Dataset Viewer
The dataset viewer is not available for this dataset.
Cannot get the config names for the dataset.
Error code: ConfigNamesError
Exception: ReadTimeout
Message: (ReadTimeoutError("HTTPSConnectionPool(host='huggingface.co', port=443): Read timed out. (read timeout=10)"), '(Request ID: 38e8a77b-986e-4d43-a10a-f306949446ae)')
Traceback: Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/dataset/config_names.py", line 66, in compute_config_names_response
config_names = get_dataset_config_names(
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/inspect.py", line 161, in get_dataset_config_names
dataset_module = dataset_module_factory(
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/load.py", line 1031, in dataset_module_factory
raise e1 from None
File "/usr/local/lib/python3.12/site-packages/datasets/load.py", line 1004, in dataset_module_factory
).get_module()
^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/load.py", line 632, in get_module
data_files = DataFilesDict.from_patterns(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/data_files.py", line 689, in from_patterns
else DataFilesList.from_patterns(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/data_files.py", line 592, in from_patterns
origin_metadata = _get_origin_metadata(data_files, download_config=download_config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/data_files.py", line 506, in _get_origin_metadata
return thread_map(
^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/tqdm/contrib/concurrent.py", line 69, in thread_map
return _executor_map(ThreadPoolExecutor, fn, *iterables, **tqdm_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/tqdm/contrib/concurrent.py", line 51, in _executor_map
return list(tqdm_class(ex.map(fn, *iterables, chunksize=chunksize), **kwargs))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/tqdm/std.py", line 1169, in __iter__
for obj in iterable:
^^^^^^^^
File "/usr/local/lib/python3.12/concurrent/futures/_base.py", line 619, in result_iterator
yield _result_or_cancel(fs.pop())
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/concurrent/futures/_base.py", line 317, in _result_or_cancel
return fut.result(timeout)
^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/concurrent/futures/_base.py", line 456, in result
return self.__get_result()
^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/concurrent/futures/_base.py", line 401, in __get_result
raise self._exception
File "/usr/local/lib/python3.12/concurrent/futures/thread.py", line 59, in run
result = self.fn(*self.args, **self.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/data_files.py", line 485, in _get_single_origin_metadata
resolved_path = fs.resolve_path(data_file)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/huggingface_hub/hf_file_system.py", line 198, in resolve_path
repo_and_revision_exist, err = self._repo_and_revision_exist(repo_type, repo_id, revision)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/huggingface_hub/hf_file_system.py", line 125, in _repo_and_revision_exist
self._api.repo_info(
File "/usr/local/lib/python3.12/site-packages/huggingface_hub/utils/_validators.py", line 114, in _inner_fn
return fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/huggingface_hub/hf_api.py", line 2816, in repo_info
return method(
^^^^^^^
File "/usr/local/lib/python3.12/site-packages/huggingface_hub/utils/_validators.py", line 114, in _inner_fn
return fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/huggingface_hub/hf_api.py", line 2673, in dataset_info
r = get_session().get(path, headers=headers, timeout=timeout, params=params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/requests/sessions.py", line 602, in get
return self.request("GET", url, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/requests/sessions.py", line 589, in request
resp = self.send(prep, **send_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/requests/sessions.py", line 703, in send
r = adapter.send(request, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/huggingface_hub/utils/_http.py", line 96, in send
return super().send(request, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/requests/adapters.py", line 690, in send
raise ReadTimeout(e, request=request)
requests.exceptions.ReadTimeout: (ReadTimeoutError("HTTPSConnectionPool(host='huggingface.co', port=443): Read timed out. (read timeout=10)"), '(Request ID: 38e8a77b-986e-4d43-a10a-f306949446ae)')Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
Variant Foundation Embeddings
Here we present the variant level embeddings for large-scale genetic analyis as described in 'Incorporating LLM Embeddings for Variation Across the Human Genome,' based on curated annotations using high quality functional data from FAVOR, ClinVar, and GWAS Catalog. We currently present embeddings using either OpenAI's text-embedding-3-large (3072-dimensional) or Qwen's Qwen3-Embedding-0.6B (1024-dimensional) models.
Genetic variants are identified with their chromosome, position (hg38 build), reference allele based on UKB coding, alternate allele based on UKB coding, and their respective LLM embeddings.
Currently we release datasets at the following scales:
- HapMap3 & MEGA (~1.5 million variants, OpenAI GPT-3.5)
- UKB Imputed (~90 million variants, OpenAI GPT-3.5)
- All FAVOR Variants (~9 billion variants, Qwen3-0.6B)
With more to come shortly.
Dataset Schema (OpenAI text-embedding-3-large)
| Field | Type | Description |
|---|---|---|
chrom |
string | Chromosome (e.g., "1", "X") |
pos |
string | Base-pair position (hg38 coordinate system) |
ref_UKB |
string | Reference allele (A, C, G, T) |
alt_UKB |
string | Alternate allele (A, C, G, T) |
embedding |
list[float] | Embedding vector (dimension 3072, float) |
Dataset Schema (Qwen qwen3-embedding-0.6B)
| Field | Type | Description |
|---|---|---|
chrom |
string | Chromosome (e.g., "1", "X") |
pos |
string | Base-pair position (hg38 coordinate system) |
ref_UKB |
string | Reference allele (A, C, G, T) |
alt_UKB |
string | Alternate allele (A, C, G, T) |
embedding |
list[float] | Embedding vector (dimension 1024, float) |
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