Incorporating feature ranking and evolutionary methods for the classification of high-dimensional DNA microarray gene expression data

Background: DNA microarray gene expression classification poses a challenging task to the machine learning domain. Typically, the dimensionality of gene expression data sets could go from several thousands to over 10,000 genes. A potential solution to this issue is using feature selection to reduce the dimensionality. Aim The aim of this paper is to investigate how we can use feature quality information to improve the precision of microarray gene expression classification tasks. Method: We propose two evolutionary machine learning models based on the eXtended Classifier System (XCS) and a typical feature selection methodology. The first one, which we call FS-XCS, uses feature selection for feature reduction purposes. The second model is GRD-XCS, which uses feature ranking to bias the rule discovery process of XCS. Results: The results indicate that the use of feature selection/ranking methods is essential for tackling high-dimensional classification tasks, such as microarray gene expression classification. However, the results also suggest that using feature ranking to bias the rule discovery process performs significantly better than using the feature reduction method. In other words, using feature quality information to develop a smarter learning procedure is more efficient than reducing the feature set. Conclusion: Our findings have shown that extracting feature quality information can assist the learning process and improve classification accuracy. On the other hand, relying exclusively on the feature quality information might potentially decrease the classification performance (e.g., using feature reduction). Therefore, we recommend a hybrid approach that uses feature quality information to direct the learning process by highlighting the more informative features, but at the same time not restricting the learning process to explore other features

Incorporating feature ranking and evolutionary methods for the classification of high-dimensional DNA microarray gene expression data

BackgroundDNA microarray gene expression classification poses a challenging task to the machine learning domain. Typically, the dimensionality of gene expression data sets could go from several thousands to over 10,000 genes. A potential solution to this issue is using feature selection to reduce the dimensionality.AimThe aim of this paper is to investigate how we can use feature quality information to improve the precision of microarray gene expression classification tasks. Method  We propose two evolutionary machine learning models based on the eXtended Classifier System (XCS) and a typical feature selection methodology. The first one, which we call FS-XCS, uses feature selection for feature reduction purposes. The second model is GRD-XCS, which uses feature ranking to bias the rule discovery process of XCS.ResultsThe  results   indicate   that  the  use  of   feature  selection / ranking methods is essential for tackling high-dimensional classification tasks, such as microarray gene expression classification. However, the results also suggest that using feature ranking to bias the rule discovery process performs significantly better than using the feature reduction method. In other words, using feature quality information to develop a smarter learning procedure is more efficient than reducing the feature set. ConclusionOur findings have shown that extracting feature quality information can assist the learning process and improve classification accuracy. On the other hand, relying exclusively on the feature quality information might potentially decrease the classification performance (e.g., using feature reduction). Therefore, we recommend a hybrid approach that uses feature quality information to direct the learning process by highlighting the more informative features, but at the same time not restricting the learning process to explore other features

A brief history of learning classifier systems: from CS-1 to XCS and its variants

© 2015, Springer-Verlag Berlin Heidelberg. The direction set by Wilson’s XCS is that modern Learning Classifier Systems can be characterized by their use of rule accuracy as the utility metric for the search algorithm(s) discovering useful rules. Such searching typically takes place within the restricted space of co-active rules for efficiency. This paper gives an overview of the evolution of Learning Classifier Systems up to XCS, and then of some of the subsequent developments of Wilson’s algorithm to different types of learning

