBank.from_path(args.data_source) + raw_dataset = db.main_data.data + vocab: GeneVocab = db.gene_vocab + for s in special_tokens: + if s not in vocab: + vocab.append_token(s) + if USE_CCE or USE_CLS or MVC: + # load or make the dataset w/ appended at the beginning + cls_prefix_datatable = Path(args.data_source) / "cls_prefix_data.parquet" + if not cls_prefix_datatable.exists(): + if args.local_rank in [0, -1]: + raw_dataset = _map_append_cls(raw_dataset) + raw_dataset.to_parquet(cls_prefix_datatable) + if IS_DATA_PARALLEL: + torch.distributed.barrier() # wait for the mapping to finish + raw_dataset = load_dataset( + "parquet", + data_files=str(cls_prefix_datatable), + split="train", + cache_dir=args.data_source, + ) + logger.info(f"Loaded {len(raw_dataset)} examples from {cls_prefix_datatable}") +elif Path(args.data_source).is_dir(): + # collection of parquet files + parquet_files = [str(f) for f in Path(args.data_source).glob("*.parquet")] + cache_dir = Path(args.data_source).parent / "cache" + vocab = GeneVocab.from_file(Path(args.vocab_path)) + for s in special_tokens: + if s not in vocab: + vocab.append_token(s) + if USE_CCE or USE_CLS or MVC: + # load or make the dataset w/ appended at the beginning + cls_prefix_datatable = Path(args.data_source) / "cls_prefix_data.parquet" + if not cls_prefix_datatable.exists(): + if args.local_rank in [0, -1]: + logger.info(f"Rank {args.local_rank}: Preparing dataset") + raw_dataset = load_dataset( + "parquet", + data_files=parquet_files, + split="train", + cache_dir=str(cache_dir), + ) + raw_dataset = _map_append_cls(raw_dataset) + raw_dataset.to_parquet(str(cls_prefix_datatable)) + if IS_DATA_PARALLEL: + torch.distributed.barrier() # wait for the mapping to finish + raw_dataset = load_dataset( + "parquet", + data_files=str(cls_prefix_datatable), + split="train", + cache_dir=str(cache_dir), + ) + logger.info(f"Loaded {len(raw_dataset)} examples from {cls_prefix_datatable}") +elif Path(args.data_source).is_file(): + adata = sc.read(args.data_source, cache=True) + # Specific the required column names, when loading the data the first time. + # Store the column names for later use. + ( + celltype_col, + str_celltype_col, + gene_col, + batch_key, + ) = scg.utils.find_required_colums( + adata, + id=args.data_source, + configs_dir=Path(args.data_source).parent, + ) + if celltype_col is None: + celltype_col = "int" + str_celltype_col + adata.obs[celltype_col] = scg.utils.category_str2int( + adata.obs[str_celltype_col] + ) +elif args.data_source == "test": # Using test data + raw_dataset = Dataset.from_dict( + { + "id": [1] * 300, + "genes": [[1, 2, 3]] * 300, + "expressions": [[1.0, 2.0, 3.0]] * 300, + } + ) + vocab = GeneVocab.from_dict({"zero": 0, "a": 1, "b": 2, "c": 3}) + for s in special_tokens: + if s not in vocab: + vocab.append_token(s) + +if args.load_model is not None: + model_dir = Path(args.load_model) + model_config_file = model_dir / "args.json" + model_file = model_dir / "best_model.pt" + if len(vocab) != len(json.load(open(model_dir / "vocab.json"))): + raise ValueError( + f"The vocabulary in the model directory to load ({model_dir}) does " + "not match the current vocabulary. " + ) + with open(model_config_file, "r") as f: + model_configs = json.load(f) + if args.pad_token != model_configs["pad_token"]: + logger.warning( + f"The pad token in the model directory to load ({model_dir}) " + "does not match the current pad token. Be careful if this is not expected." + ) + if args.pad_value != model_configs["pad_value"]: + logger.warning( + f"The pad value in the model directory to load ({model_dir}) " + "does not match the current pad value. Be careful if this is not expected." + ) + logger.info( + f"Resume model from {model_file}, the model args will be overridden the " + f"config {model_config_file}." + ) + args.embsize = model_configs["embsize"] + args.nheads = model_configs["nheads"] + args.d_hid = model_configs["d_hid"] + args.nlayers = model_configs["nlayers"] + args.n_layers_cls = model_configs["n_layers_cls"] + + # resave the args with the new values + if args.local_rank in [0, -1]: + with open(save_dir / "args.json", "w") as f: + json.dump(vars(args), f, indent=2) + +# save the vocabulary +if args.local_rank in [0, -1]: + with open(save_dir / "vocab.json", "w") as f: + json.dump( + {token: index for token, index in vocab.get_stoi().items()}, + f, + indent=2, + ) +if IS_DATA_PARALLEL: + torch.distributed.barrier() # wait for saving all the files + +# %% [markdown] +# # Data processing +# convert format to return torch.tensor +raw_dataset = raw_dataset.with_format("torch") + +# split train and validation, +raw_dataset = raw_dataset.train_test_split( + test_size=args.valid_size_or_ratio, shuffle=True +) +train_dataset = raw_dataset["train"] +valid_dataset = raw_dataset["test"] +logger.info(f"train set number of samples: {len(train_dataset)}, ") +logger.info(f"valid set number of samples: {len(valid_dataset)}, ") + +# %% data loading +# data collator for online padding and sampling +# make separate two types of input and output +collator = scg.DataCollator( + do_padding=True if args.max_seq_len is not None else False, + pad_token_id=vocab[args.pad_token], + pad_value=args.pad_value, + do_mlm=True, + do_binning=True if args.input_style == "binned" else False, + mlm_probability=args.mask_ratio, + mask_value=args.mask_value, + max_length=args.max_seq_len, + sampling=args.trunc_by_sample, + data_style=args.training_tasks, +) + +# TODO: try batch sampler, train_sampler = BatchSampler() +train_sampler = ( + DistributedSampler(train_dataset) + if IS_DATA_PARALLEL + else RandomSampler(train_dataset) +) +train_loader = DataLoader( + train_dataset, + batch_size=args.batch_size, + sampler=train_sampler, + collate_fn=collator, + drop_last=False, + num_workers=min(len(os.sched_getaffinity(0)), args.batch_size), + pin_memory=True, + prefetch_factor=4, +) +valid_sampler = ( + DistributedSampler(valid_dataset, shuffle=False) + if IS_DATA_PARALLEL + else SequentialSampler(valid_dataset) +) +valid_loader = DataLoader( + valid_dataset, + batch_size=args.eval_batch_size, + sampler=valid_sampler, + collate_fn=collator, + drop_last=False, + num_workers=min(len(os.sched_getaffinity(0)), args.eval_batch_size), + pin_memory=True, +) + + +# %% [markdown] +""" +## Notes +1. TODO: remember the distributed setting +https://huggingface.co/docs/datasets/v2.3.2/en/process#distributed-usage +2. [Dataset.format](https://huggingface.co/docs/datasets/v2.3.2/en/process#format) +as pytorch conviniently convert to torch.tensors. + + ```python + >>> dataset.reset_format() + >>> dataset.format + {'type': None, + 'format_kwargs': {}, + 'columns': ['id', 'genes', 'expressions'], + 'output_all_columns': False} + >>> dataset = dataset.with_format(type="pytorch") + >>> dataset.format + {'type': 'torch', + 'format_kwargs': {}, + 'columns': ['id', 'genes', 'expressions'], + 'output_all_columns': False} + >>> dataset[0] + {'id': tensor(0), + 'genes': tensor([34797, 16936, 2745, ..., 17076, 17078, 17072]), + 'expressions': tensor([1., 1., 1., ..., 8., 5., 7.])} + ``` +3. Instruction for using with pytorch and achieving the best performance, +[here](https://huggingface.co/docs/datasets/v2.3.2/en/use_with_pytorch). +Some key points: + + - Format to device cpu or gpu + - Use multiple loading processes + - Use a BatchSampler + - Personal suggestion: use the format_transform on the fly +""" + +# %% +if USE_CLS: + celltypes_labels = raw_dataset["celltypes"] + num_types = len(set(celltypes_labels)) + celltypes_labels = np.array(celltypes_labels) + +# # TODO: check gene and other statistics +# max_num_of_non_zero_genes = db.num_genes + +# if args.local_rank in [0, -1]: +# scg.utils.histogram( +# torch.cat(train_dataset[:10000]["expressions"]).numpy(), +# torch.cat(valid_dataset[:10000]["expressions"]).numpy(), +# title="Histogram of clipped values", +# save=save_dir / "histogram_clipped_values.png", +# ) +# if IS_DATA_PARALLEL: +# torch.distributed.barrier() + +# %% [markdown] +# # Create and train scGPT +ntokens = len(vocab) # size of vocabulary +model = TransformerModel( + ntokens, + d_model=args.embsize, + nhead=args.nheads, + d_hid=args.d_hid, + nlayers=args.nlayers, + nlayers_cls=args.n_layers_cls, + n_cls=num_types if USE_CLS else 1, + vocab=vocab, + dropout=args.dropout, + pad_token=args.pad_token, + pad_value=args.pad_value, + do_mvc=MVC, + do_dab=False, + use_batch_labels=False, # TODO: try using batch labels, may help MVC + input_emb_style=args.input_emb_style, + n_input_bins=n_input_bins, + use_generative_training=USE_GENERATIVE_TRAINING, + use_fast_transformer=args.fast_transformer, + fast_transformer_backend="flash", +) +if args.load_model is not None: + try: + model.load_state_dict(torch.load(model_file)) + except: + from collections import OrderedDict + + params = OrderedDict() + for key, value in torch.load(model_file).items(): + params[key.replace("module.", "")] = value + model.load_state_dict(params) +model.to(device) +logger.info(model) +if IS_DATA_PARALLEL: + model = torch.nn.parallel.DistributedDataParallel( + model, + device_ids=[device], + output_device=device, + find_unused_parameters=False, + ) + + +criterion = masked_mse_loss +criterion_cls = nn.CrossEntropyLoss() +optimizer = torch.optim.Adam(model.parameters(), lr=args.lr) + +# setup scheduler +if args.warmup_ratio_or_step > 0: + total_num_batches = len(train_loader) * args.epochs + warmup_steps = ( + int(total_num_batches * args.warmup_ratio_or_step) + if args.warmup_ratio_or_step < 1 + else