README.md

---

language:
- en
license: apache-2.0
task_categories:
- multiple-choice
- question-answering
pretty_name: rare disease QA
tags:
- rare disease diagnosis
- rare disease identification
- rare disease question-answering
- rare disease QA
- rare-disease diagnosis
- rare-disease identification
- rare-disease question-answering
- rare-disease QA
size:
- 1K<n<10K
dataset_info:
  features:
  - name: question
    dtype: string
  - name: opa
    dtype: string
  - name: opb
    dtype: string
  - name: opc
    dtype: string
  - name: opd
    dtype: string
  - name: cop
    dtype: int64
  - name: rare disease
    sequence: string
  - name: input
    dtype: string
  splits:
  - name: test
    num_bytes: 519412
    num_examples: 1360
  download_size: 265254
  dataset_size: 519412
configs:
- config_name: default
  data_files:
  - split: test
    path: data/test-*
---


# Dataset Card for ReDis-QA

## Dataset Summary

ReDis-QA dataset contains 1360 multi-choice questions focusing on rare disease diagnosis.
It consists of 11\%, 33\%, 13\%, 15\%, 18\% of the questions corresponding to the symptoms, causes, affects, related-disorders, diagnosis of rare diseases, respectively. 
The remaining 9\% of the questions pertain to other properties of the diseases.

<img width="400" height="290" src="https://anonymous.4open.science/r/redis-bench-EBE2/figures/theme_ratio.png">

ReDis-QA dataset widely covers 205 types of rare diseases, where the most frequent disease features over 100 questions.

<img width="900" height="260" src="https://anonymous.4open.science/r/redis-bench-EBE2/figures/disease_freq.png">

Belows are examples of each property.

| Property | Example |
| --- | --- |
| __Symptom__ | __Question:__ About Achalasia Cardia: <br> 1. Dysphagia is a presenting symptom <br> 2. The cause is the absence of Auerbach's plexus <br> 3. Esophagec-tomy is the treatment <br> 4. Motility improving agents are used in treatment <br> 5. Barium swallow shows irregular filling defects in lower esophagus <br> __Choices:__ (A) 1,2,3 False \& 4,5 True (B) 1,2,4 True \& 3,5 False (C) 2,3,4 True \& 1,5 False (D) 1,3,5 True \& 2,4 False <br> __Golden Answer:__ B |
| __Causes__ | __Question:__ A mother brings her 1-year-old daughter to the physician. She says that for the last 2 days her daughter has been fussy and crying more than usual. She also refuses formula. The patient has a fever of 39.4degC (102.9degF). Meningitis is suspected, and a lumbar puncture is performed. Analysis of the cerebrospinal fluid shows an opening pressure of 98 mm H2O, a leukocyte count of 1256/mm3, a protein level of 210 mg/dL, and a glucose level of 31 mg/dL. The mother says that the patient has received no immunizations. Which of the following organisms is most likely responsible for this patient's illness? <br> __Choices:__ (A) Clostridium botulinum (B) Haemophilus influenza (C) Neisseria meningitides (D) Streptococcus pneumonia <br> __Golden Answer:__ B |
| __Affects__ | __Question:__ 23 years old female comes to OG, because she thinks pregnant. She missed her last two cycles and she feels different. Urine pregnancy test was positive. On USG, the pregnancy was confirmed to be 12 weeks. She is very concerned because she received Measles Mumps Rubella vaccine 4 months ago and she was told to wait for 3 months to conceive. The pregnancy is desired. The most appropriate step is <br> __Choices:__ (A) Vaccine risk is minimal, not itself a reason to terminate the pregnancy. (B) Vaccine risk is nil, termination is completely inappropriate. (C) Vaccine risk is high, termination should be strongly considered. (D) Vaccine risk is high, termination is mandated. <br> __Golden Answer:__ A |
| __Related-disorders__ | __Question:__ A 35-year-old female presented to the medicine OPD with paresthesias and weakness of B/L lower limbs with a band like sensation of tightness around the torso along with painful loss of vision in both eyes along with diplopia and periorbital pain.} There is a history of similar attacks in the past with period of normalcy in between O/E, Ataxia- present Papillitis (on fundus examination) Facial myokymia Bladder incontinence and constipation CSF studies revealed mononuclear cell pleocytosis along with increased IgG. Which of the following are the oral drugs approved for the above condition: 1. Fingolimod 2. Natalizumab 3. Teriflunomide 4. Glatiramer acetate <br> __Choices:__ (A) Only 1 (B) Both 1 and 3 (C) 1,2 and 3 (D) All of the above <br> __Golden Answer:__ A |
| __Diagnosis__ | __Question:__ A 29-year-old man is seen in the office after returning from a hiking trip in Colorado. He complains of feeling unwell and reports symptoms of fever, myalgia, headache, and nausea. Two days ago, he noticed a rash on his wrists and ankles that has now spread to his body. He recalls having had numerous insect bites during his trip. On examination, his blood pressure is 90/60 mmHg, pulse 100/min, and respira- tions 20/min. There are multiple 1-5 mm macules on his body and some of them have a hemorrhagic center consistent with a petechia. His neck is supple and fundi are normal. The heart sounds are normal, lungs clear, and legs are edematous. Cranial nerve, motor, and sensory examination is normal. A clinical diagnosis of Rocky Mountain Spotted Fever (RMSF) is made and he is started on appropriate therapy. Which of the following is the most common type of central nervous system (CNS) presentation in this condition? <br> __Choices:__ (A) Hemiplegia (B) Cranial nerve abnormalities (C) Paraplegia (D) Encephalitis <br> __Golden Answer:__ D |

## Loading Dataset 

Simply follow the instructions to test your models on the ReDis-QA dataset:
```

import datasets

eval_dataset = datasets.load_dataset(f"guan-wang/ReDis-QA")

for data_idx, data_instance in enumerate(eval_dataset):

    print(data_idx, data_instance["input"])

```

## Benchmark Results of LLMs 

Benchmark results of [Llama-2-7B-chat](https://huggingface.co/meta-llama/Llama-2-7b-chat), [Mistral-7B-instruct-v0.2](https://huggingface.co/mistralai/Mistral-7B-Instruct-v0.2https://huggingface.co/mistralai/Mistral-7B-Instruct-v0.2), [Phi-3-7B-instruct](https://huggingface.co/microsoft/Phi-3-small-8k-instruct), [Gemmma-1.1-7B-it](https://huggingface.co/google/gemma-1.1-7b-it), and [Qwen-2-7B-Instruct](https://huggingface.co/Qwen/Qwen2-7B-Instruct).
More details refers to our benchmark repository [**ReDis-QA-Bench**](https://github.com/guanchuwang/redis-bench).

<img width="600" height="290" src="https://anonymous.4open.science/r/redis-bench-EBE2/figures/llm_results.png">

## Citation Information

If you find this dataset useful to your project, we appreciate you citing this work:

````

@article{wang2024assessing,

  title={Assessing and Enhancing Large Language Models in Rare Disease Question-answering},

  author={Wang, Guanchu and Ran, Junhao and Tang, Ruixiang and Chang, Chia-Yuan and Chuang, Yu-Neng and Liu, Zirui and Braverman, Vladimir and Liu, Zhandong and Hu, Xia},

  journal={arXiv preprint arXiv:2408.08422},

  year={2024}

}

````