Improving the Scalability of XCS-Based Learning Classifier Systems

Using evolutionary intelligence and machine learning techniques, a broad range of intelligent machines have been designed to perform different tasks. An intelligent machine learns by perceiving its environmental status and taking an action that maximizes its chances of success. Human beings have the ability to apply knowledge learned from a smaller problem to more complex, large-scale problems of the same or a related domain, but currently the vast majority of evolutionary machine learning techniques lack this ability. This lack of ability to apply the already learned knowledge of a domain results in consuming more than the necessary resources and time to solve complex, large-scale problems of the domain. As the problem increases in size, it becomes difficult and even sometimes impractical (if not impossible) to solve due to the needed resources and time. Therefore, in order to scale in a problem domain, a systemis needed that has the ability to reuse the learned knowledge of the domain and/or encapsulate the underlying patterns in the domain. To extract and reuse building blocks of knowledge or to encapsulate the underlying patterns in a problem domain, a rich encoding is needed, but the search space could then expand undesirably and cause bloat, e.g. as in some forms of genetic programming (GP). Learning classifier systems (LCSs) are a well-structured evolutionary computation based learning technique that have pressures to implicitly avoid bloat, such as fitness sharing through niche based reproduction. The proposed thesis is that an LCS can scale to complex problems in a domain by reusing the learnt knowledge from simpler problems of the domain and/or encapsulating the underlying patterns in the domain. Wilson’s XCS is used to implement and test the proposed systems, which is a well-tested, online learning and accuracy based LCS model. To extract the reusable building blocks of knowledge, GP-tree like, code-fragments are introduced, which are more than simply another representation (e.g. ternary or real-valued alphabets). This thesis is extended to capture the underlying patterns in a problemusing a cyclic representation. Hard problems are experimented to test the newly developed scalable systems and compare them with benchmark techniques. Specifically, this work develops four systems to improve the scalability of XCS-based classifier systems. (1) Building blocks of knowledge are extracted fromsmaller problems of a Boolean domain and reused in learning more complex, large-scale problems in the domain, for the first time. By utilizing the learnt knowledge from small-scale problems, the developed XCSCFC (i.e. XCS with Code-Fragment Conditions) system readily solves problems of a scale that existing LCS and GP approaches cannot, e.g. the 135-bitMUX problem. (2) The introduction of the code fragments in classifier actions in XCSCFA (i.e. XCS with Code-Fragment Actions) enables the rich representation of GP, which when couples with the divide and conquer approach of LCS, to successfully solve various complex, overlapping and niche imbalance Boolean problems that are difficult to solve using numeric action based XCS. (3) The underlying patterns in a problem domain are encapsulated in classifier rules encoded by a cyclic representation. The developed XCSSMA system produces general solutions of any scale n for a number of important Boolean problems, for the first time in the field of LCS, e.g. parity problems. (4) Optimal solutions for various real-valued problems are evolved by extending the existing real-valued XCSR system with code-fragment actions to XCSRCFA. Exploiting the combined power of GP and LCS techniques, XCSRCFA successfully learns various continuous action and function approximation problems that are difficult to learn using the base techniques. This research work has shown that LCSs can scale to complex, largescale problems through reusing learnt knowledge. The messy nature, disassociation of message to condition order, masking, feature construction, and reuse of extracted knowledge add additional abilities to the XCS family of LCSs. The ability to use rich encoding in antecedent GP-like codefragments or consequent cyclic representation leads to the evolution of accurate, maximally general and compact solutions in learning various complex Boolean as well as real-valued problems. Effectively exploiting the combined power of GP and LCS techniques, various continuous action and function approximation problems are solved in a simple and straight forward manner. The analysis of the evolved rules reveals, for the first time in XCS, that no matter how specific or general the initial classifiers are, all the optimal classifiers are converged through the mechanism ‘be specific then generalize’ near the final stages of evolution. Also that standard XCS does not use all available information or all available genetic operators to evolve optimal rules, whereas the developed code-fragment action based systems effectively use figure and ground information during the training process. Thiswork has created a platformto explore the reuse of learnt functionality, not just terminal knowledge as present, which is needed to replicate human capabilities

Learning Feature Selection and Combination Strategies for Generic Salient Object Detection

