From a fresh data science perspective, this thesis discusses the prediction of coronary artery disease based on genetic variations at the DNA base pair level, called Single-Nucleotide Polymorphisms (SNPs), collected from the Ontario Heart Genomics Study (OHGS). First, the thesis explains two commonly used supervised learning algorithms, the k-Nearest Neighbour (k-NN) and Random Forest classifiers, and includes a complete proof that the k-NN classifier is universally consistent in any finite dimensional normed vector space. Second, the thesis introduces two dimensionality reduction steps, Random Projections, a known feature extraction technique based on the Johnson-Lindenstrauss lemma, and a new method termed Mass Transportation Distance (MTD) Feature Selection for discrete domains. Then, this thesis compares the performance of Random Projections with the k-NN classifier against MTD Feature Selection and Random Forest, for predicting artery disease based on accuracy, the F-Measure, and area under the Receiver Operating Characteristic (ROC) curve. The comparative results demonstrate that MTD Feature Selection with Random Forest is vastly superior to Random Projections and k-NN. The Random Forest classifier is able to obtain an accuracy of 0.6660 and an area under the ROC curve of 0.8562 on the OHGS genetic dataset, when 3335 SNPs are selected by MTD Feature Selection for classification. This area is considerably better than the previous high score of 0.608 obtained by Davies et al. in 2010 on the same dataset.

This paper explores combinatorial optimization for problems of max-weight graph matching on multi-partite graphs, which arise in integrating multiple data sources. Entity resolution-the data integration problem of performing noisy joins on structured data-typically proceeds by first hashing each record into zero or more blocks, scoring pairs of records that are co-blocked for similarity, and then matching pairs of sufficient similarity. In the most common case of matching two sources, it is often desirable for the final matching to be one-to-one (a record may be matched with at most one other); members of the database and statistical record linkage communities accomplish such matchings in the final stage by weighted bipartite graph matching on similarity scores. Such matchings are intuitively appealing: they leverage a natural global property of many real-world entity stores-that of being nearly deduped-and are known to provide significant improvements to precision and recall. Unfortunately unlike the bipartite case, exact max-weight matching on multi-partite graphs is known to be NP-hard. Our two-fold algorithmic contributions approximate multi-partite max-weight matching: our first algorithm borrows optimization techniques common to Bayesian probabilistic inference; our second is a greedy approximation algorithm. In addition to a theoretical guarantee on the latter, we present comparisons on a real-world ER problem from Bing significantly larger than typically found in the literature, publication data, and on a series of synthetic problems. Our results quantify significant improvements due to exploiting multiple sources, which are made possible by global one-to-one constraints linking otherwise independent matching sub-problems. We also discover that our algorithms are complementary: one being much more robust under noise, and the other being simple to implement and very fast to run.

We present the first public release of our generic neural network training algorithm, called SkyNet. This efficient and robust machine learning tool is able to train large and deep feed-forward neural networks, including autoencoders, for use in a wide range of supervised and unsupervised learning applications, such as regression, classification, density estimation, clustering and dimensionality reduction. SkyNet uses a `pre-training' method to obtain a set of network parameters that has empirically been shown to be close to a good solution, followed by further optimisation using a regularised variant of Newton's method, where the level of regularisation is determined and adjusted automatically; the latter uses second-order derivative information to improve convergence, but without the need to evaluate or store the full Hessian matrix, by using a fast approximate method to calculate Hessian-vector products. This combination of methods allows for the training of complicated networks that are difficult to optimise using standard backpropagation techniques. SkyNet employs convergence criteria that naturally prevent overfitting, and also includes a fast algorithm for estimating the accuracy of network outputs. The utility and flexibility of SkyNet are demonstrated by application to a number of toy problems, and to astronomical problems focusing on the recovery of structure from blurred and noisy images, the identification of gamma-ray bursters, and the compression and denoising of galaxy images. The SkyNet software, which is implemented in standard ANSI C and fully parallelised using MPI, is available at http://www.mrao.cam.ac.uk/software/skynet/.

Data mining techniques on the biological analysis are spreading for most of the areas including the health care and medical information. We have applied the data mining techniques, such as KNN, SVM, MLP or decision trees over a unique dataset, which is collected from 16,380 analysis results for a year. Furthermore we have also used meta-classifiers to question the increased correlation rate between the liver disorder and the liver analysis outputs. The results show that there is a correlation among ALT, AST, Billirubin Direct and Billirubin Total down to 15% of error rate. Also the correlation coefficient is up to 94%. This makes possible to predict the analysis results from each other or disease patterns can be applied over the linear correlation of the parameters.

