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南京理工大学发表最新JCIM论文

  • 2026-03-22 09:22:53
南京理工大学发表最新JCIM论文

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利用带交叉注意力机制的残差图卷积网络实现高精度蛋白质功能预测
论文信息
南京理工大学於东军教授团队鉴于蛋白质功能的精确测定对揭示细胞过程与病理机制、推动靶向药物设计具有重要意义，而传统湿实验方法存在周期长、成本高、难以大规模开展的局限，提出了一种名为 RCHGO 的新型深度学习框架。该框架通过引入融合交叉注意力机制的残差图卷积网络，直接从蛋白质序列出发推断基因本体论注释；其核心在于利用两个深度学习模块分别提取人工构建特征与基于蛋白质语言模型的特征，并在决策层进行融合，同时借助残差图卷积网络与交叉注意力模块的协同作用，使模型能够有效学习蛋白质及残基层面的多层次表示，并与基因本体论语义实现精准对齐。在 1,493 条非冗余蛋白质上的综合评估表明，RCHGO 的性能超越了 16 种现有主流方法，为高精度蛋白质功能预测提供了新的解决方案。
研究成果于2026年3月20日以题为“Leveraging Residual Graph Convolutional Networks with Cross-Attention Mechanisms for High-Accuracy Protein Function Prediction”发表在《Journal of Chemical Information and Modeling》上。
图文解读
图1：RCHGO 的工作流程。图一系统展示了 RCHGO 的双路并行架构。左侧 A 支路基于人工构建特征（如 PSSM、结构编码）构建蛋白质图，经残差图卷积与蛋白质-基因本体交叉注意力解码；右侧 B 支路利用 ProtT5 语言模型提取序列深层嵌入，通过残差图卷积与残基-基因本体交叉注意力实现细粒度对齐。两条支路在决策层经全连接网络融合，结合 C 支路的基因本体嵌入，最终输出高一致性功能预测。
图2：RCHGO/RCHGO+ 与 16 种代表性功能预测方法在未见物种与非同源蛋白上的性能对比。图二从泛化能力维度对比了各方法性能。A–C 显示，在来源于149个未见物种的240条蛋白上，RCHGO及其集成版本RCHGO+在Fmax、Smin与AUPRC三项指标上均持续领先，表明模型对进化远缘蛋白具备良好适应性。D–F 进一步聚焦303条与训练集无同源关系的蛋白，结果显示尽管所有方法因缺失同源信号而整体性能下降，RCHGO仍稳居前列，验证了其脱离序列同源性依赖的稳健表征能力。
文章小结
本文提出 RCHGO 深度学习框架，通过融合残差图卷积网络与交叉注意力机制，直接从蛋白质序列预测其基因本体论功能。该模型包含两条互补通路：MCFGP 利用人工构建特征，PLMGP 借助蛋白质语言模型提取深度表征，二者经残差图卷积与交叉注意力模块分别解码后，通过全连接网络在决策层融合，实现蛋白质与残基层级特征的有效对齐及语义关联。在 1,493 条非冗余蛋白的基准测试中，RCHGO 显著优于 16 种主流方法，展现出卓越的泛化能力。未来工作将聚焦于扩展更大规模语言模型并整合多源生物信息，以进一步提升预测精度。
文献来源
Li, Peixuan; Wang, Weifu; Yu, Dong-Jun (2026). Leveraging Residual Graph Convolutional Networks with Cross-Attention Mechanisms for High-Accuracy Protein Function Prediction. ACS Publications. Collection. 
DOI：https://doi.org/10.1021/acs.jcim.6c00101

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  1. CONNECT:[ UseTime:0.000842s ] mysql:host=127.0.0.1;port=3306;dbname=b460;charset=utf8mb4
  2. SHOW FULL COLUMNS FROM `fenlei` [ RunTime:0.001431s ]
  3. SELECT * FROM `fenlei` WHERE `fid` = 0 [ RunTime:0.000677s ]
  4. SELECT * FROM `fenlei` WHERE `fid` = 63 [ RunTime:0.000605s ]
  5. SHOW FULL COLUMNS FROM `set` [ RunTime:0.001044s ]
  6. SELECT * FROM `set` [ RunTime:0.000425s ]
  7. SHOW FULL COLUMNS FROM `article` [ RunTime:0.001234s ]
  8. SELECT * FROM `article` WHERE `id` = 511713 LIMIT 1 [ RunTime:0.002017s ]
  9. UPDATE `article` SET `lasttime` = 1774148932 WHERE `id` = 511713 [ RunTime:0.026252s ]
  10. SELECT * FROM `fenlei` WHERE `id` = 65 LIMIT 1 [ RunTime:0.000511s ]
  11. SELECT * FROM `article` WHERE `id` < 511713 ORDER BY `id` DESC LIMIT 1 [ RunTime:0.001341s ]
  12. SELECT * FROM `article` WHERE `id` > 511713 ORDER BY `id` ASC LIMIT 1 [ RunTime:0.000940s ]
  13. SELECT * FROM `article` WHERE `id` < 511713 ORDER BY `id` DESC LIMIT 10 [ RunTime:0.001651s ]
  14. SELECT * FROM `article` WHERE `id` < 511713 ORDER BY `id` DESC LIMIT 10,10 [ RunTime:0.001957s ]
  15. SELECT * FROM `article` WHERE `id` < 511713 ORDER BY `id` DESC LIMIT 20,10 [ RunTime:0.004670s ]
0.153666s