int(args.warmup_ratio_or_step) + ) + scheduler = transformers.get_cosine_schedule_with_warmup( + optimizer, + num_warmup_steps=warmup_steps, + num_training_steps=total_num_batches, + last_epoch=-1, + ) +else: + scheduler = torch.optim.lr_scheduler.StepLR( + optimizer, args.scheduler_interval, gamma=args.scheduler_factor + ) + +# amp fp16 training +scaler = torch.cuda.amp.GradScaler(enabled=args.fp16) + + +def train(model: nn.Module, train_loader: DataLoader, epoch: int) -> None: + """ + Train the model for one epoch. + """ + model.train() + total_loss, total_mse, total_cls, total_gen, total_mvc = 0.0, 0.0, 0.0, 0.0, 0.0 + total_error = 0.0 + log_interval = args.log_interval + start_time = time.time() + + num_batches = len(train_loader) + for batch, data_dict in enumerate(train_loader): + global_iter = epoch * num_batches + batch + + data_dict = {k: v.to(device) for k, v in data_dict.items()} + if USE_GENERATIVE_TRAINING: + pcpt_gene = data_dict["pcpt_gene"] + pcpt_expr = data_dict["pcpt_expr"] + pcpt_key_padding_mask = pcpt_gene.eq(vocab[args.pad_token]) + gen_gene = data_dict["gen_gene"] + gen_expr_target = target_values = data_dict["gen_expr_target"] + gen_key_padding_mask = gen_gene.eq(vocab[args.pad_token]) + else: + input_gene_ids = data_dict["gene"] + input_values = data_dict["masked_expr"] + target_values = data_dict["expr"] + src_key_padding_mask = input_gene_ids.eq(vocab[args.pad_token]) + + with torch.cuda.amp.autocast(enabled=args.fp16): + if USE_GENERATIVE_TRAINING: + output_dict = model( + pcpt_gene, + pcpt_expr, + pcpt_key_padding_mask, + gen_gene, + gen_key_padding_mask, + CLS=USE_CLS, + MVC=MVC, + generative_training=True, + ) + gen_expr_preds = output_values = output_dict["gen_preds"] + + positions_to_match = ~gen_key_padding_mask + loss = loss_mse = criterion( + gen_expr_preds, gen_expr_target, positions_to_match + ) + writer.add_scalar("train/mse", loss_mse, global_iter) + if MVC: + loss_mvc = criterion( + output_dict["mvc_output"][:, pcpt_gene.shape[1] :], + gen_expr_target, + positions_to_match, + ) + loss = loss + loss_mvc + writer.add_scalar("train/mvc", loss_mvc, global_iter) + else: + output_dict = model( + input_gene_ids, + input_values, + src_key_padding_mask=src_key_padding_mask, + CLS=USE_CLS, + CCE=USE_CCE, # TODO: move these flags to model's attributes + MVC=MVC, + generative_training=False, + ) + output_values = output_dict["mlm_output"] + + positions_to_match = input_values.eq( + args.mask_value + ) # the postions to predict + loss = loss_mse = criterion( + output_values, target_values, positions_to_match + ) + writer.add_scalar("train/mse", loss_mse, global_iter) + if USE_CLS: + target_labels = data_dict["celltypes"] + loss_cls = criterion_cls(output_dict["cls_output"], target_labels) + loss = loss + loss_cls + writer.add_scalar("train/cls", loss_cls, global_iter) + if USE_CCE: + loss_cce = 10 * output_dict["loss_cce"] + loss = loss + loss_cce + writer.add_scalar("train/cce", loss_cce, global_iter) + if MVC: + loss_mvc = criterion( + output_dict["mvc_output"], target_values, positions_to_match + ) + loss = loss + loss_mvc + writer.add_scalar("train/mvc", loss_mvc, global_iter) + writer.add_scalar("train/loss", loss, global_iter) + + if USE_GENERATIVE_TRAINING and global_iter > 1000: + previous_cell_embs = output_dict["cell_emb"].detach() + preds = model( + pcpt_gene, + pcpt_expr, + pcpt_key_padding_mask, + gen_gene, + gen_key_padding_mask, + CLS=False, + MVC=False, + input_cell_emb=previous_cell_embs, + generative_training=True, + )["gen_preds"] + loss_gen = criterion(preds, gen_expr_target, positions_to_match) + loss = loss + loss_gen + writer.add_scalar("train/gen", loss_gen, global_iter) + + # TODO: try this choice of using a separate backprop + # # this part is for the choice of using a separate backprop + # model.zero_grad() + # scaler.scale(loss_gen).backward() + # scaler.unscale_(optimizer) + # torch.nn.utils.clip_grad_norm_( + # model.parameters(), + # 1.0, + # error_if_nonfinite=False if scaler.is_enabled() else True, + # ) + # scaler.step(optimizer) + # scaler.update() + + if args.grad_accu_steps > 1: + loss = loss / args.grad_accu_steps + scaler.scale(loss).backward() + scaler.unscale_(optimizer) + torch.nn.utils.clip_grad_norm_(model.parameters(), 1.0) + scaler.step(optimizer) + scaler.update() + + if args.grad_accu_steps > 1: + if batch % args.grad_accu_steps == 0 or batch == num_batches - 1: + scheduler.step() + optimizer.zero_grad() + else: + scheduler.step() + optimizer.zero_grad() + + with torch.no_grad(): + mre = masked_relative_error( + output_values, target_values, positions_to_match + ) + writer.add_scalar("train/mre", mre, global_iter) + + total_loss += loss.item() + total_mse += loss_mse.item() + total_cls += loss_cls.item() if USE_CLS else 0.0 + total_gen += loss_gen.item() if "loss_gen" in locals() else 0.0 + total_mvc += loss_mvc.item() if MVC else 0.0 + total_error += mre.item() + if args.local_rank in [0, -1] and batch % log_interval == 0 and batch > 0: + # Writer logs gradients distribution + for name, param in model.named_parameters(): + if param.requires_grad and param.grad is not None: + writer.add_histogram(name + "_grad", param.grad, global_iter) + writer.add_histogram(name + "_param", param, global_iter) + + # Log scalar values + lr = scheduler.get_last_lr()[0] + ms_per_batch = (time.time() - start_time) * 1000 / log_interval + cur_loss = total_loss / log_interval + cur_mse = total_mse / log_interval + cur_cls = total_cls / log_interval if USE_CLS else 0.0 + cur_gen = total_gen / log_interval if "loss_gen" in locals() else 0.0 + cur_mvc = total_mvc / log_interval if MVC else 0.0 + cur_error = total_error / log_interval + # ppl = math.exp(cur_loss) + logger.info( + f"| epoch {epoch:3d} | {batch:3d}/{num_batches:3d} batches | " + f"lr {lr:05.4f} | ms/batch {ms_per_batch:5.2f} | " + f"loss {cur_loss:5.2f} | mse {cur_mse:5.2f} | mre {cur_error:5.2f} |" + + (f"cls {cur_cls:5.2f} | " if USE_CLS else "") + + (f"gen {cur_gen:5.2f} |" if "loss_gen" in locals() else "") + + (f"mvc {cur_mvc:5.2f} |" if MVC else "") + ) + writer.add_scalar("lr", lr, global_iter) + + total_loss = 0 + total_mse = 0 + total_cls = 0 + total_gen = 0 + total_mvc = 0 + total_error = 0 + start_time = time.time() + + # immediately eval and save + if batch % args.save_interval == 0 and batch > 0: + eval_and_save(model, valid_loader, global_iter) + model.train() # important, reset to train mode + + +def evaluate(model: nn.Module, valid_loader: DataLoader) -> Dict[str, torch.Tensor]: + """ + Evaluate the model on the evaluation data. + """ + model.eval() + total_loss = 0.0 + total_error = 0.0 + with torch.no_grad(): + for data_dict in valid_loader: + data_dict = {k: v.to(device) for k, v in data_dict.items()} + if USE_GENERATIVE_TRAINING: + pcpt_gene = data_dict["pcpt_gene"] + pcpt_expr = data_dict["pcpt_expr"] + pcpt_key_padding_mask = pcpt_gene.eq(vocab[args.pad_token]) + gen_gene = data_dict["gen_gene"] + gen_expr_target = target_values = data_dict["gen_expr_target"] + gen_key_padding_mask = gen_gene.eq(vocab[args.pad_token]) + else: + input_gene_ids = data_dict["gene"] + input_values = data_dict["masked_expr"] + target_values = data_dict["expr"] + src_key_padding_mask = input_gene_ids.eq(vocab[args.pad_token]) + + with torch.cuda.amp.autocast(enabled=args.fp16): + if USE_GENERATIVE_TRAINING: + output_dict = model( + pcpt_gene, + pcpt_expr, + pcpt_key_padding_mask, + gen_gene, + gen_key_padding_mask, + CLS=False, + MVC=False, + generative_training=True, + ) + gen_expr_preds = output_values = output_dict["gen_preds"] + + positions_to_match = ~gen_key_padding_mask + else: + output_dict = model( + input_gene_ids, + input_values, + src_key_padding_mask=src_key_padding_mask, + CLS=False, # evaluation does not need CLS or CCE + CCE=False, + MVC=False, + generative_training=False, + ) + output_values = output_dict["mlm_output"] + positions_to_match = input_values.eq(args.mask_value) + + loss = criterion(output_values, target_values, positions_to_match) + total_loss += loss.item() + total_error += masked_relative_error( + output_values, target_values, positions_to_match + ).item() + total_loss = total_loss / len(valid_loader) + total_error = total_error / len(valid_loader) + return { + "mse": torch.tensor(total_loss, device=device, dtype=torch.float), + "mre": torch.tensor(total_error, device=device, dtype=torch.float), + } + + +def eval_and_save( + model: nn.Module, + valid_loader: DataLoader, + iter_or_epoch: int, + is_epoch: bool = False, + save: bool = True, +) -> None: + # perform evaluation in distributed data parallel + val_loss, val_mre = evaluate(model, valid_loader).values() + if IS_DATA_PARALLEL: + # gather the results from all the processes + val_loss_list = [torch.zeros_like(val_loss) for _ in range(world_size)] + val_mre_list = [torch.zeros_like(val_mre) for _ in range(world_size)] + torch.distributed.all_gather(val_loss_list, val_loss) + torch.distributed.all_gather(val_mre_list, val_mre) + val_loss = torch.mean(torch.stack(val_loss_list)) + val_mre = torch.mean(torch.stack(val_mre_list)) + val_loss, val_mre = val_loss.item(), val_mre.item() + if args.local_rank in [0, -1]: + if is_epoch: + elapsed = time.time() - epoch_start_time + logger.info("-" * 89) + logger.info( + f"| end of epoch {iter_or_epoch:3d} | time: {elapsed:5.2f}s | " + f"valid loss/mse {val_loss:5.4f} | mre {val_mre:5.4f}" + ) + logger.info(f"{'-' * 89}\n") + writer.add_scalar("valid/mse", val_loss, iter_or_epoch * len(valid_loader)) + writer.add_scalar("valid/mre", val_mre, iter_or_epoch * len(valid_loader)) + else: + logger.info(f"valid loss/mse {val_loss:5.4f} | mre {val_mre:5.4f}") + writer.add_scalar("valid/mse", val_loss, iter_or_epoch) + writer.add_scalar("valid/mre", val_mre, iter_or_epoch) + + global best_val_loss + if val_loss < best_val_loss: + best_val_loss = val_loss + # save the best model + logger.info(f"Saving the best model to {args.save_dir}") + torch.save( + model.module.state_dict() + if isinstance( + model, (nn.DataParallel, nn.parallel.DistributedDataParallel) + ) + else model.state_dict(), + args.save_dir + "/best_model.pt", + ) + + if save: + torch.save( + model.module.state_dict() + if isinstance( + model, (nn.DataParallel, nn.parallel.DistributedDataParallel) + ) + else model.state_dict(), + args.save_dir + f"/model-{'ep' if is_epoch else ''}{iter_or_epoch}.pt", + ) + if IS_DATA_PARALLEL: + torch.distributed.barrier() + + +# %% +best_val_loss = float("inf") +logger.info("Start training") +for epoch in range(1, args.epochs + 1): + epoch_start_time = time.time() + train(model, train_loader, epoch=epoch) + eval_and_save(model, valid_loader, iter_or_epoch=epoch, is_epoch=True) + +writer.flush() +writer.close() + +# %% +# compare with the naive baseline of all ones +data_dict = next(iter(valid_loader)) +input_values = data_dict["masked_expr"] +tagert_values = data_dict["expr"] +predict_ones = torch.ones(input_values.shape, dtype=torch.float32) +mse = masked_mse_loss(predict_ones, tagert_values, input_values.eq(args.mask_value)) +mre = masked_relative_error( + predict_ones, tagert_values, input_values.eq(args.mask_value) +) +logger.info(f"MSE: {mse.item()}, MRE: {mre.item()}") + +# %% [markdown] +# # Analysis +model.to(device) +model.eval() + +# %% [markdown] +# ## Cell embeddings + + +# def map_transform(examples: Dict[str, List]) -> Dict[str, torch.Tensor]: +# """ +# Transform batch examples to a tensor. +# """ +# # tensorize the examples +# examples = { +# k: [torch.tensor(v_i) for v_i in v] for k, v in examples.items() if k != "id" +# } +# examples = collator(examples) +# return examples + + +# valid_dataset.set_transform(map_transform) + +# cell_gene_embeddings = model.encoder(valid_dataset[:10000]["gene"].to(device)) +# cell_gene_embeddings = cell_gene_embeddings.detach().cpu().numpy() + +# cell_embeddings = np.mean(cell_gene_embeddings, axis=1) diff --git a/examples/sbatch_census.sh b/examples/sbatch_census.sh new file mode 100644 index 00000000..c817a446 --- /dev/null +++ b/examples/sbatch_census.sh @@ -0,0 +1,70 @@ +#!/bin/sh +#SBATCH --nodes=1 +#SBATCH --ntasks-per-node=1 +#SBATCH --cpus-per-task=24 +#SBATCH --job-name=scGPT +#SBATCH --mem=150GB +#SBATCH --gres=gpu:4 +#SBATCH --partition=a100 +#SBATCH --output=logs/%x-%j.out +#SBATCH --error=logs/%x-%j.err +#SBATCH --time=10-00:00:00 + +# log the sbatch environment +echo "SLURM_JOBID="$SLURM_JOBID +echo "SLURM_JOB_NODELIST"=$SLURM_JOB_NODELIST +echo "SLURM_JOB_PARTITION"=$SLURM_JOB_PARTITION +echo "SLURM_NNODES"=$SLURM_NNODES +echo "SLURM_GPUS_ON_NODE"=$SLURM_GPUS_ON_NODE +echo "SLURM_SUBMIT_DIR"=$SLURM_SUBMIT_DIR +export NCCL_IB_DISABLE=1 + +# . /etc/profile.d/lmod.sh +bash ~/.bashrc +nvcc --version + +alias python_=path_to_python_env +python_ -c "import torch; print(torch.version.cuda)" + +NPROC=$SLURM_GPUS_ON_NODE +# DATASET="path_to/datasets/3faad104-2ab8-4434-816d-474d8d2641db.scb" +# JOB_NAME="cellxgene_3faad1" +# LOG_INTERVAL=1000 +# VALID_SIZE_OR_RATIO=0.1 +QUERY_NAME="pan-cancer" +DATASET="/scratch/ssd004/datasets/cellxgene/scb_strict/${QUERY_NAME}/all_counts" +JOB_NAME="cellxgene_census_${QUERY_NAME}" +LOG_INTERVAL=2000 +VALID_SIZE_OR_RATIO=0.03 +MAX_LENGTH=1200 +per_proc_batch_size=32 +LAYERS=12 +MODEL_SCALE=8 +SAVE_DIR="/scratch/ssd004/datasets/cellxgene/save" +VOCAB_PATH="path_to/tokenizer/default_census_vocab.json" + +python_ -m torch.distributed.launch \ + --nproc_per_node=$NPROC \ + pretrain.py \ + --data-source $DATASET \ + --save-dir ./save/$JOB_NAME-$(date +%b%d-%H-%M-%Y) \ + --vocab-path ${VOCAB_PATH} \ + --valid-size-or-ratio $VALID_SIZE_OR_RATIO \ + --max-seq-len $MAX_LENGTH \ + --batch-size $per_proc_batch_size \ + --eval-batch-size $(($per_proc_batch_size * 2)) \ + --nlayers $LAYERS \ + --nheads 8 \ + --embsize $((MODEL_SCALE * 64)) \ + --d-hid $((MODEL_SCALE * 64)) \ + --grad-accu-steps 1 \ + --epochs 6 \ + --lr 0.0001 \ + --warmup-ratio-or-step 10000 \ + --log-interval $LOG_INTERVAL \ + --save-interval $(($LOG_INTERVAL * 3)) \ + --trunc-by-sample \ + --no-cls \ + --no-cce \ + --fp16 | + awk '{ print strftime("[%Y-%m-%d %H:%M:%S]"), $0; fflush(); }' diff --git a/scgpt/data_collator.py b/scgpt/data_collator.py index 9769eba2..7ad53e46 100644 --- a/scgpt/data_collator.py +++ b/scgpt/data_collator.py @@ -1,4 +1,4 @@ -from dataclasses import dataclass +from dataclasses import dataclass, field from typing import Any, Dict, List, Mapping, Optional, Tuple, Union import torch @@ -28,10 +28,18 @@ class DataCollator: This is required if do_padding is True. sampling (:obj:`bool`): whether to do sampling instead of truncation if length > max_length. + reserve_keys (:obj:`List[str]`, optional): a list of keys in the examples + to reserve in the output dictionary. Default to []. These fields + will be kept unchanged in the output. keep_first_n_tokens (:obj:`int`): the number of tokens in the beginning of the sequence to keep unchanged from sampling. This is useful when special tokens have been added to the beginning of the sequence. Default to 1. + data_style (:obj:`str`): the style of the data. If "pcpt", the data is + masked and padded for perception training. If "gen", only the gene + tokens are provided, but not the expression values, for pure generative + training setting. If "both", the output will contain both fields above. + Choices: "pcpt", "gen", "both". Default to "pcpt". """ do_padding: bool = True @@ -43,7 +51,9 @@ class DataCollator: mask_value: int = -1 max_length: Optional[int] = None sampling: bool = True + reserve_keys: List[str] = field(default_factory=lambda: []) keep_first_n_tokens: int = 1 + data_style: str = "pcpt" def __post_init__(self): if self.do_padding: @@ -52,8 +62,17 @@ def __post_init__(self): if self.max_length is None: raise ValueError("`max_length` is required if `do_padding`.") - if self.mlm_probability <= 0 or self.mlm_probability >= 1: - raise ValueError("`mlm_probability` must be between 0 and 1.") + if isinstance(self.mlm_probability, float): + if self.mlm_probability <= 0 or self.mlm_probability >= 1: + raise ValueError("`mlm_probability` must be between 0 and 1.") + elif isinstance(self.mlm_probability, (list, tuple)): + if min(self.mlm_probability) <= 0 or max(self.mlm_probability) >= 1: + raise ValueError("`mlm_probability` must be between 0 and 1.") + else: + raise ValueError("`mlm_probability` must be a float or iterable of floats.") + + if isinstance(self.reserve_keys, str): + self.reserve_keys = [self.reserve_keys] if self.keep_first_n_tokens < 0 or self.keep_first_n_tokens > self.max_length: raise ValueError( @@ -61,14 +80,60 @@ def __post_init__(self): f"({self.max_length})." ) + if self.data_style not in ["pcpt", "gen", "both"]: + raise ValueError("`data_style` must be one of 'pcpt', 'gen', 'both'.") + def __call__( self, examples: List[Dict[str, torch.Tensor]] + ) -> Dict[str, torch.Tensor]: + """ + Args: + examples (:obj:`List[Dict[str, torch.Tensor]]`): a list of data dicts. + Each dict is for one cell. It contains multiple 1 dimensional tensors + like the following exmaple: + {'id': tensor(184117), + 'genes': tensor([36572, 17868, ..., 17072]), + 'expressions': tensor([ 0., 2., ..., 18.])} + + Returns: + :obj:`Dict[str, torch.Tensor]`: a dict of tensors. + """ + + if len(self.reserve_keys) > 0: + assert all(key in examples[0] for key in self.reserve_keys), ( + f"reserve_keys must be a subset of the keys in the examples. " + f"Got {self.reserve_keys} but expected keys in {list(examples[0].keys())}." + ) + + if self.data_style == "pcpt": + data_dict = self._call_pcpt(examples) + elif self.data_style == "gen": + data_dict = self._call_gen(examples) + elif self.data_style == "both": + data_dict = self._call_both(examples) + + # add reserved keys + device = examples[0]["genes"].device + for key in self.reserve_keys: + data_ = [example[key] for example in examples] + data_dict[key] = torch.stack(data_, dim=0).to(device) + + return data_dict + + def _call_pcpt( + self, examples: List[Dict[str, torch.Tensor]] ) -> Dict[str, torch.Tensor]: """ Each example is like: {'id': tensor(184117), 'genes': tensor([36572, 17868, ..., 17072]), 'expressions': tensor([ 0., 2., ..., 18.])} + + Args: + examples (:obj:`List[Dict[str, torch.Tensor]]`): a list of examples. + Each example is a dictionary of tensors. + Returns: + :obj:`Dict[str, torch.Tensor]`: a dictionary of tensors. """ if not isinstance(examples[0], Mapping): return NotImplementedError @@ -105,21 +170,261 @@ def __call__( # mask if self.do_mlm: - masked_expressions = self._mask(padded_expressions) + masked_expressions = self._mask( + padded_expressions, self.keep_first_n_tokens + ) else: masked_expressions = padded_expressions data_dict["masked_expr"] = masked_expressions return data_dict - def _mask(self, expressions: torch.Tensor) -> torch.Tensor: + def _call_gen( + self, examples: List[Dict[str, torch.Tensor]] + ) -> Dict[str, torch.Tensor]: + """ + This method will simply return the gene ids, with needed padding. There is + no masking for pure generative training, and no input of expr values. + + Each example is like: + {'id': tensor(184117), + 'genes': tensor([36572, 17868, ..., 17072])} + + Returns: + Dict[str, torch.Tensor]: a dict of tensors. + Example: + {'pcpt_gene': tensor([[36572, 17868, ..., 17072], + [36572, 17868, ..., 17072], + ..., + [36572, 17868, ..., 17072]]), + 'pcpt_expr': tensor([[ 0., 2., ..., 18.], + [ 0., 2., ..., 18.], + ..., + [ 0., 2., ..., 18.]])