Reading the Cell, Designing the Cure: Perturbation-Conditioned Molecular Diffusion for Function-Oriented Drug Design
A new approach to drug design, termed Transcriptome-based Drug Design (TBDD), has been proposed to address challenges in creating effective drug molecules. The method utilizes a multi-resolution transcriptome-guided diffusion framework called the Cell Response Engine. This framework aims to bridge the gap between biology and chemistry by generating drug candidates based on desired transcriptomic state transitions.
- ▪The study formalizes drug design as a generative inverse problem based on transcriptomic perturbations.
- ▪A specialized feature extractor is used to distill function-oriented perturbation embeddings and align them with chemical views.
- ▪The proposed model outperforms existing baselines in both structural quality and functional consistency.
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Computer Science > Machine Learning arXiv:2605.15243 (cs) [Submitted on 14 May 2026] Title:Reading the Cell, Designing the Cure: Perturbation-Conditioned Molecular Diffusion for Function-Oriented Drug Design Authors:Ziyu Xu, Zijian Zhang, Liang Wang, Zhiyuan Liu, Qiang Liu, Shu Wu, Liang Wang View a PDF of the paper titled Reading the Cell, Designing the Cure: Perturbation-Conditioned Molecular Diffusion for Function-Oriented Drug Design, by Ziyu Xu and 6 other authors View PDF HTML (experimental) Abstract:When reliable target structures are unavailable at scale or phenotypes arise from dysregulated pathways, transcriptomic perturbations provide a system-level functional readout for drug action.
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