Applicability Condition Extraction for Therapeutic Drug-Disease Relations
- URL: http://arxiv.org/abs/2606.14031v2
- Date: Thu, 18 Jun 2026 05:23:32 GMT
- Title: Applicability Condition Extraction for Therapeutic Drug-Disease Relations
- Abstract summary: We introduce the task of applicability condition extraction for therapeutic drug-disease relations from biomedical research literature.<n>We create the first dataset that has manually annotated triples of drugs, diseases, and applicability conditions on biomedical paper abstracts with 1,119 drug-disease pairs.<n>We propose a new method that enhances LoRA to consider relations between drugs and diseases.
- Score: 11.102832431694956
- License: http://creativecommons.org/licenses/by/4.0/
- Abstract: Identifying conditions that a certain drug takes therapeutic effect on a target disease is crucial for clinical decision-making support. However, most existing biomedical information extraction methods have focused on identifying only relations between drugs and diseases, while largely overlooking the context-specific conditions where such relations can apply. To address this problem, we introduce the task of applicability condition extraction for therapeutic drug-disease relations from biomedical research literature. We create the first dataset that has manually annotated triples of drugs, diseases, and applicability conditions on biomedical paper abstracts with 1,119 drug-disease pairs. Using this dataset, we systematically evaluate the performance of a range of existing methods. In addition, we propose a new method that enhances LoRA to consider relations between drugs and diseases. Our method consistently outperforms strong baselines across different evaluation settings.
Related papers
- DrugReason: Dynamic Multi-View Reasoning over Knowledge Graph and Language Evidence for Drug Repurposing [55.45112712244231]
DrugReason is a multi-view reasoning framework that integrates grounded KG reasoning with LLM-generated mechanistic inference for drug repurposing.<n> Experiments on PharmaDB, DDInter, and DrugBank show that DrugReason improves average performance over strong single-view reasoning baselines.
arXiv Detail & Related papers (2026-09-06T18:54:26Z) - OPBench: A Graph Benchmark to Combat the Opioid Crisis [50.31950155687914]
graph learning methods have emerged as a promising paradigm for modeling complex drug-related phenomena.<n>There is no comprehensive benchmark for systematically evaluating these methods across real-world opioid crisis scenarios.<n>OPBench is the first comprehensive opioid benchmark comprising five datasets across three critical application domains.
arXiv Detail & Related papers (2026-02-16T10:04:57Z) - DREaM: Drug-Drug Relation Extraction via Transfer Learning Method [12.05102643799087]
We propose DREAM, a method that first employs a trained relation extraction model to discover relations between entities.<n>The extracted relations are subsequently validated using a large language model.<n>Our qualitative analysis indicates that this approach can uncover ambiguities in the medical domain.
arXiv Detail & Related papers (2025-10-27T10:27:00Z) - Natural Language-Assisted Multi-modal Medication Recommendation [97.07805345563348]
We introduce the Natural Language-Assisted Multi-modal Medication Recommendation(NLA-MMR)<n>The NLA-MMR is a multi-modal alignment framework designed to learn knowledge from the patient view and medication view jointly.<n>In this vein, we employ pretrained language models(PLMs) to extract in-domain knowledge regarding patients and medications.
arXiv Detail & Related papers (2025-01-13T09:51:50Z) - Multiscale Topology in Interactomic Network: From Transcriptome to
Antiaddiction Drug Repurposing [0.3683202928838613]
The escalating drug addiction crisis in the United States underscores the urgent need for innovative therapeutic strategies.
This study embarked on an innovative and rigorous strategy to unearth potential drug repurposing candidates for opioid and cocaine addiction treatment.
arXiv Detail & Related papers (2023-12-03T04:01:38Z) - A clustering and graph deep learning-based framework for COVID-19 drug
repurposing [0.3359875577705538]
This study presents a novel unsupervised machine learning framework that utilizes a graph-based autoencoder for multi-feature type clustering on heterogeneous drug data.
The dataset consists of 438 drugs, of which 224 are under clinical trials for COVID-19.
Our framework relies on reported drug data, including its pharmacological properties, chemical/physical properties, interaction with the host, and efficacy in different publicly available COVID-19 assays.
arXiv Detail & Related papers (2023-06-24T15:00:47Z) - Transcriptomics-based matching of drugs to diseases with deep learning [1.590243405031747]
We present a deep learning approach to conduct hypothesis-free, transcriptomics-based matching of drugs for diseases.
