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The dataset generation failed because of a cast error
Error code: DatasetGenerationCastError
Exception: DatasetGenerationCastError
Message: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 7 new columns ({'Subject', 'Context', 'Question', 'Solution', 'ID', 'Choices', 'Answer'}) and 2 missing columns ({'explanation', 'id'}).
This happened while the csv dataset builder was generating data using
hf://datasets/SeanWu25/NEJM-AI_Benchmarking_Medical_Language_Models/NEJM_All_Questions_And_Answers.csv (at revision 7839934224e0c50e50143d98f8db1d56462b87b1)
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback: Traceback (most recent call last):
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 2011, in _prepare_split_single
writer.write_table(table)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 585, 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 2302, in table_cast
return cast_table_to_schema(table, schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2256, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
ID: int64
Context: string
Question: string
Choices: string
Answer: string
Solution: string
Subject: string
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 1048
to
{'id': Value(dtype='int64', id=None), 'explanation': Value(dtype='string', id=None)}
because column names don't match
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1321, 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 935, in convert_to_parquet
builder.download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1027, in download_and_prepare
self._download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1122, 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 1882, 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 2013, in _prepare_split_single
raise DatasetGenerationCastError.from_cast_error(
datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 7 new columns ({'Subject', 'Context', 'Question', 'Solution', 'ID', 'Choices', 'Answer'}) and 2 missing columns ({'explanation', 'id'}).
This happened while the csv dataset builder was generating data using
hf://datasets/SeanWu25/NEJM-AI_Benchmarking_Medical_Language_Models/NEJM_All_Questions_And_Answers.csv (at revision 7839934224e0c50e50143d98f8db1d56462b87b1)
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)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.
id
int64 | explanation
string |
|---|---|
2,464 | Answer D: About 50% of people with hypertension are controlled |
2,465 | Answer A: Increased long-term BP variability is associated with an increased risk of cardiovascular events despite adequate BP control on most visits |
2,466 | Answer D: Low dietary potassium promotes hypertension by increasing the activity of the sodium-chloride cotransporter (on a high sodium diet) |
2,467 | Answer D: Add amiloride |
2,468 | Answer B: In 1 year |
2,469 | Answer B: Obtain 24-hour ambulatory BP monitoring |
2,470 | Answer D: Add spironolactone |
2,471 | Answer B: Home BP tele-monitoring supervised by a health care provider results in higher rates of BP control than usual care Home BP monitoring, with or without remote telemonitoring, is associated with better BP control; therefore, choice B is correct, and choice A is incorrect. The best results occur when a healthcare provider, such as a physician, clinical pharmacist, or nurse, pairs the monitoring with interventions. Protocols involving patient education for self-titration of therapy are also quite effective for individuals with hypertension regardless of comorbid conditions, but it is estimated that only about 20% of hypertensive patients may be suitable to this intervention (incorrect choices C and D). Financial incentives to physicians result in modest increases in rates of BP control in hypertensive patients (incorrect choice E). |
2,472 | Answer D: 110/75 mmHg |
2,473 | Answer A: Droxidopa |
2,474 | Answer D: Make no changes to the current regimen |
2,475 | Answer D: Her BMI |
2,476 | Answer C: Inappropriately low atrial natriuretic peptide levels |
2,477 | Answer D: Regular use of continuous positive airway pressure for at least 4 hours per night Patients with obesity have an increased incidence of both sleep apnea and resistant hypertension. A recent study has shown that the combination of weight loss with regular use of CPAP improves BP and can reverse abnormal dipping patterns. The effects of CPAP on BP are also more pronounced with use of CPAP for more than 4 hours per night; hence, choice D is correct. Use of nocturnal oxygen supplementation has not been shown to be effective to reduce BP (choice A is incorrect). Behavioral and self-help psychotherapy are not effective in lowering BP as assessed by ambulatory blood pressure monitoring (choice B is incorrect). A randomized, double-blind, sham-controlled trial and a meta-analysis of device-guided breathing by Landman and coworkers found no benefit of device-guided breathing in lowering BP; thus, choice C is incorrect. |
