# Medical Coding with Biomedical Transformer Ensembles and Zero/Few-shot Learning

arXiv: https://arxiv.org/abs/2206.02662 · HTML: https://mlsanity.com/paper/2206.02662/

## Key facts

- Cited by 6 papers in the map (data through 14 Oct 2026).
- Builds on 18 of its 32 references that are in the map.
- First posted on arXiv 1 May 2022.

## Builds on (most cited first, 18 of 18)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Model-Agnostic Meta-Learning for Fast Adaptation of Deep Networks](https://mlsanity.com/paper/1703.03400/) (2017)
- [Dropout as a Bayesian Approximation: Representing Model Uncertainty in Deep Learning](https://mlsanity.com/paper/1506.02142/) (2015)
- [Simple and Scalable Predictive Uncertainty Estimation using Deep Ensembles](https://mlsanity.com/paper/1612.01474/) (2016)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Underspecification Presents Challenges for Credibility in Modern Machine Learning](https://mlsanity.com/paper/2011.03395/) (2020)
- [Deep Ensembles: A Loss Landscape Perspective](https://mlsanity.com/paper/1912.02757/) (2019)
- [Benchmarking Zero-shot Text Classification: Datasets, Evaluation and Entailment Approach](https://mlsanity.com/paper/1909.00161/) (2019)
- [Explainable Prediction of Medical Codes from Clinical Text](https://mlsanity.com/paper/1802.05695/) (2018)
- [Construction of the Literature Graph in Semantic Scholar](https://mlsanity.com/paper/1805.02262/) (2018)
- [Induction Networks for Few-Shot Text Classification](https://mlsanity.com/paper/1902.10482/) (2019)
- [Diverse Few-Shot Text Classification with Multiple Metrics](https://mlsanity.com/paper/1805.07513/) (2018)
- [An Empirical Study on Large-Scale Multi-Label Text Classification Including Few and Zero-Shot Labels](https://mlsanity.com/paper/2010.01653/) (2020)
- [Multi-Label Classification of Patient Notes a Case Study on ICD Code Assignment](https://mlsanity.com/paper/1709.09587/) (2017)
- [Towards Automated ICD Coding Using Deep Learning](https://mlsanity.com/paper/1711.04075/) (2017)
- [Read, Attend, and Code: Pushing the Limits of Medical Codes Prediction from Clinical Notes by Machines](https://mlsanity.com/paper/2107.10650/) (2021)

## Built on by (most cited first, 6 of 6)

- [Knowledge Injected Prompt Based Fine-tuning for Multi-label Few-shot ICD Coding](https://mlsanity.com/paper/2210.03304/) (2022)
- [Multi-label Few-shot ICD Coding as Autoregressive Generation with Prompt](https://mlsanity.com/paper/2211.13813/) (2022)
- [Generalizing over Long Tail Concepts for Medical Term Normalization](https://mlsanity.com/paper/2210.11947/) (2022)
- [Generating patient cohorts from electronic health records using two-step retrieval-augmented text-to-SQL generation](https://mlsanity.com/paper/2502.21107/) (2025)
- [From Zero to Hero: Harnessing Transformers for Biomedical Named Entity Recognition in Zero- and Few-shot Contexts](https://mlsanity.com/paper/2305.04928/) (2023)
- [RxSafeBench: Identifying Medication Safety Issues of Large Language Models in Simulated Consultation](https://mlsanity.com/paper/2511.04328/) (2025)

## Abstract (arXiv)

Medical coding (MC) is an essential pre-requisite for reliable data retrieval and reporting. Given a free-text reported term (RT) such as "pain of right thigh to the knee", the task is to identify the matching lowest-level term (LLT) - in this case "unilateral leg pain" - from a very large and continuously growing repository of standardized medical terms. However, automating this task is challenging due to a large number of LLT codes (as of writing over 80,000), limited availability of training data for long tail/emerging classes, and the general high accuracy demands of the medical domain. With this paper, we introduce the MC task, discuss its challenges, and present a novel approach called xTARS that combines traditional BERT-based classification with a recent zero/few-shot learning approach (TARS). We present extensive experiments that show that our combined approach outperforms strong baselines, especially in the few-shot regime. The approach is developed and deployed at Bayer, live since November 2021. As we believe our approach potentially promising beyond MC, and to ensure reproducibility, we release the code to the research community.