Libra / libra /train /train.py
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# Copyright 2024 Xi Zhang
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import os
import copy
import numpy as np
from dataclasses import dataclass, field
import json
import logging
import pathlib
from typing import Dict, Optional, Sequence, List, Union
import random
import torch
import shutil
import evaluate
import transformers
import tokenizers
from transformers import EvalPrediction, TrainerCallback
from libra.constants import IGNORE_INDEX, IMAGE_TOKEN_INDEX, DEFAULT_IMAGE_TOKEN, DEFAULT_IM_START_TOKEN, DEFAULT_IM_END_TOKEN
from torch.utils.data import Dataset
from libra.train.libra_trainer import LibraTrainer
from libra import conversation as conversation_lib
from libra.model import *
from libra.mm_utils import tokenizer_image_token
from libra.eval import temporal_f1_score
from PIL import Image
import pydicom
from pydicom.pixel_data_handlers.util import apply_voi_lut
local_rank = None
def rank0_print(*args):
if local_rank == 0:
print(*args)
from packaging import version
IS_TOKENIZER_GREATER_THAN_0_14 = version.parse(tokenizers.__version__) >= version.parse('0.14')
@dataclass
class ModelArguments:
model_name_or_path: Optional[str] = field(default="libra")
version: Optional[str] = field(default="libra_v1")
freeze_backbone: bool = field(default=False)
tune_mm_mlp_adapter: bool = field(default=False)
vision_tower: Optional[str] = field(default=None)
mm_vision_select_layer: Optional[Union[int, str]] = field(
default=-1,
metadata={"help": "Select specific vision layer (e.g., -1, -2) or 'all' for all layers."}
)
pretrain_mm_mlp_adapter: Optional[str] = field(default=None)
mm_projector_type: Optional[str] = field(default='linear')
mm_use_im_start_end: bool = field(default=False)
mm_use_im_patch_token: bool = field(default=True)
mm_vision_select_feature: Optional[str] = field(
default="patch",
metadata={"help": "Select feature type: 'patch' or 'cls_patch'."}
)
compute_metrics: bool = field(
default=False,
metadata={"help": "Optional callable for computing metrics during evaluation during training."}
)
@dataclass
class DataArguments:
data_path: str = field(default=None,
metadata={"help": "Path to the training data."})
lazy_preprocess: bool = False
is_multimodal: bool = False
image_folder: Optional[str] = field(default=None)
image_aspect_ratio: str = 'square'
validation_data_path: Optional[str] = field(
default=None,
metadata={"help": "Path to the validation data."}
)
@dataclass
class TrainingArguments(transformers.TrainingArguments):
cache_dir: Optional[str] = field(default=None)
optim: str = field(default="adamw_torch")
remove_unused_columns: bool = field(default=False)
freeze_mm_mlp_adapter: bool = field(default=False)
mpt_attn_impl: Optional[str] = field(default="triton")
model_max_length: int = field(
default=512,
metadata={
"help":
"Maximum sequence length. Sequences will be right padded (and possibly truncated)."
},
)
double_quant: bool = field(
default=True,
metadata={"help": "Compress the quantization statistics through double quantization."}
)
quant_type: str = field(
default="nf4",
metadata={"help": "Quantization data type to use. Should be one of `fp4` or `nf4`."}
)
bits: int = field(
default=16,
metadata={"help": "How many bits to use."}
)
lora_enable: bool = False
lora_r: int = 64
lora_alpha: int = 16
lora_dropout: float = 0.05
lora_weight_path: str = ""
lora_bias: str = "none"
mm_projector_lr: Optional[float] = None
group_by_modality_length: bool = field(default=False)
def maybe_zero_3(param, ignore_status=False, name=None):
from deepspeed import zero
from deepspeed.runtime.zero.partition_parameters import ZeroParamStatus
if hasattr(param, "ds_id"):
if param.ds_status == ZeroParamStatus.NOT_AVAILABLE:
if not ignore_status:
logging.warning(f"{name}: param.ds_status != ZeroParamStatus.NOT_AVAILABLE: {param.ds_status}")
with zero.GatheredParameters([param]):
param = param.data.detach().cpu().clone()
else:
param = param.detach().cpu().clone()
return param
# Borrowed from peft.utils.get_peft_model_state_dict
def get_peft_state_maybe_zero_3(named_params, bias):
if bias == "none":
to_return = {k: t for k, t in named_params if "lora_" in k}
elif bias == "all":
to_return = {k: t for k, t in named_params if "lora_" in k or "bias" in k}
elif bias == "lora_only":
to_return = {}
maybe_lora_bias = {}
lora_bias_names = set()
for k, t in named_params:
if "lora_" in k:
to_return[k] = t
bias_name = k.split("lora_")[0] + "bias"
lora_bias_names.add(bias_name)
elif "bias" in k:
maybe_lora_bias[k] = t
for k, t in maybe_lora_bias:
if bias_name in lora_bias_names:
to_return[bias_name] = t
else:
raise NotImplementedError
to_return = {k: maybe_zero_3(v, ignore_status=True) for k, v in to_return.items()}
return to_return
def get_peft_state_non_lora_maybe_zero_3(named_params, require_grad_only=True):
to_return = {k: t for k, t in named_params if "lora_" not in k}
if require_grad_only:
to_return = {k: t for k, t in to_return.items() if t.requires_grad}
to_return = {k: maybe_zero_3(v, ignore_status=True).cpu() for k, v in to_return.items()}
return to_return
def get_non_vision_tower_state_maybe_zero_3(named_params):
to_return = {k: t for k, t in named_params if "vision_tower" not in k}
to_return = {k: maybe_zero_3(v, ignore_status=True).cpu() for k, v in to_return.items()}
return to_return
def get_mm_adapter_state_maybe_zero_3(named_params, keys_to_match):
to_return = {k: t for k, t in named_params if any(key_match in k for key_match in keys_to_match)}
to_return = {k: maybe_zero_3(v, ignore_status=True).cpu() for k, v in to_return.items()}
return to_return
def find_all_linear_names(model):
cls = torch.nn.Linear
lora_module_names = set()
multimodal_keywords = ['mm_projector', 'vision_tower', 'vision_resampler']
for name, module in model.named_modules():
if any(mm_keyword in name for mm_keyword in multimodal_keywords):
continue
if isinstance(module, cls):
names = name.split('.')