} + """ + + if not isinstance(examples[0], Mapping): + return NotImplementedError + + device = examples[0]["genes"].device + + max_ori_len = max(len(example["genes"]) for example in examples) + _max_length = self.max_length if max_ori_len >= self.max_length else max_ori_len + + # pad and truncate + padded_pcpt_genes = [] + padded_pcpt_expressions = [] + for i in range(len(examples)): + genes = examples[i]["genes"] + expressions = examples[i]["expressions"] + if self.do_binning: + expressions[self.keep_first_n_tokens :] = binning( + row=expressions[self.keep_first_n_tokens :], + n_bins=51, # FIXME: replace with self.n_bins + ) + genes, expressions = self._sample_or_truncate_plus_pad( + genes, expressions, _max_length + ) + padded_pcpt_genes.append(genes) + padded_pcpt_expressions.append(expressions) + + padded_pcpt_genes = torch.stack(padded_pcpt_genes, dim=0).to(device) + padded_pcpt_expressions = torch.stack(padded_pcpt_expressions, dim=0).to(device) + + data_dict = { + "pcpt_gene": padded_pcpt_genes, + "pcpt_expr": padded_pcpt_expressions, + } + return data_dict + + def _call_both( + self, + examples: List[Dict[str, torch.Tensor]], + gen_prob: Optional[float] = None, + ) -> Dict[str, torch.Tensor]: + """ + This method will split the input into the peception part and the generation + part. The perception part will be processed into gene ids and expr values, + and the generation part will be processed into gene ids only. + + By default, the mlm_probability will be used to select the genese assigned to + the generation part. + + Each example is like: + {'id': tensor(184117), + 'genes': tensor([36572, 17868, ..., 17072]), + 'expressions': tensor([ 0., 2., ..., 18.])} + + Args: + gen_prob (float, optional): the probability of a gene being assigned to + the generation part. If not provided, the mlm_probability will be used. + + Returns: + Dict[str, torch.Tensor]: a dict of tensors. + Example: + {'pcpt_gene': tensor([[36572, 17868, ..., 17072], + [36572, 17868, ..., 17072], + ..., + [36572, 17868, ..., 17072]]), + 'pcpt_expr': tensor([[ 0., 2., ..., 18.], + [ 0., 2., ..., 18.], + ..., + [ 0., 2., ..., 18.]]), + 'gen_gene': tensor([[36573, 17869, ..., 17073], + [36573, 17869, ..., 17073], + ..., + [36573, 17869, ..., 17073]]), + 'gen_expr_target': tensor([[ 1., 3., ..., 19.], + [ 1., 3., ..., 19.], + ..., + [ 1., 3., ..., 19.]])} + """ + if not isinstance(examples[0], Mapping): + return NotImplementedError + + if not self.do_mlm: + # if not doing mlm, then the perceptrual part is the whole input + return self._call_gen(examples) + + if gen_prob is None: + gen_prob = self.get_mlm_probability() + + device = examples[0]["genes"].device + + max_ori_len = max(len(example["genes"]) for example in examples) + _max_length = self.max_length if max_ori_len >= self.max_length else max_ori_len + + gen_length = int((_max_length - self.keep_first_n_tokens) * gen_prob) + pcpt_length = _max_length - gen_length # perception part length + + # pad and truncate + padded_pcpt_genes = [] + padded_pcpt_expressions = [] + padded_gen_genes = [] + padded_gen_expressions = [] + for i in range(len(examples)): + genes = examples[i]["genes"] + expressions = examples[i]["expressions"] + if self.do_binning: + expressions[self.keep_first_n_tokens :] = binning( + row=expressions[self.keep_first_n_tokens :], + n_bins=51, + ) + + ( + gen_genes, + gen_expressions, + pcpt_genes, + pcpt_expressions, + ) = self._random_split( + genes[self.keep_first_n_tokens :], + expressions[self.keep_first_n_tokens :], + ratio=gen_prob, + ) + pcpt_genes = torch.cat( + (genes[: self.keep_first_n_tokens], pcpt_genes), dim=0 + ) + pcpt_expressions = torch.cat( + (expressions[: self.keep_first_n_tokens], pcpt_expressions), dim=0 + ) + + pcpt_genes, pcpt_expressions = self._sample_or_truncate_plus_pad( + pcpt_genes, pcpt_expressions, pcpt_length + ) # torch tensors of length pcpt_length + padded_pcpt_genes.append(pcpt_genes) + padded_pcpt_expressions.append(pcpt_expressions) + + gen_genes, gen_expressions = self._sample_or_truncate_plus_pad( + gen_genes, gen_expressions, gen_length + ) # torch tensors of length gen_length + padded_gen_genes.append(gen_genes) + padded_gen_expressions.append(gen_expressions) + + padded_pcpt_genes = torch.stack(padded_pcpt_genes, dim=0) + padded_pcpt_expressions = torch.stack(padded_pcpt_expressions, dim=0) + padded_gen_genes = torch.stack(padded_gen_genes, dim=0) + padded_gen_expressions = torch.stack(padded_gen_expressions, dim=0) + + data_dict = { + "pcpt_gene": padded_pcpt_genes, + "pcpt_expr": padded_pcpt_expressions, + "gen_gene": padded_gen_genes, + "gen_expr_target": padded_gen_expressions, + } + + return data_dict + + def _random_split( + self, + *arrays: torch.Tensor, + ratio: float, + ) -> Tuple[torch.Tensor, ...]: + """ + Randomly split the arrays into two parts. The first part will have the + length of `ratio * length`, and the second part will have the length of + `(1 - ratio) * length`. When multiple arrays are provided, they are supposed + to have the same length. + + This method reflects the behavior of `sklearn.model_selection.train_test_split` + + Args: + *arrays (torch.Tensor): the arrays to be split. + ratio (float): the ratio of the first part. + + Returns: + Tuple[torch.Tensor, ...]: the split arrays. + """ + assert len(arrays) > 0 + assert 0 < ratio < 1 + if len(arrays) > 1: + assert all( + array.shape[0] == arrays[0].shape[0] for array in arrays + ), "The arrays must have the same length." + + length = arrays[0].shape[0] + split_index = int(length * ratio) + + indices = torch.randperm(length, device=arrays[0].device) + first_part_indices = indices[:split_index] + second_part_indices = indices[split_index:] + + first_parts = tuple(array[first_part_indices] for array in arrays) + second_parts = tuple(array[second_part_indices] for array in arrays) + + return first_parts + second_parts + + def get_mlm_probability(self) -> float: + """ + Get the mlm probability for the current step. + """ + if isinstance(self.mlm_probability, float): + return self.mlm_probability + elif isinstance(self.mlm_probability, list): + # random choose a probability + return np.random.choice(self.mlm_probability) + else: + raise ValueError( + "mlm_probability must be a float or a list of floats, " + f"but got {self.mlm_probability}." + ) + + def _mask( + self, expressions: torch.Tensor, keep_first_n_tokens: int = 0 + ) -> torch.Tensor: """ Mask the expression values with MLM. """ + if keep_first_n_tokens > 0: + result_ = self._mask( + expressions[:, keep_first_n_tokens:], + keep_first_n_tokens=0, + ) + return torch.cat([expressions[:, :keep_first_n_tokens], result_], dim=1) + device = expressions.device shape = expressions.shape - probability_matrix = torch.full(shape, self.mlm_probability) + probability_matrix = torch.full(shape, self.get_mlm_probability()) # set padded postion probability to 0 probability_matrix[expressions.eq(self.pad_value)] = 0 if self.keep_first_n_tokens > 0: diff --git a/scgpt/model/flash_layers.py b/scgpt/model/flash_layers.py new file mode 100644 index 00000000..af1fefd4 --- /dev/null +++ b/scgpt/model/flash_layers.py @@ -0,0 +1,427 @@ +from functools import lru_cache +import math +from typing import Optional + +from einops import rearrange +import torch +import torch.nn as nn +import torch.nn.functional as F +from torch import Tensor +from torch.nn.modules.transformer import _get_clones + +from flash_attn.flash_attn_interface import flash_attn_unpadded_qkvpacked_func +from flash_attn.bert_padding import unpad_input, pad_input +from flash_attn.flash_attention import FlashAttention +from flash_attn.modules.mha import FlashCrossAttention +from .layers import MultiheadAttention + + +class FlashscGPTMHA(nn.Module): + """ + Custom MHA layer for scGPT. This takes two separate forward passes on the pect + genes, and on the gen genes. + """ + + def __init__( + self, + embed_dim, + num_heads, + bias=True, + batch_first=True, + attention_dropout=0.0, + causal=False, + device=None, + dtype=None, + ) -> None: + assert batch_first + factory_kwargs = {"device": device, "dtype": dtype} + super().