SciHorizon-GENE: Benchmarking LLM for Life Sciences Inference from Gene Knowledge to Functional Understanding
Paper
•
2601.12805
•
Published
Dataset Viewer
The dataset viewer is not available for this split.
Cannot extract the features (columns) for the split 'train' of the config 'default' of the dataset.
Error code: FeaturesError
Exception: ArrowInvalid
Message: JSON parse error: Column(/answer) changed from string to array in row 8
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/json/json.py", line 183, in _generate_tables
df = pandas_read_json(f)
^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/json/json.py", line 38, in pandas_read_json
return pd.read_json(path_or_buf, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/pandas/io/json/_json.py", line 815, in read_json
return json_reader.read()
^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/pandas/io/json/_json.py", line 1014, in read
obj = self._get_object_parser(self.data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/pandas/io/json/_json.py", line 1040, in _get_object_parser
obj = FrameParser(json, **kwargs).parse()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/pandas/io/json/_json.py", line 1176, in parse
self._parse()
File "/usr/local/lib/python3.12/site-packages/pandas/io/json/_json.py", line 1392, in _parse
ujson_loads(json, precise_float=self.precise_float), dtype=None
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: Trailing data
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/split/first_rows.py", line 243, in compute_first_rows_from_streaming_response
iterable_dataset = iterable_dataset._resolve_features()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 3608, in _resolve_features
features = _infer_features_from_batch(self.with_format(None)._head())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2368, in _head
return next(iter(self.iter(batch_size=n)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2573, in iter
for key, example in iterator:
^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2060, in __iter__
for key, pa_table in self._iter_arrow():
^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2082, in _iter_arrow
yield from self.ex_iterable._iter_arrow()
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 544, in _iter_arrow
for key, pa_table in iterator:
^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 383, 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/json/json.py", line 186, in _generate_tables
raise e
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/json/json.py", line 160, in _generate_tables
pa_table = paj.read_json(
^^^^^^^^^^^^^^
File "pyarrow/_json.pyx", line 342, in pyarrow._json.read_json
File "pyarrow/error.pxi", line 155, in pyarrow.lib.pyarrow_internal_check_status
File "pyarrow/error.pxi", line 92, in pyarrow.lib.check_status
pyarrow.lib.ArrowInvalid: JSON parse error: Column(/answer) changed from string to array in row 8Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
🧬 SciHorizon-GENE
SciHorizon-GENE is a large-scale benchmark for evaluating the capability of large language models (LLMs) to perform understanding-to-reasoning in human gene knowledge.
It focuses on assessing whether LLMs can reliably infer biological function and interpretation from gene-level knowledge - a core requirement for knowledge-driven biological analysis.
🔗 Project Page: https://horizon.scidb.cn/verticalCategory/SciHorizonGene
🔗 Github Repository: https://github.com/XiaohanHwang/SciHorizonGene
📖 Overview
SciHorizon-GENE is a large-scale gene-centric benchmark constructed from authoritative biological databases to systematically evaluate LLM performance in gene-level biological understanding and reasoning.
The benchmark is designed to analyze model behavior in realistic scientific scenarios and to identify limitations that affect the reliability of LLMs in biological research settings.
🧬 Dataset & Benchmark Scale
SciHorizon-GENE integrates curated knowledge for:
- 190K+ human genes
- 540K+ gene-centric questions
All questions are constructed from authoritative biological databases and curated knowledge sources, ensuring high biological relevance and scientific grounding.
📊 Intended Use
This benchmark is NOT intended for:
- Clinical diagnosis
- Medical treatment decisions
- Any real-world healthcare deployment
SciHorizon-GENE is for research and evaluation purposes only.
🌐 SciHorizon Project
For more information about the SciHorizon project:
👉 https://horizon.scidb.cn
📑Paper:
Qin C, Chen X, Wang C, et al. Scihorizon: Benchmarking ai-for-science readiness from scientific data to large language models[C]//Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining V. 2. 2025: 5754-5765.
📄 Citation
If you use this benchmark, please cite:
SciHorizon-GENE: Benchmarking LLM for Life Sciences Inference from Gene Knowledge to Functional Understanding
arXiv: https://arxiv.org/abs/2601.12805
@article{huang2026scihorizon,
title={SciHorizon-GENE: Benchmarking LLM for Life Sciences Inference from Gene Knowledge to Functional Understanding},
author={Huang, Xiaohan and Xiao, Meng and Qin, Chuan and Long, Qingqing and Chen, Jinmiao and Zhou, Yuanchun and Zhu, Hengshu},
journal={arXiv preprint arXiv:2601.12805},
year={2026}
}
- Downloads last month
- 3