tdpeuter/2025ML-project-neural_compression
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feat: Smaller genome dataset

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This commit is contained in:
Tibo De Peuter 2025-12-11 13:38:52 +01:00
parent d0457b6571
commit cd74949b74
Signed by: tdpeuter
GPG key ID: 38297DE43F75FFE2
5 changed files with 337 additions and 77 deletions
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2
job.pbs
View file

@ -30,7 +30,7 @@ source "${VENV}/bin/activate"
UV_PYTHON_INSTALL_DIR="${UV_DIR}/python" UV_PYTHON_INSTALL_DIR="${UV_DIR}/python" \ UV_PYTHON_INSTALL_DIR="${UV_DIR}/python" UV_PYTHON_INSTALL_DIR="${UV_DIR}/python" \
uv --cache-dir="${CACHE_DIR}/uv" \ uv --cache-dir="${CACHE_DIR}/uv" \
sync --active --no-dev sync --active --no-dev # I hope this includes dataset code as well
cd "${PBS_O_WORKDIR}" || exit cd "${PBS_O_WORKDIR}" || exit

7
pyproject.toml
View file

@ -5,8 +5,7 @@ description = "Add your description here"
readme = "README.md" readme = "README.md"
requires-python = ">=3.11" requires-python = ">=3.11"
dependencies = [ dependencies = [
"datasets>=3.2.0", "datasets<4.0.0",
"huggingface_hub==0.27.0",
"fsspec==2024.9.0", "fsspec==2024.9.0",
"lorem>=0.1.1", "lorem>=0.1.1",
] ]
@ -21,3 +20,7 @@ dev = [
"torchdata==0.7.1", "torchdata==0.7.1",
"torchvision==0.24.0", "torchvision==0.24.0",
] ]
dataset = [
"biopython>=1.86",
"regex>=2025.11.3",
]

48
src/dataset_loaders/HumanReferenceGenomeDataset.py Normal file
View file

@ -0,0 +1,48 @@
from typing import Callable
from datasets import load_dataset
from .Dataset import Dataset
class HumanReferenceGenomeDataset(Dataset):
"""
Hugging Face: https://huggingface.co/datasets/InstaDeepAI/human_reference_genome
:param split: 'train' | 'validation' | 'test'
:param config: '6kbp' | '12kbp' (chunk length in the HF builder config)
"""
def __init__(self,
root: str | None = None,
split: str = "train",
transform: Callable = None,
size: int = -1,
config: str = "6kbp",
):
super().__init__("human_reference_genome", root, split, transform, size)
print(f"Loading from HuggingFace (config: {config}, split: {split})")
ds = load_dataset("InstaDeepAI/human_reference_genome", config, split=split,
cache_dir=self.root, trust_remote_code=True)
# Your Dataset.process_data() expects a list[str]; use the 'sequence' field
self.data = ds["sequence"]
self.context_length = 2048
self.process_data()
print("Done initializing dataset")
def __len__(self):
return self.chunk_offsets[-1] - self.context_length
def __getitem__(self, idx):
x = self.tensor[idx: idx + self.context_length]
y = self.tensor[idx + self.context_length]
if self.transform:
x = self.transform(x)
return x, y

4
src/dataset_loaders/__init__.py
View file

@ -1,10 +1,12 @@
from .Dataset import Dataset from .Dataset import Dataset
from .EnWik9 import EnWik9DataSet from .EnWik9 import EnWik9DataSet
from .HumanReferenceGenomeDataset import HumanReferenceGenomeDataset
from .LoremIpsumDataset import LoremIpsumDataset from .LoremIpsumDataset import LoremIpsumDataset
from .OpenGenomeDataset import OpenGenomeDataset from .OpenGenomeDataset import OpenGenomeDataset
dataset_called: dict[str, type[Dataset]] = { dataset_called: dict[str, type[Dataset]] = {
'enwik9': EnWik9DataSet, 'enwik9': EnWik9DataSet,
'lorem_ipsum': LoremIpsumDataset, 'lorem_ipsum': LoremIpsumDataset,
'opengenome': OpenGenomeDataset 'opengenome': OpenGenomeDataset,
'humanreference': HumanReferenceGenomeDataset
} }

353
uv.lock generated
View file

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version = "1.86"
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