__init__() + self.embed_dim = embed_dim + self.causal = causal + + self.num_heads = num_heads + assert ( + self.embed_dim % num_heads == 0 + ), "self.kdim must be divisible by num_heads" + self.head_dim = self.embed_dim // num_heads + assert ( + self.head_dim % 8 == 0 and self.head_dim <= 128 + ), "Only support head_dim <= 128 and divisible by 8" + + self.Wqkv = nn.Linear(embed_dim, 3 * embed_dim, bias=bias, **factory_kwargs) + self.self_attn = FlashAttention(attention_dropout=attention_dropout) + self.cross_attn = MultiheadAttention( + embed_dim, + num_heads, + dropout=attention_dropout, + batch_first=batch_first, + **factory_kwargs, + ) + # self.cross_attn = FlashCrossAttention(attention_dropout=attention_dropout) + # for cross attetion, launch multiple queries in parallel, each query is just + # a single gen gene. Then each kv is the entire set of pect genes plus this gen + # gene together. + # In practice, we can simply put these queries in the batch dimension, and then + # they can be processed in parallel. + self.out_proj = nn.Linear(embed_dim, embed_dim, bias=bias, **factory_kwargs) + + def forward( + self, + pcpt_total_embs: Tensor, + gen_total_embs: Tensor, + pcpt_key_padding_mask: Optional[Tensor] = None, + gen_key_padding_mask: Optional[Tensor] = None, + need_weights=False, + ): + """ + pcpt_total_embs: (batch, pcpt_len, hidden_dim) (where hidden_dim = num heads * head dim) + gen_total_embs: (batch, gen_len, hidden_dim) + pcpt_key_padding_mask: bool tensor of shape (batch, pcpt_len), 1 means valid and 0 means not valid. + gen_key_padding_mask: bool tensor of shape (batch, gen_len), 1 means valid and 0 means not valid. + """ + pcpt_qkv = self.Wqkv(pcpt_total_embs) + + pcpt_qkv = rearrange( + pcpt_qkv, "b s (three h d) -> b s three h d", three=3, h=self.num_heads + ) + + # full self attention on pcpt genes + pcpt_context, pcpt_attn_weights = self.self_attn( + pcpt_qkv, + key_padding_mask=pcpt_key_padding_mask, + need_weights=need_weights, + causal=self.causal, + ) + pcpt_context = self.out_proj(rearrange(pcpt_context, "b s h d -> b s (h d)")) + + if gen_total_embs is None: + return (pcpt_context, None), (pcpt_attn_weights, None) + + gen_qkv = self.Wqkv(gen_total_embs) + gen_qkv = rearrange( + gen_qkv, "b s (three h d) -> b s three h d", three=3, h=self.num_heads + ) + + # CROSS ATTENTION USING RAW PYTORCH IMPLEMENTATION + cross_q = gen_qkv[:, :, 0, :, :] # (batch, gen_len, nheads, head_dim) + cross_q = rearrange(cross_q, "b gen_s h d -> b gen_s (h d)") + cross_kv = torch.cat( + [pcpt_qkv[:, :, 1:, :, :], gen_qkv[:, :, 1:, :, :]], dim=1 + ) # (batch, pcpt_seq+gen_seq, 2, nheads, head_dim) + cross_kv = rearrange(cross_kv, "b pcpt_gen_s two h d -> b pcpt_gen_s two (h d)") + + # make the attention mask, for pytorch implementation, true means attention is not allowed + @lru_cache(maxsize=1) + def make_mask(q_len, k_len, device): + attention_mask = torch.zeros( + (q_len, k_len), device=device, dtype=torch.bool + ) # (gen_len, pcpt_len+gen_len) + # make the last gen_len by gen_gen to be true, only the diagonal is allowed with false + attention_mask[:, -q_len:] = ~torch.eye( + q_len, device=device, dtype=torch.bool + ) + return attention_mask + + attention_mask = make_mask(cross_q.shape[1], cross_kv.shape[1], cross_q.device) + + if pcpt_key_padding_mask is None and gen_key_padding_mask is None: + key_padding_mask = None + else: + if pcpt_key_padding_mask is None: + pcpt_key_padding_mask = torch.ones( + (pcpt_qkv.shape[0], pcpt_qkv.shape[1]), + device=pcpt_qkv.device, + dtype=torch.bool, + ) + elif gen_key_padding_mask is None: + gen_key_padding_mask = torch.ones( + (gen_qkv.shape[0], gen_qkv.shape[1]), + device=gen_qkv.device, + dtype=torch.bool, + ) + key_padding_mask = ~torch.cat( + [pcpt_key_padding_mask, gen_key_padding_mask], dim=1 + ) + cross_context, _ = self.cross_attn( + cross_q, + cross_kv[:, :, 0, :], + cross_kv[:, :, 1, :], + key_padding_mask=key_padding_mask, + attn_mask=attention_mask, + ) + gen_context = cross_context # (batch, gen_len, hidden_dim) + gen_attn_weights = None + + # # CROSS ATTENTION ON GEN GENES + # # prepare cross_q, where each query is per only one gen gene + # cross_q = gen_qkv[:, :, 0, :, :] # (batch, gen_len, nheads, head_dim) + # cross_q = rearrange(cross_q, "b s h d -> b s (h d)") + # cross_q_unpad, indices_q, cu_seq_len_q, max_seqlen_q = unpad_input( + # cross_q, gen_key_padding_mask + # ) + # # if not care about padding (b gen_s) 1 (h d) + + # # the input to cross attention, q needs to be (total_q, nheads, head_dim) + + # # prepare gen_kv, where each kv is this gen gene plus the entire set of pect genes + # # if not care about padding (b gen_s) pcpt_seq+1 (h d) + + # # call cross attention + # gen_context, gen_attn_weights = self.cross_attn( + # gen_q, + # gen_kv, + # q_padding_mask=gen_key_padding_mask, + # kv_padding_mask=pcpt_key_padding_mask, + # need_weights=need_weights, + # ) + # # rearrange output to (batch, gen_len, hidden_dim) + + # # TEMP TEST + # gen_context, gen_attn_weights = self.self_attn( + # gen_qkv, + # key_padding_mask=gen_key_padding_mask, + # need_weights=need_weights, + # causal=self.causal, + # ) + # gen_context = self.out_proj(rearrange(gen_context, "b s h d -> b s (h d)")) + + return (pcpt_context, gen_context), (pcpt_attn_weights, gen_attn_weights) + + +class FlashscGPTLayer(nn.Module): + r"""TransformerEncoderLayer is made up of self-attn and feedforward network. + The class is modified from torch.nn.TransformerEncoderLayer to support the + FlashAttention. + + Args: + d_model: the number of expected features in the input (required). + nhead: the number of heads in the multiheadattention models (required). + dim_feedforward: the dimension of the feedforward network model (default=2048). + dropout: the dropout value (default=0.1). + activation: the activation function of intermediate layer, relu or gelu (default=relu). + layer_norm_eps: the eps value in layer normalization components (default=1e-5). + batch_first: If ``True``, then the input and output tensors are provided + as (batch, seq, feature). Default: ``False``. + + Examples:: + >>> encoder_layer = nn.TransformerEncoderLayer(d_model=512, nhead=8) + >>> src = torch.rand(10, 32, 512) + >>> out = encoder_layer(src) + + Alternatively, when ``batch_first`` is ``True``: + >>> encoder_layer = nn.TransformerEncoderLayer(d_model=512, nhead=8, batch_first=True) + >>> src = torch.rand(32, 10, 512) + >>> out = encoder_layer(src) + """ + __constants__ = ["batch_first"] + + def __init__( + self, + d_model, + nhead, + dim_feedforward=2048, + dropout=0.1, + activation="relu", + layer_norm_eps=1e-5, + batch_first=True, + device=None, + dtype=None, + norm_scheme="post", # "pre" or "post" + ) -> None: + super().__init__() + factory_kwargs = {"device": device, "dtype": dtype} + self.self_attn = FlashscGPTMHA( + embed_dim=d_model, + num_heads=nhead, + batch_first=batch_first, + attention_dropout=dropout, + **factory_kwargs, + ) + # Implementation of Feedforward model + self.linear1 = nn.Linear(d_model, dim_feedforward, **factory_kwargs) + self.dropout = nn.Dropout(dropout) + self.linear2 = nn.Linear(dim_feedforward, d_model, **factory_kwargs) + + self.norm1 = nn.LayerNorm(d_model, eps=layer_norm_eps, **factory_kwargs) + self.norm2 = nn.LayerNorm(d_model, eps=layer_norm_eps, **factory_kwargs) + self.dropout1 = nn.Dropout(dropout) + self.dropout2 = nn.Dropout(dropout) + + self.activation = self._get_activation_fn(activation) + self.norm_scheme = norm_scheme + if norm_scheme not in ["pre", "post"]: + raise ValueError("norm_scheme must be either pre or post") + + @staticmethod + def _get_activation_fn(activation): + if activation == "relu": + return F.relu + elif activation == "gelu": + return F.gelu + + raise RuntimeError("activation should be relu/gelu, not {}".format(activation)) + + def __setstate__(self, state): + if "activation" not in state: + state["activation"] = F.relu + super().__setstate__(state) + + def _reverse_key_padding_mask(self, src_key_padding_mask): + """ + Reverse the true false values of the key padding mask. This is because + we follow pytorch rule that the mask is True for padded tokens, but + in the inner flash MHA, it assumes the mask is False for padded tokens. + """ + if src_key_padding_mask is None: + return None + + if not src_key_padding_mask.any().item(): + # no padding tokens in src + return None + return ~src_key_padding_mask + + def forward( + self, + pcpt_total_embs: Tensor, + gen_total_embs: Tensor, + pcpt_key_padding_mask: Optional[Tensor] = None, + gen_key_padding_mask: Optional[Tensor] = None, + ) -> Tensor: + r"""Pass the input through the encoder layer. + + Args: + src: the sequence to the encoder layer (required). + src_mask: the mask for the src sequence (optional). + src_key_padding_mask: the mask for the src keys per batch (optional). + + Shape: + see the docs in Transformer class. + """ + + pcpt_key_padding_mask_ = self._reverse_key_padding_mask(pcpt_key_padding_mask) + gen_key_padding_mask_ = self._reverse_key_padding_mask(gen_key_padding_mask) + + if self.norm_scheme == "pre": + pcpt_total_embs = self.norm1(pcpt_total_embs) + if gen_total_embs is not None: + gen_total_embs = self.norm1(gen_total_embs) + pcpt_total_embs2, gen_total_embs2 = self.self_attn( + pcpt_total_embs, + gen_total_embs, + pcpt_key_padding_mask=pcpt_key_padding_mask_, + gen_key_padding_mask=gen_key_padding_mask_, + )[0] + pcpt_total_embs = pcpt_total_embs + self.dropout1(pcpt_total_embs2) + pcpt_total_embs = self.norm2(pcpt_total_embs) + pcpt_total_embs2 = self.linear2( + self.dropout(self.activation(self.linear1(pcpt_total_embs))) + ) + pcpt_total_embs = pcpt_total_embs + self.dropout2(pcpt_total_embs2) + + if gen_total_embs is not None: + gen_total_embs = gen_total_embs + self.dropout1(gen_total_embs2) + gen_total_embs = self.norm2(gen_total_embs) + gen_total_embs2 = self.linear2( + self.dropout(self.activation(self.linear1(gen_total_embs))) + ) + gen_total_embs = gen_total_embs + self.dropout2(gen_total_embs2) + else: + pcpt_total_embs2, gen_total_embs2 = self.self_attn( + pcpt_total_embs, + gen_total_embs, + pcpt_key_padding_mask=pcpt_key_padding_mask_, + gen_key_padding_mask=gen_key_padding_mask_, + )[0] + pcpt_total_embs = pcpt_total_embs + self.dropout1(pcpt_total_embs2) + pcpt_total_embs = self.norm1(pcpt_total_embs) + pcpt_total_embs2 = self.linear2( + self.dropout(self.activation(self.linear1(pcpt_total_embs))) + ) + pcpt_total_embs = pcpt_total_embs + self.dropout2(pcpt_total_embs2) + pcpt_total_embs = self.norm2(pcpt_total_embs) + + if gen_total_embs is not None: + gen_total_embs = gen_total_embs + self.dropout1(gen_total_embs2) + gen_total_embs = self.norm1(gen_total_embs) + gen_total_embs2 = self.linear2( + self.dropout(self.activation(self.linear1(gen_total_embs))) + ) + gen_total_embs = gen_total_embs + self.dropout2(gen_total_embs2) + gen_total_embs = self.norm2(gen_total_embs) + + return pcpt_total_embs, gen_total_embs + + +class FlashscGPTGenerator(nn.Module): + # takes in the set of different inputs in an mapping + r"""TransformerEncoder is a stack of N encoder layers. Users can build the + BERT(https://arxiv.org/abs/1810.04805) model with corresponding parameters. + + Args: + encoder_layer: an instance of the TransformerEncoderLayer() class (required). + num_layers: the number of sub-encoder-layers in the encoder (required). + norm: the layer normalization component (optional). + enable_nested_tensor: if True, input will automatically convert to nested tensor + (and convert back on output). This will improve the overall performance of + TransformerEncoder when padding rate is high. Default: ``True`` (enabled). + + Examples:: + >>> encoder_layer = nn.TransformerEncoderLayer(d_model=512, nhead=8) + >>> transformer_encoder = nn.TransformerEncoder(encoder_layer, num_layers=6) + >>> src = torch.rand(10, 32, 512) + >>> out = transformer_encoder(src) + """ + __constants__ = ["norm"] + + def __init__( + self, + encoder_layer, + num_layers, + norm=None, + mask_check=True, + ): + super().