# Extracting Biomedical Entities from Noisy Audio Transcripts

arXiv: https://arxiv.org/abs/2403.17363 · HTML: https://mlsanity.com/paper/2403.17363/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 16 of its 49 references that are in the map.
- First posted on arXiv 26 Mar 2024.

## Builds on (most cited first, 16 of 16)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [Robust Speech Recognition via Large-Scale Weak Supervision](https://mlsanity.com/paper/2212.04356/) (2022)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Neural Architectures for Named Entity Recognition](https://mlsanity.com/paper/1603.01360/) (2016)
- [SSAST: Self-Supervised Audio Spectrogram Transformer](https://mlsanity.com/paper/2110.09784/) (2021)
- [GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information](https://mlsanity.com/paper/2304.09667/) (2023)
- [Thinking about GPT-3 In-Context Learning for Biomedical IE? Think Again](https://mlsanity.com/paper/2203.08410/) (2022)
- [HunFlair: An Easy-to-Use Tool for State-of-the-Art Biomedical Named Entity Recognition](https://mlsanity.com/paper/2008.07347/) (2020)
- [Inexpensive Domain Adaptation of Pretrained Language Models: Case Studies on Biomedical NER and Covid-19 QA](https://mlsanity.com/paper/2004.03354/) (2020)
- [Few-shot learning for medical text: A systematic review](https://mlsanity.com/paper/2204.14081/) (2022)
- [Effective Unsupervised Domain Adaptation with Adversarially Trained Language Models](https://mlsanity.com/paper/2010.01739/) (2020)
- [Hardness-guided domain adaptation to recognise biomedical named entities under low-resource scenarios](https://mlsanity.com/paper/2211.05980/) (2022)
- [BioAug: Conditional Generation based Data Augmentation for Low-Resource Biomedical NER](https://mlsanity.com/paper/2305.10647/) (2023)
- [Improving Speech Recognition for Indic Languages using Language Model](https://mlsanity.com/paper/2203.16595/) (2022)

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

- [Auto Review: Second Stage Error Detection for Highly Accurate Information Extraction from Phone Conversations](https://mlsanity.com/paper/2506.05400/) (2025)

## Abstract (arXiv)

Automatic Speech Recognition (ASR) technology is fundamental in transcribing spoken language into text, with considerable applications in the clinical realm, including streamlining medical transcription and integrating with Electronic Health Record (EHR) systems. Nevertheless, challenges persist, especially when transcriptions contain noise, leading to significant drops in performance when Natural Language Processing (NLP) models are applied. Named Entity Recognition (NER), an essential clinical task, is particularly affected by such noise, often termed the ASR-NLP gap. Prior works have primarily studied ASR's efficiency in clean recordings, leaving a research gap concerning the performance in noisy environments. This paper introduces a novel dataset, BioASR-NER, designed to bridge the ASR-NLP gap in the biomedical domain, focusing on extracting adverse drug reactions and mentions of entities from the Brief Test of Adult Cognition by Telephone (BTACT) exam. Our dataset offers a comprehensive collection of almost 2,000 clean and noisy recordings. In addressing the noise challenge, we present an innovative transcript-cleaning method using GPT4, investigating both zero-shot and few-shot methodologies. Our study further delves into an error analysis, shedding light on the types of errors in transcription software, corrections by GPT4, and the challenges GPT4 faces. This paper aims to foster improved understanding and potential solutions for the ASR-NLP gap, ultimately supporting enhanced healthcare documentation practices.