Datasets:

chenxz
/

RareBench

@@ -15,149 +15,88 @@ viewer: false
 # RareBench
-<!-- Provide a quick summary of the dataset. -->
-This dataset card aims to be a base template for new datasets. It has been generated using [this raw template](https://github.com/huggingface/huggingface_hub/blob/main/src/huggingface_hub/templates/datasetcard_template.md?plain=1).
 Github Repo for RareBench: https://github.com/chenxz1111/RareBench
 Arxiv Paper for RareBench: https://arxiv.org/pdf/2402.06341.pdf
-## Dataset Details
-### Dataset Description
-<!-- Provide a longer summary of what this dataset is. -->
-- **Curated by:** [More Information Needed]
-- **Funded by [optional]:** [More Information Needed]
-- **Shared by [optional]:** [More Information Needed]
-- **Language(s) (NLP):** [More Information Needed]
-- **License:** [More Information Needed]
-### Dataset Sources [optional]
-<!-- Provide the basic links for the dataset. -->
-- **Repository:** [More Information Needed]
-- **Paper [optional]:** [More Information Needed]
-- **Demo [optional]:** [More Information Needed]
-## Uses
-<!-- Address questions around how the dataset is intended to be used. -->
-### Direct Use
-<!-- This section describes suitable use cases for the dataset. -->
-[More Information Needed]
-### Out-of-Scope Use
-<!-- This section addresses misuse, malicious use, and uses that the dataset will not work well for. -->
-[More Information Needed]
-## Dataset Structure
-<!-- This section provides a description of the dataset fields, and additional information about the dataset structure such as criteria used to create the splits, relationships between data points, etc. -->
-[More Information Needed]
-## Dataset Creation
-### Curation Rationale
-<!-- Motivation for the creation of this dataset. -->
-[More Information Needed]
-### Source Data
-<!-- This section describes the source data (e.g. news text and headlines, social media posts, translated sentences, ...). -->
-#### Data Collection and Processing
-<!-- This section describes the data collection and processing process such as data selection criteria, filtering and normalization methods, tools and libraries used, etc. -->
-[More Information Needed]
-#### Who are the source data producers?
-<!-- This section describes the people or systems who originally created the data. It should also include self-reported demographic or identity information for the source data creators if this information is available. -->
-[More Information Needed]
-### Annotations [optional]
-<!-- If the dataset contains annotations which are not part of the initial data collection, use this section to describe them. -->
-#### Annotation process
-<!-- This section describes the annotation process such as annotation tools used in the process, the amount of data annotated, annotation guidelines provided to the annotators, interannotator statistics, annotation validation, etc. -->
-[More Information Needed]
-#### Who are the annotators?
-<!-- This section describes the people or systems who created the annotations. -->
-[More Information Needed]
 #### Personal and Sensitive Information
-<!-- State whether the dataset contains data that might be considered personal, sensitive, or private (e.g., data that reveals addresses, uniquely identifiable names or aliases, racial or ethnic origins, sexual orientations, religious beliefs, political opinions, financial or health data, etc.). If efforts were made to anonymize the data, describe the anonymization process. -->
-[More Information Needed]
-## Bias, Risks, and Limitations
-<!-- This section is meant to convey both technical and sociotechnical limitations. -->
-[More Information Needed]
-### Recommendations
-<!-- This section is meant to convey recommendations with respect to the bias, risk, and technical limitations. -->
-Users should be made aware of the risks, biases and limitations of the dataset. More information needed for further recommendations.
-## Citation [optional]
-<!-- If there is a paper or blog post introducing the dataset, the APA and Bibtex information for that should go in this section. -->
-**BibTeX:**
-[More Information Needed]
-**APA:**
-[More Information Needed]
-## Glossary [optional]
-<!-- If relevant, include terms and calculations in this section that can help readers understand the dataset or dataset card. -->
-[More Information Needed]
-## More Information [optional]
-[More Information Needed]