lora_module_names.add(names[0] if len(names) == 1 else names[-1])
if 'lm_head' in lora_module_names: # needed for 16-bit
lora_module_names.remove('lm_head')
return list(lora_module_names)
def safe_save_model_for_hf_trainer(trainer: transformers.Trainer,
output_dir: str):
"""Collects the state dict and dump to disk."""
if getattr(trainer.args, "tune_mm_mlp_adapter", False):
# Only save Adapter
keys_to_match = ['mm_projector']
if getattr(trainer.args, "use_im_start_end", False):
keys_to_match.extend(['embed_tokens', 'embed_in'])
weight_to_save = get_mm_adapter_state_maybe_zero_3(trainer.model.named_parameters(), keys_to_match)
trainer.model.config.save_pretrained(output_dir)
current_folder = output_dir.split('/')[-1]
parent_folder = os.path.dirname(output_dir)
if trainer.args.local_rank == 0 or trainer.args.local_rank == -1:
if current_folder.startswith('checkpoint-'):
mm_projector_folder = os.path.join(parent_folder, "mm_projector")
os.makedirs(mm_projector_folder, exist_ok=True)
torch.save(weight_to_save, os.path.join(mm_projector_folder, f'{current_folder}.bin'))
else:
torch.save(weight_to_save, os.path.join(output_dir, f'mm_projector.bin'))
return
if trainer.deepspeed:
torch.cuda.synchronize()
trainer.save_model(output_dir)
return
state_dict = trainer.model.state_dict()
if trainer.args.should_save:
cpu_state_dict = {
key: value.cpu()
for key, value in state_dict.items()
}
del state_dict
trainer._save(output_dir, state_dict=cpu_state_dict)
def smart_tokenizer_and_embedding_resize(
special_tokens_dict: Dict,
tokenizer: transformers.PreTrainedTokenizer,
model: transformers.PreTrainedModel,
):
"""Resize tokenizer and embedding. You can add some new tokens <video> etc
Note: This is the unoptimized version that may make your embedding size not be divisible by 64.
"""
num_new_tokens = tokenizer.add_special_tokens(special_tokens_dict)
model.resize_token_embeddings(len(tokenizer))
if num_new_tokens > 0:
input_embeddings = model.get_input_embeddings().weight.data
output_embeddings = model.get_output_embeddings().weight.data
input_embeddings_avg = input_embeddings[:-num_new_tokens].mean(
dim=0, keepdim=True)
output_embeddings_avg = output_embeddings[:-num_new_tokens].mean(
dim=0, keepdim=True)
input_embeddings[-num_new_tokens:] = input_embeddings_avg
output_embeddings[-num_new_tokens:] = output_embeddings_avg
def _tokenize_fn(strings: Sequence[str],
tokenizer: transformers.PreTrainedTokenizer) -> Dict:
"""
Tokenizes a list of input strings and returns tokenized results along with sequence lengths.
"""
tokenized_list = [
tokenizer(
text,
return_tensors="pt",
padding="longest",
max_length=tokenizer.model_max_length,
truncation=True,
) for text in strings
]
input_ids = labels = [
tokenized.input_ids[0] for tokenized in tokenized_list
]
input_ids_lens = labels_lens = [
tokenized.input_ids.ne(tokenizer.pad_token_id).sum().item()
for tokenized in tokenized_list
]
return dict(
input_ids=input_ids,
labels=labels,
input_ids_lens=input_ids_lens,
labels_lens=labels_lens,
)
def _mask_targets(target, tokenized_lens, speakers):
# cur_idx = 0
cur_idx = tokenized_lens[0]
tokenized_lens = tokenized_lens[1:]
target[:cur_idx] = IGNORE_INDEX
for tokenized_len, speaker in zip(tokenized_lens, speakers):
if speaker == "human":
target[cur_idx+2:cur_idx + tokenized_len] = IGNORE_INDEX
cur_idx += tokenized_len
def _add_speaker_and_signal(header, source, get_conversation=True):
"""Add speaker and start/end signal on each round."""
