A Particle Swarm Optimization-based Flexible Convolutional Auto-Encoder for Image Classification

Convolutional auto-encoders have shown their remarkable performance in stacking to deep convolutional neural networks for classifying image data during past several years. However, they are unable to construct the state-of-the-art convolutional neural networks due to their intrinsic architectures. In this regard, we propose a flexible convolutional auto-encoder by eliminating the constraints on the numbers of convolutional layers and pooling layers from the traditional convolutional auto-encoder. We also design an architecture discovery method by using particle swarm optimization, which is capable of automatically searching for the optimal architectures of the proposed flexible convolutional auto-encoder with much less computational resource and without any manual intervention. We use the designed architecture optimization algorithm to test the proposed flexible convolutional auto-encoder through utilizing one graphic processing unit card on four extensively used image classification datasets. Experimental results show that our work in this paper significantly outperform the peer competitors including the state-of-the-art algorithm.Comment: Accepted by IEEE Transactions on Neural Networks and Learning Systems, 201

Mixed Order Hyper-Networks for Function Approximation and Optimisation

Many systems take inputs, which can be measured and sometimes controlled, and outputs, which can also be measured and which depend on the inputs. Taking numerous measurements from such systems produces data, which may be used to either model the system with the goal of predicting the output associated with a given input (function approximation, or regression) or of finding the input settings required to produce a desired output (optimisation, or search). Approximating or optimising a function is central to the field of computational intelligence. There are many existing methods for performing regression and optimisation based on samples of data but they all have limitations. Multi layer perceptrons (MLPs) are universal approximators, but they suffer from the black box problem, which means their structure and the function they implement is opaque to the user. They also suffer from a propensity to become trapped in local minima or large plateaux in the error function during learning. A regression method with a structure that allows models to be compared, human knowledge to be extracted, optimisation searches to be guided and model complexity to be controlled is desirable. This thesis presents such as method. This thesis presents a single framework for both regression and optimisation: the mixed order hyper network (MOHN). A MOHN implements a function f:{-1,1}^n ->R to arbitrary precision. The structure of a MOHN makes the ways in which input variables interact to determine the function output explicit, which allows human insights and complexity control that are very difficult in neural networks with hidden units. The explicit structure representation also allows efficient algorithms for searching for an input pattern that leads to a desired output. A number of learning rules for estimating the weights based on a sample of data are presented along with a heuristic method for choosing which connections to include in a model. Several methods for searching a MOHN for inputs that lead to a desired output are compared. Experiments compare a MOHN to an MLP on regression tasks. The MOHN is found to achieve a comparable level of accuracy to an MLP but suffers less from local minima in the error function and shows less variance across multiple training trials. It is also easier to interpret and combine from an ensemble. The trade-off between the fit of a model to its training data and that to an independent set of test data is shown to be easier to control in a MOHN than an MLP. A MOHN is also compared to a number of existing optimisation methods including those using estimation of distribution algorithms, genetic algorithms and simulated annealing. The MOHN is able to find optimal solutions in far fewer function evaluations than these methods on tasks selected from the literature

Learning Discriminative Bayesian Networks from High-dimensional Continuous Neuroimaging Data

Due to its causal semantics, Bayesian networks (BN) have been widely employed to discover the underlying data relationship in exploratory studies, such as brain research. Despite its success in modeling the probability distribution of variables, BN is naturally a generative model, which is not necessarily discriminative. This may cause the ignorance of subtle but critical network changes that are of investigation values across populations. In this paper, we propose to improve the discriminative power of BN models for continuous variables from two different perspectives. This brings two general discriminative learning frameworks for Gaussian Bayesian networks (GBN). In the first framework, we employ Fisher kernel to bridge the generative models of GBN and the discriminative classifiers of SVMs, and convert the GBN parameter learning to Fisher kernel learning via minimizing a generalization error bound of SVMs. In the second framework, we employ the max-margin criterion and build it directly upon GBN models to explicitly optimize the classification performance of the GBNs. The advantages and disadvantages of the two frameworks are discussed and experimentally compared. Both of them demonstrate strong power in learning discriminative parameters of GBNs for neuroimaging based brain network analysis, as well as maintaining reasonable representation capacity. The contributions of this paper also include a new Directed Acyclic Graph (DAG) constraint with theoretical guarantee to ensure the graph validity of GBN.Comment: 16 pages and 5 figures for the article (excluding appendix

