Learning rule sets from survival data

• Published in: BMC bioinformatics 2017-05, Vol.18 (1), p.285-285, Article 285
• Main Authors: Wróbel, Łukasz, Gudyś, Adam, Sikora, Marek
• Format: Article
• Language: English
• Subjects: Algorithms; Artificial intelligence; Aversion learning; Bioinformatics; Bone marrow; Breast cancer; Breast Neoplasms - metabolism; Breast Neoplasms - mortality; Breast Neoplasms - pathology; Cancer; Case studies; Classification; Data analysis; Data mining; Data processing; Datasets; Deoxyribonucleic acid; Design of experiments; Diseases; DNA; DNA Copy Number Variations; DNA Methylation; Esophagus; Female; Gene expression; Genes; Genomes; High throughput sequencing; Humans; Kaplan-Meier Estimate; Learning; Leukemia; Log-rank test; Lungs; Medicine; Methods; MicroRNAs - metabolism; miRNA; Neural networks; Patients; Polymorphism, Single Nucleotide; Problem solving; Proteomics; Reasoning; Rule induction; Separate-and-conquer; Serial learning; Studies; Survival; Survival analysis; Thyroid; Thyroid gland; Transcription; Transcriptome
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-017-1693-x

Survival analysis is an important element of reasoning from data. Applied in a number of fields, it has become particularly useful in medicine to estimate the survival rate of patients on the basis of their condition, examination results, and undergoing treatment. The recent developments in the next generation sequencing open new opportunities in survival study as they allow vast amount of genome-, transcriptome-, and proteome-related features to be investigated. These include single nucleotide and structural variants, expressions of genes and microRNAs, DNA methylation, and many others. We present LR-Rules, a new algorithm for rule induction from survival data. It works according to the separate-and-conquer heuristics with a use of log-rank test for establishing rule body. Extensive experiments show LR-Rules to generate models of superior accuracy and comprehensibility. The detailed analysis of rules rendered by the presented algorithm on four medical datasets concerning leukemia as well as breast, lung, and thyroid cancers, reveals the ability to discover true relations between attributes and patients' survival rate. Two of the case studies incorporate features obtained with a use of high throughput technologies showing the usability of the algorithm in the analysis of bioinformatics data. LR-Rules is a viable alternative to existing approaches to survival analysis, particularly when the interpretability of a resulting model is crucial. Presented algorithm may be especially useful when applied on the genomic and proteomic data as it may contribute to the better understanding of the background of diseases and support their treatments.