We propose a novel diverse feature selection method based on determinantal point processes (DPPs). Our model enables one to flexibly define diversity based on the covariance of features (similar to orthogonal matching pursuit) or alternatively based on side information. We introduce our approach in the context of Bayesian sparse regression, employing a DPP as a variational approximation to the true spike and slab posterior distribution. We subsequently show how this variational DPP approximation generalizes and extends mean-field approximation, and can be learned efficiently by exploiting the fast sampling properties of DPPs. Our motivating application comes from bioinformatics, where we aim to identify a diverse set of genes whose expression profiles predict a tumor type where the diversity is defined with respect to a gene-gene interaction network. We also explore an application in spatial statistics. In both cases, we demonstrate that the proposed method yields significantly more diverse feature sets than classic sparse methods, without compromising accuracy.

According to Cobanoglu et al and Murphy, it is now widely acknowledged that the single target paradigm (one protein or target, one disease, one drug) that has been the dominant premise in drug development in the recent past is untenable. More often than not, a drug-like compound (ligand) can be promiscuous - that is, it can interact with more than one target protein. In recent years, in in silico target prediction methods the promiscuity issue has been approached computationally in different ways. In this study we confine attention to the so-called ligand-based target prediction machine learning approaches, commonly referred to as target-fishing. With a few exceptions, the target-fishing approaches that are currently ubiquitous in cheminformatics literature can be essentially viewed as single-label multi-classification schemes; these approaches inherently bank on the single target paradigm assumption that a ligand can home in on one specific target. In order to address the ligand promiscuity issue, one might be able to cast target-fishing as a multi-label multi-class classification problem. For illustrative and comparison purposes, single-label and multi-label Naive Bayes classification models (denoted here by SMM and MMM, respectively) for target-fishing were implemented. The models were constructed and tested on 65,587 compounds and 308 targets retrieved from the ChEMBL17 database. SMM and MMM performed differently: for 16,344 test compounds, the MMM model returned recall and precision values of 0.8058 and 0.6622, respectively; the corresponding recall and precision values yielded by the SMM model were 0.7805 and 0.7596, respectively. However, at a significance level of 0.05 and one degree of freedom McNemar test performed on the target prediction results returned by SMM and MMM for the 16,344 test ligands gave a chi-squared value of 15.656, in favour of the MMM approach.

Empirical risk minimization (ERM) is a fundamental learning rule for statistical learning problems where the data is generated according to some unknown distribution $\mathsf{P}$ and returns a hypothesis $f$ chosen from a fixed class $\mathcal{F}$ with small loss $\ell$. In the parametric setting, depending upon $(\ell, \mathcal{F},\mathsf{P})$ ERM can have slow $(1/\sqrt{n})$ or fast $(1/n)$ rates of convergence of the excess risk as a function of the sample size $n$. There exist several results that give sufficient conditions for fast rates in terms of joint properties of $\ell$, $\mathcal{F}$, and $\mathsf{P}$, such as the margin condition and the Bernstein condition. In the non-statistical prediction with expert advice setting, there is an analogous slow and fast rate phenomenon, and it is entirely characterized in terms of the mixability of the loss $\ell$ (there being no role there for $\mathcal{F}$ or $\mathsf{P}$). The notion of stochastic mixability builds a bridge between these two models of learning, reducing to classical mixability in a special case. The present paper presents a direct proof of fast rates for ERM in terms of stochastic mixability of $(\ell,\mathcal{F}, \mathsf{P})$, and in so doing provides new insight into the fast-rates phenomenon. The proof exploits an old result of Kemperman on the solution to the general moment problem. We also show a partial converse that suggests a characterization of fast rates for ERM in terms of stochastic mixability is possible.

Conditional Value at Risk (CVaR) is a prominent risk measure that is being used extensively in various domains. We develop a new formula for the gradient of the CVaR in the form of a conditional expectation. Based on this formula, we propose a novel sampling-based estimator for the CVaR gradient, in the spirit of the likelihood-ratio method. We analyze the bias of the estimator, and prove the convergence of a corresponding stochastic gradient descent algorithm to a local CVaR optimum. Our method allows to consider CVaR optimization in new domains. As an example, we consider a reinforcement learning application, and learn a risk-sensitive controller for the game of Tetris.

Human computation or crowdsourcing involves joint inference of the ground-truth-answers and the worker-abilities by optimizing an objective function, for instance, by maximizing the data likelihood based on an assumed underlying model. A variety of methods have been proposed in the literature to address this inference problem. As far as we know, none of the objective functions in existing methods is convex. In machine learning and applied statistics, a convex function such as the objective function of support vector machines (SVMs) is generally preferred, since it can leverage the high-performance algorithms and rigorous guarantees established in the extensive literature on convex optimization. One may thus wonder if there exists a meaningful convex objective function for the inference problem in human computation. In this paper, we investigate this convexity issue for human computation. We take an axiomatic approach by formulating a set of axioms that impose two mild and natural assumptions on the objective function for the inference. Under these axioms, we show that it is unfortunately impossible to ensure convexity of the inference problem. On the other hand, we show that interestingly, in the absence of a requirement to model "spammers", one can construct reasonable objective functions for crowdsourcing that guarantee convex inference.