__init__() + self.layers = _get_clones(encoder_layer, num_layers) + self.num_layers = num_layers + self.norm = norm + self.mask_check = mask_check + + def forward( + self, + pcpt_total_embs: Tensor, + gen_total_embs: Tensor, + pcpt_key_padding_mask: Optional[Tensor] = None, + gen_key_padding_mask: Optional[Tensor] = None, + ) -> Tensor: + r"""Pass the input through the encoder layers in turn. + + Args: + src: the sequence to the encoder (required). + mask: the mask for the src sequence (optional). + src_key_padding_mask: the mask for the src keys per batch (optional). + + Shape: + see the docs in Transformer class. + """ + if pcpt_key_padding_mask is not None: + _skpm_dtype = pcpt_key_padding_mask.dtype + if _skpm_dtype != torch.bool and not torch.is_floating_point( + pcpt_key_padding_mask + ): + raise AssertionError( + "only bool and floating types of key_padding_mask are supported" + ) + + for mod in self.layers: + pcpt_total_embs, gen_total_embs = mod( + pcpt_total_embs, + gen_total_embs, + pcpt_key_padding_mask, + gen_key_padding_mask, + ) + + if self.norm is not None: + pcpt_total_embs = self.norm(pcpt_total_embs) + gen_total_embs = self.norm(gen_total_embs) + + return pcpt_total_embs, gen_total_embs diff --git a/scgpt/model/layers.py b/scgpt/model/layers.py new file mode 100644 index 00000000..40d84f63 --- /dev/null +++ b/scgpt/model/layers.py @@ -0,0 +1,165 @@ +from typing import Optional, Tuple + +import torch +from torch import Tensor +from torch.nn import Module +from torch.nn import functional as F +from torch.nn.init import constant_, xavier_normal_, xavier_uniform_ +from torch.nn.parameter import Parameter + + +class MultiheadAttention(Module): + r"""Allows the model to jointly attend to information + from different representation subspaces as described in the paper: + `Attention Is All You Need `_. + + This module is modified from the original torch.nn.MultiheadAttention + + """ + __constants__ = ["batch_first"] + + def __init__( + self, + embed_dim, + num_heads, + dropout=0.0, + batch_first=True, + device=None, + dtype=None, + ) -> None: + factory_kwargs = {"device": device, "dtype": dtype} + super(MultiheadAttention, self).__init__() + self.embed_dim = embed_dim + self._qkv_same_embed_dim = True + + self.num_heads = num_heads + self.dropout = dropout + self.batch_first = batch_first + self.head_dim = embed_dim // num_heads + assert ( + self.head_dim * num_heads == self.embed_dim + ), "embed_dim must be divisible by num_heads" + + # an identity out_proj + self.in_proj_weight = torch.eye(embed_dim, **factory_kwargs) + self.out_proj_weight = torch.eye(embed_dim, **factory_kwargs) + + def __setstate__(self, state): + # Support loading old MultiheadAttention checkpoints generated by v1.1.0 + if "_qkv_same_embed_dim" not in state: + state["_qkv_same_embed_dim"] = True + + super(MultiheadAttention, self).__setstate__(state) + + def _apply(self, fn): + self.in_proj_weight = fn(self.in_proj_weight) + self.out_proj_weight = fn(self.out_proj_weight) + return super()._apply(fn) + + def forward( + self, + query: Tensor, + key: Tensor, + value: Tensor, + key_padding_mask: Optional[Tensor] = None, + need_weights: bool = True, + attn_mask: Optional[Tensor] = None, + average_attn_weights: bool = True, + ) -> Tuple[Tensor, Optional[Tensor]]: + r""" + Args: + query: Query embeddings of shape :math:`(L, E_q)` for unbatched input, :math:`(L, N, E_q)` when ``batch_first=False`` + or :math:`(N, L, E_q)` when ``batch_first=True``, where :math:`L` is the target sequence length, + :math:`N` is the batch size, and :math:`E_q` is the query embedding dimension ``embed_dim``. + Queries are compared against key-value pairs to produce the output. + See "Attention Is All You Need" for more details. + key: Key embeddings of shape :math:`(S, E_k)` for unbatched input, :math:`(S, N, E_k)` when ``batch_first=False`` + or :math:`(N, S, E_k)` when ``batch_first=True``, where :math:`S` is the source sequence length, + :math:`N` is the batch size, and :math:`E_k` is the key embedding dimension ``kdim``. + See "Attention Is All You Need" for more details. + value: Value embeddings of shape :math:`(S, E_v)` for unbatched input, :math:`(S, N, E_v)` when + ``batch_first=False`` or :math:`(N, S, E_v)` when ``batch_first=True``, where :math:`S` is the source + sequence length, :math:`N` is the batch size, and :math:`E_v` is the value embedding dimension ``vdim``. + See "Attention Is All You Need" for more details. + key_padding_mask: If specified, a mask of shape :math:`(N, S)` indicating which elements within ``key`` + to ignore for the purpose of attention (i.e. treat as "padding"). For unbatched `query`, shape should be :math:`(S)`. + Binary and byte masks are supported. + For a binary mask, a ``True`` value indicates that the corresponding ``key`` value will be ignored for + the purpose of attention. For a float mask, it will be directly added to the corresponding ``key`` value. + need_weights: If specified, returns ``attn_output_weights`` in addition to ``attn_outputs``. + Default: ``True``. + attn_mask: If specified, a 2D or 3D mask preventing attention to certain positions. Must be of shape + :math:`(L, S)` or :math:`(N\cdot\text{num\_heads}, L, S)`, where :math:`N` is the batch size, + :math:`L` is the target sequence length, and :math:`S` is the source sequence length. A 2D mask will be + broadcasted across the batch while a 3D mask allows for a different mask for each entry in the batch. + Binary, byte, and float masks are supported. For a binary mask, a ``True`` value indicates that the + corresponding position is not allowed to attend. For a byte mask, a non-zero value indicates that the + corresponding position is not allowed to attend. For a float mask, the mask values will be added to + the attention weight. + average_attn_weights: If true, indicates that the returned ``attn_weights`` should be averaged across + heads. Otherwise, ``attn_weights`` are provided separately per head. Note that this flag only has an + effect when ``need_weights=True``. Default: ``True`` (i.e. average weights across heads) + + Outputs: + - **attn_output** - Attention outputs of shape :math:`(L, E)` when input is unbatched, + :math:`(L, N, E)` when ``batch_first=False`` or :math:`(N, L, E)` when ``batch_first=True``, + where :math:`L` is the target sequence length, :math:`N` is the batch size, and :math:`E` is the + embedding dimension ``embed_dim``. + - **attn_output_weights** - Only returned when ``need_weights=True``. If ``average_attn_weights=True``, + returns attention weights averaged across heads of shape :math:`(L, S)` when input is unbatched or + :math:`(N, L, S)`, where :math:`N` is the batch size, :math:`L` is the target sequence length, and + :math:`S` is the source sequence length. If ``average_attn_weights=False``, returns attention weights per + head of shape :math:`(\text{num\_heads}, L, S)` when input is unbatched or :math:`(N, \text{num\_heads}, L, S)`. + + .. note:: + `batch_first` argument is ignored for unbatched inputs. + """ + is_batched = query.dim() == 3 + if key_padding_mask is not None: + _kpm_dtype = key_padding_mask.dtype + if _kpm_dtype != torch.bool and not torch.is_floating_point( + key_padding_mask + ): + raise AssertionError( + "only bool and floating types of key_padding_mask are supported" + ) + + if self.batch_first and is_batched: + # make sure that the transpose op does not affect the "is" property + if key is value: + if query is key: + query = key = value = query.transpose(1, 0) + else: + query, key = [x.transpose(1, 0) for x in (query, key)] + value = key + else: + query, key, value = [x.transpose(1, 0) for x in (query, key, value)] + + attn_output, attn_output_weights = F.multi_head_attention_forward( + query, + key, + value, + self.embed_dim, + self.num_heads, + in_proj_weight=None, + in_proj_bias=None, + bias_k=None, + bias_v=None, + add_zero_attn=False, + dropout_p=self.dropout, + out_proj_weight=self.out_proj_weight, + out_proj_bias=None, + training=self.training, + key_padding_mask=key_padding_mask, + need_weights=need_weights, + attn_mask=attn_mask, + use_separate_proj_weight=True, + q_proj_weight=self.in_proj_weight, + k_proj_weight=self.in_proj_weight, + v_proj_weight=self.in_proj_weight, + average_attn_weights=average_attn_weights, + ) + if self.batch_first and is_batched: + return attn_output.transpose(1, 0), attn_output_weights + else: + return attn_output, attn_output_weights diff --git a/scgpt/model/model.py b/scgpt/model/model.py index 40bf87d2..368f449f 100644 --- a/scgpt/model/model.py +++ b/scgpt/model/model.py @@ -1,6 +1,7 @@ import gc import math from typing import Dict, Mapping, Optional, Tuple, Any, Union +import warnings import torch import numpy as np @@ -13,6 +14,7 @@ try: from flash_attn.flash_attention import FlashMHA + from .flash_layers import FlashscGPTLayer, FlashscGPTGenerator except ImportError: import warnings @@ -47,9 +49,11 @@ def __init__( mvc_decoder_style: str = "inner product", ecs_threshold: float = 0.3, explicit_zero_prob: bool = False, + use_generative_training=False, use_fast_transformer: bool = False, fast_transformer_backend: str = "flash", pre_norm: bool = False, + use_sim_decoder: bool = False, ): super().