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Error code: DatasetGenerationError Exception: ArrowInvalid Message: Failed to parse string: '4781916-1' as a scalar of type int64 Traceback: Traceback (most recent call last): File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1870, in _prepare_split_single writer.write_table(table) File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 622, in write_table pa_table = table_cast(pa_table, self._schema) File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2292, in table_cast return cast_table_to_schema(table, schema) File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2245, in cast_table_to_schema arrays = [ File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2246, in <listcomp> cast_array_to_feature( File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1795, in wrapper return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks]) File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1795, in <listcomp> return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks]) File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2102, in cast_array_to_feature return array_cast( File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1797, in wrapper return func(array, *args, **kwargs) File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1949, in array_cast return array.cast(pa_type) File "pyarrow/array.pxi", line 996, in pyarrow.lib.Array.cast File "/src/services/worker/.venv/lib/python3.9/site-packages/pyarrow/compute.py", line 404, in cast return call_function("cast", [arr], options, memory_pool) File "pyarrow/_compute.pyx", line 590, in pyarrow._compute.call_function File "pyarrow/_compute.pyx", line 385, in pyarrow._compute.Function.call File "pyarrow/error.pxi", line 154, in pyarrow.lib.pyarrow_internal_check_status File "pyarrow/error.pxi", line 91, in pyarrow.lib.check_status pyarrow.lib.ArrowInvalid: Failed to parse string: '4781916-1' as a scalar of type int64 The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1417, in compute_config_parquet_and_info_response parquet_operations = convert_to_parquet(builder) File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1049, in convert_to_parquet builder.download_and_prepare( File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 924, in download_and_prepare self._download_and_prepare( File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1000, in _download_and_prepare self._prepare_split(split_generator, **prepare_split_kwargs) File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1741, in _prepare_split for job_id, done, content in self._prepare_split_single( File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1897, in _prepare_split_single raise DatasetGenerationError("An error occurred while generating the dataset") from e datasets.exceptions.DatasetGenerationError: An error occurred while generating the dataset
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query-id
string | corpus-id
int64 | score
int64 |
---|---|---|
7665777-1 | 32,320,506 | 1 |
7665777-1 | 32,293,716 | 1 |
7665777-1 | 23,219,649 | 1 |
7665777-1 | 30,339,549 | 1 |
7665777-1 | 17,470,624 | 1 |
7665777-1 | 32,280,973 | 1 |
7665777-1 | 34,789,437 | 1 |
7665777-1 | 30,427,933 | 1 |
7665777-1 | 32,191,813 | 1 |
7665777-1 | 31,064,802 | 1 |
7665777-1 | 12,493,078 | 1 |
7665777-1 | 23,688,302 | 1 |
7665777-1 | 24,552,321 | 1 |
7665777-1 | 34,602,603 | 1 |
7665777-1 | 29,208,005 | 1 |
7665777-1 | 32,312,646 | 1 |
7665777-1 | 20,046,114 | 1 |
