Identifying molecular cancer subtypes from multi-omics data is an important step in the personalized medicine. We introduce CancerSubtypes, an R package for identifying cancer subtypes using multi-omics data, including gene expression, miRNA expression and DNA methylation data. CancerSubtypes integrates four main computational methods which are highly cited for cancer subtype identification and provides a standardized framework for data pre-processing, feature selection, and result follow-up analyses, including results computing, biology validation and visualization. The input and output of each step in the framework are packaged in the same data format, making it convenience to compare different methods. The package is useful for inferring cancer subtypes from an input genomic dataset, comparing the predictions from different well-known methods and testing new subtype discovery methods, as shown with different application scenarios in the Supplementary Material . The package is implemented in R and available under GPL-2 license from the Bioconductor website (http://bioconductor.org/packages/CancerSubtypes/). Supplementary data are available at Bioinformatics online.

Discovering causal relationships from observational data is a crucial problem and it has applications in many research areas. The PC algorithm is the state-of-the-art constraint based method for causal discovery. However, runtime of the PC algorithm, in the worst-case, is exponential to the number of nodes (variables), and thus it is inefficient when being applied to high dimensional data, e.g., gene expression datasets. On another note, the advancement of computer hardware in the last decade has resulted in the widespread availability of multi-core personal computers. There is a significant motivation for designing a parallelized PC algorithm that is suitable for personal computers and does not require end users' parallel computing knowledge beyond their competency in using the PC algorithm. In this paper, we develop parallel-PC, a fast and memory efficient PC algorithm using the parallel computing technique. We apply our method to a range of synthetic and real-world high dimensional datasets. Experimental results on a dataset from the DREAM 5 challenge show that the original PC algorithm could not produce any results after running more than 24 hours; meanwhile, our parallel-PC algorithm managed to finish within around 12 hours with a 4-core CPU computer, and less than six hours with a 8-core CPU computer. Furthermore, we integrate parallel-PC into a causal inference method for inferring miRNA-mRNA regulatory relationships. The experimental results show that parallel-PC helps improve both the efficiency and accuracy of the causal inference algorithm.

Causal feature selection has attracted much attention in recent years, as the causal features selected imply the causal mechanism related to the class attribute, leading to more reliable prediction models built using them. Currently there is a need of developing multi-source feature selection methods, since in many applications data for studying the same problem has been collected from various sources, such as multiple gene expression datasets obtained from different experiments for studying the causes of the same disease. However, the state-of-the-art causal feature selection methods generally tackle a single dataset, and a direct application of the methods to multiple datasets will result in unreliable results as the datasets may have different distributions. To address the challenges, by utilizing the concept of causal invariance in causal inference, we firstly formulate the problem of causal feature selection with multiple datasets as a search problem for an invariant set across the datasets, then give the upper and lower bounds of the invariant set, and finally we propose a new Multi-source Causal Feature Selection algorithm, MCFS. Using synthetic and real world datasets and 16 feature selection methods, the extensive experiments have validated the effectiveness of MCFS.

In this article, we aim to develop a unified view of causal and non-causal feature selection methods. The unified view will fill in the gap in the research of the relation between the two types of methods. Based on the Bayesian network framework and information theory, we first show that causal and non-causal feature selection methods share the same objective. That is to find the Markov blanket of a class attribute, the theoretically optimal feature set for classification. We then examine the assumptions made by causal and non-causal feature selection methods when searching for the optimal feature set, and unify the assumptions by mapping them to the restrictions on the structure of the Bayesian network model of the studied problem. We further analyze in detail how the structural assumptions lead to the different levels of approximations employed by the methods in their search, which then result in the approximations in the feature sets found by the methods with respect to the optimal feature set. With the unified view, we can interpret the output of non-causal methods from a causal perspective and derive the error bounds of both types of methods. Finally, we present practical understanding of the relation between causal and non-causal methods using extensive experiments with synthetic data and various types of real-world data.