A Reliability-Based Multisensor Data Fusion with Application in Target Classification.

The theory of belief functions has been extensively utilized in many practical applications involving decision making. One such application is the classification of target based on the pieces of information extracted from the individual attributes describing the target. Each piece of information is usually modeled as the basic probability assignment (BPA), also known as the mass function. The determination of the BPA has remained an open problem. Although fuzzy membership functions such as triangular and Gaussian functions have been widely used to model the likelihood estimation function based on the historical data, it has been observed that less emphasis has been placed on the impact of the spread of the membership function on the decision accuracy of the reasoning process. Conflict in the combination of BPAs may arise due to poor characterization of fuzzy membership functions to induce belief mass. In this work, we propose a multisensor data fusion within the framework of belief theory for target classification where shape/spread of the membership function is adjusted during the training/modeling stage to improve on the classification accuracy while removing the need for the computation of the credibility. To further enhance the performance of the proposed method, the reliability factor is deployed not only to effectively manage the possible conflict among participating bodies of evidence for better decision accuracy but also to reduce the number of sources for improved efficiency. The effectiveness of the proposed method was evaluated using both the real-world and the artificial datasets.

Identifying time-delayed gene regulatory networks via an evolvable hierarchical recurrent neural network.

BACKGROUND: The modeling of genetic interactions within a cell is crucial for a basic understanding of physiology and for applied areas such as drug design. Interactions in gene regulatory networks (GRNs) include effects of transcription factors, repressors, small metabolites, and microRNA species. In addition, the effects of regulatory interactions are not always simultaneous, but can occur after a finite time delay, or as a combined outcome of simultaneous and time delayed interactions. Powerful biotechnologies have been rapidly and successfully measuring levels of genetic expression to illuminate different states of biological systems. This has led to an ensuing challenge to improve the identification of specific regulatory mechanisms through regulatory network reconstructions. Solutions to this challenge will ultimately help to spur forward efforts based on the usage of regulatory network reconstructions in systems biology applications. METHODS: We have developed a hierarchical recurrent neural network (HRNN) that identifies time-delayed gene interactions using time-course data. A customized genetic algorithm (GA) was used to optimize hierarchical connectivity of regulatory genes and a target gene. The proposed design provides a non-fully connected network with the flexibility of using recurrent connections inside the network. These features and the non-linearity of the HRNN facilitate the process of identifying temporal patterns of a GRN. RESULTS: Our HRNN method was implemented with the Python language. It was first evaluated on simulated data representing linear and nonlinear time-delayed gene-gene interaction models across a range of network sizes and variances of noise. We then further demonstrated the capability of our method in reconstructing GRNs of the Saccharomyces cerevisiae synthetic network for in vivo benchmarking of reverse-engineering and modeling approaches (IRMA). We compared the performance of our method to TD-ARACNE, HCC-CLINDE, TSNI and ebdbNet across different network sizes and levels of stochastic noise. We found our HRNN method to be superior in terms of accuracy for nonlinear data sets with higher amounts of noise. CONCLUSIONS: The proposed method identifies time-delayed gene-gene interactions of GRNs. The topology-based advancement of our HRNN worked as expected by more effectively modeling nonlinear data sets. As a non-fully connected network, an added benefit to HRNN was how it helped to find the few genes which regulated the target gene over different time delays.

Stable Gene Regulatory Network Modeling From Steady-State Data.

Gene regulatory networks represent an abstract mapping of gene regulations in living cells. They aim to capture dependencies among molecular entities such as transcription factors, proteins and metabolites. In most applications, the regulatory network structure is unknown, and has to be reverse engineered from experimental data consisting of expression levels of the genes usually measured as messenger RNA concentrations in microarray experiments. Steady-state gene expression data are obtained from measurements of the variations in expression activity following the application of small perturbations to equilibrium states in genetic perturbation experiments. In this paper, the least absolute shrinkage and selection operator-vector autoregressive (LASSO-VAR) originally proposed for the analysis of economic time series data is adapted to include a stability constraint for the recovery of a sparse and stable regulatory network that describes data obtained from noisy perturbation experiments. The approach is applied to real experimental data obtained for the SOS pathway in Escherichia coli and the cell cycle pathway for yeast Saccharomyces cerevisiae. Significant features of this method are the ability to recover networks without inputting prior knowledge of the network topology, and the ability to be efficiently applied to large scale networks due to the convex nature of the method.