Skip to main content
Log in

DC programming and DCA for sparse Fisher linear discriminant analysis

  • Original Article
  • Published:
Neural Computing and Applications Aims and scope Submit manuscript

Abstract

We consider the supervised pattern classification in the high-dimensional setting, in which the number of features is much larger than the number of observations. We present a novel approach to the sparse Fisher linear discriminant problem using the \(\ell _0\)-norm. The resulting optimization problem is nonconvex, discontinuous and very hard to solve. We overcome the discontinuity by using appropriate approximations to the \(\ell _0\)-norm such that the resulting problems can be formulated as difference of convex functions (DC) programs to which DC programming and DC Algorithms (DCA) are investigated. The experimental results on both simulated and real datasets demonstrate the efficiency of the proposed algorithms compared to some state-of-the-art methods.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2

Similar content being viewed by others

Notes

  1. http://cran.r-project.org/.

References

  1. Alon U, Barkai N, Notterman DA, Gish K, Ybarra S, Mack D, Levine AJ (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci USA 96(12):6745–6750

    Article  Google Scholar 

  2. Bickel PJ, Levina E (2004) Some theory for Fisher’s linear discriminant function, naive Bayes, and some alternatives when there are many more variables than observations. Bernoulli 10(6):989–1010

    Article  MathSciNet  MATH  Google Scholar 

  3. Boyd S, Parikh N, Chu E, Peleato B, Eckstein J (2011) Distributed optimization and statistical learning via the alternating direction method of multipliers. Found. Trends Mach. Learn. 3(1):1–124

    Article  MATH  Google Scholar 

  4. Bradley PS, Mangasarian OL (1998) Feature selection via concave minimization and support vector machines. In: Proceeding of international conference on machine learning ICML98

  5. Chen X, Xu FM, Ye Y (2010) Lower bound theory of nonzero entries in solutions of l2-lp minimization. SIAM J Sci Comput 32(5):2832–2852

    Article  MathSciNet  MATH  Google Scholar 

  6. Cheng S, Le Thi HA (2013) Learning sparse classifiers with difference of convex functions algorithms. Optim Methods Softw 28(4):830–854

    Article  MathSciNet  MATH  Google Scholar 

  7. Clemmensen L, Hansen M, Ersboll B, Frisvad J (2007) A method for comparison of growth media in objective identification of penicillium based on multi-spectral imaging. J Microbiol Methods 69:249–255

    Article  Google Scholar 

  8. Clemmensen L, Hastie T, Witten D, Ersbøll B (2011) Sparse discriminant analysis. Technometrics 53(4):406–413

    Article  MathSciNet  Google Scholar 

  9. Collobert R, Sinz F, Weston J, Bottou L (2006) Trading convexity for scalability. In Proceedings of the 23rd international conference on machine learning, NY, USA, pp 201–208

  10. Fisher RA (1936) The use of multiple measurements in taxonomic problems. Ann Eugen 7:179–188

    Article  Google Scholar 

  11. Friedman J, Hastie T, Hoefling H, Tibshirani R (2007) Pathwise coordinate optimization. An Appl Stat 1:302–332

    Article  MathSciNet  MATH  Google Scholar 

  12. Gasso G, Rakotomamonjy A, Canu S (2009) Recovering sparse signals with a certain family of nonconvex penalties and dc programming. IEEE Trans Signal Process 57:4686–4698

    Article  MathSciNet  Google Scholar 

  13. Gordon GJ, Jensen RV, Hsiao LL, Gullans SR, Blumenstock JE, Ramaswamy S, Richards WG, Sugarbaker DJ, Bueno R (2002) Translation of microarray data into clinically relevant cancer diagnostic tests using gene expression ratios in lung cancer and mesothelioma. Cancer Res 62:4963–4967

    Google Scholar 

  14. Grosenick L, Greer S, Knutson B (2008) Interpretable classifiers for fmri improve prediction of purchases. IEEE Trans Neural Syst Rehabil Eng 16(6):539–547

    Article  Google Scholar 

  15. Guo Y, Hastie T, Tibshirani R (2007) Regularized linear discriminant analysis and its application in microarrays. Biostatistics 8(1):86–100

