Shiyuan Yin, Ruizhi Zhang
· Knowledge-Based Systems · 0 citations
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The Membership Decoding method is a plug-and-play replacement for standard decoding that requires only black-box token probabilities, and a new token-level membership inference method is proposed by leveraging likelihood from reference models, shifting the generation from the original token distribution to the member token distribution.
Zi-Tai Chen, Reza Shokri
· Proceedings on Privacy Enhan... · 0 citations
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Tianlin Liu, Cheng Yang, Hyungchul Chung et al.
· Transportation Research Part... · 0 citations
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Haichao Du, Dongwei Zheng, An Guo et al.
· Engineering applications of... · 0 citations
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Accurate classification of long non-coding RNAs (lncRNAs) is essential for transcriptome annotation and understanding gene regulation. Existing computational methods predominantly rely on nucleotide sequence features, frequently overlooking biologically relevant peptide signals encoded within lncRNAs. To overcome this limitation, we developed LncPNdeep, an integrative deep learning framework that combines nucleotide and peptide embeddings extracted via masked language models, specifically utilizing contextual representations from BigBird, Longformer, and ProtTrans. By fusing both features in a concatenated neural architecture, LncPNdeep robustly captures complex sequence relationships and improves discrimination between lncRNAs and coding RNAs. Benchmarking on the human transcriptome achieved state-of-the-art performance with 97.1% accuracy, surpassing established lncRNA classification tools and baseline machine learning models. LncPNdeep also demonstrated superior generalization ability across cross-species datasets, maintaining consistently high accuracy and F1 scores. Permutation analysis highlighted the pivotal role of peptide embeddings, especially Average Peptide Embedding, in model performance, while t-SNE visualizations confirmed that integrating multiple embeddings markedly enhances the separation of lncRNAs from coding RNAs. These results position LncPNdeep as a versatile and powerful tool for transcriptomic research, facilitating lncRNA discovery, biomarker identification, and comparative genomics. The model and instructions are freely available at https://github.com/yatoka233/LncPNdeep.
Zongrui Dai, Feiyang Deng, Hsiao H. Sung
· Non-coding RNA Research · 0 citations
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Xiamei Wen, D. Duives, Serge P. Hoogendoorn
· Transportation Research Part... · 0 citations
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Shenghua Zhou, Jiawen Wang, Ioannis K. Brilakis et al.
· Engineering applications of... · 0 citations
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M. Renigier‐Biłozor, Piotr Artiemjew, Jakub Jurewicz
· Engineering applications of... · 0 citations
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Anni Meng, Weijiao Zhang, Miaomiao Qi
· Engineering applications of... · 3 citations
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Jimin Park, Karen Seojin Kim, Zuhdi Faturrahman et al.
· Journal of manufacturing sys... · 0 citations
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Yongqi Zhang
· Computers & electrical engin... · 0 citations
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Yuqi Zhang, Haochen Lv, Danyang Zheng et al.
· Comput. Networks · 0 citations
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