Binary Shapelet Transform for Multiclass Time Series Classification

Shapelets have recently been proposed as a new primitive for time series classification. Shapelets are subseries of series that best split the data into its classes. In the original research, shapelets were found recursively within a decision tree through enumeration of the search space. Subsequent research indicated that using shapelets as the basis for transforming datasets leads to more accurate classifiers. Both these approaches evaluate how well a shapelet splits all the classes. However, often a shapelet is most useful in distinguishing between members of the class of the series it was drawn from against all others. To assess this conjecture, we evaluate a one vs all encoding scheme. This technique simplifies the quality assessment calculations, speeds up the execution through facilitating more frequent early abandon and increases accuracy for multi-class problems. We also propose an alternative shapelet evaluation scheme which we demonstrate significantly speeds up the full search

Predictive Modelling of Bone Age through Classification and Regression of Bone Shapes

Bone age assessment is a task performed daily in hospitals worldwide. This involves a clinician estimating the age of a patient from a radiograph of the non-dominant hand. Our approach to automated bone age assessment is to modularise the algorithm into the following three stages: segment and verify hand outline; segment and verify bones; use the bone outlines to construct models of age. In this paper we address the final question: given outlines of bones, can we learn how to predict the bone age of the patient? We examine two alternative approaches. Firstly, we attempt to train classifiers on individual bones to predict the bone stage categories commonly used in bone ageing. Secondly, we construct regression models to directly predict patient age. We demonstrate that models built on summary features of the bone outline perform better than those built using the one dimensional representation of the outline, and also do at least as well as other automated systems. We show that models constructed on just three bones are as accurate at predicting age as expert human assessors using the standard technique. We also demonstrate the utility of the model by quantifying the importance of ethnicity and sex on age development. Our conclusion is that the feature based system of separating the image processing from the age modelling is the best approach for automated bone ageing, since it offers flexibility and transparency and produces accurate estimate

An Experimental Evaluation of Nearest Neighbour Time Series Classification

Data mining research into time series classification (TSC) has focussed on alternative distance measures for nearest neighbour classifiers. It is standard practice to use 1-NN with Euclidean or dynamic time warping (DTW) distance as a straw man for comparison. As part of a wider investigation into elastic distance measures for TSC~\cite{lines14elastic}, we perform a series of experiments to test whether this standard practice is valid. Specifically, we compare 1-NN classifiers with Euclidean and DTW distance to standard classifiers, examine whether the performance of 1-NN Euclidean approaches that of 1-NN DTW as the number of cases increases, assess whether there is any benefit of setting $k$ for $k$-NN through cross validation whether it is worth setting the warping path for DTW through cross validation and finally is it better to use a window or weighting for DTW. Based on experiments on 77 problems, we conclude that 1-NN with Euclidean distance is fairly easy to beat but 1-NN with DTW is not, if window size is set through cross validation

Finding Motif Sets in Time Series

Time-series motifs are representative subsequences that occur frequently in a time series; a motif set is the set of subsequences deemed to be instances of a given motif. We focus on finding motif sets. Our motivation is to detect motif sets in household electricity-usage profiles, representing repeated patterns of household usage. We propose three algorithms for finding motif sets. Two are greedy algorithms based on pairwise comparison, and the third uses a heuristic measure of set quality to find the motif set directly. We compare these algorithms on simulated datasets and on electricity-usage data. We show that Scan MK, the simplest way of using the best-matching pair to find motif sets, is less accurate on our synthetic data than Set Finder and Cluster MK, although the latter is very sensitive to parameter settings. We qualitatively analyse the outputs for the electricity-usage data and demonstrate that both Scan MK and Set Finder can discover useful motif sets in such data

Time Series Data Mining Algorithms for Identifying Short RNA in Arabidopsis thaliana

The class of molecules called short RNAs (sRNAs) are known to play a key role in gene regulation. Th are typically sequences of nucleotides between 21-25 nucleotides in length. They are known to play a key role in gene regulation. The identification, clustering and classification of sRNA has recently become the focus of much research activity. The basic problem involves detecting regions of interest on the chromosome where the pattern of candidate matches is somehow unusual. Currently, there are no published algorithms for detecting regions of interest, and the unpublished methods that we are aware of involve bespoke rule based systems designed for a specific organism. Work in this very new field has understandably focused on the outcomes rather than the methods used to obtain the results. In this paper we propose two generic approaches that place the specific biological problem in the wider context of time series data mining problems. Both methods are based on treating the occurrences on a chromosome, or “hit count” data, as a time series, then running a sliding window along a chromosome and measuring unusualness. This formulation means we can treat finding unusual areas of candidate RNA activity as a variety of time series anomaly detection problem. The first set of approaches is model based. We specify a null hypothesis distribution for not being a sRNA, then estimate the p-values along the chromosome. The second approach is instance based. We identify some typical shapes from known sRNA, then use dynamic time warping and fourier trans-form based distance to measure how closely the candidate series matches. We demonstrate that these methods can find known sRNA on Arabidopsis thaliana chromosomes and illustrate the benefits of the added information provided by these algorithms

Benchmarking the Semi-Supervised Naïve Bayes Classifier

Semi-supervised learning involves constructing predictive models with both labelled and unlabelled training data. The need for semi-supervised learning is driven by the fact that unlabelled data are often easy and cheap to obtain, whereas labelling data requires costly and time consuming human intervention and expertise. Semi-supervised methods commonly use self training, which involves using the labelled data to predict the unlabelled data, then iteratively reconstructing classifiers using the predicted labels. Our aim is to determine whether self training classifiers actually improves performance. Expectation maximization is a commonly used self training scheme. We investigate whether an expectation maximization scheme improves a naïve Bayes classifier through experimentation with 30 discrete and 20 continuous real world benchmark UCI datasets. Rather surprisingly we find that in practice the self training actually makes the classifier worse. The cause for this detrimental affect on performance could either be with the self training scheme itself, or how self training works in conjunction with the classifier. Our hypothesis is that it is the latter cause, and the violation of the naïve Bayes model assumption of independence of attributes means predictive errors propagate through the self training scheme. To test whether this is the case, we generate simulated data with the same attribute distribution as the UCI data, but where the attributes are independent. Experiments with this data demonstrate that semi-supervised learning does improve performance, leading to significantly more accurate classifiers. These results demonstrate that semi-supervised learning cannot be applied blindly without considering the nature of the classifier, because the assumptions implicit in the classifier may result in a degradation in performance