For a diverse range of applications in machine vision from social media searches to robotic home care providers, it is important to replicate the mechanism by which the human brain selects the most important visual information, while suppressing the remaining non-usable information. Many computational methods attempt to model this process by following the traditional model of visual attention. The traditional model of attention involves feature extraction, conditioning and combination to capture this behaviour of human visual attention. Consequently, the model has inherent design choices at its various stages. These choices include selection of parameters related to the feature computation process, setting a conditioning approach, feature importance and setting a combination approach. Despite rapid research and substantial improvements in benchmark performance, the performance of many models depends upon tuning these design choices in an ad hoc fashion. Additionally, these design choices are heuristic in nature, thus resulting in good performance only in certain settings. Consequentially, many such models exhibit low robustness to difficult stimuli and the complexities of real-world imagery. Machine learning and optimisation technique have long been used to increase the generalisability of a system to unseen data. Surprisingly, artificial learning techniques have not been investigated to their full potential to improve generalisation of visual attention methods. The proposed thesis is that artificial learning can increase the generalisability of the traditional model of visual attention by effective selection and optimal combination of features. The following new techniques have been introduced at various stages of the traditional model of visual attention to improve its generalisation performance, specifically on challenging cases of saliency detection: 1. Joint optimisation of feature related parameters and feature importance weights is introduced for the first time to improve the generalisation of the traditional model of visual attention. To evaluate the joint learning hypothesis, a new method namely GAOVSM is introduced for the tasks of eye fixation prediction. By finding the relationships between feature related parameters and feature importance, the developed method improves the generalisation performance of baseline method (that employ human encoded parameters). 2. Spectral matting based figure-ground segregation is introduced to overcome the artifacts encountered by region-based salient object detection approaches. By suppressing the unwanted background information and assigning saliency to object parts in a uniform manner, the developed FGS approach overcomes the limitations of region based approaches. 3. Joint optimisation of feature computation parameters and feature importance weights is introduced for optimal combination of FGS with complementary features for the first time for salient object detection. By learning feature related parameters and their respective importance at multiple segmentation thresholds and by considering the performance gaps amongst features, the developed FGSopt method improves the object detection performance of the FGS technique also improving upon several state-of-the-art salient object detection models. 4. The introduction of multiple combination schemes/rules further extends the generalisability of the traditional attention model beyond that of joint optimisation based single rules. The introduction of feature composition based grouping of images, enables the developed IGA method to autonomously identify an appropriate combination strategy for an unseen image. The results of a pair-wise ranksum test confirm that the IGA method is significantly better than the deterministic and classification based benchmark methods on the 99% confidence interval level. Extending this line of research, a novel relative encoding approach enables the adapted XCSCA method to group images having similar saliency prediction ability. By keeping track of previous inputs, the introduced action part of the XCSCA approach enables learning of generalised feature importance rules. By more accurate grouping of images as compared with IGA, generalised learnt rules and appropriate application of feature importance rules, the XCSCA approach improves upon the generalisation performance of the IGA method. 5. The introduced uniform saliency assignment and segmentation quality cues enable label free evaluation of a feature/saliency map. By accurate ranking and effective clustering, the developed DFS method successfully solves the complex problem of finding appropriate features for combination (on an-image-by-image basis) for the first time in saliency detection. The DFS method enables ground truth free evaluation of saliency methods and advances the state-of-the-art in data driven saliency aggregation by detection and deselection of redundant information. The final contribution is that the developed methods are formed into a complete system where analysis shows the effects of their interactions on the system. Based on the saliency prediction accuracy versus computational time trade-off, specialised variants of the proposed methods are presented along with the recommendations for further use by other saliency detection systems. This research work has shown that artificial learning can increase the generalisation of the traditional model of attention by effective selection and optimal combination of features. Overall, this thesis has shown that it is the ability to autonomously segregate images based on their types and subsequent learning of appropriate combinations that aid generalisation on difficult unseen stimuli

Learning classifier systems from first principles: A probabilistic reformulation of learning classifier systems from the perspective of machine learning

Learning Classifier Systems (LCS) are a family of rule-based machine learning methods. They aim at the autonomous production of potentially human readable results that are the most compact generalised representation whilst also maintaining high predictive accuracy, with a wide range of application areas, such as autonomous robotics, economics, and multi-agent systems. Their design is mainly approached heuristically and, even though their performance is competitive in regression and classification tasks, they do not meet their expected performance in sequential decision tasks despite being initially designed for such tasks. It is out contention that improvement is hindered by a lack of theoretical understanding of their underlying mechanisms and dynamics.EThOS - Electronic Theses Online ServiceGBUnited Kingdo