2,478 | Answer D: Order a CT angiogram |
2,479 | Answer D: Refer for adrenal vein sampling |
2,480 | Answer C: A lateralization index of 6 |
2,481 | Answer D: Plasma metanephrines |
2,482 | Answer C: Genetic testing |
2,483 | Answer D: Maintenance of his systolic BP at <120 mmHg |
2,484 | Answer C: Reversal of INR to <1.3 plus lowering of systolic BP <160 mmHg within 4 hours |
2,485 | Answer D: The absence of nocturnal dipping |
2,486 | Answer B: Underlying CKD |
2,488 | Answer D: Add amlodipine, targeting a systolic BP of <120 mmHg |
2,489 | Answer C: The low BP target (120 mmHg) resulted in a 38% reduction in the risk of heart failure In SPRINT, a systolic BP target of <120 mmHg, compared to a target of 140 mmHg, resulted in lower risk of several cardiovascular endpoints as well as all-cause death. Specifically, the composite endpoint of myocardial infarction and other coronary syndromes, stroke, heart failure, or cardiovascular death was decreased by 25%. This was driven largely by less heart failure (38%) and cardiovascular deaths (22%). All cause death was also decreased by 27%. Other components of the endpoint were also improved, but did not reach statistical significance (stroke was decreased by 11%, P=0.50, and myocardial infarction was decreased by 17%, P=0.19; other coronary syndromes were identical between the two groups). All subgroups benefited from the lower target, including patients older than 75 years. The differences between the two groups were substantial (15/8 mmHg at 12 months) an dpersisted for the duration of the trial. The risk of AKI was increased by 71% in the low BP target group, but the absolute risk was 4.4% (vs. 2.6% in the standard group, P<0.001). |
2,490 | Answer C: Refer for percutaneous renal angioplasty |
2,491 | Answer E: 25OHD replacement has no effect on BP in hypertensive patients with 25OHD deficiency |
2,492 | Answer C: Beetroot juice lowers ambulatory BP by about 8/5 mmHg compared with placebo Beetroot juice is a good source of nitrates, resulting in BP lowering through the provision of nitrates that result in vasodilatation, improved endothelial function, and lower BP (-7.7/5.2 mmHg on 24h ABPM). There is no known effect of beetroot juice on aldosterone. In the available clinical studies, the effect was sustained at least up to 4 weeks. Pulse wave reflections have not been studied with beetroot therapy, but pulse wave velocity tends to decrease, thus suggesting that wave reflection would also likely decrease. There are no reports of hypertension associated with beetroot juice. |
2,493 | Answer B: Target the hemoglobin A1c to <7.0 % before conception |
2,494 | Answer C: Increased AST and ALT |
2,495 | Answer E: Make no changes to the current regimen |
2,496 | Answer A: Induction of labor and delivery |
2,497 | Answer D: Continue intravenous magnesium and transition to oral antihypertensive medications |
2,498 | Answer A: Labetalol |
2,499 | Answer C: Aspirin at 81 mg daily |
2,500 | Answer C: It increases the risk of cardiovascular disease |
2,501 | Answer B: She is at increased risk of urinary tract infection |
2,502 | Answer D: Acute fatty liver of pregnancy (AFLP) |
2,503 | Answer A: Transfuse platelets and packed red blood cells |
2,504 | Answer B: Long-chain 3-hydroxyl CoA dehydrogenase |
2,505 | Answer C: Observation with expectant medical management |
2,506 | Answer D: Renal blood flow returns to pre-pregnancy levels |
2,507 | Answer D: Preeclampsia |
2,508 | Answer A: Intravenous normal saline plus furosemide |
2,509 | Answer D: Hemodialysis totaling ≥36 h/wk |
2,510 | Answer C: A low soluble fms-like tyrosine kinase-1 to placental growth factor ratio |
2,511 | Answer C: Enalapril |
2,512 | Answer B: She should start aspirin 81 mg daily immediately after pregnancy is diagnosed Approximately one in three women who have received a kidney transplant develop preeclampsia during pregnancy. Therefore, prophylaxis with low-dose aspirin is appropriate. In addition, heightened antenatal surveillance should be offered, including fetal growth and Doppler monitoring starting at 28 weeks gestation. The majority of women with kidney transplants are delivered by caesarean section. However, the indications for surgical delivery are the standard obstetric maternal or fetal indications, and vaginal delivery is not contraindicated. Therefore, option A is incorrect. Mycophenolate mofetil should be changed to azathioprine at least 3 months prior to attempting to conceive, to ensure graft stability; hence, option C is incorrect. Risk factors for adverse graft outcomes include hypertension, pre-pregnancy serum creatinine levels >1.5 mg/dl, and black ethnicity. There is no evidence to support an increased incidence of graft rejection after delivery, therefore commencing prednisone postpartum (option D) is incorrect. |
