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README.md

@@ -1,3 +1,282 @@
----
-license: cc-by-4.0
----
+---
+TODO:
+language:
+    - en
+language_creators:
+    - TODO
+license:
+    - cc by 4.0
+multilinguality:
+    - monolingual
+pretty_name: nirschl_et_al_2018
+size_categories:
+    - TODO
+source_datasets: []
+tags:
+    - H&E, cardiac pathology, heart, heart disease, heart failure, histology,pathology
+task_categories:
+    - multi_class
+task_ids:
+    - TODO
+---
+
+# Dataset Card for nirschl_et_al_2018
+
+<div align="center">
+ 🌐 <a href=""><strong>Homepage</strong></a> •
+ 🤗 <a href="https://huggingface.co/jnirschl/nirschl_et_al_2018"><strong>HF Dataset</strong></a> •
+ 📚 <a href=""><strong>Paper</strong></a> •
+ 🏆 <a href="TODO"><strong>Leaderboard</strong></a> •
+ 👩‍💻 <a href="mailto:jnirschl@stanford.edu"><strong>Point of Contact</strong></a> •
+  <a href="https://creativecommons.org/licenses/[]/4.0/"><img src="https://img.shields.io/badge/License-CC_BY_4.0-lightgrey.svg" alt="CC BY 4.0"></a>
+<br><br>
+ This is a dataset card for nirschl_et_al_2018 dataset, which has been
+ used under the CC BY 4.0 license. The original data have been
+ updated, extended, and incorporated into the <a href="TODO_BRAVURA_URL">Biomedical Reasoning And image
+ Understanding for Robust AI agents (BRAVURA) benchmark</a>.
+</div>
+
+## Table of Contents
+
+-   [Table of Contents](#table-of-contents)
+-   [Dataset Description](#dataset-description)
+    -   [Dataset Summary](#dataset-summary)
+    -   [Supported Tasks and Leaderboards](#supported-tasks-and-leaderboards)
+    -   [Languages](#languages)
+-   [Dataset Structure](#dataset-structure)
+    -   [Data Instances](#data-instances)
+    -   [Data Fields](#data-fields)
+    -   [Data Splits](#data-splits)
+-   [Dataset Creation](#dataset-creation)
+    -   [Curation Rationale](#curation-rationale)
+    -   [Source Data](#source-data)
+    -   [Annotations](#annotations)
+    -   [Personal and Sensitive Information](#personal-and-sensitive-information)
+-   [Considerations for Using the Data](#considerations-for-using-the-data)
+    -   [Social Impact of Dataset](#social-impact-of-dataset)
+    -   [Discussion of Biases](#discussion-of-biases)
+    -   [Other Known Limitations](#other-known-limitations)
+-   [Additional Information](#additional-information)
+    -   [Dataset Curators](#dataset-curators)
+    -   [Licensing Information](#licensing-information)
+    -   [Citation Information](#citation-information)
+    -   [Contributions](#contributions)
+
+## Dataset Description
+
+The original nirschl_et_al_2018 has been cleaned, updated, and
+extended to include additional metadata and then converted to a Hugging Face
+dataset by [jnirschl](https://huggingface.co/jnirschl) and [lozanoe](https://huggingface.co/ale9806). This is part of the Biomedical Reasoning
+And image Understanding for Robust AI agents (BRAVURA) benchmark. If you use
+this updated and extended dataset in your research, please cite both the original paper
+and the BRAVURA benchmark paper.
