Enhancing Transcription Factor Prediction through Multi-Task Learning


Transcription factors (TFs) play a fundamental role in gene regulation by selectively binding to specific DNA sequences. Understanding the nature and behavior of these TFs is essential for insights into gene regulation dynamics. In this study, we introduce a robust multi-task learning framework specifically tailored to harness both TF-specific annotations and TF-related domain annotations, thereby enhancing the accuracy of TF predictions. Notably, we incorporate cutting-edge language models that have recently garnered attention for their outstanding performance across various fields, particularly in biological computations like protein sequence modeling. Comparative experimental analysis with existing models, DeepTFactor and TFpredict, reveals that our multi-task learning framework achieves an accuracy exceeding 92% across four evaluation metrics on the TF prediction task, surpassing both competitors. Our work marks a significant leap in the domain of TF prediction, enriching our comprehension of gene regulatory mechanisms and paving the way for the discovery of novel regulatory motifs.


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Gao, L., Zhang, M., & Sheng, V.S.. 2024. Enhancing Transcription Factor Prediction through Multi-Task Learning. Proceedings of the AAAI Conference on Artificial Intelligence, 38(21). https://doi.org/10.1609/aaai.v38i21.30446