As a technology to read brain states from measurable brain activities, brain decoding are widely applied in industries and medical sciences. In spite of high demands in these applications for a universal decoder that can be applied to all individuals simultaneously, large variation in brain activities across individuals has limited the scope of many studies to the development of individual-specific decoders. In this study, we used deep neural network (DNN), a nonlinear hierarchical model, to construct a subject-transfer decoder. Our decoder is the first successful DNN-based subject-transfer decoder. When applied to a large-scale functional magnetic resonance imaging (fMRI) database, our DNN-based decoder achieved higher decoding accuracy than other baseline methods, including support vector machine (SVM). In order to analyze the knowledge acquired by this decoder, we applied principal sensitivity analysis (PSA) to the decoder and visualized the discriminative features that are common to all subjects in the dataset. Our PSA successfully visualized the subject-independent features contributing to the subject-transferability of the trained decoder.

The problem of finding itemsets that are statistically significantly enriched in a class of transactions is complicated by the need to correct for multiple hypothesis testing. Pruning untestable hypotheses was recently proposed as a strategy for this task of significant itemset mining. It was shown to lead to greater statistical power, the discovery of more truly significant itemsets, than the standard Bonferroni correction on real-world datasets. An open question, however, is whether this strategy of excluding untestable hypotheses also leads to greater statistical power in subgraph mining, in which the number of hypotheses is much larger than in itemset mining. Here we answer this question by an empirical investigation on eight popular graph benchmark datasets. We propose a new efficient search strategy, which always returns the same solution as the state-of-the-art approach and is approximately two orders of magnitude faster. Moreover, we exploit the dependence between subgraphs by considering the effective number of tests and thereby further increase the statistical power.

Identification of the influential clinical symptoms and laboratory features that help in the diagnosis of dengue fever in early phase of the illness would aid in designing effective public health management and virological surveillance strategies. Keeping this as our main objective we develop in this paper, a new computational intelligence based methodology that predicts the diagnosis in real time, minimizing the number of false positives and false negatives. Our methodology consists of three major components (i) a novel missing value imputation procedure that can be applied on any data set consisting of categorical (nominal) and/or numeric (real or integer) (ii) a wrapper based features selection method with genetic search for extracting a subset of most influential symptoms that can diagnose the illness and (iii) an alternating decision tree method that employs boosting for generating highly accurate decision rules. The predictive models developed using our methodology are found to be more accurate than the state-of-the-art methodologies used in the diagnosis of the dengue fever.

We study regularized estimation in high-dimensional longitudinal classification problems, using the lasso and fused lasso regularizers. The constructed coefficient estimates are piecewise constant across the time dimension in the longitudinal problem, with adaptively selected change points (break points). We present an efficient algorithm for computing such estimates, based on proximal gradient descent. We apply our proposed technique to a longitudinal data set on Alzheimer's disease from the Cardiovascular Health Study Cognition Study, and use this data set to motivate and demonstrate several practical considerations such as the selection of tuning parameters, and the assessment of model stability.

Binary Hashing is widely used for effective approximate nearest neighbors search. Even though various binary hashing methods have been proposed, very few methods are feasible for extremely high-dimensional features often used in visual tasks today. We propose a novel highly sparse linear hashing method based on pairwise rotations. The encoding cost of the proposed algorithm is $\mathrm{O}(n \log n)$ for n-dimensional features, whereas that of the existing state-of-the-art method is typically $\mathrm{O}(n^2)$. The proposed method is also remarkably faster in the learning phase. Along with the efficiency, the retrieval accuracy is comparable to or slightly outperforming the state-of-the-art. Pairwise rotations used in our method are formulated from an analytical study of the trade-off relationship between quantization error and entropy of binary codes. Although these hashing criteria are widely used in previous researches, its analytical behavior is rarely studied. All building blocks of our algorithm are based on the analytical solution, and it thus provides a fairly simple and efficient procedure.

Accurate approximations to density functionals have recently been obtained via machine learning (ML). By applying ML to a simple function of one variable without any random sampling, we extract the qualitative dependence of errors on hyperparameters. We find universal features of the behavior in extreme limits, including both very small and very large length scales, and the noise-free limit. We show how such features arise in ML models of density functionals.

Determining the 3D structures of biological molecules is a key problem for both biology and medicine. Electron Cryomicroscopy (Cryo-EM) is a promising technique for structure estimation which relies heavily on computational methods to reconstruct 3D structures from 2D images. This paper introduces the challenging Cryo-EM density estimation problem as a novel application for stochastic optimization techniques. Structure discovery is formulated as MAP estimation in a probabilistic latent-variable model, resulting in an optimization problem to which an array of seven stochastic optimization methods are applied. The methods are tested on both real and synthetic data, with some methods recovering reasonable structures in less than one epoch from a random initialization. Complex quasi-Newton methods are found to converge more slowly than simple gradient-based methods, but all stochastic methods are found to converge to similar optima. This method represents a major improvement over existing methods as it is significantly faster and is able to converge from a random initialization.

We introduce and study methods for inferring and learning from correspondences among neurons. The approach enables alignment of data from distinct multiunit studies of nervous systems. We show that the methods for inferring correspondences combine data effectively from cross-animal studies to make joint inferences about behavioral decision making that are not possible with the data from a single animal. We focus on data collection, machine learning, and prediction in the representative and long-studied invertebrate nervous system of the European medicinal leech. Acknowledging the computational intractability of the general problem of identifying correspondences among neurons, we introduce efficient computational procedures for matching neurons across animals. The methods include techniques that adjust for missing cells or additional cells in the different data sets that may reflect biological or experimental variation. The methods highlight the value harnessing inference and learning in new kinds of computational microscopes for multiunit neurobiological studies.

Pointwise-competitive classifier from class F is required to classify identically to the best classifier in hindsight from F. For noisy, agnostic settings we present a strategy for learning pointwise-competitive classifiers from a finite training sample provided that the classifier can abstain from prediction at a certain region of its choice. For some interesting hypothesis classes and families of distributions, the measure of this rejected region is shown to be diminishing at a fast rate, with high probability. Exact implementation of the proposed learning strategy is dependent on an ERM oracle that can be hard to compute in the agnostic case. We thus consider a heuristic approximation procedure that is based on SVMs, and show empirically that this algorithm consistently outperforms a traditional rejection mechanism based on distance from decision boundary.

We provide a general theory of the expectation-maximization (EM) algorithm for inferring high dimensional latent variable models. In particular, we make two contributions: (i) For parameter estimation, we propose a novel high dimensional EM algorithm which naturally incorporates sparsity structure into parameter estimation. With an appropriate initialization, this algorithm converges at a geometric rate and attains an estimator with the (near-)optimal statistical rate of convergence. (ii) Based on the obtained estimator, we propose new inferential procedures for testing hypotheses and constructing confidence intervals for low dimensional components of high dimensional parameters. For a broad family of statistical models, our framework establishes the first computationally feasible approach for optimal estimation and asymptotic inference in high dimensions. Our theory is supported by thorough numerical results.