+
+### Dataset Summary
+
+| Dataset Name        | Nirschl et al 2018                                                                   |
+| ------------------- | ------------------------------------------------------------------------------------ |
+| Dataset description | Classification of clinical chronic heart failure from cardiac histopathology images. |
+| Tasks               | multi_class                                                                          |
+| Languages           | en                                                                                   |
+| Homepage            | []()                                                                                 |
+| Paper               | [Paper](https://pubmed.ncbi.nlm.nih.gov/29614076/)                                   |
+| Leaderboard         | [Leaderboard](TODO)                                                                  |
+| Dataset curator     | [jnirschl](mailto:jnirschl@stanford.edu)                                             |
+| License             | [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/)                            |
+| Last updated        | 2024-04-17 20:38:57                                                                  |
+| Version             | 0.1.0                                                                                |
+| Comment             |                                                                                      |
+
+### Dataset Statistics
+
+|                           |                           | Missing | Overall          | Test set         | Train            | Validation       |
+| ------------------------- | ------------------------- | ------- | ---------------- | ---------------- | ---------------- | ---------------- |
+| n                         |                           |         | 2299             | 1155             | 770              | 374              |
+| Age (yrs), median [Q1,Q3] |                           | 22      | 58.0 [48.0,63.0] | 57.0 [48.0,62.0] | 58.0 [51.0,63.0] | 58.0 [52.0,62.0] |
+| Sex, n (%)                | Female                    | 11      | 825 (36.1)       | 462 (40.0)       | 231 (30.0)       | 132 (36.4)       |
+|                           | Male                      |         | 1463 (63.9)      | 693 (60.0)       | 539 (70.0)       | 231 (63.6)       |
+| Institution, n (%)        | UPenn                     | 0       | 2299 (100.0)     | 1155 (100.0)     | 770 (100.0)      | 374 (100.0)      |
+| Label, n (%)              | Chronic heart failure     | 0       | 1034 (45.0)      | 517 (44.8)       | 352 (45.7)       | 165 (44.1)       |
+|                           | Heart tissue pathology    |         | 22 (1.0)         | 22 (1.9)         |                  |                  |
+|                           | Not chronic heart failure |         | 1243 (54.1)      | 616 (53.3)       | 418 (54.3)       | 209 (55.9)       |
+| Domain, n (%)             | Pathology                 | 0       | 2299 (100.0)     | 1155 (100.0)     | 770 (100.0)      | 374 (100.0)      |
+| Subdomain, n (%)          | Cardiovascular pathology  | 0       | 2299 (100.0)     | 1155 (100.0)     | 770 (100.0)      | 374 (100.0)      |
+| Stain, n (%)              | H&E                       | 0       | 2299 (100.0)     | 1155 (100.0)     | 770 (100.0)      | 374 (100.0)      |
+| Modality, n (%)           | Light microscopy          | 0       | 2299 (100.0)     | 1155 (100.0)     | 770 (100.0)      | 374 (100.0)      |
+| Submodality, n (%)        | Brightfield               | 0       | 2299 (100.0)     | 1155 (100.0)     | 770 (100.0)      | 374 (100.0)      |
+| Tasks, n (%)              | multi_class               | 0       | 2299 (100.0)     | 1155 (100.0)     | 770 (100.0)      | 374 (100.0)      |
+
+[More Information Needed]
+
+### Supported Tasks and Leaderboards
+
+multi_class
+[More Information Needed]
+
+### Languages
+
+en
+
+## Dataset Structure
+
+### Data Instances
+
+An example of 'train' looks as follows.
+
+```console
+{
+    "image_id": d54bb7ec-284f-4218-a47d-af87bb371de5,
+    "image": np.array([250, 250, 3], dtype="uint8"),
+    "label": datasets.ClassLabel(names={'chronic heart failure': 0, 'heart tissue pathology': 1, 'not chronic heart failure': 2},
+                                 num_classes=3),
+    "label_name": datasets.Value("string"),
+    "domain": pathology,
+    "subdomain": cardiovascular pathology,
+    "modality": light microscopy,
+    "submodality": brightfield microscopy,
+    "stain": H&E,
+    "microns_per_pixel": 2.0,
+    ...
+}
+```
+
+[More Information Needed]
+
+### Data Fields
+
+[More Information Needed]
+
+```console
+{
+    "image_id": datasets.Value("string"),
+    "image": datasets.Array3D(shape=[250, 250, 3], dtype="uint8"),
+    "label": datasets.ClassLabel(names={'chronic heart failure': 0, 'heart tissue pathology': 1, 'not chronic heart failure': 2},
+                                 num_classes=3),
+    "label_name": datasets.Value("string"),
+    "domain": datasets.Value("string"),
+    "subdomain": datasets.Value("string"),
+    "modality": datasets.Value("string"),
+    "submodality": datasets.Value("string"),
+    "stain": datasets.Value("string"),
+    "microns_per_pixel": datasets.Value("float32"),
+    ...
