Pedigrees, or family trees, are directed graphs used to identify sites of the genome that are correlated with the presence or absence of a disease. With the advent of genotyping and sequencing technologies, there has been an explosion in the amount of data available, both in the number of individuals and in the number of sites. Some pedigrees number in the thousands of individuals. Meanwhile, analysis methods have remained limited to pedigrees of <100 individuals which limits analyses to many small independent pedigrees. Disease models, such those used for the linkage analysis log-odds (LOD) estimator, have similarly been limited. This is because linkage anlysis was originally designed with a different task in mind, that of ordering the sites in the genome, before there were technologies that could reveal the order. LODs are difficult to interpret and nontrivial to extend to consider interactions among sites. These developments and difficulties call for the creation of modern methods of pedigree analysis. Drawing from recent advances in graphical model inference and transducer theory, we introduce a simple yet powerful formalism for expressing genetic disease models. We show that these disease models can be turned into accurate and efficient estimators. The technique we use for constructing the variational approximation has potential applications to inference in other large-scale graphical models. This method allows inference on larger pedigrees than previously analyzed in the literature, which improves disease site prediction.

Sparse graphical modelling/inverse covariance selection is an important problem in machine learning and has seen significant advances in recent years. A major focus has been on methods which perform model selection in high dimensions. To this end, numerous convex $\ell_1$ regularization approaches have been proposed in the literature. It is not however clear which of these methods are optimal in any well-defined sense. A major gap in this regard pertains to the rate of convergence of proposed optimization methods. To address this, an iterative thresholding algorithm for numerically solving the $\ell_1$-penalized maximum likelihood problem for sparse inverse covariance estimation is presented. The proximal gradient method considered in this paper is shown to converge at a linear rate, a result which is the first of its kind for numerically solving the sparse inverse covariance estimation problem. The convergence rate is provided in closed form, and is related to the condition number of the optimal point. Numerical results demonstrating the proven rate of convergence are presented.

Imitation Learning has been shown to be successful in solving many challenging real-world problems. Some recent approaches give strong performance guarantees by training the policy iteratively. However, it is important to note that these guarantees depend on how well the policy we found can imitate the oracle on the training data. When there is a substantial difference between the oracle's ability and the learner's policy space, we may fail to find a policy that has low error on the training set. In such cases, we propose to use a coach that demonstrates easy-to-learn actions for the learner and gradually approaches the oracle. By a reduction of learning by demonstration to online learning, we prove that coaching can yield a lower regret bound than using the oracle. We apply our algorithm to a novel cost-sensitive dynamic feature selection problem, a hard decision problem that considers a user-specified accuracy-cost trade-off. Experimental results on UCI datasets show that our method outperforms state-of-the-art imitation learning methods in dynamic features selection and two static feature selection methods.

In conventional causal discovery, structural equation models (SEM) are directly applied to the observed variables, meaning that the causal effect can be represented as a function of the direct causes themselves. However, in many real world problems, there are significant dependencies in the variances or energies, which indicates that causality may possibly take place at the level of variances or energies. In this paper, we propose a probabilistic causal scale-mixture model with spatiotemporal variance dependencies to represent a specific type of generating mechanism of the observations. In particular, the causal mechanism including contemporaneous and temporal causal relations in variances or energies is represented by a Structural Vector AutoRegressive model (SVAR). We prove the identifiability of this model under the non-Gaussian assumption on the innovation processes. We also propose algorithms to estimate the involved parameters and discover the contemporaneous causal structure. Experiments on synthesis and real world data are conducted to show the applicability of the proposed model and algorithms.

We prove a new exponential concentration inequality for a plug-in estimator of the Shannon mutual information. Previous results on mutual information estimation only bounded expected error. The advantage of having the exponential inequality is that, combined with the union bound, we can guarantee accurate estimators of the mutual information for many pairs of random variables simultaneously. As an application, we show how to use such a result to optimally estimate the density function and graph of a distribution which is Markov to a forest graph.

We study the problem of diverse feature selection in linear regression: selecting a small subset of diverse features that can predict a given objective. Diversity is useful for several reasons such as interpretability, robustness to noise, etc. We propose several spectral regularizers that capture a notion of diversity of features and show that these are all submodular set functions. These regularizers, when added to the objective function for linear regression, result in approximately submodular functions, which can then be maximized approximately by efficient greedy and local search algorithms, with provable guarantees. We compare our algorithms to traditional greedy and $\ell_1$-regularization schemes and show that we obtain a more diverse set of features that result in the regression problem being stable under perturbations.

Positive definite operator-valued kernels generalize the well-known notion of reproducing kernels, and are naturally adapted to multi-output learning situations. This paper addresses the problem of learning a finite linear combination of infinite-dimensional operator-valued kernels which are suitable for extending functional data analysis methods to nonlinear contexts. We study this problem in the case of kernel ridge regression for functional responses with an lr-norm constraint on the combination coefficients. The resulting optimization problem is more involved than those of multiple scalar-valued kernel learning since operator-valued kernels pose more technical and theoretical issues. We propose a multiple operator-valued kernel learning algorithm based on solving a system of linear operator equations by using a block coordinate-descent procedure. We experimentally validate our approach on a functional regression task in the context of finger movement prediction in brain-computer interfaces.

This paper adresses the inverse reinforcement learning (IRL) problem, that is inferring a reward for which a demonstrated expert behavior is optimal. We introduce a new algorithm, SCIRL, whose principle is to use the so-called feature expectation of the expert as the parameterization of the score function of a multi-class classifier. This approach produces a reward function for which the expert policy is provably near-optimal. Contrary to most of existing IRL algorithms, SCIRL does not require solving the direct RL problem. Moreover, with an appropriate heuristic, it can succeed with only trajectories sampled according to the expert behavior. This is illustrated on a car driving simulator.

This paper proposes an efficient online learning algorithm to track the smoothing functions of Additive Models. The key idea is to combine the linear representation of Additive Models with a Recursive Least Squares (RLS) filter. In order to quickly track changes in the model and put more weight on recent data, the RLS filter uses a forgetting factor which exponentially weights down observations by the order of their arrival. The tracking behaviour is further enhanced by using an adaptive forgetting factor which is updated based on the gradient of the a priori errors. Using results from Lyapunov stability theory, upper bounds for the learning rate are analyzed. The proposed algorithm is applied to 5 years of electricity load data provided by the French utility company Electricite de France (EDF). Compared to state-of-the-art methods, it achieves a superior performance in terms of model tracking and prediction accuracy.

Alzheimer disease (AD) is a neurodegenerative disorder characterized by progressive impairment of memory and other cognitive functions. Regression analysis has been studied to relate neuroimaging measures to cognitive status. However, whether these measures have further predictive power to infer a trajectory of cognitive performance over time is still an under-explored but important topic in AD research. We propose a novel high-order multi-task learning model to address this issue. The proposed model explores the temporal correlations existing in data features and regression tasks by the structured sparsity-inducing norms. In addition, the sparsity of the model enables the selection of a small number of MRI measures while maintaining high prediction accuracy. The empirical studies, using the baseline MRI and serial cognitive data of the ADNI cohort, have yielded promising results.