We introduce a method called multi-scale local shape analysis, or MLSA, for extracting features that describe the local structure of points within a dataset. The method uses both geometric and topological features at multiple levels of granularity to capture diverse types of local information for subsequent machine learning algorithms operating on the dataset. Using synthetic and real dataset examples, we demonstrate significant performance improvement of classification algorithms constructed for these datasets with correspondingly augmented features.

In this manuscript we consider the problem of jointly estimating multiple graphical models in high dimensions. We assume that the data are collected from n subjects, each of which consists of T possibly dependent observations. The graphical models of subjects vary, but are assumed to change smoothly corresponding to a measure of closeness between subjects. We propose a kernel based method for jointly estimating all graphical models. Theoretically, under a double asymptotic framework, where both (T,n) and the dimension d can increase, we provide the explicit rate of convergence in parameter estimation. It characterizes the strength one can borrow across different individuals and impact of data dependence on parameter estimation. Empirically, experiments on both synthetic and real resting state functional magnetic resonance imaging (rs-fMRI) data illustrate the effectiveness of the proposed method.

We present an integer programming framework to build accurate and interpretable discrete linear classification models. Unlike existing approaches, our framework is designed to provide practitioners with the control and flexibility they need to tailor accurate and interpretable models for a domain of choice. To this end, our framework can produce models that are fully optimized for accuracy, by minimizing the 0--1 classification loss, and that address multiple aspects of interpretability, by incorporating a range of discrete constraints and penalty functions. We use our framework to produce models that are difficult to create with existing methods, such as scoring systems and M-of-N rule tables. In addition, we propose specially designed optimization methods to improve the scalability of our framework through decomposition and data reduction. We show that discrete linear classifiers can attain the training accuracy of any other linear classifier, and provide an Occam's Razor type argument as to why the use of small discrete coefficients can provide better generalization. We demonstrate the performance and flexibility of our framework through numerical experiments and a case study in which we construct a highly tailored clinical tool for sleep apnea diagnosis.

Probabilistic approaches for tensor factorization aim to extract meaningful structure from incomplete data by postulating low rank constraints. Recently, variational Bayesian (VB) inference techniques have successfully been applied to large scale models. This paper presents full Bayesian inference via VB on both single and coupled tensor factorization models. Our method can be run even for very large models and is easily implemented. It exhibits better prediction performance than existing approaches based on maximum likelihood on several real-world datasets for missing link prediction problem.

Automatic anomaly detection is a major issue in various areas. Beyond mere detection, the identification of the origin of the problem that produced the anomaly is also essential. This paper introduces a general methodology that can assist human operators who aim at classifying monitoring signals. The main idea is to leverage expert knowledge by generating a very large number of indicators. A feature selection method is used to keep only the most discriminant indicators which are used as inputs of a Naive Bayes classifier. The parameters of the classifier have been optimized indirectly by the selection process. Simulated data designed to reproduce some of the anomaly types observed in real world engines.

Statistical tests that compare classification algorithms are univariate and use a single performance measure, e.g., misclassification error, $F$ measure, AUC, and so on. In multivariate tests, comparison is done using multiple measures simultaneously. For example, error is the sum of false positives and false negatives and a univariate test on error cannot make a distinction between these two sources, but a 2-variate test can. Similarly, instead of combining precision and recall in $F$ measure, we can have a 2-variate test on (precision, recall). We use Hotelling's multivariate $T^2$ test for comparing two algorithms, and when we have three or more algorithms we use the multivariate analysis of variance (MANOVA) followed by pairwise post hoc tests. In our experiments, we see that multivariate tests have higher power than univariate tests, that is, they can detect differences that univariate tests cannot. We also discuss how multivariate analysis allows us to automatically extract performance measures that best distinguish the behavior of multiple algorithms.