BEGIN_SIGNAL = "### "
END_SIGNAL = "\n"
conversation = header
for sentence in source:
from_str = sentence["from"]
if from_str.lower() == "human":
from_str = conversation_lib.default_conversation.roles[0]
elif from_str.lower() == "gpt":
from_str = conversation_lib.default_conversation.roles[1]
else:
from_str = 'unknown'
sentence["value"] = (BEGIN_SIGNAL + from_str + ": " +
sentence["value"] + END_SIGNAL)
if get_conversation:
conversation += sentence["value"]
conversation += BEGIN_SIGNAL
return conversation
def preprocess_multimodal(
sources: Sequence[str],
data_args: DataArguments
) -> Dict:
is_multimodal = data_args.is_multimodal
if not is_multimodal:
return sources
for source in sources:
for sentence in source:
if DEFAULT_IMAGE_TOKEN in sentence['value']:
sentence['value'] = sentence['value'].replace(DEFAULT_IMAGE_TOKEN, '').strip()
sentence['value'] = DEFAULT_IMAGE_TOKEN + '\n' + sentence['value']
sentence['value'] = sentence['value'].strip()
if "mmtag" in conversation_lib.default_conversation.version:
sentence['value'] = sentence['value'].replace(DEFAULT_IMAGE_TOKEN, '<Image>' + DEFAULT_IMAGE_TOKEN + '</Image>')
replace_token = DEFAULT_IMAGE_TOKEN
if data_args.mm_use_im_start_end:
replace_token = DEFAULT_IM_START_TOKEN + replace_token + DEFAULT_IM_END_TOKEN
sentence["value"] = sentence["value"].replace(DEFAULT_IMAGE_TOKEN, replace_token)
return sources
def preprocess_llama_2(
sources,
tokenizer: transformers.PreTrainedTokenizer,
has_image: bool = False
) -> Dict:
conv = conversation_lib.default_conversation.copy()
roles = {"human": conv.roles[0], "gpt": conv.roles[1]}
# Apply prompt templates
conversations = []
for i, source in enumerate(sources):
if roles[source[0]["from"]] != conv.roles[0]:
# Skip the first one if it is not from human
source = source[1:]
conv.messages = []
for j, sentence in enumerate(source):
role = roles[sentence["from"]]
assert role == conv.roles[j % 2], f"{i}"
conv.append_message(role, sentence["value"])
conversations.append(conv.get_prompt())
# Tokenize conversations
if has_image:
input_ids = torch.stack([tokenizer_image_token(prompt, tokenizer, return_tensors='pt') for prompt in conversations], dim=0)
else:
input_ids = tokenizer(
conversations,
return_tensors="pt",
padding="longest",
max_length=tokenizer.model_max_length,
truncation=True,
).input_ids
targets = input_ids.clone()
assert conv.sep_style == conversation_lib.SeparatorStyle.LLAMA_2
# Mask targets
sep = "[/INST] "
for conversation, target in zip(conversations, targets):
total_len = int(target.ne(tokenizer.pad_token_id).sum())
rounds = conversation.split(conv.sep2)
cur_len = 1
target[:cur_len] = IGNORE_INDEX
for i, rou in enumerate(rounds):
if rou == "":
break
parts = rou.split(sep)
if len(parts) != 2:
break
parts[0] += sep
if has_image:
round_len = len(tokenizer_image_token(rou, tokenizer))
instruction_len = len(tokenizer_image_token(parts[0], tokenizer)) - 2
else:
round_len = len(tokenizer(rou).input_ids)
instruction_len = len(tokenizer(parts[0]).input_ids) - 2
target[cur_len : cur_len + instruction_len] = IGNORE_INDEX
cur_len += round_len
target[cur_len:] = IGNORE_INDEX
if cur_len < tokenizer.model_max_length:
if cur_len != total_len:
target[:] = IGNORE_INDEX
print(
f"WARNING: tokenization mismatch: {cur_len} vs. {total_len}."
f" (ignored)"
)
return dict(
input_ids=input_ids,
labels=targets,
)
# llama_3
def preprocess_llama_3(
sources,
tokenizer: transformers.PreTrainedTokenizer,
has_image: bool = False
) -> Dict:
special_token = "<|finetune_right_pad_id|>"
if tokenizer.pad_token_id is None:
pad_token_id = tokenizer.convert_tokens_to_ids(special_token)
if pad_token_id is None:
raise ValueError(f"Cannot find ID for {special_token}. Please check the tokenizer.")
tokenizer.pad_token_id = pad_token_id
conv = conversation_lib.default_conversation.copy()
roles = {"human": conv.roles[0], "gpt": conv.roles[1]}
# Apply prompt templates
conversations = []
for i, source in enumerate(sources):
if roles[source[0]["from"]] != conv.roles[0]:
# Skip the first one if it is not from human
source = source[1:]
conv.messages = []
for j, sentence in enumerate(source):
role = roles[sentence["from"]]
assert role == conv.roles[j % 2], f"{i}"
conv.append_message(role, sentence["value"])
conversations.append(conv.get_prompt())
if has_image:
input_ids = torch.stack([tokenizer_image_token(prompt, tokenizer, return_tensors='pt') for prompt in conversations], dim=0)
else:
input_ids = tokenizer(
conversations,
return_tensors="pt",
padding="longest",
max_length=tokenizer.model_max_length,
truncation=True,
).input_ids
targets = input_ids.clone()
assert conv.sep_style == conversation_lib.SeparatorStyle.LLAMA_3
sep_round = "<|eot_id|>\n<|start_header_id|>user<|end_header_id|>"
sep_user = "<|eot_id|>\n<|start_header_id|>assistant<|end_header_id|>\n\n"
for conversation, target in zip(conversations, targets):
total_len = int(target.ne(tokenizer.pad_token_id).sum())
rounds = conversation.split(sep_round)
cur_len = 1
target[:cur_len] = IGNORE_INDEX
for i, rou in enumerate(rounds):
if rou == "":
break
parts = rou.split(sep_user)
if len(parts) != 2:
break
parts[0] += sep_user
if has_image:
round_len = len(tokenizer_image_token(rou, tokenizer)) - 1
instruction_len = len(tokenizer_image_token(parts[0], tokenizer)) - 1
else:
round_len = len(tokenizer(rou).input_ids) - 1
instruction_len = len(tokenizer(parts[0]).input_ids) - 1
target[cur_len : cur_len + instruction_len] = IGNORE_INDEX
cur_len += round_len
target[cur_len:] = IGNORE_INDEX
if cur_len < tokenizer.model_max_length:
if cur_len != total_len:
target[:] = IGNORE_INDEX
print(
f"WARNING: tokenization mismatch: {cur_len} vs. {total_len}."