+}
+```
+
+### Data Splits
+
+[//]: # 'The data are split by the patient identifier such that all data from a single patient is either in the train, dev, or test set. The data are split as follows:'
+
+[More Information Needed]
+
+| Split | # Instances |
+| ----- | ----------- |
+| Train | 770         |
+| Dev   | 374         |
+| Test  | 1155        |
+| Total | 1155        |
+
+LICENSE
+
+## Dataset Creation
+
+### Curation Rationale
+
+There is a need for well curated and annotated biomedical datasets to train and evaluate biomedical machine learning models. The original dataset was cleaned, updated, and extended to include additional metadata. The dataset was then converted to a Hugging Face dataset by [jnirschl](https://huggingface.co/jnirschl) and is incorporated into the Biomedical Reasoning And image Understanding for Robust AI agents (BRAVURA) benchmark. If you use this extended dataset in your research, please cite both the original paper and the BRAVURA benchmark paper.
+
+Each instance has been assigned a UUID and the original identifiers and filenames have been retained in the metadata to ensure that the data can be traced back to the original source if needed.
+
+[More Information Needed]
+
+### Source Data
+
+#### Initial Data Collection and Normalization
+
+[More Information Needed]
+
+#### Who are the source language producers?
+
+[More Information Needed]
+
+### Annotations
+
+#### Annotation process
+
+[More Information Needed]
+
+#### Who are the annotators?
+
+[More Information Needed]
+
+### Personal and Sensitive Information
+
+The original dataset authors have anonymized the data and removed any personal or sensitive information prior to making the dataset public. The original dataset authors obtained appropriate institutional review board (IRB) approval for the data collection process, and users are referred to the original data sources for more information on the ethical considerations and data collection process.
+
+[More Information Needed]
+
+## Considerations for Using the Data
+
+### Social Impact of Dataset
+
+[More Information Needed]
+
+### Discussion of Biases
+
+[More Information Needed]
+
+### Other Known Limitations
+
+[More Information Needed]
+
+## Additional Information
+
+### Dataset Curators
+
+Jeff Nirschl
+Alejandro Lozano
+
+[More Information Needed]
+
+### Licensing Information
+
+The datasets were curated and extended while adhering to the original copyright and licensing rules.
+We specifically avoided materials that restricted or prohibited copying, adapting, remixing, redistributing,
+or otherwise using the data for research purposes. We recommend users refer to the original data sources'
+terms of use and licensing information. In case of any concerns or issues, please contact us at [jnirschl](mailto:jnirschl)
+Should you encounter any oversight or data samples potentially breaching the copyright or licensing regulations of any site, we encourage you to notify us.
+
+[More Information Needed]
+
+### Citation Information
+
+The original authors of nirschl_et_al_2018 have requested that the dataset be cited as follows:
+
+```bibtex
+@ARTICLE{Nirschl2018-pc,
+  title    = "A deep-learning classifier identifies patients with clinical
+              heart failure using whole-slide images of {H&E} tissue",
+  author   = "Nirschl, Jeffrey J and Janowczyk, Andrew and Peyster, Eliot G and
+              Frank, Renee and Margulies, Kenneth B and Feldman, Michael D and
+              Madabhushi, Anant",
+  journal  = "PLoS One",
+  volume   =  13,
+  number   =  4,
+  pages    = "e0192726",
+  month    =  apr,
+  year     =  2018,
+  language = "en"
+}
+```
+
+The extended nirschl_et_al_2018 dataset is part of the Biomedical Reasoning And image Understanding for Robust AI agents (BRAVURA) benchmark. If you use this extended dataset in your research, please cite both the original paper and the BRAVURA benchmark paper.
+
+```bibtex
+@article{TODO,
+}
+```
+
+[More Information Needed]
+
+### Contributions
+
+Thanks to [@jnirschl](https://github.com/jnirschl) for adding this dataset.

all-ce7e9e0f06cb90b8/0.1.0/LICENSE

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