A cDNA Microarray Gene Expression Data Classifier for Clinical Diagnostics Based on Graph Theory

Despite great advances in discovering cancer molecular profiles, the proper application of microarray technology to routine clinical diagnostics is still a challenge. Current practices in the classification of microarrays' data show two main limitations: the reliability of the training data sets used to build the classifiers, and the classifiers' performances, especially when the sample to be classified does not belong to any of the available classes. In this case, state-of-the-art algorithms usually produce a high rate of false positives that, in real diagnostic applications, are unacceptable. To address this problem, this paper presents a new cDNA microarray data classification algorithm based on graph theory and is able to overcome most of the limitations of known classification methodologies. The classifier works by analyzing gene expression data organized in an innovative data structure based on graphs, where vertices correspond to genes and edges to gene expression relationships. To demonstrate the novelty of the proposed approach, the authors present an experimental performance comparison between the proposed classifier and several state-of-the-art classification algorithm

A probabilistic classifier ensemble weighting scheme based on cross-validated accuracy estimates

Our hypothesis is that building ensembles of small sets of strong classifiers constructed with different learning algorithms is, on average, the best approach to classification for real world problems. We propose a simple mechanism for building small heterogeneous ensembles based on exponentially weighting the probability estimates of the base classifiers with an estimate of the accuracy formed through cross-validation on the train data. We demonstrate through extensive experimentation that, given the same small set of base classifiers, this method has measurable benefits over commonly used alternative weighting, selection or meta classifier approaches to heterogeneous ensembles. We also show how an ensemble of five well known, fast classifiers can produce an ensemble that is not significantly worse than large homogeneous ensembles and tuned individual classifiers on datasets from the UCI archive. We provide evidence that the performance of the Cross-validation Accuracy Weighted Probabilistic Ensemble (CAWPE) generalises to a completely separate set of datasets, the UCR time series classification archive, and we also demonstrate that our ensemble technique can significantly improve the state-of-the-art classifier for this problem domain. We investigate the performance in more detail, and find that the improvement is most marked in problems with smaller train sets. We perform a sensitivity analysis and an ablation study to demonstrate the robustness of the ensemble and the significant contribution of each design element of the classifier. We conclude that it is, on average, better to ensemble strong classifiers with a weighting scheme rather than perform extensive tuning and that CAWPE is a sensible starting point for combining classifiers

Multiple Instance Learning: A Survey of Problem Characteristics and Applications

Multiple instance learning (MIL) is a form of weakly supervised learning where training instances are arranged in sets, called bags, and a label is provided for the entire bag. This formulation is gaining interest because it naturally fits various problems and allows to leverage weakly labeled data. Consequently, it has been used in diverse application fields such as computer vision and document classification. However, learning from bags raises important challenges that are unique to MIL. This paper provides a comprehensive survey of the characteristics which define and differentiate the types of MIL problems. Until now, these problem characteristics have not been formally identified and described. As a result, the variations in performance of MIL algorithms from one data set to another are difficult to explain. In this paper, MIL problem characteristics are grouped into four broad categories: the composition of the bags, the types of data distribution, the ambiguity of instance labels, and the task to be performed. Methods specialized to address each category are reviewed. Then, the extent to which these characteristics manifest themselves in key MIL application areas are described. Finally, experiments are conducted to compare the performance of 16 state-of-the-art MIL methods on selected problem characteristics. This paper provides insight on how the problem characteristics affect MIL algorithms, recommendations for future benchmarking and promising avenues for research

Time Series classification through transformation and ensembles

The problem of time series classification (TSC), where we consider any real-valued ordered data a time series, offers a specific challenge. Unlike traditional classification problems, the ordering of attributes is often crucial for identifying discriminatory features between classes. TSC problems arise across a diverse range of domains, and this variety has meant that no single approach outperforms all others. The general consensus is that the benchmark for TSC is nearest neighbour (NN) classifiers using Euclidean distance or Dynamic Time Warping (DTW). Though conceptually simple, many have reported that NN classifiers are very diffi�cult to beat and new work is often compared to NN classifiers. The majority of approaches have focused on classification in the time domain, typically proposing alternative elastic similarity measures for NN classification. Other work has investigated more specialised approaches, such as building support vector machines on variable intervals and creating tree-based ensembles with summary measures. We wish to answer a specific research question: given a new TSC problem without any prior, specialised knowledge, what is the best way to approach the problem? Our thesis is that the best methodology is to first transform data into alternative representations where discriminatory features are more easily detected, and then build ensemble classifiers on each representation. In support of our thesis, we propose an elastic ensemble classifier that we believe is the first ever to significantly outperform DTW on the widely used UCR datasets. Next, we propose the shapelet-transform, a new data transformation that allows complex classifiers to be coupled with shapelets, which outperforms the original algorithm and is competitive with DTW. Finally, we combine these two works with with heterogeneous ensembles built on autocorrelation and spectral-transformed data to propose a collective of transformation-based ensembles (COTE). The results of COTE are, we believe, the best ever published on the UCR datasets

Ant colony optimization approach for stacking configurations

In data mining, classifiers are generated to predict the class labels of the instances. An ensemble is a decision making system which applies certain strategies to combine the predictions of different classifiers and generate a collective decision. Previous research has empirically and theoretically demonstrated that an ensemble classifier can be more accurate and stable than its component classifiers in most cases. Stacking is a well-known ensemble which adopts a two-level structure: the base-level classifiers to generate predictions and the meta-level classifier to make collective decisions. A consequential problem is: what learning algorithms should be used to generate the base-level and meta-level classifier in the Stacking configuration? It is not easy to find a suitable configuration for a specific dataset. In some early works, the selection of a meta classifier and its training data are the major concern. Recently, researchers have tried to apply metaheuristic methods to optimize the configuration of the base classifiers and the meta classifier. Ant Colony Optimization (ACO), which is inspired by the foraging behaviors of real ant colonies, is one of the most popular approaches among the metaheuristics. In this work, we propose a novel ACO-Stacking approach that uses ACO to tackle the Stacking configuration problem. This work is the first to apply ACO to the Stacking configuration problem. Different implementations of the ACO-Stacking approach are developed. The first version identifies the appropriate learning algorithms in generating the base-level classifiers while using a specific algorithm to create the meta-level classifier. The second version simultaneously finds the suitable learning algorithms to create the base-level classifiers and the meta-level classifier. Moreover, we study how different kinds on local information of classifiers will affect the classification results. Several pieces of local information collected from the initial phase of ACO-Stacking are considered, such as the precision, f-measure of each classifier and correlative differences of paired classifiers. A series of experiments are performed to compare the ACO-Stacking approach with other ensembles on a number of datasets of different domains and sizes. The experiments show that the new approach can achieve promising results and gain advantages over other ensembles. The correlative differences of the classifiers could be the best local information in this approach. Under the agile ACO-Stacking framework, an application to deal with a direct marketing problem is explored. A real world database from a US-based catalog company, containing more than 100,000 customer marketing records, is used in the experiments. The results indicate that our approach can gain more cumulative response lifts and cumulative profit lifts in the top deciles. In conclusion, it is competitive with some well-known conventional and ensemble data mining methods