Bayesian Networks: a Non-Frequentist Approach for Parametrization, and a more Accurate Structural Complexity Measure

The problem of calibrating relations from examples is a classical problem in learning theory. This problem has in particular been studied in the theory of empirical processes (providing asymptotic results), and through statistical learning theory. The application of learning theory to bayesian networks is still uncomplete and we propose a contribution, especially through the use of covering numbers. We deduce multiple corollaries, among which a non-frequentist approach for parameters learning and a score taking into account a measure of structural entropy that has never been taken into account before. We then investigate the algorithmic aspects of our theoretical solution, based on BFGS and adaptive refining of gradient calculus. Empirical results show the relevance of both the statistical results and the algorithmic solution

Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network

Abstract Background Despite large amounts of available genomic and proteomic data, predicting the structure and response of signaling networks is still a significant challenge. While statistical method such as Bayesian network has been explored to meet this challenge, employing existing biological knowledge for network prediction is difficult. The objective of this study is to develop a novel approach that integrates prior biological knowledge in the form of the Ontology Fingerprint to infer cell-type-specific signaling networks via data-driven Bayesian network learning; and to further use the trained model to predict cellular responses. Results We applied our novel approach to address the Predictive Signaling Network Modeling challenge of the fourth (2009) Dialog for Reverse Engineering Assessment's and Methods (DREAM4) competition. The challenge results showed that our method accurately captured signal transduction of a network of protein kinases and phosphoproteins in that the predicted protein phosphorylation levels under all experimental conditions were highly correlated (R2 = 0.93) with the observed results. Based on the evaluation of the DREAM4 organizer, our team was ranked as one of the top five best performers in predicting network structure and protein phosphorylation activity under test conditions. Conclusions Bayesian network can be used to simulate the propagation of signals in cellular systems. Incorporating the Ontology Fingerprint as prior biological knowledge allows us to efficiently infer concise signaling network structure and to accurately predict cellular responses.http://deepblue.lib.umich.edu/bitstream/2027.42/109490/1/12918_2012_Article_989.pd

Breast Cancer Classification by Gene Expression Analysis using Hybrid Feature Selection and Hyper-heuristic Adaptive Universum Support Vector Machine

Comprehensive assessments of the molecular characteristics of breast cancer from gene expression patterns can aid in the early identification and treatment of tumor patients. The enormous scale of gene expression data obtained through microarray sequencing increases the difficulty of training the classifier due to large-scale features. Selecting pivotal gene features can minimize high dimensionality and the classifier complexity with improved breast cancer detection accuracy. However, traditional filter and wrapper-based selection methods have scalability and adaptability issues in handling complex gene features. This paper presents a hybrid feature selection method of Mutual Information Maximization - Improved Moth Flame Optimization (MIM-IMFO) for gene selection along with an advanced Hyper-heuristic Adaptive Universum Support classification model Vector Machine (HH-AUSVM) to improve cancer detection rates. The hybrid gene selection method is developed by performing filter-based selection using MIM in the first stage followed by the wrapper method in the second stage, to obtain the pivotal features and remove the inappropriate ones. This method improves standard MFO by a hybrid exploration/exploitation phase to accomplish a better trade-off between exploration and exploitation phases. The classifier HH-AUSVM is formulated by integrating the Adaptive Universum learning approach to the hyper- heuristics-based parameter optimized SVM to tackle the class samples imbalance problem. Evaluated on breast cancer gene expression datasets from Mendeley Data Repository, this proposed MIM-IMFO gene selection-based HH-AUSVM classification approach provided better breast cancer detection with high accuracies of 95.67%, 96.52%, 97.97% and 95.5% and less processing time of 4.28, 3.17, 9.45 and 6.31 seconds, respectively