Quantitative structure-activity relationship assumes a smooth relationship between molecular structure and biological activity. However, activity cliffs defined as pairs of structurally similar compounds with large potency differences break this continuity. Recent benchmarks targeting activity cliffs have revealed that classical machine learning models with extended connectivity fingerprints outperform graph neural networks. Our analysis shows that graph embeddings fail to adequately separate structurally similar molecules in the embedding space, making it difficult to distinguish between structurally similar but functionally different molecules. Despite this limitation, molecular graph structures are inherently expressive and attractive, as they preserve molecular topology. To preserve the structural representation of molecules as graphs, we propose a new model, Graph-Cliff, which integrates short-and long-range information through a gating mechanism. Experimental results demonstrate that GraphCliff consistently improves performance on both non-cliff and cliff compounds. Furthermore, layer-wise node embedding analyses reveal reduced over-smoothing and enhanced discriminative power relative to strong baseline graph models. Quantitative Structure-Activity Relationship (QSAR) is based on the premise that molecules with similar structures have similar biological activity.

The vast amount of biomedical information available today presents a significant challenge for investigators seeking to digest, process, and understand these findings effectively. Large Language Models (LLMs) have emerged as powerful tools to navigate this complex and challenging data landscape. However, LLMs may lead to hallucinatory responses, making Retrieval Augmented Generation (RAG) crucial for achieving accurate information. In this protocol, we present RUGGED (Retrieval Under Graph-Guided Explainable disease Distinction), a comprehensive workflow designed to support investigators with knowledge integration and hypothesis generation, identifying validated paths forward. Relevant biomedical information from publications and knowledge bases are reviewed, integrated, and extracted via text-mining association analysis and explainable graph prediction models on disease nodes, forecasting potential links among drugs and diseases. These analyses, along with biomedical texts, are integrated into a framework that facilitates user-directed mechanism elucidation as well as hypothesis exploration through RAG-enabled LLMs. A clinical use-case demonstrates RUGGED's ability to evaluate and recommend therapeutics for Arrhythmogenic Cardiomyopathy (ACM) and Dilated Cardiomyopathy (DCM), analyzing prescribed drugs for molecular interactions and unexplored uses. The platform minimizes LLM hallucinations, offers actionable insights, and improves the investigation of novel therapeutics.