f" (ignored)"
)
return dict(
input_ids=input_ids,
labels=targets,
)
def preprocess_libra(
sources,
tokenizer: transformers.PreTrainedTokenizer,
has_image: bool = False
) -> Dict:
conv = conversation_lib.default_conversation.copy()
roles = {"human": conv.roles[0], "gpt": conv.roles[1]}
# Apply prompt templates
conversations = []
for i, source in enumerate(sources):
if roles[source[0]["from"]] != conv.roles[0]:
# Skip the first one if it is not from human
source = source[1:]
conv.messages = []
for j, sentence in enumerate(source):
role = roles[sentence["from"]]
assert role == conv.roles[j % 2], f"{i}"
conv.append_message(role, sentence["value"])
conversations.append(conv.get_prompt())
# Tokenize conversations
if has_image:
input_ids = torch.stack([tokenizer_image_token(prompt, tokenizer, return_tensors='pt') for prompt in conversations], dim=0)
else:
input_ids = tokenizer(
conversations,
return_tensors="pt",
padding="longest",
max_length=tokenizer.model_max_length,
truncation=True,
).input_ids
targets = input_ids.clone()
assert conv.sep_style == conversation_lib.SeparatorStyle.TWO
# Mask targets
sep = conv.sep + conv.roles[1] + ": "
for conversation, target in zip(conversations, targets):
total_len = int(target.ne(tokenizer.pad_token_id).sum())
rounds = conversation.split(conv.sep2)
cur_len = 1
target[:cur_len] = IGNORE_INDEX
for i, rou in enumerate(rounds):
if rou == "":
break
parts = rou.split(sep)
if len(parts) != 2:
break
parts[0] += sep
if has_image:
round_len = len(tokenizer_image_token(rou, tokenizer))
instruction_len = len(tokenizer_image_token(parts[0], tokenizer)) - 2
else:
round_len = len(tokenizer(rou).input_ids)
instruction_len = len(tokenizer(parts[0]).input_ids) - 2
if i != 0 and not tokenizer.legacy and IS_TOKENIZER_GREATER_THAN_0_14:
round_len -= 1
instruction_len -= 1
target[cur_len : cur_len + instruction_len] = IGNORE_INDEX
cur_len += round_len
target[cur_len:] = IGNORE_INDEX
if cur_len < tokenizer.model_max_length:
if cur_len != total_len:
target[:] = IGNORE_INDEX
print(
f"WARNING: tokenization mismatch: {cur_len} vs. {total_len}."
f" (ignored)"
)
return dict(
input_ids=input_ids,
labels=targets,
)
def preprocess_mpt(
sources,
tokenizer: transformers.PreTrainedTokenizer,
has_image: bool = False
) -> Dict:
conv = conversation_lib.default_conversation.copy()
roles = {"human": conv.roles[0], "gpt": conv.roles[1]}
# Apply prompt templates
conversations = []
for i, source in enumerate(sources):
if roles[source[0]["from"]] != conv.roles[0]:
# Skip the first one if it is not from human
source = source[1:]
conv.messages = []
for j, sentence in enumerate(source):
role = roles[sentence["from"]]
assert role == conv.roles[j % 2], f"{i}"
conv.append_message(role, sentence["value"])
conversations.append(conv.get_prompt())
# Tokenize conversations
if has_image:
input_ids = torch.stack([tokenizer_image_token(prompt, tokenizer, return_tensors='pt') for prompt in conversations], dim=0)
else:
input_ids = tokenizer(
conversations,
return_tensors="pt",
padding="longest",
max_length=tokenizer.model_max_length,
truncation=True,
).input_ids
targets = input_ids.clone()
assert conv.sep_style == conversation_lib.SeparatorStyle.MPT
# Mask targets
sep = conv.sep + conv.roles[1]
for conversation, target in zip(conversations, targets):
total_len = int(target.ne(tokenizer.pad_token_id).sum())
rounds = conversation.split(conv.sep)
re_rounds = [conv.sep.join(rounds[:3])] # system + user + gpt
for conv_idx in range(3, len(rounds), 2):
re_rounds.append(conv.sep.join(rounds[conv_idx:conv_idx+2])) # user + gpt
cur_len = 0
target[:cur_len] = IGNORE_INDEX
for i, rou in enumerate(re_rounds):
if rou == "":
break
parts = rou.split(sep)
if len(parts) != 2:
break
parts[0] += sep
if has_image:
round_len = len(tokenizer_image_token(rou, tokenizer))
instruction_len = len(tokenizer_image_token(parts[0], tokenizer)) - 1
else:
round_len = len(tokenizer(rou).input_ids)
instruction_len = len(tokenizer(parts[0]).input_ids) - 1
if i != 0 and getattr(tokenizer, 'legacy', False) and IS_TOKENIZER_GREATER_THAN_0_14:
round_len += 1
instruction_len += 1
target[cur_len : cur_len + instruction_len] = IGNORE_INDEX
cur_len += round_len
target[cur_len:] = IGNORE_INDEX
if cur_len < tokenizer.model_max_length:
if cur_len != total_len:
target[:] = IGNORE_INDEX
print(
f"WARNING: tokenization mismatch: {cur_len} vs. {total_len}."
f" (ignored)"
)
return dict(
input_ids=input_ids,
labels=targets,
)
def preprocess_plain(
sources: Sequence[str],
tokenizer: transformers.PreTrainedTokenizer,
) -> Dict:
# add end signal and concatenate together
conversations = []
for source in sources:
assert len(source) == 2
assert DEFAULT_IMAGE_TOKEN in source[0]['value']
source[0]['value'] = DEFAULT_IMAGE_TOKEN
conversation = source[0]['value'] + source[1]['value'] + conversation_lib.default_conversation.sep
conversations.append(conversation)
# tokenize conversations
input_ids = [tokenizer_image_token(prompt, tokenizer, return_tensors='pt') for prompt in conversations]
targets = copy.deepcopy(input_ids)
for target, source in zip(targets, sources):
tokenized_len = len(tokenizer_image_token(source[0]['value'], tokenizer))
target[:tokenized_len] = IGNORE_INDEX
return dict(input_ids=input_ids, labels=targets)
def load_images(image_file):
"""
Load an image from a local file, a URL, or a DICOM file.
Args:
image_file (str): The path or URL of the image file to load.
Returns:
PIL.Image.Image: The loaded image in RGB format.
Raises:
ValueError: If the DICOM file does not contain image data.
TypeError: If the input is neither a valid file path nor a URL.