-## Dataset Card Authors [optional]
-[More Information Needed]
-## Dataset Card Contact
-[More Information Needed]
-<a name="citation"></a>
-## 📝 Citation
 ```
 @article{chen2024rarebench,
   title={RareBench: Can LLMs Serve as Rare Diseases Specialists?},

 # RareBench
+**RareBench** is a pioneering benchmark designed to systematically evaluate the capabilities of LLMs on 4 critical dimensions within the realm of rare diseases.
+Meanwhile, we have compiled the largest open-source dataset on rare disease patients, establishing a benchmark for future studies in this domain. To facilitate differential diagnosis of rare diseases, we develop a dynamic few-shot prompt methodology, leveraging a comprehensive rare disease knowledge graph synthesized from multiple knowledge bases, significantly enhancing LLMs’ diagnos-
+tic performance. Moreover, we present an exhaustive comparative study of GPT-4’s diagnostic capabilities against those of specialist physicians. Our experimental findings underscore the promising potential of integrating LLMs into the clinical diagnostic process for rare diseases.
 Github Repo for RareBench: https://github.com/chenxz1111/RareBench
 Arxiv Paper for RareBench: https://arxiv.org/pdf/2402.06341.pdf
+## How to use it?
+#### Loading Data
+```python
+from datasets import load_dataset
+datasets = ["RAMEDIS", "MME", "HMS", "LIRICAL", "PUMCH_ADM"]
+for dataset in datasets:
+    data = load_dataset('chenxz/RareBench', dataset, split='test')
+    print(data)
+```
+#### Data Format
+```json
+{
+    "Phenotype": "The list of phenotypes presented in HPO codes",
+    "RareDisease": "The list of rare diseases code including OMIM, Orphanet and CCRD format",
+    "Department": "(Optional) Only provided in PUMCH_ADM"
+}
+```
+#### Evaluation
+This repository provides data and mapping files for **RareBench**. Please refer to our [github](https://github.com/chenxz1111/RareBench) for further automated evaluation.
+## Source Data
+#### Data Collection and statistics
+This study categorizes datasets into two main groups: publicly available datasets and the Peking Union Medical College Hospital (PUMCH) datasets.
+| Dataset           | RAMEDIS | MME      |  HMS    | LIRICAL       | PUMCH_ADM |
+| :---------------- | :------:| :------: |:------: | :-----------: |:--------: |
+| Countries/Regions | Europe  | Canada   | Germany | Multi-Country | China     |
+| \#Cases           | 624     | 40       | 88      | 370           | 75        |
+| \#Disease         | 624     | 17       | 39      | 252           | 16        |
+| \#Department      | N/A     | N/A      | N/A     | N/A           | 5         |
+|\#Cases per disease|         |          |         |               |           |
+|--- Minimum        | 1       | 1        | 1       | 1             |  3        |
+|--- Median         | 2       | 1        | 1       | 1             |  5        |
+|--- Maximum        |82       |11        |11       | 19            |  8        |
+|\#HPO terms per case|        |          |         |               |           |
+|--- Minimum        | 3       | 3        | 5       | 3             |  3        |
+|--- Median         | 9       | 10.5     | 17.5    | 11            |  16       |
+|--- Maximum        |46       |26        |54       | 95            |  47       |
+> Note: The total number of cases in PUMCH is 1,650. We have currently only made public the 75 cases used in the Human versus LLMs experiment.
+#### Data Processing
+We apply reasonable filtering criteria to identify and remove cases of low quality that may be caused by recording errors or missing information, such as those with uncertain or imprecise diagnoses and those lacking sufficient relevant information, i.e., fewer than three phenotypes.
 #### Personal and Sensitive Information
+Doctors from PUMCH monitored all cases before uploading text information, ensuring the absence of any potential personal information leaks.
+#### Mapping Files
+Files in mapping directory, including:
+`phenotype_mapping.json`: HPO phenotype code mapping to term name
+`disease_mapping.json`: OMIM/Orphanet/CCRD code mapping to disease name
+`ic_dict.json`: HPO phenotype terms' Information Content(IC) values obtained from HPO hierarchical structure
+`phe2embedding.json`: HPO phenotype terms' 256 dimension embedding vectors learned by IC-based random walk
+## Citation
 ```
 @article{chen2024rarebench,
   title={RareBench: Can LLMs Serve as Rare Diseases Specialists?},