A tree-like Bayesian structure learning algorithm for small-sample datasets from complex biological model systems

Enhanced virtual sample generation based on manifold features: Applications to developing soft sensor using small data

In the process industry, it is essential to establish a data-driven soft sensor to predict the key variable that is difficult to online measure directly. The accuracy performance of data-driven soft sensors relies heavily on data. Unfortunately, it is hard to acquire sufficient and informative data from the samples with limited number, which is called as the small sample problem. For handling the small sample problem, it is a good solution to generating virtual samples according to the distribution of original data. This paper proposes an enhanced method of virtual sample generation utilizing manifold features to develop soft sensors using small data. First, T-Distribution Stochastic Neighbor Embedding (t-SNE) is utilized to extract the features of input data. The main idea of generating virtual samples is to use the interpolation algorithm to obtain virtual t-SNE input features and then the random forest algorithm is utilized to get the virtual outputs using virtual t-SNE input features. Finally, virtual samples using the proposed t-SNE based virtual sample generation (t-SNE-VSG) can be achieved. For the sake of confirming the effectiveness and feasibility of the presented t-SNE-VSG, a standard data set is first used. What is more, a small data set from an actual industrial process of Purified Terephthalic Acid is used to establish a soft sensor model. The results from simulations show that the accuracy performance of the soft sensor established with small data can be effectively improved by adding the virtual samples generated by t-SNE-VSG. In addition, t-SNE-VSG achieves superior accuracy to state-of-the-art virtual sample generation methods.

New Algorithm and Software (BNOmics) for Inferring and Visualizing Bayesian Networks from Heterogeneous Big Biological and Genetic Data

Bayesian network (BN) reconstruction is a prototypical systems biology data analysis approach that has been successfully used to reverse engineer and model networks reflecting different layers of biological organization (ranging from genetic to epigenetic to cellular pathway to metabolomic). It is especially relevant in the context of modern (ongoing and prospective) studies that generate heterogeneous high-throughput omics datasets. However, there are both theoretical and practical obstacles to the seamless application of BN modeling to such big data, including computational inefficiency of optimal BN structure search algorithms, ambiguity in data discretization, mixing data types, imputation and validation, and, in general, limited scalability in both reconstruction and visualization of BNs. To overcome these and other obstacles, we present BNOmics, an improved algorithm and software toolkit for inferring and analyzing BNs from omics datasets. BNOmics aims at comprehensive systems biology—type data exploration, including both generating new biological hypothesis and testing and validating the existing ones. Novel aspects of the algorithm center around increasing scalability and applicability to varying data types (with different explicit and implicit distributional assumptions) within the same analysis framework. An output and visualization interface to widely available graph-rendering software is also included. Three diverse applications are detailed. BNOmics was originally developed in the context of genetic epidemiology data and is being continuously optimized to keep pace with the ever-increasing inflow of available large-scale omics datasets. As such, the software scalability and usability on the less than exotic computer hardware are a priority, as well as the applicability of the algorithm and software to the heterogeneous datasets containing many data types—single-nucleotide polymorphisms and other genetic/epigenetic/transcriptome variables, metabolite levels, epidemiological variables, endpoints, and phenotypes, etc.