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--- |
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license: mit |
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--- |
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<h1 align="center"> |
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MedTok: Multimodal Medical Code Tokenizer |
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</h1> |
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## Overview of MedTok |
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MEDTOK is a multimodal tokenizer of medical codes that combines text descriptions of codes with graph-based representations of dependencies between codes derived from clinical ontologies and standard medical terminologies. MEDTOK is a general-purpose tokenizer that can be integrated into any transformer-based model or system that requires tokenization. |
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## How to use MedTok? |
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```bash |
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from transformers import AutoTokenizer |
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tokenizer = AutoTokenizer.from_pretrained("mims-harvard/MedTok", trust_remote_code=True) |
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tokens = tokenizer("E11.9") |
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embed = tokenizer.embed("E11.9") |
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``` |
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- embed means the quantized embedding for this input medical code. |
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If you want to use the tokenized embedding for each medical code, please download it from [mims-harvard/MedTok](https://huggingface.co/mims-harvard/MedTok) or [code2embeddings.json.zip](https://doi.org/10.7910/DVN/7XNT3M) directly. And the downloaded embedding file could be put into 'MedTok/embedding.npy' to run EHR or QA tasks based on MedTok. |
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### 🏥MedTok for EHR & MedicalQA |
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Please reference our github repo [MedTok](https://github.com/mims-harvard/MedTok) |
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### Note |
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MedTok tokenizer V1.0 now only supports those medical codes adopted in our paper. For those unseen codes, the output will be '<unk>' token. We will also continue to update our MedTok to make it apply to more coding system and tokenize medical code dynamically. |
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## Citation |
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```bash |
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@article{su2025multimodal, |
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title={Multimodal Medical Code Tokenizer}, |
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author={Su, Xiaorui and Messica, Shvat and Huang, Yepeng and Johnson, Ruth and Fesser, Lukas and Gao, Shanghua and Sahneh, Faryad and Zitnik, Marinka}, |
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journal={International Conference on Machine Learning, ICML}, |
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year={2025} |
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} |
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``` |
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## Contact |
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Thank you for your support! |
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If you have any questions or suggestions, please email [Xiaorui Su](xiaorui_su@hms.harvard.edu) and [Marinka Zitnik](marinka@hms.harvard.edu). |
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</details> |
