Cyclednn-a novel deep neural network model for cetsa feature prediction cross cell lines

Z Zeng, S Zhao, Q Da, P Qian… - 2022 44th Annual …, 2022 - ieeexplore.ieee.org
2022 44th Annual International Conference of the IEEE Engineering …, 2022ieeexplore.ieee.org
Cellular Thermal Shift Assay (CETSA) has been widely used in drug discovery, cancer cell
biology, immunology, etc. One of the barriers for CETSA applications is that CETSA
experiments have to be conducted on various cell lines, which is extremely time-consuming
and costly. In this study, we make an effort to explore the translation of CETSA features cross
cell lines, ie, known CETSA feature of a given protein in one cell line, can we automatically
predict the CETSA feature of this protein in another cell line, and vice versa? Inspired by …
Cellular Thermal Shift Assay (CETSA) has been widely used in drug discovery, cancer cell biology, immunology, etc. One of the barriers for CETSA applications is that CETSA experiments have to be conducted on various cell lines, which is extremely time-consuming and costly. In this study, we make an effort to explore the translation of CETSA features cross cell lines, i.e., known CETSA feature of a given protein in one cell line, can we automatically predict the CETSA feature of this protein in another cell line, and vice versa? Inspired by pix2pix and CycleGAN, which perform well on image-to-image translation cross various domains in computer vision, we propose a novel deep neural network model called CycleDNN for CETSA feature translation cross cell lines. Given cell lines and B, the proposed CycleDNN consists of two auto-encoders, the first one encodes the CETSA feature from cell line into in the latent space , then decodes into the CETSA feature in cell line ., Similarly, the second one translates the CETSA feature from cell line to cell line through the latent space . In such a way, the two auto-encoders form a cyclic feature translation between cell lines. The reconstructed loss, cycle-consistency loss, and latent vector regularization loss are used to guide the training of the model. The experimental results on a public CETSA dataset demonstrate the effectiveness of the proposed approach.
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