# A Structure-aware Generative Model for Biomedical Event Extraction

arXiv: https://arxiv.org/abs/2408.06583 · HTML: https://mlsanity.com/paper/2408.06583/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 23 of its 35 references that are in the map.
- First posted on arXiv 13 Aug 2024.

## Builds on (most cited first, 23 of 23)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [BART: Denoising Sequence-to-Sequence Pre-training for Natural Language Generation, Translation, and Comprehension](https://mlsanity.com/paper/1910.13461/) (2019)
- [Prefix-Tuning: Optimizing Continuous Prompts for Generation](https://mlsanity.com/paper/2101.00190/) (2021)
- [Instruction Tuning for Large Language Models: A Survey](https://mlsanity.com/paper/2308.10792/) (2023)
- [Entity, Relation, and Event Extraction with Contextualized Span Representations](https://mlsanity.com/paper/1909.03546/) (2019)
- [Structured Prediction as Translation between Augmented Natural Languages](https://mlsanity.com/paper/2101.05779/) (2021)
- [Event Extraction by Answering (Almost) Natural Questions](https://mlsanity.com/paper/2004.13625/) (2020)
- [Document-Level Event Argument Extraction by Conditional Generation](https://mlsanity.com/paper/2104.05919/) (2021)
- [Text2Event: Controllable Sequence-to-Structure Generation for End-to-end Event Extraction](https://mlsanity.com/paper/2106.09232/) (2021)
- [DEGREE: A Data-Efficient Generation-Based Event Extraction Model](https://mlsanity.com/paper/2108.12724/) (2021)
- [How would Stance Detection Techniques Evolve after the Launch of ChatGPT?](https://mlsanity.com/paper/2212.14548/) (2022)
- [LasUIE: Unifying Information Extraction with Latent Adaptive Structure-aware Generative Language Model](https://mlsanity.com/paper/2304.06248/) (2023)
- [PHEE: A Dataset for Pharmacovigilance Event Extraction from Text](https://mlsanity.com/paper/2210.12560/) (2022)
- [Dynamic Prefix-Tuning for Generative Template-based Event Extraction](https://mlsanity.com/paper/2205.06166/) (2022)
- [Document-level Entity-based Extraction as Template Generation](https://mlsanity.com/paper/2109.04901/) (2021)
- [TextEE: Benchmark, Reevaluation, Reflections, and Future Challenges in Event Extraction](https://mlsanity.com/paper/2311.09562/) (2023)
- [AMPERE: AMR-Aware Prefix for Generation-Based Event Argument Extraction Model](https://mlsanity.com/paper/2305.16734/) (2023)
- [TAGPRIME: A Unified Framework for Relational Structure Extraction](https://mlsanity.com/paper/2205.12585/) (2022)

## Built on by (most cited first, 2 of 2)

- [Understanding LLM Reasoning for Abstractive Summarization](https://mlsanity.com/paper/2512.03503/) (2025)
- [Wi-Chat: Large Language Model Powered Wi-Fi Sensing](https://mlsanity.com/paper/2502.12421/) (2025)

## Abstract (arXiv)

Biomedical Event Extraction (BEE) is a challenging task that involves modeling complex relationships between fine-grained entities in biomedical text. BEE has traditionally been formulated as a classification problem. With recent advancements in large language models (LLMs), generation-based models that cast event extraction as a sequence generation problem have attracted attention in the NLP research community. However, current generative models often overlook cross-instance information in complex event structures, such as nested and overlapping events, which constitute over 20% of events in benchmark datasets. In this paper, we propose GenBEE, an event structure-aware generative model that captures complex event structures in biomedical text for biomedical event extraction. GenBEE constructs event prompts that distill knowledge from LLMs to incorporate both label semantics and argument dependency relationships. In addition, GenBEE generates prefixes with event structural prompts to incorporate structural features to improve the model's overall performance. We have evaluated the proposed GenBEE model on three widely used BEE benchmark datasets, namely MLEE, GE11, and PHEE. Experimental results show that GenBEE has achieved state-of-the-art performance on the MLEE and GE11 datasets, and achieved competitive results when compared to the state-of-the-art classification-based models on the PHEE dataset.