2,513 | Answer A: The probability of achieving pregnancy is reduced compared with spontaneous conception |
2,514 | Answer B: Stop mycophenolate mofetil and start azathioprine |
2,515 | Answer D: Anti-Ro and anti-La antibodies |
2,516 | Answer C: Furosemide |
2,517 | Answer B: Reduce the tacrolimus dose |
2,518 | Answer B: Enzyme replacement therapy |
2,519 | Answer D: It does not increase the risk for a small gestation baby |
2,520 | Answer C: A reduction in the loading dose and maintenance dose |
2,521 | Answer C: Empiric therapy with predisone and azathioprine, followed by adjusted treatment after delivery based on kidney biopsy performed postpartum |
2,522 | Answer A: Her risk of progression to ESRD during or shortly postpartum is about 20% |
2,523 | Answer D: IgA nephropathy |
2,524 | Answer C: Measure or estimate 24-hour creatinine excretion rate |
2,525 | Answer E: Rituximab |
2,526 | Answer D: Stain prior kidney biopsy with Congo Red |
2,527 | Answer E: No additional diagnostic studies are required |
2,528 | Answer A: Oral angiotensin receptor blockers (ARBs)d |
2,529 | Answer A: Oral glucocorticoids |
2,530 | Answer B: Oral cyclosporine and low-dose steroids for ≥4 months |
2,531 | Answer C: As in A plus widespread effacement of the podocyte foot processes by electron microscopy |
2,532 | Answer C: Hyperexpression of PLA2R antigen by immunohistochemical studies of pronasedigested, paraffin-preserved specimens |
2,533 | Answer E: Continued supportive care and observation |
2,534 | Answer B: Pronase digestion of paraffin-embedded material and staining for monoclonal IgG (light and heavy chains) |
2,535 | Answer A: Sarcoidosis causing secondary membranous nephropathy |
2,536 | Answer B: Oral ACEIs or ARBs |
2,537 | Answer D: Perform a laser dissection/mass spectrometry analysis of the biopsy specimen |
2,538 | Answer E: Serum immunofixation and free light-chain assays |
2,539 | Answer B: An underlying autoimmune disorder |
2,540 | Answer B: Staining the kidney biopsy for hepatitis B surface antigen and core antigen |
2,541 | Answer D: Sofosbuvir plus simeprevir plus rituximab |
2,542 | Answer C: IgA−dominant, infection−related GN |
2,543 | Answer C: Kidney prognosis is likely to be good long term, but uncertainty exists; therefore, yearly follow-up is advisable |
2,544 | Answer A: A calcineurin inhibitor |
2,545 | Answer C: Treat with cyclophosphamide and corticosteroids as outlined in choice B but reduce the doses by ≥20% |
2,546 | Answer B: Either intravenous cyclophosphamide or intravenous rituximab |
2,547 | Answer A: Rituximab > azathioprine > mycophenolate > extended cyclophosphamide |
2,548 | Answer A: Plasmapheresis, high−dose corticosteroids, and cyclophosphamide |
2,549 | Answer A: Provide supportive care and management for ESRD |
2,550 | Answer A: The long−term prognosis is favorable, because the proteinuria declined to <0.7 g/d after 1 year |
2,551 | Answer B: Add low−dose Euro lupus cyclophosphamide for 3 months to corticosteroids |
2,552 | Answer B: A sustained remission for at least 24 months |
2,553 | Answer E: Conduct a detailed evaluation of his diet |
2,554 | Answer E: Adynamic bone disease |
2,555 | Answer B: All surgical approaches, such as partial, subtotal, or total parathyroidectomy with or without autotransplantation, are effective |
2,556 | Answer B: Begin cinacalcet therapy |
2,557 | Answer D: Cinacalcet |
2,558 | Answer D: Add teriparatide |
2,559 | Answer A: The effect of phosphate binders does not increase linearly with dose |
2,560 | Answer C: Lithium-related primary hyperparathyroidism |
2,561 | Answer C: Elevated IgGκ monoclonal protein |
2,564 | Answer D: Add sodium thiosulfate |
2,566 | Answer A: Start bisphosphonate therapy |
2,567 | Answer C: Identify the method of serum phosphate measurement |
End of preview.
A Comparative Study of Open-Source Large Language Models
Dataset Overview
Welcome to the dataset repository for our paper, "A Comparative Study of Open-Source Large Language Models, GPT-4 and Claude 2: Multiple-Choice Test Taking in Nephrology." The preprint of the paper can be accessed here.
Files
This repository contains two key files:
NEJM_All_Questions_And_Answers.csv: This file includes all the questions and corresponding answers used in the study.
Ground_Truth_Answers.csv: This file provides ground truth explanations associated with the questions in the main dataset.
Usage
To utilize this dataset for your research or experimentation:
- Download: Obtain the dataset files from this repository.
- Load: Import the dataset into your preferred data analysis or machine learning environment.
- Explore: Investigate the questions, answers, and ground truth explanations for your specific use case.
Paper
Our paper is accepted to NEJM-AI. For now please read the pre-print at the link: https://arxiv.org/abs/2308.04709
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