Automatic anomaly detection is a major issue in various areas. Beyond mere detection, the identification of the source of the problem that produced the anomaly is also essential. This is particularly the case in aircraft engine health monitoring where detecting early signs of failure (anomalies) and helping the engine owner to implement efficiently the adapted maintenance operations (fixing the source of the anomaly) are of crucial importance to reduce the costs attached to unscheduled maintenance. This paper introduces a general methodology that aims at classifying monitoring signals into normal ones and several classes of abnormal ones. The main idea is to leverage expert knowledge by generating a very large number of binary indicators. Each indicator corresponds to a fully parametrized anomaly detector built from parametric anomaly scores designed by experts. A feature selection method is used to keep only the most discriminant indicators which are used at inputs of a Naive Bayes classifier. This give an interpretable classifier based on interpretable anomaly detectors whose parameters have been optimized indirectly by the selection process. The proposed methodology is evaluated on simulated data designed to reproduce some of the anomaly types observed in real world engines.

Many diseases cause significant changes to the concentrations of small molecules (aka metabolites) that appear in a person's biofluids, which means such diseases can often be readily detected from a person's "metabolic profile". This information can be extracted from a biofluid's NMR spectrum. Today, this is often done manually by trained human experts, which means this process is relatively slow, expensive and error-prone. This paper presents a tool, Bayesil, that can quickly, accurately and autonomously produce a complex biofluid's (e.g., serum or CSF) metabolic profile from a 1D1H NMR spectrum. This requires first performing several spectral processing steps then matching the resulting spectrum against a reference compound library, which contains the "signatures" of each relevant metabolite. Many of these steps are novel algorithms and our matching step views spectral matching as an inference problem within a probabilistic graphical model that rapidly approximates the most probable metabolic profile. Our extensive studies on a diverse set of complex mixtures, show that Bayesil can autonomously find the concentration of all NMR-detectable metabolites accurately (~90% correct identification and ~10% quantification error), in <5minutes on a single CPU. These results demonstrate that Bayesil is the first fully-automatic publicly-accessible system that provides quantitative NMR spectral profiling effectively -- with an accuracy that meets or exceeds the performance of trained experts. We anticipate this tool will usher in high-throughput metabolomics and enable a wealth of new applications of NMR in clinical settings. Available at http://www.bayesil.ca.

Many applications in translational medicine require the understanding of how diseases progress through the accumulation of persistent events. Specialized Bayesian networks called monotonic progression networks offer a statistical framework for modeling this sort of phenomenon. Current machine learning tools to reconstruct Bayesian networks from data are powerful but not suited to progression models. We combine the technological advances in machine learning with a rigorous philosophical theory of causation to produce Polaris, a scalable algorithm for learning progression networks that accounts for causal or biological noise as well as logical relations among genetic events, making the resulting models easy to interpret qualitatively. We tested Polaris on synthetically generated data and showed that it outperforms a widely used machine learning algorithm and approaches the performance of the competing special-purpose, albeit clairvoyant algorithm that is given a priori information about the model parameters. We also prove that under certain rather mild conditions, Polaris is guaranteed to converge for sufficiently large sample sizes. Finally, we applied Polaris to point mutation and copy number variation data in Prostate cancer from The Cancer Genome Atlas (TCGA) and found that there are likely three distinct progressions, one major androgen driven progression, one major non-androgen driven progression, and one novel minor androgen driven progression.

We describe a state-of-the-art sentiment analysis system that detects (a) the sentiment of short informal textual messages such as tweets and SMS (message-level task) and (b) the sentiment of a word or a phrase within a message (term-level task). The system is based on a supervised statistical text classification approach leveraging a variety of surface-form, semantic, and sentiment features. The sentiment features are primarily derived from novel high-coverage tweet-specific sentiment lexicons. These lexicons are automatically generated from tweets with sentiment-word hashtags and from tweets with emoticons. To adequately capture the sentiment of words in negated contexts, a separate sentiment lexicon is generated for negated words. The system ranked first in the SemEval-2013 shared task `Sentiment Analysis in Twitter' (Task 2), obtaining an F-score of 69.02 in the message-level task and 88.93 in the term-level task. Post-competition improvements boost the performance to an F-score of 70.45 (message-level task) and 89.50 (term-level task). The system also obtains state-of-the-art performance on two additional datasets: the SemEval-2013 SMS test set and a corpus of movie review excerpts. The ablation experiments demonstrate that the use of the automatically generated lexicons results in performance gains of up to 6.5 absolute percentage points.