Bidirectional compressive sensing for classification of gene expression data
Xiaohua Xu
Department of Computer Science, Yangzhou University, Yangzhou, China
Search for more papers by this authorBaichuan Fan
Department of Computer Science, Yangzhou University, Yangzhou, China
Search for more papers by this authorCorresponding Author
Ping He
Department of Computer Science, Yangzhou University, Yangzhou, China
Ping He, Department of Computer Science, Yangzhou University, Yangzhou 225000, China.
Email: [email protected]
Search for more papers by this authorYali Liang
Department of Computer Science, Yangzhou University, Yangzhou, China
Search for more papers by this authorJie Ding
Department of Computer Science, Yangzhou University, Yangzhou, China
Search for more papers by this authorYuan Lou
Department of Computer Science, Yangzhou University, Yangzhou, China
Search for more papers by this authorZhijun Zhang
Department of Computer Science, Yangzhou University, Yangzhou, China
Search for more papers by this authorXincheng Chang
Department of Computer Science, Yangzhou University, Yangzhou, China
Search for more papers by this authorXiaohua Xu
Department of Computer Science, Yangzhou University, Yangzhou, China
Search for more papers by this authorBaichuan Fan
Department of Computer Science, Yangzhou University, Yangzhou, China
Search for more papers by this authorCorresponding Author
Ping He
Department of Computer Science, Yangzhou University, Yangzhou, China
Ping He, Department of Computer Science, Yangzhou University, Yangzhou 225000, China.
Email: [email protected]
Search for more papers by this authorYali Liang
Department of Computer Science, Yangzhou University, Yangzhou, China
Search for more papers by this authorJie Ding
Department of Computer Science, Yangzhou University, Yangzhou, China
Search for more papers by this authorYuan Lou
Department of Computer Science, Yangzhou University, Yangzhou, China
Search for more papers by this authorZhijun Zhang
Department of Computer Science, Yangzhou University, Yangzhou, China
Search for more papers by this authorXincheng Chang
Department of Computer Science, Yangzhou University, Yangzhou, China
Search for more papers by this authorPresent Address:
Jie Ding, China Institute of FTZ Supply Chain, Shanghai Maritime University, Shanghai, China
Summary
The classification of gene expression data is significantly important for medical diagnosis. In recent years, compressive sensing emerges as a popular sparse learning method and has been applied in different areas. It is featured with the sparse representation of data with a few atoms in the dictionary. However, the traditional compressive sensing model only focuses on the relationship among different samples but neglects the relationship among different genes. In order to take into account of the both kinds of correlation, we propose a novel bidirectional compressive sensing model for the classification of gene expression data. Under this model, we develop a novel Bi-ADMM algorithm with three different variants to solve the optimization problem. The promising experimental results on the real-world gene expression datasets demonstrate both the effectiveness and efficiency of our proposed approach.
REFERENCES
- 1Zhang Y, Gravina R, Lu H, Villari M, Fortino G. PEA: parallel electrocardiogram-based authentication for smart healthcare systems. J Netw Comput Appl. 2018; 117: 10-16.
- 2Chen M, Shi X, Zhang Y, Wu D, Guizani M. Deep features learning for medical image analysis with convolutional autoencoder neural network. IEEE Trans Big Data. 2017; PP(1): 1-1.
- 3Wolf FA, Angerer P, Theis FJ. SCANPY: large-scale single-cell gene expression data analysis. Genome Biology. 2018; 19(1): 15.
- 4Chatterjee S, Hore S, Dey N, Chakraborty S, Ashour AS. Dengue fever classification using gene expression data: a PSO based artificial neural network approach. In: Proceedings of the 5th International Conference on Frontiers in Intelligent Computing: Theory and Applications: FICTA 2016, Volume 2. Singapore: Springer Nature Singapore Pte Ltd; 2017: 331-341.
10.1007/978-981-10-3156-4_34 Google Scholar
- 5Monika R, Dhanalakshmi S, Sreejith S. Coefficient random permutation based compressed sensing for medical image compression. In: Advances in Electronics, Communication and Computing: ETAEERE-2016. Singapore: Springer Nature Singapore Pte Ltd; 2018: 529-536.
10.1007/978-981-10-4765-7_56 Google Scholar
- 6Gibson RM, Amira A, Ramzan N, Casaseca-de-la-Higuera P, Pervez Z. Matching pursuit-based compressive sensing in a wearable biomedical accelerometer fall diagnosis device. Biomed Signal Process Control. 2017; 33: 96-108.
- 7Peller J, Thompson KJ, Siddiqui I, Martinie J, Iannitti DA, Trammell SR. Hyperspectral imaging based on compressive sensing to determine cancer margins in human pancreatic tissue ex vivo. In: Proceedings Vol 10060, Optical Biopsy XV: Toward Real-Time Spectroscopic Imaging and Diagnosis; 2017; San Francisco, CA.
- 8Bioucas-Dias JM, Figueiredo MAT. Alternating direction algorithms for constrained sparse regression: application to hyperspectral unmixing. Paper presented at: 2010 2nd Workshop on Hyperspectral Image and Signal Processing: Evolution in Remote Sensing (WHISPERS); 2010; Reykjavik, Iceland.
