# An Automatic SOAP Classification System Using Weakly Supervision And Transfer Learning

arXiv: https://arxiv.org/abs/2211.14539 · HTML: https://mlsanity.com/paper/2211.14539/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 14 of its 43 references that are in the map.
- First posted on arXiv 26 Nov 2022.

## Builds on (most cited first, 14 of 14)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Pre-train, Prompt, and Predict: A Systematic Survey of Prompting Methods in Natural Language Processing](https://mlsanity.com/paper/2107.13586/) (2021)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [How Contextual are Contextualized Word Representations? Comparing the Geometry of BERT, ELMo, and GPT-2 Embeddings](https://mlsanity.com/paper/1909.00512/) (2019)
- [Bidirectional LSTM-CRF Models for Sequence Tagging](https://mlsanity.com/paper/1508.01991/) (2015)
- [BioSentVec: creating sentence embeddings for biomedical texts](https://mlsanity.com/paper/1810.09302/) (2018)
- [Launching into clinical space with medspaCy: a new clinical text processing toolkit in Python](https://mlsanity.com/paper/2106.07799/) (2021)
- [NSP-BERT: A Prompt-based Few-Shot Learner Through an Original Pre-training Task--Next Sentence Prediction](https://mlsanity.com/paper/2109.03564/) (2021)
- [Bidirectional Recurrent Neural Networks for Medical Event Detection in Electronic Health Records](https://mlsanity.com/paper/1606.07953/) (2016)
- [MedJEx: A Medical Jargon Extraction Model with Wiki's Hyperlink Span and Contextualized Masked Language Model Score](https://mlsanity.com/paper/2210.05875/) (2022)
- [Deep EHR: Chronic Disease Prediction Using Medical Notes](https://mlsanity.com/paper/1808.04928/) (2018)
- [Structured prediction models for RNN based sequence labeling in clinical text](https://mlsanity.com/paper/1608.00612/) (2016)
- [Hierarchical Annotation for Building A Suite of Clinical Natural Language Processing Tasks: Progress Note Understanding](https://mlsanity.com/paper/2204.03035/) (2022)
- [Towards an Automated SOAP Note: Classifying Utterances from Medical Conversations](https://mlsanity.com/paper/2007.08749/) (2020)

## Built on by (most cited first, 1 of 1)

- [UMASS_BioNLP at MEDIQA-Chat 2023: Can LLMs generate high-quality synthetic note-oriented doctor-patient conversations?](https://mlsanity.com/paper/2306.16931/) (2023)

## Abstract (arXiv)

In this paper, we introduce a comprehensive framework for developing a machine learning-based SOAP (Subjective, Objective, Assessment, and Plan) classification system without manually SOAP annotated training data or with less manually SOAP annotated training data. The system is composed of the following two parts: 1) Data construction, 2) A neural network-based SOAP classifier, and 3) Transfer learning framework. In data construction, since a manual construction of a large size training dataset is expensive, we propose a rule-based weak labeling method utilizing the structured information of an EHR note. Then, we present a SOAP classifier composed of a pre-trained language model and bi-directional long-short term memory with conditional random field (Bi-LSTM-CRF). Finally, we propose a transfer learning framework that re-uses the trained parameters of the SOAP classifier trained with the weakly labeled dataset for datasets collected from another hospital. The proposed weakly label-based learning model successfully performed SOAP classification (89.99 F1-score) on the notes collected from the target hospital. Otherwise, in the notes collected from other hospitals and departments, the performance dramatically decreased. Meanwhile, we verified that the transfer learning framework is advantageous for inter-hospital adaptation of the model increasing the models' performance in every cases. In particular, the transfer learning approach was more efficient when the manually annotated data size was smaller. We showed that SOAP classification models trained with our weakly labeling algorithm can perform SOAP classification without manually annotated data on the EHR notes from the same hospital. The transfer learning framework helps SOAP classification model's inter-hospital migration with a minimal size of the manually annotated dataset.