"""
if isinstance(image_file, str):
# Case 1: Load from URL
if image_file.startswith(('http://', 'https://')):
try:
response = requests.get(image_file)
response.raise_for_status()
image = Image.open(BytesIO(response.content)).convert('RGB')
except Exception as e:
raise ValueError(f"Error loading image from URL: {image_file}\n{e}")
# Case 2: Load from DICOM file
elif image_file.lower().endswith('.dcm'):
try:
dicom = pydicom.dcmread(image_file)
if 'PixelData' in dicom:
data = apply_voi_lut(dicom.pixel_array, dicom)
# Handle MONOCHROME1 images
if dicom.PhotometricInterpretation == "MONOCHROME1":
data = np.max(data) - data
# Normalize the image data
data = data - np.min(data)
data = data / np.max(data)
data = (data * 255).astype(np.uint8)
# Convert to 3-channel RGB if necessary
if data.ndim == 2:
data = np.stack([data] * 3, axis=-1)
image = Image.fromarray(data).convert('RGB')
else:
raise ValueError("DICOM file does not contain image data")
except Exception as e:
raise ValueError(f"Error loading DICOM file: {image_file}\n{e}")
# Case 3: Load standard image files (e.g., PNG, JPG)
else:
try:
image = Image.open(image_file).convert('RGB')
except Exception as e:
raise ValueError(f"Error loading standard image file: {image_file}\n{e}")
else:
raise TypeError("image_file must be a string representing a file path or URL")
return image
def preprocess(
sources: Sequence[str],
tokenizer: transformers.PreTrainedTokenizer,
has_image: bool = False
) -> Dict:
"""
Given a list of sources, each is a conversation list. This transform:
1. Add signal '### ' at the beginning each sentence, with end signal '\n';
2. Concatenate conversations together;
3. Tokenize the concatenated conversation;
4. Make a deepcopy as the target. Mask human words with IGNORE_INDEX.
"""
if conversation_lib.default_conversation.sep_style == conversation_lib.SeparatorStyle.PLAIN:
return preprocess_plain(sources, tokenizer)
if conversation_lib.default_conversation.sep_style == conversation_lib.SeparatorStyle.LLAMA_2:
return preprocess_llama_2(sources, tokenizer, has_image=has_image)
if conversation_lib.default_conversation.sep_style == conversation_lib.SeparatorStyle.LLAMA_3:
return preprocess_llama_3(sources, tokenizer, has_image=has_image)
if conversation_lib.default_conversation.version.startswith("v1"):
return preprocess_libra(sources, tokenizer, has_image=has_image)
if conversation_lib.default_conversation.version == "mpt":
return preprocess_mpt(sources, tokenizer)
conversations = []
for source in sources:
header = f"{conversation_lib.default_conversation.system}\n\n"
conversation = _add_speaker_and_signal(header, source)
conversations.append(conversation)
# tokenize conversations
def get_tokenize_len(prompts):
return [len(tokenizer_image_token(prompt, tokenizer)) for prompt in prompts]
if has_image:
input_ids = [tokenizer_image_token(prompt, tokenizer, return_tensors='pt') for prompt in conversations]
else:
conversations_tokenized = _tokenize_fn(conversations, tokenizer)
input_ids = conversations_tokenized["input_ids"]
targets = copy.deepcopy(input_ids)
for target, source in zip(targets, sources):
if has_image:
tokenized_lens = get_tokenize_len([header] + [s["value"] for s in source])
else:
tokenized_lens = _tokenize_fn([header] + [s["value"] for s in source], tokenizer)["input_ids_lens"]
speakers = [sentence["from"] for sentence in source]
_mask_targets(target, tokenized_lens, speakers)
return dict(input_ids=input_ids, labels=targets)
def create_compute_metrics(tokenizer, num_patches: int, sep2: str):
"""
Creates a function to compute evaluation metrics (e.g., BLEU, ROUGE-L, Temple-F1) for the model.
based on the given tokenizer and 'num_patches' parameter.
Args:
tokenizer: The tokenizer used for encoding/decoding text.
num_patches (int): The number of patches to be adjusted in the labels.
sep2 (str): A separator token used to identify a special token ID.
Returns:
A callable function 'compute_metrics(eval_pred)' that computes evaluation metrics.
"""
# Pre-fetch special token IDs to avoid repeated calls
bos_token_id = tokenizer.convert_tokens_to_ids(sep2)
newline_token_id = tokenizer.convert_tokens_to_ids('<0x0A>')
# 0 is commonly used as the <pad> token ID
special_token_ids = [bos_token_id, newline_token_id, 0]
# Pre-load evaluation metrics (adjust if needed for your scenario)
bleu_metric = evaluate.load("bleu")
rouge_metric = evaluate.load("rouge")
def compute_metrics(eval_pred: EvalPrediction) -> dict:
"""
Compute various evaluation metrics including BLEU, ROUGE, F1 for RadGraph and CheXbert, and BERTScore.
Args:
eval_pred (EvalPrediction): Contains model predictions and true labels.
Returns:
dict: Dictionary containing evaluation metric scores.
"""
logits, labels = eval_pred.predictions, eval_pred.label_ids
predicted_ids = np.argmax(logits, axis=-1)
# Store processed predicted token IDs
processed_predicted_ids = []
for label, predicted in zip(labels, predicted_ids):
# (1) Find ignore_count: the position of the first non-IGNORE_INDEX token in the label
ignore_count = next(
(i for i, token in enumerate(label) if token != IGNORE_INDEX),
len(label) # If all are -100, use the length of the label
)
