Papers with biomedical relation extraction
Syntax-aware Multi-task Graph Convolutional Networks for Biomedical Relation Extraction (D19-62)
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| Challenge: | 80% of the data sets for relation extraction tasks are negative instances, resulting in a lack of syntactic information between two entity mentions. |
| Approach: | They propose a graph convolutional networks model that incorporates dependency parsing and contextualized embedding to capture comprehensive contextual information. |
| Outcome: | The proposed model achieves state-of-the-art F-score on the 2013 drug-drug interaction extraction task. |
Extraction of Diagnostic Reasoning Relations for Clinical Knowledge Graphs (2022.acl-srw)
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| Challenge: | Existing methods for analyzing knowledge graphs focus on concept relations and clinical processes. |
| Approach: | They propose to extract clinical knowledge graphs from a wiki and consumer health resource texts by using a clinical reasoning ontology. |
| Outcome: | The proposed methods evaluate the correctness of extracted triples in the zero-shot setting. |
Can NLI Provide Proper Indirect Supervision for Low-resource Biomedical Relation Extraction? (2023.acl-long)
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| Challenge: | Existing approaches to biomedical relation extraction (RE) are limited due to the scarcity of annotations and the prevalence of instances without explicitly pre-defined labels. |
| Approach: | They propose a method which converts biomedical relation extraction (RE) as natural language inference formulation through indirect supervision. |
| Outcome: | Extensive experiments on three widely-used biomedical RE benchmarks show that indirect supervision improves biomedically relation extraction even when a domain gap exists. |
MedDistant19: Towards an Accurate Benchmark for Broad-Coverage Biomedical Relation Extraction (2022.coling-1)
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| Challenge: | Relation extraction in the biomedical domain is challenging due to the lack of labeled data and high annotation costs. |
| Approach: | They propose to use distant supervision to pair knowledge graph relationships with raw texts to tackle the scarcity of annotated data and to validate their results. |
| Outcome: | The proposed benchmarks are more accurate and consistent with existing benchmarks and show that there is no train-test leakage. |
Decorate the Examples: A Simple Method of Prompt Design for Biomedical Relation Extraction (2022.lrec-1)
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| Challenge: | Recent research shows that prompt-based learning improves performance on relation extraction tasks. |
| Approach: | They propose a prompt-based learning method that generates comprehensive prompts for biomedical relation extraction using a ChemProt dataset. |
| Outcome: | The proposed method improves fine-tuning on a biomedical relation extraction task with a cloze-test task and fewer training examples to make reasonable predictions. |
Federated Document-Level Biomedical Relation Extraction with Localized Context Contrast (2024.lrec-main)
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| Challenge: | Existing studies on relation extraction focus on document-level training without sharing raw medical texts. |
| Approach: | They propose a federated framework for relation extraction that enables collaborative training without sharing raw medical texts. |
| Outcome: | The proposed framework extends document-level relation extraction to a federated environment. |
Improving Automatic Evaluation of Large Language Models (LLMs) in Biomedical Relation Extraction via LLMs-as-the-Judge (2025.acl-long)
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| Challenge: | Large Language Models generate human-like text, making them unreliable for biomedical relation extraction tasks. |
| Approach: | They propose to use Large Language Models as judges to evaluate biomedical relation extraction . they propose structured output formatting for LLM-generated responses that helps LLMs improve their performance by 15%. |
| Outcome: | The proposed method improves LLM-Judges' performance by 15% . it is cheaper and more efficient than human evaluation metrics, the authors say . |
Enhanced Reasoning for Biomedical Document-Level Relation Extraction via a Novel Cascade Language Model Framework (2026.acl-long)
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| Challenge: | Pre-trained language models (PLMs) are the leading paradigm in document-level relation extraction. |
| Approach: | They propose a cascade framework that leverages the complementary strengths of PLMs and LLMs through a detect-then-rethink paradigm. |
| Outcome: | The proposed framework improves on BioRED and CDR datasets and improves existing models. |