Advancing Target Discovery Through Disease-Specific Integration of Multi-Modal Target Identification Models and Comprehensive Target Benchmarking System

Leung, H.; Duan, C.; Gou, W.; Chen, J.; Xin, Y.; Zheng, Z.; Naumov, V.; Gennert, D.; Zhang, M.; Aliper, A.; Ren, F.; Izumchenko, E.; Pun, F. W.; Zhavoronkov, A.

doi:10.1101/2025.08.06.668866

bioRxiv · 10.1101/2025.08.06.668866

Advancing Target Discovery Through Disease-Specific Integration of Multi-Modal Target Identification Models and Comprehensive Target Benchmarking System

Leung, H.·Duan, C.·Gou, W.·Chen, J.·Xin, Y.·Zheng, Z.·Naumov, V.·Gennert, D.·Zhang, M.·Aliper, A.·Ren, F.·Izumchenko, E.·Pun, F. W.·Zhavoronkov, A.

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Abstract

Target identification is crucial for drug development. AI-driven approaches leveraging multi-omics and computational modeling can accelerate this process. However, integrating multi-modal data for disease-specific target identification and predicting translational potential remains challenging. Moreover, the absence of a systematic evaluation framework for model performance limits confidence in target reliability. We present a unified platform combining machine learning-based target identification with comprehensive benchmarking. As a testbed, we developed Target Identification Pro (TargetPro), a disease-specific model spanning 38 diseases across oncology, metabolic, immune, fibrotic, and neurological categories. TargetPro shows strong predictive performance for clinical-stage targets and reveals disease-specific patterns, underscoring the need for tailored target detection models. We next created Target Identification Benchmark (TargetBench 1.0) to rigorously assess target identification systems, including large language models, based on their ability to recover established targets and find high-quality novel candidates. This integrated approach offers a streamlined strategy to evaluate target discovery models, ultimately improving drug development efficiency.

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Leung, H., Duan, C., Gou, W., Chen, J., Xin, Y., Zheng, Z., Naumov, V., Gennert, D., Zhang, M., Aliper, A., Ren, F., Izumchenko, E., Pun, F. W., Zhavoronkov, A.. 2025-08-08. Advancing Target Discovery Through Disease-Specific Integration of Multi-Modal Target Identification Models and Comprehensive Target Benchmarking System. https://doi.org/10.1101/2025.08.06.668866

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