    Article  MATH  Google Scholar 

  16. Hastie T, Buja A, Tibshirani R (1995) Penalized discriminant analysis. Ann Stat 23(1):73–102

    Article  MathSciNet  MATH  Google Scholar 

  17. Hastie T, Tibshirani R, Friedman J (2009) The elements of statistical learning. Springer Verlag, New York

    Book  MATH  Google Scholar 

  18. Khan J, Wei JS, Ringner M, Saal LH, Ladanyi M, Westermann F, Berthold F, Schab M, Antonescu CR, Peterson C, Meltzer PS (2001) Classification and diagnostic prediction of cancers using expression profiling and artificial neural networks. Nat Med 7:673–679

    Article  Google Scholar 

  19. Krause N, Singer Y (2004) Leveraging the margin more carefully. In: Proceedings of the twenty first international conference on machine learning, NY, USA

  20. Krzanowski W, Jonathan P, Mccarthy W, Thomas M (1995) Discriminant analysis with singular covariance matrices: methods and applications to spectroscopic data. J R Stat Soc 44(1):101–115

    MATH  Google Scholar 

  21. Le Hoai M, Le Thi HA, Pham Dinh T, Huynh VN (2013) Block clustering based on difference of convex functions (DC) programming and DC algorithms. Neural Comput 25:259–278

    Article  MathSciNet  Google Scholar 

  22. Le Thi HA (2000) An efficient algorithm for globally minimizing a quadratic function under convex quadratic constraints. Math Program 87:401–426

    Article  MathSciNet  MATH  Google Scholar 

  23. Le Thi HA, Le Hoai M, Nguyen VV, Pham Dinh T (2008) A DC programming approach for feature selection in support vector machines learning. J Adv Data Anal Classif 2(3):259–278

    Article  MathSciNet  MATH  Google Scholar 

  24. Le Thi HA, Le Hoai M, Pham Dinh T (2007) Optimization based DC programming and DCA for hierarchical clustering. Eur J Oper Res 183:1067–1085

    Article  MathSciNet  MATH  Google Scholar 

  25. Le Thi HA, Le HM, Dinh TP (2014a) New and efficient DCA based algorithms for minimum sum-of-squares clustering. Pattern Recognit 47:388–401

    Article  MATH  Google Scholar 

  26. Le Thi HA, Le Hoai M, Pham Dinh T (2015a) Feature selection in machine learning: an exact penalty approach using a difference of convex function algorithm. Mach Learn 101:163–186

    Article  MathSciNet  MATH  Google Scholar 

  27. Le Thi HA, Nguyen MC (2014) Self-organizing maps by difference of convex functions optimization. Data Min Knowl Discov 28:1336–1365

    Article  MathSciNet  MATH  Google Scholar 

  28. Le Thi HA, Nguyen VV, Ouchani S (2009) Gene selection for cancer classification using DCA. J Front Comput Sci Technol 3:612–620

    Google Scholar 

  29. Le Thi HA, Pham Dinh T (2005) The DC (difference of convex functions) programming and DCA revisited with DC models of real world nonconvex optimization problems. Ann Oper Res 133:23–46

    Article  MathSciNet  MATH  Google Scholar 

  30. Le Thi HA, Pham Dinh T, Huynh VN (2012) Exact penalty and error bounds in DC programming. J Glob Optim 52(3):509–535

    Article  MathSciNet  MATH  Google Scholar 

  31. Le Thi HA, Pham Dinh T, Le Hoai M, Vo Xuan T (2015b) DC approximation approaches for sparse optimization. Eur J Oper Res 244:26–44

    Article  MathSciNet  MATH  Google Scholar 

  32. Le Thi HA, Vo Xuan T, Pham Dinh T (2014b) Feature selection for linear SVMs under uncertain data: robust optimization based on difference of convex functions algorithms. Neural Netw 59:36–50

    Article  MATH  Google Scholar 

  33. Leng C (2008) Sparse optimal scoring for multiclass cancer diagnosis and biomarker detection using microarray data. Comput Biol Chem 32:417–425

    Article  MathSciNet  MATH  Google Scholar 

  34. Liu Y, Shen X, Doss H (2005) Multicategory \(\psi \)-learning and support vector machine: computational tools. J Comput Graph Stat 14:219–236

    Article  MathSciNet  Google Scholar 

  35. Mai Q, Zou H (2013) A note on the connection and equivalence of three sparse linear discriminant analysis methods. Technometrics 55(2):243–246

    Article  MathSciNet  Google Scholar 

  36. Mai Q, Zou H, Yuan M (2012) A direct approach to sparse discriminant analysis in ultra-high dimensions. Biometrika 99(1):29–42