Originally designed to model text, topic modeling has become a powerful tool for uncovering latent structure in domains including medicine, finance, and vision. The goals for the model vary depending on the application: in some cases, the discovered topics may be used for prediction or some other downstream task. In other cases, the content of the topic itself may be of intrinsic scientific interest. Unfortunately, even using modern sparse techniques, the discovered topics are often difficult to interpret due to the high dimensionality of the underlying space. To improve topic interpretability, we introduce Graph-Sparse LDA, a hierarchical topic model that leverages knowledge of relationships between words (e.g., as encoded by an ontology). In our model, topics are summarized by a few latent concept-words from the underlying graph that explain the observed words. Graph-Sparse LDA recovers sparse, interpretable summaries on two real-world biomedical datasets while matching state-of-the-art prediction performance.

We study the problem of predicting the future, though only in the probabilistic sense of estimating a future state of a time-varying probability distribution. This is not only an interesting academic problem, but solving this extrapolation problem also has many practical application, e.g. for training classifiers that have to operate under time-varying conditions. Our main contribution is a method for predicting the next step of the time-varying distribution from a given sequence of sample sets from earlier time steps. For this we rely on two recent machine learning techniques: embedding probability distributions into a reproducing kernel Hilbert space, and learning operators by vector-valued regression. We illustrate the working principles and the practical usefulness of our method by experiments on synthetic and real data. We also highlight an exemplary application: training a classifier in a domain adaptation setting without having access to examples from the test time distribution at training time.

Estimating the difficulty level of math word problems is an important task for many educational applications. Identification of relevant and irrelevant sentences in math word problems is an important step for calculating the difficulty levels of such problems. This paper addresses a novel application of text categorization to identify two types of sentences in mathematical word problems, namely relevant and irrelevant sentences. A novel joint probabilistic classification model is proposed to estimate the joint probability of classification decisions for all sentences of a math word problem by utilizing the correlation among all sentences along with the correlation between the question sentence and other sentences, and sentence text. The proposed model is compared with i) a SVM classifier which makes independent classification decisions for individual sentences by only using the sentence text and ii) a novel SVM classifier that considers the correlation between the question sentence and other sentences along with the sentence text. An extensive set of experiments demonstrates the effectiveness of the joint probabilistic classification model for identifying relevant and irrelevant sentences as well as the novel SVM classifier that utilizes the correlation between the question sentence and other sentences. Furthermore, empirical results and analysis show that i) it is highly beneficial not to remove stopwords and ii) utilizing part of speech tagging does not make a significant improvement although it has been shown to be effective for the related task of math word problem type classification.

In this thesis, we propose several modelling strategies to tackle evolving data in different contexts. In the framework of static clustering, we start by introducing a soft kernel spectral clustering (SKSC) algorithm, which can better deal with overlapping clusters with respect to kernel spectral clustering (KSC) and provides more interpretable outcomes. Afterwards, a whole strategy based upon KSC for community detection of static networks is proposed, where the extraction of a high quality training sub-graph, the choice of the kernel function, the model selection and the applicability to large-scale data are key aspects. This paves the way for the development of a novel clustering algorithm for the analysis of evolving networks called kernel spectral clustering with memory effect (MKSC), where the temporal smoothness between clustering results in successive time steps is incorporated at the level of the primal optimization problem, by properly modifying the KSC formulation. Later on, an application of KSC to fault detection of an industrial machine is presented. Here, a smart pre-processing of the data by means of a proper windowing operation is necessary to catch the ongoing degradation process affecting the machine. In this way, in a genuinely unsupervised manner, it is possible to raise an early warning when necessary, in an online fashion. Finally, we propose a new algorithm called incremental kernel spectral clustering (IKSC) for online learning of non-stationary data. This ambitious challenge is faced by taking advantage of the out-of-sample property of kernel spectral clustering (KSC) to adapt the initial model, in order to tackle merging, splitting or drifting of clusters across time. Real-world applications considered in this thesis include image segmentation, time-series clustering, community detection of static and evolving networks.

This paper proposed a new regression model called $l_1$-regularized outlier isolation and regression (LOIRE) and a fast algorithm based on block coordinate descent to solve this model. Besides, assuming outliers are gross errors following a Bernoulli process, this paper also presented a Bernoulli estimate model which, in theory, should be very accurate and robust due to its complete elimination of affections caused by outliers. Though this Bernoulli estimate is hard to solve, it could be approximately achieved through a process which takes LOIRE as an important intermediate step. As a result, the approximate Bernoulli estimate is a good combination of Bernoulli estimate's accuracy and LOIRE regression's efficiency with several simulations conducted to strongly verify this point. Moreover, LOIRE can be further extended to realize robust rank factorization which is powerful in recovering low-rank component from massive corruptions. Extensive experimental results showed that the proposed method outperforms state-of-the-art methods like RPCA and GoDec in the aspect of computation speed with a competitive performance.