使用端到端深度学习模型完成PPI任务两篇论文笔记

1.“Multifaceted protein–protein interaction prediction based on Siamese residual RCNN”

1.1PPI任务的难点：

（1）蛋白质的表征需要一个模型来有效地过滤和聚合它们的局部特征，同时保留重要的上下文和序列的氨基酸信息
(2)扩展深度神经结构经常导致低效的学习过程，并遭受臭名昭著的消失梯度问题
(iii)还需要一个有效的机制来理解蛋白质对在PPI预测中的相互影响。此外，框架必须具有大数据的可伸缩性（我们的任务要求用在多长的数据上？）可推广到不同的预测任务。

1.2 作者对于自己工作的概括

（1）训练端到端网络PIPR，从而减少了用户数据预处理的工作量。
PIPR requires only the primary protein sequences as the input, and is trained to automatically preserve the critical features from the sequences.
补充：

（2）强调了在PPI任务中考虑上下文化和顺序信息的需求。（也就是说序列信息和局部信息都很重要，可是现在我们思考的模型中还没有加入局部信息）
（3）Third, the architecture of PIPR can be flexibly used to address different PPI tasks
（4）这个工作中也预测了亲和度！且表现很良好，可以对细微变化做出反应。

1.3PPI任务相较于NLP任务的不同之处

（1）序列
In contrast to sentences, proteins are profiled in sequences with more intractable patterns, as well as in a drastically larger range of lengths.
（2）Precisely capturing the PPI requires much more comprehensive learning architectures to distill the latent information from the entire sequences, and to preserve the long-term ordering information.

1.4 处理PPI任务上，基于深度学习的方法的发展：

（1）第一项工作是基于深层CNN
One recent work (Hashemifar et al., 2018), DPPI, uses a deep CNN-based architecture which focuses on capturing local features from protein profiles. DPPI represents the first work to deploy deep learning to PPI prediction, and has achieved the state-of-the-art performance on the binary prediction task. However, it requires excessive efforts for data