__init__() self.model_type = "Transformer" @@ -72,6 +76,7 @@ def __init__( # TODO: add dropout in the GeneEncoder self.encoder = GeneEncoder(ntoken, d_model, padding_idx=vocab[pad_token]) + self.flag_encoder = nn.Embedding(2, d_model) # Value Encoder, NOTE: the scaling style is also handled in _encode method if input_emb_style == "continuous": @@ -96,11 +101,22 @@ def __init__( self.dsbn = DomainSpecificBatchNorm1d( d_model, num_batch_labels, eps=6.1e-5, affine=use_affine ) - else: - print("Using simple batchnorm instead of domain specific batchnorm") - self.bn = nn.BatchNorm1d(d_model, eps=6.1e-5) + # else: + # print("Using simple batchnorm instead of domain specific batchnorm") + # self.bn = nn.BatchNorm1d(d_model, eps=6.1e-5) + # bug - if use_fast_transformer: + if use_generative_training: + encoder_layers = FlashscGPTLayer( + d_model, + nhead, + d_hid, + dropout, + batch_first=True, + norm_scheme=self.norm_scheme, + ) + self.transformer_encoder = FlashscGPTGenerator(encoder_layers, nlayers) + elif use_fast_transformer: if fast_transformer_backend == "linear": self.transformer_encoder = FastTransformerEncoderWrapper( d_model, nhead, d_hid, nlayers, dropout @@ -126,7 +142,13 @@ def __init__( explicit_zero_prob=explicit_zero_prob, use_batch_labels=use_batch_labels, ) - self.cls_decoder = ClsDecoder(d_model, n_cls, nlayers=nlayers_cls) + + if n_cls > 1: + if use_sim_decoder: + self.cls_decoder = SimDecoder(d_model, n_cls, nlayers=nlayers_cls) + else: + self.cls_decoder = ClsDecoder(d_model, n_cls, nlayers=nlayers_cls) + if do_mvc: self.mvc_decoder = MVCDecoder( d_model, @@ -142,8 +164,8 @@ def __init__( reverse_grad=True, ) - self.sim = Similarity(temp=0.5) # TODO: auto set temp - self.creterion_cce = nn.CrossEntropyLoss() + # self.sim = Similarity(temp=0.5) # TODO: auto set temp + # self.creterion_cce = nn.CrossEntropyLoss() self.init_weights() @@ -176,14 +198,73 @@ def _encode( total_embs = self.dsbn(total_embs.permute(0, 2, 1), batch_label).permute( 0, 2, 1 ) # the batch norm always works on dim 1 - else: - total_embs = self.bn(total_embs.permute(0, 2, 1)).permute(0, 2, 1) + # else: + # total_embs = self.bn(total_embs.permute(0, 2, 1)).permute(0, 2, 1) output = self.transformer_encoder( total_embs, src_key_padding_mask=src_key_padding_mask ) return output # (batch, seq_len, embsize) + def transformer_generate( + self, + pcpt_genes: Tensor, + pcpt_values: Tensor, + pcpt_key_padding_mask: Tensor, + gen_genes: Tensor, + gen_key_padding_mask: Tensor, + batch_labels: Optional[Tensor] = None, # (batch,) + input_cell_emb: Optional[Tensor] = None, # (batch, seq_len, embsize) + ) -> Tuple[Tensor, Tensor]: + self._check_batch_labels(batch_labels) + + pcpt_token_embs = self.encoder(pcpt_genes) # (batch, pcpt_len, embsize) + pcpt_values = self.value_encoder(pcpt_values) # (batch, pcpt_len, embsize) + pcpt_total_embs = pcpt_token_embs + pcpt_values + + assert self.input_emb_style != "scaling" + if gen_genes is not None: + gen_token_embs = self.encoder(gen_genes) # (batch, gen_len, embsize) + self.cur_gene_token_embs = torch.cat( + [pcpt_token_embs, gen_token_embs], dim=1 + ) + gen_flags = self.flag_encoder( + torch.tensor(1).to(pcpt_values.device) + ).expand(gen_genes.shape[0], gen_genes.shape[1], -1) + + gen_total_embs = gen_token_embs + gen_flags + else: + self.cur_gene_token_embs = pcpt_token_embs + gen_total_embs = None + + if self.domain_spec_batchnorm: + batch_label = int(batch_labels[0].item()) + pcpt_total_embs = self.dsbn( + pcpt_total_embs.permute(0, 2, 1), batch_label + ).permute(0, 2, 1) + if gen_genes is not None: + gen_total_embs = self.dsbn( + gen_total_embs.permute(0, 2, 1), batch_label + ).permute(0, 2, 1) + # else: + # pcpt_total_embs = self.bn(pcpt_total_embs.permute(0, 2, 1)).permute(0, 2, 1) + # if gen_genes is not None: + # gen_total_embs = self.bn(gen_total_embs.permute(0, 2, 1)).permute( + # 0, 2, 1 + # ) + + if input_cell_emb is not None: + pcpt_total_embs[:, 0, :] = input_cell_emb + + pcpt_output, gen_output = self.transformer_encoder( + pcpt_total_embs, + gen_total_embs, + pcpt_key_padding_mask=pcpt_key_padding_mask, + gen_key_padding_mask=gen_key_padding_mask, + ) + + return pcpt_output, gen_output + def _get_cell_emb_from_layer( self, layer_output: Tensor, weights: Tensor = None ) -> Tensor: @@ -242,8 +323,6 @@ def generate( try: self._check_batch_labels(batch_labels) except: - import warnings - warnings.warn( "batch_labels is required but not provided, using zeros instead" ) @@ -299,7 +378,173 @@ def generate( return output # (batch, seq_len) + def _extend_output( + self, + output: Mapping[str, Tensor], + transformer_output: Tensor, + batch_emb: Optional[Tensor] = None, + CLS: bool = False, + MVC: bool = False, + ECS: bool = False, + do_sample: bool = False, + ) -> Mapping[str, Tensor]: + cell_emb = self._get_cell_emb_from_layer(transformer_output) + output["cell_emb"] = cell_emb + + if CLS: + output["cls_output"] = self.cls_decoder(cell_emb) # (batch, n_cls) + if MVC: + mvc_output = self.mvc_decoder( + cell_emb + if not self.use_batch_labels + else torch.cat([cell_emb, batch_emb], dim=1), + # else cell_emb + batch_emb, + self.cur_gene_token_embs, + ) + if self.explicit_zero_prob and do_sample: + bernoulli = Bernoulli(probs=mvc_output["zero_probs"]) + output["mvc_output"] = bernoulli.sample() * mvc_output["pred"] + else: + output["mvc_output"] = mvc_output["pred"] # (batch, seq_len) + if self.explicit_zero_prob: + output["mvc_zero_probs"] = mvc_output["zero_probs"] + if ECS: + # Here using customized cosine similarity instead of F.cosine_similarity + # to avoid the pytorch issue of similarity larger than 1.0, pytorch # 78064 + # normalize the embedding + cell_emb_normed = F.normalize(cell_emb, p=2, dim=1) + cos_sim = torch.mm(cell_emb_normed, cell_emb_normed.t()) # (batch, batch) + + # mask out diagnal elements + mask = torch.eye(cos_sim.size(0)).bool().to(cos_sim.device) + cos_sim = cos_sim.masked_fill(mask, 0.0) + # only optimize positive similarities + cos_sim = F.relu(cos_sim) + + output["loss_ecs"] = torch.mean(1 - (cos_sim - self.ecs_threshold) ** 2) + + if self.do_dab: + output["dab_output"] = self.grad_reverse_discriminator(cell_emb) + + return output + def forward( + self, + *args, + **kwargs, + ) -> Mapping[str, Tensor]: + """ + Wrapper to call either generative_forward or perceptual_forward, depending + on the value of the "generative_training" kwarg. + """ + if "generative_training" not in kwargs: + # raise ValueError("generative_training kwarg is required") + warnings.warn( + "generative_training kwarg is required but not provided! " + "Using False and calling perceptual_forward instead" + ) + return self.perceptual_forward(*args, **kwargs) + + # get the generative training flag and pop it out + do_generative_training = kwargs.pop("generative_training") + if do_generative_training: + return self.generative_forward(*args, **kwargs) + else: + return self.perceptual_forward(*args, **kwargs) + + def generative_forward( + self, + pcpt_genes: Tensor, + pcpt_values: Tensor, + pcpt_key_padding_mask: Tensor, + gen_genes: Tensor, + gen_key_padding_mask: Tensor, + batch_labels: Optional[Tensor] = None, + CLS: bool = False, + CCE: bool = False, + MVC: bool = False, + ECS: bool = False, + do_sample: bool = False, + input_cell_emb: Optional[Tensor] = None, + ) -> Mapping[str, Tensor]: + """ + Args: + pcpt_genes (:obj:`Tensor`): token ids of the perceptual part, shape + [batch_size, seq_len] + pcpt_values (:obj:`Tensor`): token values of the perceptual part, shape + [batch_size, seq_len] + pcpt_key_padding_mask (:obj:`Tensor`): mask for pcpt_genes, shape + [batch_size, seq_len] + gen_genes (:obj:`Tensor`): token ids of the generative part, shape + [batch_size, seq_len] + gen_key_padding_mask (:obj:`Tensor`): mask for gen_genes, shape + [batch_size, seq_len] + batch_labels (:obj:`Tensor`): batch labels, shape [batch_size] + do_sample (:obj:`bool`): whether to do sampling from bernoulli for + generated zero predictions. + input_cell_emb (:obj:`Tensor`): cell embeddings, shape [batch_size, + embsize] + + Returns: + :obj:`Mapping[str, Tensor]`: + - pred (:obj:`Tensor`): prediction, shape [batch_size, seq_len] + - cell_emb (:obj:`Tensor`): cell embeddings, shape [batch_size, + embsize] + """ + + pcpt_output, gen_output = self.transformer_generate( + pcpt_genes, + pcpt_values, + pcpt_key_padding_mask, + gen_genes, + gen_key_padding_mask, + batch_labels, + input_cell_emb=input_cell_emb, + ) + if gen_output is