Our proposed neural network architecture is trained on approved drug-disease indications, taking as input the relevant disease and drug differential gene expression profiles.
We evaluate our approach against the most widely used transcriptomics-based matching baselines, CMap and the Characteristic Direction.
arXiv Detail & Related papers (2023-03-21T09:32:31Z) - Drug Synergistic Combinations Predictions via Large-Scale Pre-Training
and Graph Structure Learning [82.93806087715507]
Drug combination therapy is a well-established strategy for disease treatment with better effectiveness and less safety degradation.
Deep learning models have emerged as an efficient way to discover synergistic combinations.
Our framework achieves state-of-the-art results in comparison with other deep learning-based methods.
arXiv Detail & Related papers (2023-01-14T15:07:43Z) - Neural Bandits for Data Mining: Searching for Dangerous Polypharmacy [63.135687276599114]
Some polypharmacies, deemed inappropriate, may be associated with adverse health outcomes such as death or hospitalization.
We propose the OptimNeuralTS strategy to efficiently mine claims datasets and build a predictive model of the association between drug combinations and health outcomes.
Our method can detect up to 72% of PIPs while maintaining an average precision score of 99% using 30 000 time steps.
arXiv Detail & Related papers (2022-12-10T03:43:23Z) - Knowledge-Driven New Drug Recommendation [88.35607943144261]
We develop a drug-dependent multi-phenotype few-shot learner to bridge the gap between existing and new drugs.
EDGE eliminates the false-negative supervision signal using an external drug-disease knowledge base.
Results show that EDGE achieves 7.3% improvement on the ROC-AUC score over the best baseline.
arXiv Detail & Related papers (2022-10-11T16:07:52Z) - A Dataset for N-ary Relation Extraction of Drug Combinations [39.281113345967995]
Combination therapies have become the standard of care for diseases such as cancer, tuberculosis, malaria and HIV.
We construct an expert-annotated dataset for extracting information about the efficacy of drug combinations from the scientific literature.
arXiv Detail & Related papers (2022-05-04T19:01:16Z) - Deep learning for drug repurposing: methods, databases, and applications [54.08583498324774]
Repurposing existing drugs for new therapies is an attractive solution that accelerates drug development at reduced experimental costs.
In this review, we introduce guidelines on how to utilize deep learning methodologies and tools for drug repurposing.
arXiv Detail & Related papers (2022-02-08T09:42:08Z) - Discovering Drug-Target Interaction Knowledge from Biomedical Literature [107.98712673387031]
The Interaction between Drugs and Targets (DTI) in human body plays a crucial role in biomedical science and applications.
As millions of papers come out every year in the biomedical domain, automatically discovering DTI knowledge from literature becomes an urgent demand in the industry.
We explore the first end-to-end solution for this task by using generative approaches.
We regard the DTI triplets as a sequence and use a Transformer-based model to directly generate them without using the detailed annotations of entities and relations.
arXiv Detail & Related papers (2021-09-27T17:00:14Z) - Extracting Adverse Drug Events from Clinical Notes [1.6244541005112747]
Adverse drug events (ADEs) are unexpected incidents caused by the administration of a drug or medication.
This paper explores the relationship between a drug and its associated attributes using relation extraction techniques.
arXiv Detail & Related papers (2021-04-21T23:10:20Z) - Clinical Temporal Relation Extraction with Probabilistic Soft Logic
Regularization and Global Inference [50.029659413650194]
Existing methods either require expensive feature engineering or are incapable of modeling the global dependencies among the events.
In this paper, we propose a novel method, Clinical Temporal ReLation Exaction with Probabilistic Soft Logic Regularization and Global Inference.
arXiv Detail & Related papers (2020-12-16T08:23:03Z) - Text Mining to Identify and Extract Novel Disease Treatments From
Unstructured Datasets [56.38623317907416]
We use Google Cloud to transcribe podcast episodes of an NPR radio show.
We then build a pipeline for systematically pre-processing the text.
Our model successfully identified that Omeprazole can help treat heartburn.
arXiv Detail & Related papers (2020-10-22T19:52:49Z)
This list is automatically generated from the titles and abstracts of the papers in this site.
This site does not guarantee the quality of this site (including all information) and is not responsible for any consequences.