Time series are ubiquitous, and a measure to assess their similarity is a core part of many computational systems. In particular, the similarity measure is the most essential ingredient of time series clustering and classification systems. Because of this importance, countless approaches to estimate time series similarity have been proposed. However, there is a lack of comparative studies using empirical, rigorous, quantitative, and large-scale assessment strategies. In this article, we provide an extensive evaluation of similarity measures for time series classification following the aforementioned principles. We consider 7 different measures coming from alternative measure `families', and 45 publicly-available time series data sets coming from a wide variety of scientific domains. We focus on out-of-sample classification accuracy, but in-sample accuracies and parameter choices are also discussed. Our work is based on rigorous evaluation methodologies and includes the use of powerful statistical significance tests to derive meaningful conclusions. The obtained results show the equivalence, in terms of accuracy, of a number of measures, but with one single candidate outperforming the rest. Such findings, together with the followed methodology, invite researchers on the field to adopt a more consistent evaluation criteria and a more informed decision regarding the baseline measures to which new developments should be compared.

This paper presents an approach to multilabel classification (MLC) with a large number of labels. Our approach is a reduction to binary classification in which label sets are represented by low dimensional binary vectors. This representation follows the principle of Bloom filters, a space-efficient data structure originally designed for approximate membership testing. We show that a naive application of Bloom filters in MLC is not robust to individual binary classifiers' errors. We then present an approach that exploits a specific feature of real-world datasets when the number of labels is large: many labels (almost) never appear together. Our approch is provably robust, has sublinear training and inference complexity with respect to the number of labels, and compares favorably to state-of-the-art algorithms on two large scale multilabel datasets.

With simultaneous measurements from ever increasing populations of neurons, there is a growing need for sophisticated tools to recover signals from individual neurons. In electrophysiology experiments, this classically proceeds in a two-step process: (i) threshold the waveforms to detect putative spikes and (ii) cluster the waveforms into single units (neurons). We extend previous Bayesian nonparamet- ric models of neural spiking to jointly detect and cluster neurons using a Gamma process model. Importantly, we develop an online approximate inference scheme enabling real-time analysis, with performance exceeding the previous state-of-the- art. Via exploratory data analysis—using data with partial ground truth as well as two novel data sets—we find several features of our model collectively contribute to our improved performance including: (i) accounting for colored noise, (ii) de- tecting overlapping spikes, (iii) tracking waveform dynamics, and (iv) using mul- tiple channels. We hope to enable novel experiments simultaneously measuring many thousands of neurons and possibly adapting stimuli dynamically to probe ever deeper into the mysteries of the brain.

One approach to computer object recognition and modeling the brain's ventral stream involves unsupervised learning of representations that are invariant to common transformations. However, applications of these ideas have usually been limited to 2D affine transformations, e.g., translation and scaling, since they are easiest to solve via convolution. In accord with a recent theory of transformation-invariance, we propose a model that, while capturing other common convolutional networks as special cases, can also be used with arbitrary identity-preserving transformations. The model's wiring can be learned from videos of transforming objects---or any other grouping of images into sets by their depicted object. Through a series of successively more complex empirical tests, we study the invariance/discriminability properties of this model with respect to different transformations. First, we empirically confirm theoretical predictions for the case of 2D affine transformations. Next, we apply the model to non-affine transformations: as expected, it performs well on face verification tasks requiring invariance to the relatively smooth transformations of 3D rotation-in-depth and changes in illumination direction. Surprisingly, it can also tolerate clutter transformations'' which map an image of a face on one background to an image of the same face on a different background. Motivated by these empirical findings, we tested the same model on face verification benchmark tasks from the computer vision literature: Labeled Faces in the Wild, PubFig and a new dataset we gathered---achieving strong performance in these highly unconstrained cases as well."

We investigate the relationship between three fundamental problems in machine learning: binary classification, bipartite ranking, and binary class probability estimation (CPE). It is known that a good binary CPE model can be used to obtain a good binary classification model (by thresholding at 0.5), and also to obtain a good bipartite ranking model (by using the CPE model directly as a ranking model); it is also known that a binary classification model does not necessarily yield a CPE model. However, not much is known about other directions. Formally, these relationships involve regret transfer bounds. In this paper, we introduce the notion of weak regret transfer bounds, where the mapping needed to transform a model from one problem to another depends on the underlying probability distribution (and in practice, must be estimated from data). We then show that, in this weaker sense, a good bipartite ranking model can be used to construct a good classification model (by thresholding at a suitable point), and more surprisingly, also to construct a good binary CPE model (by calibrating the scores of the ranking model).

We use the notion of local Rademacher complexity to design new algorithms for learning kernels. Our algorithms thereby benefit from the sharper learning bounds based on that notion which, under certain general conditions, guarantee a faster convergence rate. We devise two new learning kernel algorithms: one based on a convex optimization problem for which we give an efficient solution using existing learning kernel techniques, and another one that can be formulated as a DC-programming problem for which we describe a solution in detail. We also report the results of experiments with both algorithms in both binary and multi-class classification tasks.