# (2) Calculate the truncation start index
# This depends on 'num_patches' and the ignored tokens.
start_index = ignore_count + num_patches - 2
# If start_index exceeds the predicted sequence length, append an empty list
if start_index >= len(predicted):
processed_predicted_ids.append([])
continue
# (3) Slice the prediction from 'start_index' onwards
temp_predicted = predicted[start_index:]
# (4) Find the earliest occurrence of any special token to truncate
matching_indices = []
for token_id in special_token_ids:
idx = np.where(temp_predicted == token_id)[0]
if idx.size > 0:
matching_indices.append(idx)
if matching_indices:
# Merge all matching indices and take the smallest
all_indices = np.concatenate(matching_indices)
first_match_index = np.min(all_indices)
# Truncate up to the first special token
temp_predicted = temp_predicted[:first_match_index]
# Append the processed sequence to the results
processed_predicted_ids.append(temp_predicted)
# Decode the processed prediction IDs
decoded_preds = tokenizer.batch_decode(
processed_predicted_ids,
skip_special_tokens=True
)
# Filter labels by removing IGNORE_INDEX tokens
filtered_labels = [
[token for token in label_group if token != IGNORE_INDEX]
for label_group in labels
]
decoded_labels = tokenizer.batch_decode(
filtered_labels,
skip_special_tokens=True
)
references = [[lbl] for lbl in decoded_labels]
# Calculate BLEU score
bleu_score = bleu_metric.compute(
predictions=decoded_preds,
references=references,
max_order=4
)["bleu"]
# Calculate ROUGE-L score
rouge_score = rouge_metric.compute(
predictions=decoded_preds,
references=references
)["rougeL"]
# Calculate Temporal-F1 score
tem_f1_score = temporal_f1_score(
predictions=decoded_preds,
references=references
)["f1"]
# Clean up memory
del logits, labels, decoded_preds, decoded_labels, references
torch.cuda.empty_cache()
# Return metrics
return {
"BLEU4": bleu_score,
"ROUGE-L": rouge_score,
"TEM-F1": tem_f1_score
}
return compute_metrics
def check_trainable_parameters(model: torch.nn.Module) -> None:
"""
Print the names, shapes, and data types of all trainable parameters in the model.
Args:
model (torch.nn.Module): The model to inspect.
"""
total_params = sum(
p.numel() for p in model.parameters() if p.requires_grad
)
print(f"Total number of trainable parameters: {total_params:,d}\n")
# (Optional) Print the model structure for reference
print("Overall model structure:")
print(model)
print("\nTrainable parameters:")
# Print details of each trainable parameter
for name, param in model.named_parameters():
if param.requires_grad:
param_info = (
f"Shape: {list(param.shape)}, "
f"Dtype: {param.dtype}"
)
print(f" - {name} -> {param_info}")
class LazySupervisedDataset(Dataset):
"""Dataset for supervised fine-tuning."""
def __init__(self, data_path: str,
tokenizer: transformers.PreTrainedTokenizer,
data_args: DataArguments,
sample_rate=1.0):
super(LazySupervisedDataset, self).__init__()
list_data_dict = json.load(open(data_path, "r"))
# Apply sampling if sample_rate < 1.0
if 0 < sample_rate < 1.0:
random.seed(27) # Fixed seed for consistent behavior across different runs
sampled_size = int(len(list_data_dict) * sample_rate)
list_data_dict = random.sample(list_data_dict, sampled_size)
rank0_print("Formatting inputs...Skip in lazy mode")
self.tokenizer = tokenizer
self.list_data_dict = list_data_dict
self.data_args = data_args
def __len__(self):
return len(self.list_data_dict)
@property
def lengths(self):
length_list = []
for sample in self.list_data_dict:
img_tokens = 128 if 'image' in sample else 0
length_list.append(sum(len(conv['value'].split()) for conv in sample['conversations']) + img_tokens)
return length_list
@property
def modality_lengths(self):
length_list = []
for sample in self.list_data_dict:
cur_len = sum(len(conv['value'].split()) for conv in sample['conversations'])
cur_len = cur_len if 'image' in sample else -cur_len
length_list.append(cur_len)
return length_list
def __getitem__(self, i) -> Dict[str, torch.Tensor]:
sources = self.list_data_dict[i]
if isinstance(i, int):
sources = [sources]
assert len(sources) == 1, "Don't know why it is wrapped to a list" # FIXME
if 'image' in sources[0]:
image_file = self.list_data_dict[i]['image']
image_folder = self.data_args.image_folder
processor = self.data_args.image_processor
if isinstance(image_file, str):
image=[]
image_path = os.path.join(image_folder, image_file)
img = load_images(image_path)
image.append(img)
# set dummy prior image
image.append(img)
elif isinstance(image_file, (list, tuple)):
image=[]
image_paths = [os.path.join(image_folder, file_name) for file_name in image_file]
for path in image_paths:
img = load_images(path)
image.append(img)
# set dummy prior image
if len(image) == 1:
print("Contains only current image. Adding a dummy prior image.")
image.append(image[0])
else:
raise TypeError("image_file must be a string or a list/tuple of strings")
if self.data_args.image_aspect_ratio == 'pad':
def expand2square(pil_img, background_color=(0, 0, 0)):
width, height = pil_img.size
if width == height:
return pil_img
elif width > height:
result = Image.new(pil_img.mode, (width, width), background_color)
result.paste(pil_img, (0, (width - height) // 2))
return result
else:
result = Image.new(pil_img.mode, (height, height), background_color)
result.paste(pil_img, ((height - width) // 2, 0))
return result
processed_images = []
for img_data in image:
pad_image = expand2square(img_data, (0, 0, 0))
image_temp = processor.preprocess(pad_image, return_tensors='pt')['pixel_values'][0]
processed_images.append(image_temp)
image = processed_images
else:
processed_images = []
for img_data in image:
image_temp = processor.preprocess(img_data, return_tensors='pt')['pixel_values'][0]
processed_images.append(image_temp)
image = processed_images
sources = preprocess_multimodal(
copy.deepcopy([e["conversations"] for e in sources]),
self.data_args)
else:
sources = copy.deepcopy([e["conversations"] for e in sources])
data_dict = preprocess(
sources,
self.tokenizer,
has_image=('image' in self.list_data_dict[i]))
if isinstance(i, int):
data_dict = dict(input_ids=data_dict["input_ids"][0],
labels=data_dict["labels"][0])
# image exist in the data
if 'image' in self.list_data_dict[i]:
data_dict['image'] = image
elif self.data_args.is_multimodal:
# image does not exist in the data, but the model is multimodal
crop_size = self.data_args.image_processor.crop_size
data_dict['image'] = torch.zeros(3, crop_size['height'], crop_size['width'])
return data_dict
@dataclass
class DataCollatorForSupervisedDataset(object):
"""Collate examples for supervised fine-tuning."""
