Finding Hidden Relationships Between Medical Concepts by Leveraging Metamap and Text Mining Techniques

In this digital world, data is everything and significantly impacts our everyday lives. Interestingly, in this small world, everything is part of an ecosystem, where everything is connected, directly or indirectly. The same thing happens to data as well. In most cases, it may seem like a particular topic does not have any connection with another one, but in reality, they are connected through a mutually related topic. Therefore, in this research, we will discuss an adaptive model modified from the ABC model by Don R. Swanson, a Literature-Based Discovery (LBD) Model, to find the hidden connections between Concepts of Interest. The model demonstrates that two topics, A and C are different and have no relationship. But they have a common topic, B that can be used to connect topics A and C This famous model will be used in this discussion to connect Medical Concepts.

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.

Causal relation extraction (CRE) is central to biomedical text mining, but current resources often conflate causal relations with broader associations, restrict annotation to sentence-level examples, or focus mainly on explicit causal cues. This limits their usefulness for evaluating whether models can recover causal claims as they are actually expressed in biomedical text. We introduce PubMedCausal, a span-level annotated corpus for biomedical CRE built from PubMed abstracts. The corpus contains 30,000 paragraph-level rows, including 3,945 causal rows and 6,491 adjudicated cause--effect pairs. Each causal relation is annotated with full-text cause and effect spans, causality type, and sententiality, enabling evaluation of both causal detection and full-span causal extraction. We benchmark discriminative encoders and open-source generative models across detection and extraction settings. For causal detection, biomedical encoders are strongest, with PubMedBERT reaching an F$_1$ score of 0.7391. For span-level extraction, the best generative baseline is DeepSeek-R1-32B with few-shot prompting, reaching a Cosine Pair F$_1$ of 0.6765. We further test transfer learning by evaluating PubMedCausal-trained encoders on external causal relation datasets, showing that the resource supports cross-dataset evaluation. Our results show that biomedical CRE remains difficult under class imbalance, long causal spans, implicit causality, inter-sentential relations, and prompt sensitivity. Code and Data can be found here: https://github.com/josiahpaul07/PubMedCausal_Exp