# WHERE and WHICH: Iterative Debate for Biomedical Synthetic Data Augmentation

arXiv: https://arxiv.org/abs/2503.23673 · HTML: https://mlsanity.com/paper/2503.23673/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Placed in Medical synthetic data and agents, one of 13 directions in Synthetic data and self-improvement for LLMs.
- Builds on 20 of its 33 references that are in the map.
- First posted on arXiv 31 Mar 2025.

## Placed in

- Synthetic data and self-improvement for LLMs / [Medical synthetic data and agents](https://mlsanity.com/synth/medical-synthetic-data-and-agents/)

## Builds on (most cited first, 20 of 20)

- [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)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [EDA: Easy Data Augmentation Techniques for Boosting Performance on Text Classification Tasks](https://mlsanity.com/paper/1901.11196/) (2019)
- [DoLa: Decoding by Contrasting Layers Improves Factuality in Large Language Models](https://mlsanity.com/paper/2309.03883/) (2023)
- [LinkBERT: Pretraining Language Models with Document Links](https://mlsanity.com/paper/2203.15827/) (2022)
- [Not Enough Data? Deep Learning to the Rescue!](https://mlsanity.com/paper/1911.03118/) (2019)
- [Fine-Tuning Large Neural Language Models for Biomedical Natural Language Processing](https://mlsanity.com/paper/2112.07869/) (2021)
- [Neural Data Augmentation via Example Extrapolation](https://mlsanity.com/paper/2102.01335/) (2021)
- [DARE: Data Augmented Relation Extraction with GPT-2](https://mlsanity.com/paper/2004.13845/) (2020)
- [MELM: Data Augmentation with Masked Entity Language Modeling for Low-Resource NER](https://mlsanity.com/paper/2108.13655/) (2021)
- [Data Manipulation: Towards Effective Instance Learning for Neural Dialogue Generation via Learning to Augment and Reweight](https://mlsanity.com/paper/2004.02594/) (2020)
- [Data Augmentation in Natural Language Processing: A Novel Text Generation Approach for Long and Short Text Classifiers](https://mlsanity.com/paper/2103.14453/) (2021)
- [Open Source Language Models Can Provide Feedback: Evaluating LLMs' Ability to Help Students Using GPT-4-As-A-Judge](https://mlsanity.com/paper/2405.05253/) (2024)
- [Incidental Supervision: Moving beyond Supervised Learning](https://mlsanity.com/paper/2005.12339/) (2020)
- [Can NLI Provide Proper Indirect Supervision for Low-resource Biomedical Relation Extraction?](https://mlsanity.com/paper/2212.10784/) (2022)
- [GDA: Generative Data Augmentation Techniques for Relation Extraction Tasks](https://mlsanity.com/paper/2305.16663/) (2023)
- [Incorporating Relation Paths in Neural Relation Extraction](https://mlsanity.com/paper/1609.07479/) (2016)
- [ACLM: A Selective-Denoising based Generative Data Augmentation Approach for Low-Resource Complex NER](https://mlsanity.com/paper/2306.00928/) (2023)
- [GPT-4 is judged more human than humans in displaced and inverted Turing tests](https://mlsanity.com/paper/2407.08853/) (2024)

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

- [Error-Aware Curriculum Learning for Biomedical Relation Classification](https://mlsanity.com/paper/2507.14374/) (2025)

## Abstract (arXiv)

In Biomedical Natural Language Processing (BioNLP) tasks, such as Relation Extraction, Named Entity Recognition, and Text Classification, the scarcity of high-quality data remains a significant challenge. This limitation poisons large language models to correctly understand relationships between biological entities, such as molecules and diseases, or drug interactions, and further results in potential misinterpretation of biomedical documents. To address this issue, current approaches generally adopt the Synthetic Data Augmentation method which involves similarity computation followed by word replacement, but counterfactual data are usually generated. As a result, these methods disrupt meaningful word sets or produce sentences with meanings that deviate substantially from the original context, rendering them ineffective in improving model performance. To this end, this paper proposes a biomedical-dedicated rationale-based synthetic data augmentation method. Beyond the naive lexicon similarity, specific bio-relation similarity is measured to hold the augmented instance having a strong correlation with bio-relation instead of simply increasing the diversity of augmented data. Moreover, a multi-agents-involved reflection mechanism helps the model iteratively distinguish different usage of similar entities to escape falling into the mis-replace trap. We evaluate our method on the BLURB and BigBIO benchmark, which includes 9 common datasets spanning four major BioNLP tasks. Our experimental results demonstrate consistent performance improvements across all tasks, highlighting the effectiveness of our approach in addressing the challenges associated with data scarcity and enhancing the overall performance of biomedical NLP models.