Multi-class protein fold classification using a new ensemble machine learning approach.

Protein structure classification represents an important process in understanding the associations between sequence and structure as well as possible functional and evolutionary relationships. Recent structural genomics initiatives and other high-throughput experiments have populated the biological databases at a rapid pace. The amount of structural data has made traditional methods such as manual inspection of the protein structure become impossible. Machine learning has been widely applied to bioinformatics and has gained a lot of success in this research area. This work proposes a novel ensemble machine learning method that improves the coverage of the classifiers under the multi-class imbalanced sample sets by integrating knowledge induced from different base classifiers, and we illustrate this idea in classifying multi-class SCOP protein fold data. We have compared our approach with PART and show that our method improves the sensitivity of the classifier in protein fold classification. Furthermore, we have extended this method to learning over multiple data types, preserving the independence of their corresponding data sources, and show that our new approach performs at least as well as the traditional technique over a single joined data source. These experimental results are encouraging, and can be applied to other bioinformatics problems similarly characterised by multi-class imbalanced data sets held in multiple data sources

Learning Hybrid Neuro-Fuzzy Classifier Models From Data: To Combine or Not to Combine?

To combine or not to combine? Though not a question of the same gravity as the Shakespeare’s to be or not to be, it is examined in this paper in the context of a hybrid neuro-fuzzy pattern classifier design process. A general fuzzy min-max neural network with its basic learning procedure is used within six different algorithm independent learning schemes. Various versions of cross-validation, resampling techniques and data editing approaches, leading to a generation of a single classifier or a multiple classifier system, are scrutinised and compared. The classification performance on unseen data, commonly used as a criterion for comparing different competing designs, is augmented by further four criteria attempting to capture various additional characteristics of classifier generation schemes. These include: the ability to estimate the true classification error rate, the classifier transparency, the computational complexity of the learning scheme and the potential for adaptation to changing environments and new classes of data. One of the main questions examined is whether and when to use a single classifier or a combination of a number of component classifiers within a multiple classifier system

On Time Series Classification with Dictionary-Based Classifiers

A family of algorithms for time series classification (TSC) involve running a sliding window across each series, discretising the window to form a word, forming a histogram of word counts over the dictionary, then constructing a classifier on the histograms. A recent evaluation of two of this type of algorithm, Bag of Patterns (BOP) and Bag of Symbolic Fourier Approximation Symbols (BOSS) found a significant difference in accuracy between these seemingly similar algorithms. We investigate this phenomenon by deconstructing the classifiers and measuring the relative importance of the four key components between BOP and BOSS. We find that whilst ensembling is a key component for both algorithms, the effect of the other components is mixed and more complex. We conclude that BOSS represents the state of the art for dictionary-based TSC. Both BOP and BOSS can be classed as bag of words approaches. These are particularly popular in Computer Vision for tasks such as image classification. We adapt three techniques used in Computer Vision for TSC: Scale Invariant Feature Transform; Spatial Pyramids; and Histogram Intersection. We find that using Spatial Pyramids in conjunction with BOSS (SP) produces a significantly more accurate classifier. SP is significantly more accurate than standard benchmarks and the original BOSS algorithm. It is not significantly worse than the best shapelet-based or deep learning approaches, and is only outperformed by an ensemble that includes BOSS as a constituent module

Time series classification with ensembles of elastic distance measures

Several alternative distance measures for comparing time series have recently been proposed and evaluated on time series classification (TSC) problems. These include variants of dynamic time warping (DTW), such as weighted and derivative DTW, and edit distance-based measures, including longest common subsequence, edit distance with real penalty, time warp with edit, and move–split–merge. These measures have the common characteristic that they operate in the time domain and compensate for potential localised misalignment through some elastic adjustment. Our aim is to experimentally test two hypotheses related to these distance measures. Firstly, we test whether there is any significant difference in accuracy for TSC problems between nearest neighbour classifiers using these distance measures. Secondly, we test whether combining these elastic distance measures through simple ensemble schemes gives significantly better accuracy. We test these hypotheses by carrying out one of the largest experimental studies ever conducted into time series classification. Our first key finding is that there is no significant difference between the elastic distance measures in terms of classification accuracy on our data sets. Our second finding, and the major contribution of this work, is to define an ensemble classifier that significantly outperforms the individual classifiers. We also demonstrate that the ensemble is more accurate than approaches not based in the time domain. Nearly all TSC papers in the data mining literature cite DTW (with warping window set through cross validation) as the benchmark for comparison. We believe that our ensemble is the first ever classifier to significantly outperform DTW and as such raises the bar for future work in this area

Predicting college basketball match outcomes using machine learning techniques: some results and lessons learned

Most existing work on predicting NCAAB matches has been developed in a statistical context. Trusting the capabilities of ML techniques, particularly classification learners, to uncover the importance of features and learn their relationships, we evaluated a number of different paradigms on this task. In this paper, we summarize our work, pointing out that attributes seem to be more important than models, and that there seems to be an upper limit to predictive quality