Multi-learner based recursive supervised training

In this paper, we propose the Multi-Learner Based Recursive Supervised Training (MLRT) algorithm which uses the existing framework of recursive task decomposition, by training the entire dataset, picking out the best learnt patterns, and then repeating the process with the remaining patterns. Instead of having a single learner to classify all datasets during each recursion, an appropriate learner is chosen from a set of three learners, based on the subset of data being trained, thereby avoiding the time overhead associated with the genetic algorithm learner utilized in previous approaches. In this way MLRT seeks to identify the inherent characteristics of the dataset, and utilize it to train the data accurately and efficiently. We observed that empirically, MLRT performs considerably well as compared to RPHP and other systems on benchmark data with 11% improvement in accuracy on the SPAM dataset and comparable performances on the VOWEL and the TWO-SPIRAL problems. In addition, for most datasets, the time taken by MLRT is considerably lower than the other systems with comparable accuracy. Two heuristic versions, MLRT-2 and MLRT-3 are also introduced to improve the efficiency in the system, and to make it more scalable for future updates. The performance in these versions is similar to the original MLRT system

Towards the Evolution of Multi-Layered Neural Networks: A Dynamic Structured Grammatical Evolution Approach

Current grammar-based NeuroEvolution approaches have several shortcomings. On the one hand, they do not allow the generation of Artificial Neural Networks (ANNs composed of more than one hidden-layer. On the other, there is no way to evolve networks with more than one output neuron. To properly evolve ANNs with more than one hidden-layer and multiple output nodes there is the need to know the number of neurons available in previous layers. In this paper we introduce Dynamic Structured Grammatical Evolution (DSGE): a new genotypic representation that overcomes the aforementioned limitations. By enabling the creation of dynamic rules that specify the connection possibilities of each neuron, the methodology enables the evolution of multi-layered ANNs with more than one output neuron. Results in different classification problems show that DSGE evolves effective single and multi-layered ANNs, with a varying number of output neurons

Adaptive inferential sensors based on evolving fuzzy models

A new technique to the design and use of inferential sensors in the process industry is proposed in this paper, which is based on the recently introduced concept of evolving fuzzy models (EFMs). They address the challenge that the modern process industry faces today, namely, to develop such adaptive and self-calibrating online inferential sensors that reduce the maintenance costs while keeping the high precision and interpretability/transparency. The proposed new methodology makes possible inferential sensors to recalibrate automatically, which reduces significantly the life-cycle efforts for their maintenance. This is achieved by the adaptive and flexible open-structure EFM used. The novelty of this paper lies in the following: (1) the overall concept of inferential sensors with evolving and self-developing structure from the data streams; (2) the new methodology for online automatic selection of input variables that are most relevant for the prediction; (3) the technique to detect automatically a shift in the data pattern using the age of the clusters (and fuzzy rules); (4) the online standardization technique used by the learning procedure of the evolving model; and (5) the application of this innovative approach to several real-life industrial processes from the chemical industry (evolving inferential sensors, namely, eSensors, were used for predicting the chemical properties of different products in The Dow Chemical Company, Freeport, TX). It should be noted, however, that the methodology and conclusions of this paper are valid for the broader area of chemical and process industries in general. The results demonstrate that well-interpretable and with-simple-structure inferential sensors can automatically be designed from the data stream in real time, which predict various process variables of interest. The proposed approach can be used as a basis for the development of a new generation of adaptive and evolving inferential sensors that can a- ddress the challenges of the modern advanced process industry

SUBIC: A Supervised Bi-Clustering Approach for Precision Medicine

Traditional medicine typically applies one-size-fits-all treatment for the entire patient population whereas precision medicine develops tailored treatment schemes for different patient subgroups. The fact that some factors may be more significant for a specific patient subgroup motivates clinicians and medical researchers to develop new approaches to subgroup detection and analysis, which is an effective strategy to personalize treatment. In this study, we propose a novel patient subgroup detection method, called Supervised Biclustring (SUBIC) using convex optimization and apply our approach to detect patient subgroups and prioritize risk factors for hypertension (HTN) in a vulnerable demographic subgroup (African-American). Our approach not only finds patient subgroups with guidance of a clinically relevant target variable but also identifies and prioritizes risk factors by pursuing sparsity of the input variables and encouraging similarity among the input variables and between the input and target variable

Overview of Random Forest Methodology and Practical Guidance with Emphasis on Computational Biology and Bioinformatics

The Random Forest (RF) algorithm by Leo Breiman has become a standard data analysis tool in bioinformatics. It has shown excellent performance in settings where the number of variables is much larger than the number of observations, can cope with complex interaction structures as well as highly correlated variables and returns measures of variable importance. This paper synthesizes ten years of RF development with emphasis on applications to bioinformatics and computational biology. Special attention is given to practical aspects such as the selection of parameters, available RF implementations, and important pitfalls and biases of RF and its variable importance measures (VIMs). The paper surveys recent developments of the methodology relevant to bioinformatics as well as some representative examples of RF applications in this context and possible directions for future research

Bayesian modeling of recombination events in bacterial populations

Background: We consider the discovery of recombinant segments jointly with their origins within multilocus DNA sequences from bacteria representing heterogeneous populations of fairly closely related species. The currently available methods for recombination detection capable of probabilistic characterization of uncertainty have a limited applicability in practice as the number of strains in a data set increases. Results: We introduce a Bayesian spatial structural model representing the continuum of origins over sites within the observed sequences, including a probabilistic characterization of uncertainty related to the origin of any particular site. To enable a statistically accurate and practically feasible approach to the analysis of large-scale data sets representing a single genus, we have developed a novel software tool (BRAT, Bayesian Recombination Tracker) implementing the model and the corresponding learning algorithm, which is capable of identifying the posterior optimal structure and to estimate the marginal posterior probabilities of putative origins over the sites. Conclusion: A multitude of challenging simulation scenarios and an analysis of real data from seven housekeeping genes of 120 strains of genus Burkholderia are used to illustrate the possibilities offered by our approach. The software is freely available for download at URL http://web.abo.fi/fak/ mnf//mate/jc/software/brat.html