Please use this identifier to cite or link to this item: http://hdl.handle.net/20.500.11861/7409
Title: Improving prediction of phenotypic drug response on cancer cell lines using deep convolutional network
Authors: Liu, Pengfei 
Li, Hongjian 
Li, Shuai 
Prof. LEUNG Kwong Sak 
Issue Date: Jul-2019
Source: BMC Bioinformatics, 2019, vol. 20, article no. 408.
Journal: BMC Bioinformatics 
Abstract: Background Understanding the phenotypic drug response on cancer cell lines plays a vital role in anti-cancer drug discovery and re-purposing. The Genomics of Drug Sensitivity in Cancer (GDSC) database provides open data for researchers in phenotypic screening to build and test their models. Previously, most research in these areas starts from the molecular fingerprints or physiochemical features of drugs, instead of their structures. Results In this paper, a model called twin Convolutional Neural Network for drugs in SMILES format (tCNNS) is introduced for phenotypic screening. tCNNS uses a convolutional network to extract features for drugs from their simplified molecular input line entry specification (SMILES) format and uses another convolutional network to extract features for cancer cell lines from the genetic feature vectors respectively. After that, a fully connected network is used to predict the interaction between the drugs and the cancer cell lines. When the training set and the testing set are divided based on the interaction pairs between drugs and cell lines, tCNNS achieves 0.826, 0.831 for the mean and top quartile of the coefficient of determinant (R2) respectively and 0.909, 0.912 for the mean and top quartile of the Pearson correlation (Rp) respectively, which are significantly better than those of the previous works (Ammad-Ud-Din et al., J Chem Inf Model 54:2347–9, 2014), (Haider et al., PLoS ONE 10:0144490, 2015), (Menden et al., PLoS ONE 8:61318, 2013). However, when the training set and the testing set are divided exclusively based on drugs or cell lines, the performance of tCNNS decreases significantly and Rp and R2 drop to barely above 0. Conclusions Our approach is able to predict the drug effects on cancer cell lines with high accuracy, and its performance remains stable with less but high-quality data, and with fewer features for the cancer cell lines. tCNNS can also solve the problem of outliers in other feature space. Besides achieving high scores in these statistical metrics, tCNNS also provides some insights into the phenotypic screening. However, the performance of tCNNS drops in the blind test.
Type: Peer Reviewed Journal Article
URI: http://hdl.handle.net/20.500.11861/7409
DOI: 10.1186/s12859-019-2910-6
Appears in Collections:Applied Data Science - Publication

Show full item record

SCOPUSTM   
Citations

101
checked on Dec 15, 2024

Page view(s)

41
Last Week
0
Last month
checked on Dec 20, 2024

Google ScholarTM

Impact Indices

Altmetric

PlumX

Metrics


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.