    Article  MathSciNet  MATH  Google Scholar 

  37. Mardia KV, Kent JT, Bibby JM (1979) Multivariate Analysis. Academic Press, London, New York, Toronto, Sydney, San Francisco

  38. Nakayama R, Nemoto T, Takahashi H, Ohta T, Kawai A, Yoshida T, Toyama Y, Ichikawa H, Hasegama T (2007) Gene expression analysis of soft tissue sarcomas: characterization and reclassification of malignant fibrous histiocytoma. Mod Pathol 20(7):749–759

    Article  Google Scholar 

  39. Neumann J, Schnorr G, Steidl G (2005) Combined SVM-based feature selection and classification. Mach Learn 61:129–150

    Article  MATH  Google Scholar 

  40. Peleg D, Meir R (2008) A bilinear formulation for vector sparsity optimization. Signal Process 88(2):375–389

    Article  MATH  Google Scholar 

  41. Pham Dinh T, Le Thi HA (1997) Convex analysis approach to D.C. programming: theory, algorithms and applications. Acta Math Vietnam 22(1):289–355

    MathSciNet  MATH  Google Scholar 

  42. Pham Dinh T, Le Thi HA (1998) A DC optimization algorithm for solving the trust-region subproblem. SIAM J Optim 8(2):476–505

    Article  MathSciNet  MATH  Google Scholar 

  43. Pham Dinh T, Le Thi HA (2014) Recent advances in dc programming and dca. Trans Comput Collect Intell 8342:1–37

    Google Scholar 

  44. Sun L, Hui A, Su Q, Vortmeyer A, Kotliarov Y, Pastorino S, Passaniti A, Menon J, Wlling J, Bailey R, Rosenblum M, Mikkelsen T, Fine H (2006) Neuronal and glioma-derived stem cell factor induces angiogenesis within the brain. Cancer Cell 9:287–300

    Article  Google Scholar 

  45. Tibshirani R (1996) Regression shrinkage and selection via the lasso. J R Stat Soc 58:267–288

    MathSciNet  MATH  Google Scholar 

  46. Tibshirani R, Hastie T, Narasimhan B, Chu G (2002) Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci 99:6567–6572

    Article  Google Scholar 

  47. Tibshirani R, Hastie T, Narasimhan B, Chu G (2003) Class prediction by nearest shrunken centroids, with applications to DNA microarrays. Stat Sci 18(1):104–117

    Article  MathSciNet  MATH  Google Scholar 

  48. Trendafilov NT, Jolliffe IT (2007) Dalass: Variable selection in discriminant analysis via the lasso. Comput Stat Data Anal 51:3718–3736

    Article  MathSciNet  MATH  Google Scholar 

  49. Witten D, Tibshirani R (2011) Penalized classification using Fisher’s linear discriminant. J R Stat Soc B 73:753–772

    Article  MathSciNet  MATH  Google Scholar 

  50. Wu M, Zhang L, Wang Z, Christiani D, Lin X (2009) Sparse linear discriminant analysis for simultaneous testing for the significance of a gene set/pathway and gene selection. Bioinformatics 25:1145–1151

    Article  Google Scholar 

  51. Xu P, Brock GN, Parrish RS (2009) Modified linear discriminant analysis approaches for classification of high-dimensional microarray data. Comput Stat Data Anal 53:1674–1687

    Article  MathSciNet  MATH  Google Scholar 

  52. Yeoh EJ, Ross ME, Shurtleff SA, Williams WK, Patel D, Mahfouz R, Behm FG, Raimondi SC, Relling MV, Patel A et al (2002) Classification, subtype discovery, and prediction of outcome in pediatric lymphoblastic leukemia by gene expression profiling. Cancer Cell 1:133–143

    Article  Google Scholar 

Download references

Acknowledgments

This research is funded by Foundation for Science and Technology Development of Ton Duc Thang University (FOSTECT), website: http://fostect.tdt.edu.vn, under Grant FOSTECT.2015.BR.15. The authors would like to thank the referees for their valuable comments which helped to improve the manuscript.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Hoai An Le Thi.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Le Thi, H.A., Phan, D.N. DC programming and DCA for sparse Fisher linear discriminant analysis. Neural Comput & Applic 28, 2809–2822 (2017). https://doi.org/10.1007/s00521-016-2216-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00521-016-2216-9

Keywords

Navigation