Yuchen Liu
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Research Subjects
Yuchen Liu has a total of 12 co-authors. Here are the top co-authors by number of shared publications:
- Dianwen Ju
School of Pharmaceutical Sciences, Shanghai Engineering Research Center of Immunotherapeutics, Fudan University, Shanghai 201203, China
1 shared publication - Dongyue Hou
School of Pharmaceutical Sciences, Shanghai Engineering Research Center of Immunotherapeutics, Fudan University, Shanghai 201203, China
1 shared publication - Hanbo Lin
School of Pharmaceutical Sciences, Shanghai Engineering Research Center of Immunotherapeutics, Fudan University, Shanghai 201203, China
1 shared publication - Hui Zhao
Byterna Therapeutics, Shanghai, China
1 shared publication - Jiajie Gu
School of Pharmaceutical Sciences, Shanghai Engineering Research Center of Immunotherapeutics, Fudan University, Shanghai 201203, China
1 shared publication - Juncheng Qian
School of Pharmaceutical Sciences, Shanghai Engineering Research Center of Immunotherapeutics, Fudan University, Shanghai 201203, China
1 shared publication
Latest Publications
- Open Access
Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning
The determination of RNA secondary structure (RSS) could help understand RNA’s functional mechanisms, guiding the design of RNA-based therapeutics, and advancing synthetic biology applications. However, traditional methods such as NMR for determining RSS are typically time-consuming and labor-intensive. As a result, the accurate prediction of RSS remains a fundamental yet unmet need in RNA research. Various deep learning (DL)-based methods achieved improved accuracy over thermodynamic-based methods. However, the over-parameterization nature of DL makes these methods prone to overfitting and thus limits their generalizability. Meanwhile, the inconsistency of RSS predictions between these methods further aggravated the crisis of generalizability. Here, we propose TrioFold to achieve enhanced generalizability of RSS prediction by integrating base-pairing clues learned from both thermodynamic- and DL-based methods by ensemble learning and convolutional block attention mechanism. TrioFold achieves higher accuracy in intra-family predictions and enhanced generalizability in inter-family and cross-RNA-types predictions. Additionally, we have developed an online webserver equipped with widely used RSS prediction algorithms and analysis tools, providing an accessible platform for the RNA research community. This study demonstrated new opportunities to improve generalizability for RSS predictions by efficient ensemble learning of base-pairing clues learned from both thermodynamic- and DL-based algorithms.
Open AccessEnhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning
The determination of RNA secondary structure (RSS) could help understand RNA’s functional mechanisms, guiding the design of RNA-based therapeutics, and advancing synthetic biology applications. However, traditional methods such as NMR for determining RSS are typically time-consuming and labor-intensive. As a result, the accurate prediction of RSS remains a fundamental yet unmet need in RNA research. Various deep learning (DL)-based methods achieved improved accuracy over thermodynamic-based methods. However, the over-parameterization nature of DL makes these methods prone to overfitting and thus limits their generalizability. Meanwhile, the inconsistency of RSS predictions between these methods further aggravated the crisis of generalizability. Here, we propose TrioFold to achieve enhanced generalizability of RSS prediction by integrating base-pairing clues learned from both thermodynamic- and DL-based methods by ensemble learning and convolutional block attention mechanism. TrioFold achieves higher accuracy in intra-family predictions and enhanced generalizability in inter-family and cross-RNA-types predictions. Additionally, we have developed an online webserver equipped with widely used RSS prediction algorithms and analysis tools, providing an accessible platform for the RNA research community. This study demonstrated new opportunities to improve generalizability for RSS predictions by efficient ensemble learning of base-pairing clues learned from both thermodynamic- and DL-based algorithms.