tokenizer: transformers.PreTrainedTokenizer
def __call__(self, instances: Sequence[Dict]) -> Dict[str, torch.Tensor]:
input_ids, labels = tuple([instance[key] for instance in instances]
for key in ("input_ids", "labels"))
input_ids = torch.nn.utils.rnn.pad_sequence(
input_ids,
batch_first=True,
padding_value=self.tokenizer.pad_token_id)
labels = torch.nn.utils.rnn.pad_sequence(labels,
batch_first=True,
padding_value=IGNORE_INDEX)
input_ids = input_ids[:, :self.tokenizer.model_max_length]
labels = labels[:, :self.tokenizer.model_max_length]
batch = dict(
input_ids=input_ids,
labels=labels,
attention_mask=input_ids.ne(self.tokenizer.pad_token_id),
)
if 'image' in instances[0]:
if not all(len(instance['image']) == 2 for instance in instances):
raise ValueError("Each instance['image'] must contain exactly two type images.")
cur_images = [instance['image'][0] for instance in instances]
prior_images = [instance['image'][1] for instance in instances]
if all(x is not None and x.shape == cur_images[0].shape for x in cur_images) and \
all(x is not None and x.shape == prior_images[0].shape for x in prior_images):
batch['images'] = torch.stack([torch.stack(cur_images), torch.stack(prior_images)])
else:
print("Warning: Image shapes are inconsistent. Using lists for images.")
batch['images'] = [cur_images, prior_images]
return batch
def make_supervised_data_module(tokenizer: transformers.PreTrainedTokenizer,
data_args) -> Dict:
"""Make dataset and collator for supervised fine-tuning."""
train_dataset = LazySupervisedDataset(tokenizer=tokenizer,
data_path=data_args.data_path,
data_args=data_args)
eval_dataset = LazySupervisedDataset(tokenizer=tokenizer,
data_path=data_args.validation_data_path,
data_args=data_args,
sample_rate=1.0)
data_collator = DataCollatorForSupervisedDataset(tokenizer=tokenizer)
return dict(train_dataset=train_dataset,
eval_dataset=eval_dataset,
data_collator=data_collator)
def train():
global local_rank
parser = transformers.HfArgumentParser(
(ModelArguments, DataArguments, TrainingArguments))
model_args, data_args, training_args = parser.parse_args_into_dataclasses()
local_rank = training_args.local_rank
compute_dtype = (torch.float16 if training_args.fp16 else (torch.bfloat16 if training_args.bf16 else torch.float32))
bnb_model_from_pretrained_args = {}
if training_args.bits in [4, 8]:
from transformers import BitsAndBytesConfig
bnb_model_from_pretrained_args.update(dict(
device_map={"": training_args.device},
load_in_4bit=training_args.bits == 4,
load_in_8bit=training_args.bits == 8,
quantization_config=BitsAndBytesConfig(
load_in_4bit=training_args.bits == 4,
load_in_8bit=training_args.bits == 8,
llm_int8_skip_modules=["mm_projector"],
llm_int8_threshold=6.0,
llm_int8_has_fp16_weight=False,
bnb_4bit_compute_dtype=compute_dtype,
bnb_4bit_use_double_quant=training_args.double_quant,
bnb_4bit_quant_type=training_args.quant_type # {'fp4', 'nf4'}
)
))
if model_args.vision_tower is not None:
model = LibraLlamaForCausalLM.from_pretrained(
model_args.model_name_or_path,
cache_dir=training_args.cache_dir,
torch_dtype=(torch.bfloat16 if training_args.bf16 else None),
**bnb_model_from_pretrained_args
)
else:
model = transformers.LlamaForCausalLM.from_pretrained(
model_args.model_name_or_path,
cache_dir=training_args.cache_dir,
torch_dtype=(torch.bfloat16 if training_args.bf16 else None),
**bnb_model_from_pretrained_args
)
model.config.use_cache = False
if model_args.freeze_backbone:
model.model.requires_grad_(False)
if training_args.bits in [4, 8]:
from peft import prepare_model_for_kbit_training
model.config.torch_dtype=(torch.float32 if training_args.fp16 else (torch.bfloat16 if training_args.bf16 else torch.float32))
model = prepare_model_for_kbit_training(model, use_gradient_checkpointing=training_args.gradient_checkpointing)
if training_args.gradient_checkpointing:
if hasattr(model, "enable_input_require_grads"):
model.enable_input_require_grads()
else:
def make_inputs_require_grad(module, input, output):
output.requires_grad_(True)
model.get_input_embeddings().register_forward_hook(make_inputs_require_grad)
if training_args.lora_enable:
from peft import LoraConfig, get_peft_model
lora_config = LoraConfig(
r=training_args.lora_r,
lora_alpha=training_args.lora_alpha,
target_modules=find_all_linear_names(model),
lora_dropout=training_args.lora_dropout,
bias=training_args.lora_bias,
task_type="CAUSAL_LM",
)
if training_args.bits == 16:
if training_args.bf16:
model.to(torch.bfloat16)
if training_args.fp16:
model.to(torch.float16)
rank0_print("Adding LoRA adapters...")
