Datasets:
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: CastError
Message: Couldn't cast
modality: string
node_feat: list<element: list<element: int64>>
child 0, element: list<element: int64>
child 0, element: int64
pos: list<element: list<element: double>>
child 0, element: list<element: double>
child 0, element: double
edge_index: list<element: list<element: int64>>
child 0, element: list<element: int64>
child 0, element: int64
edge_attr: list<element: list<element: double>>
child 0, element: list<element: double>
child 0, element: double
-- schema metadata --
pandas: '{"index_columns": [], "column_indexes": [], "columns": [{"name":' + 715
to
{'modality': Value('string'), 'node_feat': List(List(Value('int64'))), 'pos': List(List(Value('float64'))), 'edge_index': List(List(Value('int64'))), 'chem_edge_index': List(List(Value('int64'))), 'chem_edge_feat_cat': List(List(Value('int64'))), 'edge_feat_dist': List(List(Value('float64')))}
because column names don't match
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/parquet/parquet.py", line 209, in _generate_tables
yield Key(file_idx, batch_idx), self._cast_table(pa_table)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/parquet/parquet.py", line 147, in _cast_table
pa_table = table_cast(pa_table, self.info.features.arrow_schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2321, in table_cast
return cast_table_to_schema(table, schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2249, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
modality: string
node_feat: list<element: list<element: int64>>
child 0, element: list<element: int64>
child 0, element: int64
pos: list<element: list<element: double>>
child 0, element: list<element: double>
child 0, element: double
edge_index: list<element: list<element: int64>>
child 0, element: list<element: int64>
child 0, element: int64
edge_attr: list<element: list<element: double>>
child 0, element: list<element: double>
child 0, element: double
-- schema metadata --
pandas: '{"index_columns": [], "column_indexes": [], "columns": [{"name":' + 715
to
{'modality': Value('string'), 'node_feat': List(List(Value('int64'))), 'pos': List(List(Value('float64'))), 'edge_index': List(List(Value('int64'))), 'chem_edge_index': List(List(Value('int64'))), 'chem_edge_feat_cat': List(List(Value('int64'))), 'edge_feat_dist': List(List(Value('float64')))}
because column names don't matchNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
Cuttlefish-Encoder-Data
Encoder pretraining dataset for Cuttlefish-Encoder. Contains all-atom structural graphs for molecules, proteins, DNA, and RNA in a unified parquet format.
Dataset structure
molecules/ # molecule encoder training data
nacid/ # DNA and RNA encoder training data
protein/ # protein encoder training data (PDB structures)
test/ # held-out test samples
Schema
| Field | Description |
|---|---|
modality |
"molecule", "protein", "dna", or "rna" |
node_feat |
Atom/node features (N × d) |
pos |
3D coordinates in Å (N × 3) |
edge_index |
Spatial graph edges in COO (2 × E) |
edge_feat_dist |
Edge distances (E × 1, optional) |
Usage
from datasets import load_dataset
ds = load_dataset("zihaojing/Cuttlefish-Encoder-Data")
Related resources
| Resource | Link |
|---|---|
| Cuttlefish LLM | zihaojing/Cuttlefish |
| Cuttlefish-Encoder | zihaojing/Cuttlefish-Encoder |
| SFT instruction data | zihaojing/Cuttlefish-SFT-Data |
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