Dataset Viewer
The dataset viewer is not available for this split.
Cannot load the dataset split (in streaming mode) to extract the first rows.
Error code: StreamingRowsError
Exception: ValueError
Message: Dataset 'F1' has length 2013 but expected 2006
Traceback: Traceback (most recent call last):
File "/src/services/worker/src/worker/utils.py", line 99, in get_rows_or_raise
return get_rows(
^^^^^^^^^
File "/src/libs/libcommon/src/libcommon/utils.py", line 272, in decorator
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/src/services/worker/src/worker/utils.py", line 77, in get_rows
rows_plus_one = list(itertools.islice(ds, rows_max_number + 1))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2690, in __iter__
for key, example in ex_iterable:
^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2227, in __iter__
for key, pa_table in self._iter_arrow():
^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2251, in _iter_arrow
for key, pa_table in self.ex_iterable._iter_arrow():
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 494, in _iter_arrow
for key, pa_table in iterator:
^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 384, in _iter_arrow
for key, pa_table in self.generate_tables_fn(**gen_kwags):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/hdf5/hdf5.py", line 80, in _generate_tables
num_rows = _check_dataset_lengths(h5, self.info.features)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/hdf5/hdf5.py", line 359, in _check_dataset_lengths
raise ValueError(f"Dataset '{path}' has length {dset.shape[0]} but expected {num_rows}")
ValueError: Dataset 'F1' has length 2013 but expected 2006Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
HAEC Training Data
100 donor H5 files for 5-fold cross-validation training.
H5 structure
Each file has chunked datasets: X0, Y0, GC0, F0, X1, Y1, GC1, F1, ...
- X: one-hot encoded sequence (float32)
- Y: splice site labels (float32, 4 channels: neither, acceptor, donor, SSU)
- GC: genomic coordinates and transcript metadata
- F: fold assignment (int8)
Fold values
- 0 = always train (paralog or non-paralog not in any validation fold)
- 1-5 = validation for that split number
Usage
To train split k (e.g. split 3):
import h5py
with h5py.File("full_DD006RP2.h5", "r") as h5f:
n_chunks = sum(1 for k in h5f.keys() if k.startswith("X"))
for ci in range(n_chunks):
x = h5f[f"X{ci}"][:]
y = h5f[f"Y{ci}"][:]
f = h5f[f"F{ci}"][:]
train_mask = (f != 3) # everything except split 3 validation
valid_mask = (f == 3) # split 3 validation windows
x_train, y_train = x[train_mask], y[train_mask]
x_valid, y_valid = x[valid_mask], y[valid_mask]
Split configuration
- train chromosomes: chr2, 4, 6, 8, 10-22
- 5 CV folds, 10% validation per fold, seed=42
- validation drawn from non-paralog transcripts only
- paralogs always stay in training (from all chromosomes)
- 100 donors, gzip-9 compression
Download
pip install huggingface_hub
hf download mrunyan1/haec-training-data
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