None: + transformer_output = pcpt_output + else: + transformer_output = torch.cat([pcpt_output, gen_output], dim=1) + if self.use_batch_labels: + batch_emb = self.batch_encoder(batch_labels) + + output = {} + decoder_output = self.decoder( + transformer_output + if not self.use_batch_labels + else torch.cat( + [ + transformer_output, + batch_emb.unsqueeze(1).repeat(1, transformer_output.shape[1], 1), + ], + dim=2, + ), + ) + if self.explicit_zero_prob and do_sample: + bernoulli = Bernoulli(probs=decoder_output["zero_probs"]) + full_preds = bernoulli.sample() * decoder_output["pred"] + output["pcpt_preds"] = full_preds[:, : pcpt_genes.shape[1]] + output["gen_preds"] = full_preds[:, pcpt_genes.shape[1] :] + else: + full_preds = decoder_output["pred"] # (batch, seq_len) + output["pcpt_preds"] = full_preds[:, : pcpt_genes.shape[1]] + output["gen_preds"] = full_preds[:, pcpt_genes.shape[1] :] + if self.explicit_zero_prob: + output["zero_probs"] = decoder_output["zero_probs"] + + output = self._extend_output( + output, + transformer_output, + batch_emb=batch_emb if self.use_batch_labels else None, + CLS=CLS, + MVC=MVC, + ECS=ECS, + do_sample=do_sample, + ) + + return output + + def perceptual_forward( self, src: Tensor, values: Tensor, @@ -357,73 +602,15 @@ def forward( if self.explicit_zero_prob: output["mlm_zero_probs"] = mlm_output["zero_probs"] - cell_emb = self._get_cell_emb_from_layer(transformer_output, values) - output["cell_emb"] = cell_emb - - if CLS: - output["cls_output"] = self.cls_decoder(cell_emb) # (batch, n_cls) - if CCE: - cell1 = cell_emb - transformer_output2 = self._encode( - src, values, src_key_padding_mask, batch_labels - ) - cell2 = self._get_cell_emb_from_layer(transformer_output2) - - # Gather embeddings from all devices if distributed training - if dist.is_initialized() and self.training: - cls1_list = [ - torch.zeros_like(cell1) for _ in range(dist.get_world_size()) - ] - cls2_list = [ - torch.zeros_like(cell2) for _ in range(dist.get_world_size()) - ] - dist.all_gather(tensor_list=cls1_list, tensor=cell1.contiguous()) - dist.all_gather(tensor_list=cls2_list, tensor=cell2.contiguous()) - - # NOTE: all_gather results have no gradients, so replace the item - # of the current rank with the original tensor to keep gradients. - # See https://github.com/princeton-nlp/SimCSE/blob/main/simcse/models.py#L186 - cls1_list[dist.get_rank()] = cell1 - cls2_list[dist.get_rank()] = cell2 - - cell1 = torch.cat(cls1_list, dim=0) - cell2 = torch.cat(cls2_list, dim=0) - # TODO: should detach the second run cls2? Can have a try - cos_sim = self.sim(cell1.unsqueeze(1), cell2.unsqueeze(0)) # (batch, batch) - labels = torch.arange(cos_sim.size(0)).long().to(cell1.device) - output["loss_cce"] = self.creterion_cce(cos_sim, labels) - if MVC: - mvc_output = self.mvc_decoder( - cell_emb - if not self.use_batch_labels - else torch.cat([cell_emb, batch_emb], dim=1), - # else cell_emb + batch_emb, - self.cur_gene_token_embs, - ) - if self.explicit_zero_prob and do_sample: - bernoulli = Bernoulli(probs=mvc_output["zero_probs"]) - output["mvc_output"] = bernoulli.sample() * mvc_output["pred"] - else: - output["mvc_output"] = mvc_output["pred"] # (batch, seq_len) - if self.explicit_zero_prob: - output["mvc_zero_probs"] = mvc_output["zero_probs"] - if ECS: - # Here using customized cosine similarity instead of F.cosine_similarity - # to avoid the pytorch issue of similarity larger than 1.0, pytorch # 78064 - # normalize the embedding - cell_emb_normed = F.normalize(cell_emb, p=2, dim=1) - cos_sim = torch.mm(cell_emb_normed, cell_emb_normed.t()) # (batch, batch) - - # mask out diagnal elements - mask = torch.eye(cos_sim.size(0)).bool().to(cos_sim.device) - cos_sim = cos_sim.masked_fill(mask, 0.0) - # only optimize positive similarities - cos_sim = F.relu(cos_sim) - - output["loss_ecs"] = torch.mean(1 - (cos_sim - self.ecs_threshold) ** 2) - - if self.do_dab: - output["dab_output"] = self.grad_reverse_discriminator(cell_emb) + output = self._extend_output( + output, + transformer_output, + batch_emb=batch_emb if self.use_batch_labels else None, + CLS=CLS, + MVC=MVC, + ECS=ECS, + do_sample=do_sample, + ) return output @@ -903,6 +1090,59 @@ def forward(self, x: Tensor) -> Tensor: return self.out_layer(x) +class SimDecoder(nn.Module): + """ + Decoder for classification task with similarity matrix. + """ + + def __init__( + self, + d_model: int, + n_cls: int, + nlayers: int = 3, + activation: callable = nn.ReLU, + projection_dim: int = 2048, + ): + super().__init__() + # module list + self._decoder = nn.ModuleList() + for i in range(nlayers - 1): + self._decoder.append(nn.Linear(d_model, d_model)) + self._decoder.append(activation()) + self._decoder.append(nn.LayerNorm(d_model)) + self.out_layer = nn.Linear(d_model, projection_dim) + + self.cls_token_matrix = nn.Parameter(torch.randn(n_cls, projection_dim)) + self.embed_norm = nn.LayerNorm(projection_dim) + self.token_norm = nn.LayerNorm(projection_dim) + + def forward(self, x: Tensor) -> Tensor: + """ + Args: + x: Tensor, shape [batch_size, embsize] + """ + for layer in self._decoder: + x = layer(x) + x = self.out_layer(x) + x = self.embed_norm(x) + + sim = self.sim_matrix(x, self.cls_token_matrix) + + return sim + + def get_sim_matrix(self): + return self.cls_token_matrix + + def sim_matrix(self, a, b, eps=1e-8): + # b = self.token_norm(b) + a_n, b_n = a.norm(dim=1)[:, None], b.norm(dim=1)[:, None] + a_norm = a / torch.max(a_n, eps * torch.ones_like(a_n)) + b_norm = b / torch.max(b_n, eps * torch.ones_like(b_n)) + sim_mt = torch.mm(a_norm, b_norm.transpose(0, 1)) + # sim_mt = torch.mm(a, b.transpose(0, 1)) + return sim_mt + + class MVCDecoder(nn.Module): """ Decoder for the masked value prediction for cell embeddings. diff --git a/scgpt/preprocess.py b/scgpt/preprocess.py index 9ad92251..fb158a5f 100644 --- a/scgpt/preprocess.py +++ b/scgpt/preprocess.py @@ -184,7 +184,7 @@ def __call__(self, adata: AnnData, batch_key: Optional[str] = None) -> Dict: # bins = np.sort(np.unique(bins)) # NOTE: comment this line for now, since this will make the each category # has different relative meaning across datasets - non_zero_digits = self._digitize(non_zero_row, bins) + non_zero_digits = _digitize(non_zero_row, bins) assert non_zero_digits.min() >= 1 assert non_zero_digits.max() <= n_bins - 1 binned_row = np.zeros_like(row, dtype=np.int64) @@ -194,34 +194,6 @@ def __call__(self, adata: AnnData, batch_key: Optional[str] = None) -> Dict: adata.layers[self.result_binned_key] = np.stack(binned_rows) adata.obsm["bin_edges"] = np.stack(bin_edges) - def _digitize(self, x: np.ndarray, bins: np.ndarray) -> np.ndarray: - """ - Digitize the data into bins. This method spreads data uniformly when bins - have same values. - - Args: - - x (:class:`np.ndarray`): - The data to digitize. - bins (:class:`np.ndarray`): - The bins to use for digitization, in increasing order. - - Returns: - - :class:`np.ndarray`: - The digitized data. - """ - assert x.ndim == 1 and bins.ndim == 1 - - left_digits = np.digitize(x, bins) - right_difits = np.digitize(x, bins, right=True) - - rands = np.random.rand(len(x)) # uniform random numbers - - digits = rands * (right_difits - left_digits) + left_digits - digits = np.ceil(digits).astype(np.int64) - return digits - def check_logged(self, adata: AnnData, obs_key: Optional[str] = None) -> bool: """ Check if the data is already log1p transformed. @@ -248,6 +220,41 @@ def check_logged(self, adata: AnnData, obs_key: Optional[str] = None) -> bool: return True +def _digitize(x: np.ndarray, bins: np.ndarray, side="one") -> np.ndarray: + """ + Digitize the data into bins. This method spreads data uniformly when bins + have same values. + + Args: + + x (:class:`np.ndarray`): + The data to digitize. + bins (:class:`np.ndarray`): + The bins to use for digitization, in increasing order. + side (:class:`str`, optional): + The side to use for digitization. If "one", the left side is used. If + "both", the left and right side are used. Default to "one". + + Returns: + + :class:`np.ndarray`: + The digitized data. + """ + assert x.ndim == 1 and bins.ndim == 1 + + left_digits = np.digitize(x, bins) + if side == "one": + return left_digits + + right_difits = np.digitize(x, bins, right=True) + + rands = np.random.rand(len(x)) # uniform random numbers + + digits = rands * (right_difits - left_digits) + left_digits + digits = np.ceil(digits).astype(np.int64) + return digits + + def binning( row: Union[np.ndarray, torch.Tensor], n_bins: int ) -> Union[np.ndarray, torch.Tensor]: @@ -261,10 +268,10 @@ def binning( non_zero_ids = row.nonzero() non_zero_row = row[non_zero_ids] bins = np.quantile(non_zero_row, np.linspace(0, 1, n_bins - 1)) - non_zero_digits = np.digitize(non_zero_row, bins) + non_zero_digits = _digitize(non_zero_row, bins) binned_row = np.zeros_like(row, dtype=np.int64) binned_row[non_zero_ids] = non_zero_digits else: bins = np.quantile(row, np.linspace(0, 1, n_bins - 1)) - binned_row = np.digitize(row, bins) + 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\ No newline at end of file diff --git a/scgpt/tokenizer/gene_tokenizer.py b/scgpt/tokenizer/gene_tokenizer.py index 51a9a003..49ea6e67 100644 --- a/scgpt/tokenizer/gene_tokenizer.py +++ b/scgpt/tokenizer/gene_tokenizer.py @@ -290,7 +290,7 @@ def tokenize_batch( values = np.insert(values, 0, 0) if return_pt: genes = torch.from_numpy(genes).long() - values = torch.from_numpy(values) + values = torch.from_numpy(values).float() tokenized_data.append((genes, values)) return tokenized_data