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PIntMF: Penalized Integrative Matrix Factorization Method for Multi-Omics Data
- Source :
- Bioinformatics
- Publication Year :
- 2021
-
Abstract
- Motivation It is more and more common to perform multi-omics analyses to explore the genome at diverse levels and not only at a single level. Through integrative statistical methods, multi-omics data have the power to reveal new biological processes, potential biomarkers and subgroups in a cohort. Matrix factorization (MF) is an unsupervised statistical method that allows a clustering of individuals, but also reveals relevant omics variables from the various blocks. Results Here, we present PIntMF (Penalized Integrative Matrix Factorization), an MF model with sparsity, positivity and equality constraints. To induce sparsity in the model, we used a classical Lasso penalization on variable and individual matrices. For the matrix of samples, sparsity helps in the clustering, while normalization (matching an equality constraint) of inferred coefficients is added to improve interpretation. Moreover, we added an automatic tuning of the sparsity parameters using the famous glmnet package. We also proposed three criteria to help the user to choose the number of latent variables. PIntMF was compared with other state-of-the-art integrative methods including feature selection techniques in both synthetic and real data. PIntMF succeeds in finding relevant clusters as well as variables in two types of simulated data (correlated and uncorrelated). Next, PIntMF was applied to two real datasets (Diet and cancer), and it revealed interpretable clusters linked to available clinical data. Our method outperforms the existing ones on two criteria (clustering and variable selection). We show that PIntMF is an easy, fast and powerful tool to extract patterns and cluster samples from multi-omics data. Availability and implementation An R package is available at https://github.com/mpierrejean/pintmf. Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects :
- Statistics and Probability
Normalization (statistics)
FOS: Computer and information sciences
AcademicSubjects/SCI01060
Computer science
Feature selection
Latent variable
computer.software_genre
Biochemistry
Statistics - Applications
Matrix decomposition
Methodology (stat.ME)
03 medical and health sciences
Matrix (mathematics)
0302 clinical medicine
Lasso (statistics)
[MATH.MATH-ST]Mathematics [math]/Statistics [math.ST]
Applications (stat.AP)
Cluster analysis
Molecular Biology
Statistics - Methodology
030304 developmental biology
0303 health sciences
[STAT.AP]Statistics [stat]/Applications [stat.AP]
Genome Analysis
Original Papers
Computer Science Applications
Constraint (information theory)
Computational Mathematics
Computational Theory and Mathematics
030220 oncology & carcinogenesis
Data mining
computer
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Bioinformatics
- Accession number :
- edsair.doi.dedup.....2160fc0ae19cfab28bf68bc732b59a2c