7665777-1 | 32,250,385 | 1 |
7665777-1 | 23,886,842 | 1 |
7665777-1 | 32,345,343 | 1 |
7665777-1 | 17,885,261 | 1 |
7665777-1 | 29,023,260 | 1 |
7665777-1 | 27,940,276 | 1 |
7665777-1 | 31,768,568 | 1 |
7665777-1 | 34,953,756 | 1 |
7665777-1 | 30,113,379 | 1 |
7665777-1 | 28,847,238 | 1 |
7665777-1 | 33,492,400 | 1 |
7665777-2 | 32,320,506 | 1 |
7665777-2 | 32,293,716 | 1 |
7665777-2 | 23,219,649 | 1 |
7665777-2 | 30,339,549 | 1 |
7665777-2 | 17,470,624 | 1 |
7665777-2 | 32,280,973 | 1 |
7665777-2 | 34,789,437 | 1 |
7665777-2 | 30,427,933 | 1 |
7665777-2 | 32,191,813 | 1 |
7665777-2 | 31,064,802 | 1 |
7665777-2 | 12,493,078 | 1 |
7665777-2 | 23,688,302 | 1 |
7665777-2 | 24,552,321 | 1 |
7665777-2 | 34,602,603 | 1 |
7665777-2 | 29,208,005 | 1 |
7665777-2 | 32,312,646 | 1 |
7665777-2 | 20,046,114 | 1 |
7665777-2 | 32,250,385 | 1 |
7665777-2 | 23,886,842 | 1 |
7665777-2 | 32,345,343 | 1 |
7665777-2 | 17,885,261 | 1 |
7665777-2 | 29,023,260 | 1 |
7665777-2 | 27,940,276 | 1 |
7665777-2 | 31,768,568 | 1 |
7665777-2 | 34,953,756 | 1 |
7665777-2 | 30,113,379 | 1 |
7665777-2 | 28,847,238 | 1 |
7665777-2 | 33,492,400 | 1 |
7665777-3 | 32,320,506 | 1 |
7665777-3 | 32,293,716 | 1 |
7665777-3 | 23,219,649 | 1 |
7665777-3 | 30,339,549 | 1 |
7665777-3 | 17,470,624 | 1 |
7665777-3 | 32,280,973 | 1 |
7665777-3 | 34,789,437 | 1 |
7665777-3 | 30,427,933 | 1 |
7665777-3 | 32,191,813 | 1 |
7665777-3 | 31,064,802 | 1 |
7665777-3 | 12,493,078 | 1 |
7665777-3 | 23,688,302 | 1 |
7665777-3 | 24,552,321 | 1 |
7665777-3 | 34,602,603 | 1 |
7665777-3 | 29,208,005 | 1 |
7665777-3 | 32,312,646 | 1 |
7665777-3 | 20,046,114 | 1 |
7665777-3 | 32,250,385 | 1 |
7665777-3 | 23,886,842 | 1 |
7665777-3 | 32,345,343 | 1 |
7665777-3 | 17,885,261 | 1 |
7665777-3 | 29,023,260 | 1 |
7665777-3 | 27,940,276 | 1 |
7665777-3 | 31,768,568 | 1 |
7665777-3 | 34,953,756 | 1 |
7665777-3 | 30,113,379 | 1 |
7665777-3 | 28,847,238 | 1 |
7665777-3 | 33,492,400 | 1 |
7665777-4 | 32,320,506 | 1 |
7665777-4 | 32,293,716 | 1 |
7665777-4 | 23,219,649 | 1 |
7665777-4 | 30,339,549 | 1 |
7665777-4 | 17,470,624 | 1 |
7665777-4 | 32,280,973 | 1 |
7665777-4 | 34,789,437 | 1 |
7665777-4 | 30,427,933 | 1 |
7665777-4 | 32,191,813 | 1 |
7665777-4 | 31,064,802 | 1 |
7665777-4 | 12,493,078 | 1 |
7665777-4 | 23,688,302 | 1 |
7665777-4 | 24,552,321 | 1 |
7665777-4 | 34,602,603 | 1 |
7665777-4 | 29,208,005 | 1 |
7665777-4 | 32,312,646 | 1 |
Dataset Card for PMC-Patients-ReCDS
Dataset Summary
PMC-Patients is a first-of-its-kind dataset consisting of 167k patient summaries extracted from case reports in PubMed Central (PMC), 3.1M patient-article relevance and 293k patient-patient similarity annotations defined by PubMed citation graph.
Supported Tasks and Leaderboards
Based on PMC-Patients, we define two tasks to benchmark Retrieval-based Clinical Decision Support (ReCDS) systems: Patient-to-Article Retrieval (PAR) and Patient-to-Patient Retrieval (PPR). For details, please refer to our paper and leaderboard.
Languages
English (en).
Dataset Structure
The PMC-Patients ReCDS benchmark is presented as retrieval tasks and the data format is the same as BEIR benchmark. To be specific, there are queries, corpus, and qrels (annotations).
Queries
ReCDS-PAR and ReCDS-PPR tasks share the same query patient set and dataset split.
For each split (train, dev, and test), queries are stored a jsonl
file that contains a list of dictionaries, each with two fields:
_id
: unique query identifier represented by patient_uid.text
: query text represented by patient summary text.
