<p>Quantitative structure–activity relationship (QSAR) modeling has become a critical tool in drug design. Recently proposed Topological Regression (TR), a computationally efficient and highly interpretable QSAR model that maps distances in the chemical domain to distances in the activity domain, has shown predictive performance comparable to state-of-the-art deep learning-based models. However, TR’s dependence on simple random sampling-based anchor selection and utilization of radial basis function for response reconstruction constrain its interpretability and predictive capacity. To address these limitations, we propose Adaptive Topological Regression (AdapToR) with adaptive anchor selection and optimization-based reconstruction. We evaluated AdapToR on the NCI60 GI50 dataset, which consists of over 50,000 drug responses across 60 human cancer cell lines, and compared its performance to Transformer CNN, Graph Transformer, TR, and other baseline models. The results demonstrate that AdapToR outperforms competing QSAR models for drug response prediction with significantly lower computational cost and greater interpretability as compared to deep learning-based models.</p>