# Relation Extraction in underexplored biomedical domains: A diversity-optimised sampling and synthetic data generation approach

arXiv: https://arxiv.org/abs/2311.06364 · HTML: https://mlsanity.com/paper/2311.06364/

## 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 49 of its 115 references that are in the map.
- First posted on arXiv 10 Nov 2023.

## 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, 30 of 49)

- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
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- [ToxiGen: A Large-Scale Machine-Generated Dataset for Adversarial and Implicit Hate Speech Detection](https://mlsanity.com/paper/2203.09509/) (2022)
- [Confident Learning: Estimating Uncertainty in Dataset Labels](https://mlsanity.com/paper/1911.00068/) (2019)
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- [Prompting GPT-3 To Be Reliable](https://mlsanity.com/paper/2210.09150/) (2022)
- [Promptagator: Few-shot Dense Retrieval From 8 Examples](https://mlsanity.com/paper/2209.11755/) (2022)
- [ZeroGen: Efficient Zero-shot Learning via Dataset Generation](https://mlsanity.com/paper/2202.07922/) (2022)
- [Data-centric Artificial Intelligence: A Survey](https://mlsanity.com/paper/2303.10158/) (2023)
- [Generating Training Data with Language Models: Towards Zero-Shot Language Understanding](https://mlsanity.com/paper/2202.04538/) (2022)
- [GPT3Mix: Leveraging Large-scale Language Models for Text Augmentation](https://mlsanity.com/paper/2104.08826/) (2021)
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- [Not Enough Data? Deep Learning to the Rescue!](https://mlsanity.com/paper/1911.03118/) (2019)
- [Data Augmentation using Pre-trained Transformer Models](https://mlsanity.com/paper/2003.02245/) (2020)
- [Self-Adaptive In-Context Learning: An Information Compression Perspective for In-Context Example Selection and Ordering](https://mlsanity.com/paper/2212.10375/) (2022)
- [Does Synthetic Data Generation of LLMs Help Clinical Text Mining?](https://mlsanity.com/paper/2303.04360/) (2023)
- [Increasing Diversity While Maintaining Accuracy: Text Data Generation with Large Language Models and Human Interventions](https://mlsanity.com/paper/2306.04140/) (2023)
- [Knowledgeable or Educated Guess? Revisiting Language Models as Knowledge Bases](https://mlsanity.com/paper/2106.09231/) (2021)
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- [Exploiting Asymmetry for Synthetic Training Data Generation: SynthIE and the Case of Information Extraction](https://mlsanity.com/paper/2303.04132/) (2023)
- [Thinking about GPT-3 In-Context Learning for Biomedical IE? Think Again](https://mlsanity.com/paper/2203.08410/) (2022)

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

- [Merged ChemProt-DrugProt for Relation Extraction from Biomedical Literature](https://mlsanity.com/paper/2405.18605/) (2024)

## Abstract (arXiv)

The sparsity of labelled data is an obstacle to the development of Relation Extraction models and the completion of databases in various biomedical areas. While being of high interest in drug-discovery, the natural-products literature, reporting the identification of potential bioactive compounds from organisms, is a concrete example of such an overlooked topic. To mark the start of this new task, we created the first curated evaluation dataset and extracted literature items from the LOTUS database to build training sets. To this end, we developed a new sampler inspired by diversity metrics in ecology, named Greedy Maximum Entropy sampler, or GME-sampler (https://github.com/idiap/gme-sampler). The strategic optimization of both balance and diversity of the selected items in the evaluation set is important given the resource-intensive nature of manual curation. After quantifying the noise in the training set, in the form of discrepancies between the input abstracts text and the expected output labels, we explored different strategies accordingly. Framing the task as an end-to-end Relation Extraction, we evaluated the performance of standard fine-tuning as a generative task and few-shot learning with open Large Language Models (LLaMA 7B-65B). In addition to their evaluation in few-shot settings, we explore the potential of open Large Language Models (Vicuna-13B) as synthetic data generator and propose a new workflow for this purpose. All evaluated models exhibited substantial improvements when fine-tuned on synthetic abstracts rather than the original noisy data. We provide our best performing (f1-score=59.0) BioGPT-Large model for end-to-end RE of natural-products relationships along with all the generated synthetic data and the evaluation dataset. See more details at https://github.com/idiap/abroad-re.