Corpus
Corpus is shared by different splits. For ReCDS-PAR, the corpus contains 11.7M PubMed articles, and for ReCDS-PPR, the corpus contains 155.2k reference patients from PMC-Patients. The corpus is also presented by a jsonl
file that contains a list of dictionaries with three fields:
_id
: unique document identifier represented by PMID of the PubMed article in ReCDS-PAR, and patient_uid of the candidate patient in ReCDS-PPR.title
: : title of the article in ReCDS-PAR, and empty string in ReCDS-PPR.text
: abstract of the article in ReCDS-PAR, and patient summary text in ReCDS-PPR.
PAR corpus note
Due to its large size, we fail to upload the full PAR corpus on Huggingface. Instead, we provide PMIDs of the articles we include in PAR corpus, but we recommend you to download the dataset from Figshare which contains the full PAR corpus file.
Qrels
Qrels are TREC-style retrieval annotation files in tsv
format.
A qrels file contains three tab-separated columns, i.e. the query identifier, corpus identifier, and score in this order. The scores (2 or 1) indicate the relevance level in ReCDS-PAR or similarity level in ReCDS-PPR.
Note that the qrels may not be the same as relevant_articles
and similar_patients
in PMC-Patients.json
due to dataset split (see our manuscript for details).
Data Instances
A sample of query
{"_id": "8699387-1", "text": "A 60-year-old female patient with a medical history of hypertension came to our attention because of several neurological deficits that had developed over the last few years, significantly impairing her daily life. Four years earlier, she developed sudden weakness and hypoesthesia of the right hand. The symptoms resolved in a few days and no specific diagnostic tests were performed. Two months later, she developed hypoesthesia and weakness of the right lower limb. On neurological examination at the time, she had spastic gait, ataxia, slight pronation of the right upper limb and bilateral Babinski sign. Brain MRI showed extensive white matter hyperintensities (WMHs), so leukodystrophy was suspected. However, these WMHs were located bilaterally in the corona radiata, basal ganglia, the anterior part of the temporal lobes and the medium cerebellar peduncle (A–D), and were highly suggestive of CADASIL. Genetic testing was performed, showing heterozygous mutation of the NOTCH3 gene (c.994 C<T; exon 6). The diagnosis of CADASIL was confirmed and antiplatelet prevention therapy was started. Since then, her clinical conditions remained stable, and the lesion load was unchanged at follow-up brain MRIs for 4 years until November 2020, when the patient was diagnosed with COVID-19 after a PCR nasal swab. The patient developed only mild respiratory symptoms, not requiring hospitalization or any specific treatment. Fifteen days after the COVID-19 diagnosis, she suddenly developed aphasia, agraphia and worsened right upper limb motor deficit, but she did not seek medical attention. Some days later, she reported these symptoms to her family medical doctor, and a new brain MRI was performed, showing a subacute ischemic area in the left corona radiata (E,F). Therapy with acetylsalicylic acid was switched to clopidogrel as secondary prevention, while her symptoms improved in the next few weeks. The patient underwent a carotid doppler ultrasound and an echocardiogram, which did not reveal any pathological changes. The review of the blood pressure log, both in-hospital and the personal one the patient had kept, excluded uncontrolled hypertension."}
A sample of qrels
query-id corpus-id score
8647806-1 6437752-1 1
8647806-1 6946242-1 1
Data Splits
Refer to our paper.
Dataset Creation
If you are interested in the collection of PMC-Patients and reproducing our baselines, please refer to this reporsitory.
Citation Information
If you find PMC-Patients helpful in your research, please cite our work by:
@misc{zhao2023pmcpatients,
title={PMC-Patients: A Large-scale Dataset of Patient Summaries and Relations for Benchmarking Retrieval-based Clinical Decision Support Systems},
author={Zhengyun Zhao and Qiao Jin and Fangyuan Chen and Tuorui Peng and Sheng Yu},
year={2023},
eprint={2202.13876},
archivePrefix={arXiv},
primaryClass={cs.CL}
}
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