- 9Boyd S, Parikh N, Chu E, Peleato B, Eckstein J. Distributed optimization and statistical learning via the alternating direction method of multipliers. Found Trends Mach Learn. 2011; 3(1): 1-122.
- 10Lu H, Li Y, Mu S, Wang D, Kim H, Serikawa S. Motor anomaly detection for unmanned aerial vehicles using reinforcement learning. IEEE Internet Things J. 2018; 5(4): 2315-2322.
- 11Lu H, Li Y, Chen M, Kim H, Serikawa S. Brain intelligence: go beyond artificial intelligence. Mob Netw Appl. 2018; 23(2): 368-375.
- 12Lu H, Li B, Zhu J, et al. Wound intensity correction and segmentation with convolutional neural networks. Concurrency Computat Pract Exper. 2017; 29(6): e3927.
- 13van't Veer LJ, Dai H, van de Vijver MJ, et al. Expression profiling predicts outcome in breast cancer. Breast Cancer Res. 2002; 5(1): 57.
- 14Bhattacharjee A, Richards WG, Staunton J, et al. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci. 2001; 98(24): 13790-13795.
- 15Singh D, Febbo PG, Ross K, et al. Gene expression correlates of clinical prostate cancer behavior. Cancer Cell. 2002; 1(2): 203-209.
- 16Shipp MA, Ross KN, Tamayo P, et al. Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med. 2002; 8(1): 68.
- 17Horaira MA, Ahmed MS, Kabir MH, Mollah MNH, Shah MAR. Colon cancer prediction from gene expression profiles using kernel based support vector machine. Paper presented at: 2018 International Conference on Computer, Communication, Chemical, Material and Electronic Engineering (IC4ME2); 2018; Rajshahi, Bangladesh.
- 18Ludwig SA, Picek S, Jakobovic D. Classification of cancer data: analyzing gene expression data using a fuzzy decision tree algorithm. In: Operations Research Applications in Health Care Management. Cham, Switzerland: Springer International Publishing AG; 2018: 327-347.
10.1007/978-3-319-65455-3_13 Google Scholar
- 19Mehmood R, El-Ashram S, Bie R, Dawood H, Kos A. Clustering by fast search and merge of local density peaks for gene expression microarray data. Sci Rep. 2017; 7: 45602.
- 20Donoho DL, Elad M. Optimally sparse representation in general (nonorthogonal) dictionaries via š1 minimization. Proc Natl Acad Sci. 2003; 100(5): 2197-2202.
- 21Wright J, Yang AY, Ganesh A, Sastry SS, Ma Y. Robust face recognition via sparse representation. IEEE Trans Pattern Anal Mach Intell. 2009; 31(2): 210-227.
- 22Ding C, Zhou D, He X, Zha H. R1-PCA: rotational invariant L1-norm principal component analysis for robust subspace factorization. In: Proceedings of the 23rd International Conference on Machine learning (ICML); 2006; Pittsburgh, PA.
- 23Kolali KM, Bazrafkan M. A novel sparse coding algorithm for classification of tumors based on gene expression data. Med Biol Eng Comput. 2016; 54(6): 869-876.
- 24Iliadis M, Spinoulas L, Berahas AS, Wang H, Katsaggelos AK. Sparse representation and least squares-based classification in face recognition. In: Proceedings of the 2014 22nd European Signal Processing Conference (EUSIPCO); 2014; Lisbon, Portugal.
- 25Li W, Liao B, Zhu W, et al. Maxdenominator reweighted sparse representation for tumor classification. Sci Rep. 2017; 7: 46030.
- 26Jiang X, Lai J. Sparse and dense hybrid representation via dictionary decomposition for face recognition. IEEE Trans Pattern Anal Mach Intell. 2015; 37(5): 1067-1079.
- 27Durif G, Modolo L, Michaelsson J, Mold JE, Lambert-Lacroix S, Picard F. High dimensional classification with combined adaptive sparse PLS and logistic regression. Bioinformatics. 2018; 34(3): 485-493.
- 28Wang J, Guo Y, Guo J, Luo X, Kong X. Class-aware analysis dictionary learning for pattern classification. IEEE Signal Process Lett. 2017; 24(12): 1822-1826.
- 29Donoho DL. Compressed sensing. IEEE Trans Inf Theory. 2006; 52(4): 1289-1306.
- 30CandĆØs EJ, Wakin MB. An introduction to compressive sampling. IEEE Signal Process Mag. 2008; 25(2): 21-30.
- 31Tropp JA, Gilbert AC. Signal recovery from random measurements via orthogonal matching pursuit. IEEE Trans Inf Theory. 2007; 53(12): 4655-4666.
- 32Alizadeh F, Goldfarb D. Second-order cone programming. Math Program. 2003; 95(1): 3-51.
- 33Chen SS, Donoho DL, Saunders MA. Atomic decomposition by basis pursuit. SIAM Rev. 2001; 43(1): 129-159.