BiomedVLP-BioViL-T

The corresponding BERT language model is trained in two stages: First, we pretrain CXR-BERT-general from a randomly initialized BERT model via Masked Language Modeling (MLM) on PubMed abstracts and clinical notes from the publicly-available MIMIC-III and MIMIC-CXR. The general model can be fine-tuned for research in other clinical domains by adjusting the parameters specific to the target domain. In the second stage, BioViL-T is continually pretrained from CXR-BERT-general using a multi-modal pre-training procedure by utilising radiology reports and sequences of chest X-rays. We utilise the latent representation of [CLS] token to align text and image embeddings.

Language model variations

Image model

The image model is jointly trained with the text model in a multi-modal contrastive learning framework. It's a hybrid image encoder composed of a Vision Transformer and ResNet-50, where the latter is used as backbone network to extract features from images at each time point. The transformer is included in the design to aggregate and compare image features extracted across the temporal dimension. The corresponding model definition and its loading functions can be accessed through our HI-ML-Multimodal GitHub repository. The joint image and text model, namely BioViL-T, can be used in phrase grounding applications as shown in this python notebook example. Additionally, please check the MS-CXR benchmark for a more systematic evaluation of joint image and text models in phrase grounding tasks.

Citation

The corresponding manuscript is accepted to be presented at the Conference on Computer Vision and Pattern Recognition (CVPR) 2023

@misc{https://doi.org/10.48550/arXiv.2301.04558,
  doi = {10.48550/ARXIV.2301.04558},
  url = {https://arxiv.org/abs/2301.04558},
  author = {Bannur, Shruthi and Hyland, Stephanie and Liu, Qianchu and Perez-Garcia, Fernando and Ilse, Maximilian and Castro, Daniel C and Boecking, Benedikt and Sharma, Harshita and Bouzid, Kenza and Thieme, Anja and Schwaighofer, Anton and Wetscherek, Maria and Lungren, Matthew P and Nori, Aditya and Alvarez-Valle, Javier and Oktay, Ozan}
  title = {Learning to Exploit Temporal Structure for Biomedical Vision–Language Processing},
  publisher = {arXiv},
  year = {2023},
}

Model Use

Intended Use

This model is intended to be used solely for (I) future research on visual-language processing and (II) reproducibility of the experimental results reported in the reference paper.

Primary Intended Use

The primary intended use is to support AI researchers building on top of this work. CXR-BERT and its associated models should be helpful for exploring various clinical NLP & VLP research questions, especially in the radiology domain.

Out-of-Scope Use

Any deployed use case of the model --- commercial or otherwise --- is currently out of scope. Although we evaluated the models using a broad set of publicly-available research benchmarks, the models and evaluations are not intended for deployed use cases. Under unprecedented conditions, the models may make inaccurate predictions and display limitations, which may require additional mitigation strategies. Therefore, we discourage use of the model for automated diagnosis or in a medical device. Please refer to the associated paper for more details.

How to use