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基于神经网络的预测抗肿瘤药物反应的方法(NeuPD-A)

NeuPD-A Neural Network-Based Approach to Predict Antineoplastic Drug Response.

作者信息

Shahzad Muhammad, Tahir Muhammad Atif, Alhussein Musaed, Mobin Ansharah, Shams Malick Rauf Ahmed, Anwar Muhammad Shahid

机构信息

FAST School of Computing, National University of Computer and Emerging Sciences (NUCES-FAST), Karachi 75030, Pakistan.

Department of Computer Engineering, College of Computer and Information Sciences, King Saud University, P.O. Box 51178, Riyadh 11543, Saudi Arabia.

出版信息

Diagnostics (Basel). 2023 Jun 13;13(12):2043. doi: 10.3390/diagnostics13122043.

Abstract

With the beginning of the high-throughput screening, in silico-based drug response analysis has opened lots of research avenues in the field of personalized medicine. For a decade, many different predicting techniques have been recommended for the antineoplastic (anti-cancer) drug response, but still, there is a need for improvements in drug sensitivity prediction. The intent of this research study is to propose a framework, namely to validate the potential anti-cancer drugs against a panel of cancer cell lines in publicly available datasets. The datasets used in this work are Genomics of Drug Sensitivity in Cancer (GDSC) and Cancer Cell Line Encyclopedia (CCLE). As not all drugs are effective on cancer cell lines, we have worked on 10 essential drugs from the GDSC dataset that have achieved the best modeling results in previous studies. We also extracted 1610 essential oncogene expressions from 983 cell lines from the same dataset. Whereas, from the CCLE dataset, 16,383 gene expressions from 1037 cell lines and 24 drugs have been used in our experiments. For dimensionality reduction, Pearson correlation is applied to best fit the model. We integrate the genomic features of cell lines and drugs' fingerprints to fit the neural network model. For evaluation of the proposed framework, we have used repeated K-fold cross-validation with 5 times repeats where K = 10 to demonstrate the performance in terms of root mean square error (RMSE) and coefficient determination (R). The results obtained on the GDSC dataset that were measured using these cost functions show that our proposed framework has outperformed existing approaches with an RMSE of 0.490 and R of 0.929.

摘要

随着高通量筛选的兴起,基于计算机模拟的药物反应分析在个性化医疗领域开辟了许多研究途径。十年来,针对抗肿瘤(抗癌)药物反应推荐了许多不同的预测技术,但药物敏感性预测仍有改进的空间。本研究的目的是提出一个框架,即在公开可用的数据集中针对一组癌细胞系验证潜在的抗癌药物。本研究使用的数据集是癌症药物敏感性基因组学(GDSC)和癌细胞系百科全书(CCLE)。由于并非所有药物对癌细胞系都有效,我们研究了GDSC数据集中的10种基本药物,这些药物在先前的研究中取得了最佳的建模结果。我们还从同一数据集中的983个细胞系中提取了1610个基本癌基因表达。而在CCLE数据集中,我们的实验使用了来自1037个细胞系的16383个基因表达和24种药物。为了进行降维,应用Pearson相关性以最佳拟合模型。我们整合细胞系的基因组特征和药物的指纹图谱以拟合神经网络模型。为了评估所提出的框架,我们使用了重复5次的K折交叉验证,其中K = 10,以均方根误差(RMSE)和决定系数(R)来展示性能。使用这些成本函数在GDSC数据集上获得的结果表明,我们提出的框架优于现有方法,RMSE为0.490,R为0.929。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5e4/10297062/977052a05029/diagnostics-13-02043-g001.jpg

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