Update README.md

README.md

@@ -1,12 +1,36 @@
-# OpenPMC-VL
+# Open-PMC
 
 ----------------------------------------------------------------------------------------
 
 [![code checks](https://github.com/VectorInstitute/aieng-template/actions/workflows/code_checks.yml/badge.svg)](https://github.com/VectorInstitute/pmc-data-extraction/actions/workflows/code_checks.yml)
 [![integration tests](https://github.com/VectorInstitute/aieng-template/actions/workflows/integration_tests.yml/badge.svg)](https://github.com/VectorInstitute/pmc-data-extraction/actions/workflows/integration_tests.yml)
 [![license](https://img.shields.io/github/license/VectorInstitute/aieng-template.svg)](https://github.com/VectorInstitute/pmc-data-extraction/blob/main/LICENSE.md)
 
-A toolkit to download, augment, and benchmark OpenPMC-VL; a large dataset of image-text pairs extracted from open-access scientific articles on PubMedCentral.
+<div align="center">
+    <img src="https://github.com/VectorInstitute/pmc-data-extraction/blob/0a969136344a07267bb558d01f3fe76b36b93e1a/media/open-pmc-pipeline.png?raw=true" 
+     alt="Open-PMC Pipeline" 
+     width="1000" />
+</div>
+
+A toolkit to download, augment, and benchmark Open-PMC; a large dataset of image-text pairs extracted from open-access scientific articles on PubMedCentral.
+
+For more details, see the following resources:
+- **arXiv Paper:** [PMC-CLIP: Contrastive Language-Image Pre-training using Biomedical Documents](http://arxiv.org/abs/2503.14377)
+- **Dataset on Hugging Face:** [Open_PMC Dataset on Hugging Face](https://huggingface.co/datasets/vector-institute/open-pmc)
+- **Model Checkpoint on Hugging Face:** [Open_PMC_CLIP Model Checkpoint on Hugging Face](https://huggingface.co/vector-institute/open-pmc-clip)
+
+## Table of Contents
+
+1. [Hugging Face Dataset and Checkpoint](#hugging-face-dataset-and-checkpoint)
+2. [Installing Dependencies](#installing-dependencies)
+3. [Download and Parse Image-Caption Pairs](#download-and-parse-image-caption-pairs-from-pubmed-articles)
+4. [Run Benchmarking Experiments](#run-benchmarking-experiments)
+5. [References](#references)
+
+## Hugging Face Dataset and Checkpoint
+
+- **Dataset:** [Open_PMC Dataset on Hugging Face](https://huggingface.co/datasets/vector-institute/open_pmc)
+- **Checkpoint:** [Open_PMC_CLIP Model Checkpoint on Hugging Face](https://huggingface.co/vector-institute/open_pmc_clip)
 
 ## Installing dependencies
 
@@ -133,18 +157,27 @@ mmlearn_run \
     dataloader.test.batch_size=64 \
     resume_from_checkpoint="path/to/model/checkpoint"
 ```
-For more comprehensive examples of shell scripts that run various experiments with OpenPMC-VL, refer to `openpmcvl/experiment/scripts`.
+For more comprehensive examples of shell scripts that run various experiments with Open-PMC, refer to `openpmcvl/experiment/scripts`.
 For more information about `mmlearn`, please refer to the package's [official codebase](https://github.com/VectorInstitute/mmlearn).
 
 
+## Citation
+If you find the code useful for your research, please consider citing
+```bib
+@article{baghbanzadeh2025advancing,
+  title={Advancing Medical Representation Learning Through High-Quality Data},
+  author={Baghbanzadeh, Negin and Fallahpour, Adibvafa and Parhizkar, Yasaman and Ogidi, Franklin and Roy, Shuvendu and Ashkezari, Sajad and Khazaie, Vahid Reza and Colacci, Michael and Etemad, Ali and Afkanpour, Arash and others},
+  journal={arXiv preprint arXiv:2503.14377},
+  year={2025}
+}
+```
 
 ## References
 <a id="1">[1]</a> PMC-OA paper:
-```latex
+latex
 @article{lin2023pmc,
   title={PMC-CLIP: Contrastive Language-Image Pre-training using Biomedical Documents},
   author={Lin, Weixiong and Zhao, Ziheng and Zhang, Xiaoman and Wu, Chaoyi and Zhang, Ya and Wang, Yanfeng and Xie, Weidi},
   journal={arXiv preprint arXiv:2303.07240},
   year={2023}
 }
-```