model = get_peft_model(model, lora_config)
if 'mpt' in model_args.model_name_or_path:
tokenizer = transformers.AutoTokenizer.from_pretrained(
model_args.model_name_or_path,
cache_dir=training_args.cache_dir,
model_max_length=training_args.model_max_length,
padding_side="right"
)
else:
tokenizer = transformers.AutoTokenizer.from_pretrained(
model_args.model_name_or_path,
cache_dir=training_args.cache_dir,
model_max_length=training_args.model_max_length,
padding_side="right",
use_fast=False,
)
if model_args.version == "v0":
if tokenizer.pad_token is None:
smart_tokenizer_and_embedding_resize(
special_tokens_dict=dict(pad_token="[PAD]"),
tokenizer=tokenizer,
model=model,
)
elif model_args.version == "v0.5":
tokenizer.pad_token = tokenizer.unk_token
else:
tokenizer.pad_token = tokenizer.unk_token
if model_args.version in conversation_lib.conv_templates:
conversation_lib.default_conversation = conversation_lib.conv_templates[model_args.version]
else:
conversation_lib.default_conversation = conversation_lib.conv_templates["vicuna_v1"]
if model_args.vision_tower is not None:
model.get_model().initialize_vision_modules(
model_args=model_args,
fsdp=training_args.fsdp
)
vision_tower = model.get_vision_tower()
vision_tower.to(dtype=torch.bfloat16 if training_args.bf16 else torch.float16, device=training_args.device)
data_args.image_processor = vision_tower.image_processor
data_args.is_multimodal = True
model.config.image_aspect_ratio = data_args.image_aspect_ratio
model.config.tokenizer_padding_side = tokenizer.padding_side
model.config.tokenizer_model_max_length = tokenizer.model_max_length
model.config.tune_mm_mlp_adapter = training_args.tune_mm_mlp_adapter = model_args.tune_mm_mlp_adapter
if model_args.tune_mm_mlp_adapter:
model.requires_grad_(False)
for p in model.get_model().mm_projector.parameters():
p.requires_grad = True
model.config.freeze_mm_mlp_adapter = training_args.freeze_mm_mlp_adapter
if training_args.freeze_mm_mlp_adapter:
for p in model.get_model().mm_projector.parameters():
p.requires_grad = False
if training_args.bits in [4, 8]:
model.get_model().mm_projector.to(dtype=compute_dtype, device=training_args.device)
model.config.mm_use_im_start_end = data_args.mm_use_im_start_end = model_args.mm_use_im_start_end
model.config.mm_projector_lr = training_args.mm_projector_lr
training_args.use_im_start_end = model_args.mm_use_im_start_end
model.config.mm_use_im_patch_token = model_args.mm_use_im_patch_token
model.initialize_vision_tokenizer(model_args, tokenizer=tokenizer)
if training_args.bits in [4, 8]:
from peft.tuners.lora import LoraLayer
for name, module in model.named_modules():
if isinstance(module, LoraLayer):
if training_args.bf16:
module = module.to(torch.bfloat16)
if 'norm' in name:
module = module.to(torch.float32)
if 'lm_head' in name or 'embed_tokens' in name:
if hasattr(module, 'weight'):
if training_args.bf16 and module.weight.dtype == torch.float32:
module = module.to(torch.bfloat16)
data_module = make_supervised_data_module(tokenizer=tokenizer,
data_args=data_args)
# SaveCallback
class SaveCallback(TrainerCallback):
def __init__(self):
super().__init__()
self.best_metric = None
def on_evaluate(self, args, state, control, metrics, **kwargs):
"""
Custom logic for evaluating and saving the best model based on a chosen metric.
Saves the model and configuration if a better metric is achieved during evaluation.
"""
metric_for_best_model = 'eval_loss' # Metric used to determine the best model (e.g., eval_loss, eval_bleu, eval_rouge)
metric_value = metrics.get(metric_for_best_model)
if self.best_metric is None or metric_value < self.best_metric:
self.best_metric = metric_value
best_model_dir = os.path.join(args.output_dir, 'best_eval_model')
# Save generation configuration if present
if hasattr(model, 'generation_config'):
model.generation_config.save_pretrained(best_model_dir)
# Save model configuration
model.config.save_pretrained(best_model_dir)
if tokenizer is not None:
tokenizer.save_pretrained(best_model_dir)
# Save the best model
if args.lora_enable:
# Save LoRA-specific parameters
state_dict = get_peft_state_maybe_zero_3(
model.named_parameters(), args.lora_bias
)
non_lora_state_dict = get_peft_state_non_lora_maybe_zero_3(
model.named_parameters()
)
if args.local_rank in [-1, 0]:
model.save_pretrained(best_model_dir, state_dict=state_dict)
torch.save(non_lora_state_dict, os.path.join(best_model_dir, 'non_lora_trainables.bin'))
else:
# Save full model state when not using LoRA
state_dict = get_non_vision_tower_state_maybe_zero_3(
model.named_parameters()
)
if args.local_rank in [-1, 0]:
model.save_pretrained(best_model_dir, state_dict=state_dict)
# Save mm_projector state when tuning mm_mlp_adapter
safe_save_model_for_hf_trainer(trainer=trainer, output_dir=best_model_dir)
check_trainable_parameters(model)
compute_metrics_func = None
if model_args.compute_metrics:
compute_metrics_func = create_compute_metrics(tokenizer,vision_tower.num_patches,conversation_lib.default_conversation.sep2)
model.to(training_args.device)
trainer = LibraTrainer(model=model,
tokenizer=tokenizer,
args=training_args,
callbacks=[SaveCallback()],
compute_metrics=compute_metrics_func,
**data_module)
if list(pathlib.Path(training_args.output_dir).glob("checkpoint-*")):
trainer.train(resume_from_checkpoint=True)
else:
trainer.train()
trainer.save_state()
model.config.use_cache = True
if training_args.lora_enable:
state_dict = get_peft_state_maybe_zero_3(
model.named_parameters(), training_args.lora_bias
)
non_lora_state_dict = get_peft_state_non_lora_maybe_zero_3(
model.named_parameters()
)
if training_args.local_rank == 0 or training_args.local_rank == -1:
model.config.save_pretrained(training_args.output_dir)
model.save_pretrained(training_args.output_dir, state_dict=state_dict)
torch.save(non_lora_state_dict, os.path.join(training_args.output_dir, 'non_lora_trainables.bin'))
else:
safe_save_model_for_hf_trainer(trainer=trainer,
output_dir=training_args.output_dir)
if __name__ == "__main__":
train()