In many fields it is common to have access to information about sums of random variables and to desire information about those variables themselves. In mass spectrometry, when two (or more) analytes with similar mass-to-charge 1 are measured, the intensity of the resulting peak is a function of the sum of abundances of those analytes (this problem occurs not only in the mass spectrometry of small molecules, but also in measuring isotope measurement in elemental and nuclear mass spectrometry). In transcriptomics, the abundance of a particular non-unique read (i.e., an RNA sequence that maps to multiple locations in the transcriptome or genome) provides information about the sum of the abundances of all transcripts that contain the read (each transcript weighted by how many copies of the read it carries). Proteomics has its own version of non-unique reads, shared peptides which can be found in multiple proteins (not only are shared peptides the principal source of difficulty in protein inference [14, 17, 18], they are also responsible for the difficulty evaluating putatative sets of discovered proteins [16, 19]). In population genetics, the prior knowledge about population structure can suggest an expected number of individuals with a particular genotype, which in turn yields probabilistic information about the individuals whose aggregate genotypes are expected to produce that sum (inference is particularly pronounced in polyploids, which increase the dimensionality of the problem [15]).

With an eye towards human-centered automation, we contribute to the development of a systematic means to infer features of human decision-making from behavioral data. Motivated by the common use of softmax selection in models of human decision-making, we study the maximum likelihood parameter estimation problem for softmax decision-making models with linear objective functions. We present conditions under which the likelihood function is convex. These allow us to provide sufficient conditions for convergence of the resulting maximum likelihood estimator and to construct its asymptotic distribution. In the case of models with nonlinear objective functions, we show how the estimator can be applied by linearizing about a nominal parameter value. We apply the estimator to fit the stochastic UCL (Upper Credible Limit) model of human decision-making to human subject data. We show statistically significant differences in behavior across related, but distinct, tasks.

We develop a new compressive sensing (CS) inversion algorithm by utilizing the Gaussian mixture model (GMM). While the compressive sensing is performed globally on the entire image as implemented in our lensless camera, a low-rank GMM is imposed on the local image patches. This low-rank GMM is derived via eigenvalue thresholding of the GMM trained on the projection of the measurement data, thus learned {\em in situ}. The GMM and the projection of the measurement data are updated iteratively during the reconstruction. Our GMM algorithm degrades to the piecewise linear estimator (PLE) if each patch is represented by a single Gaussian model. Inspired by this, a low-rank PLE algorithm is also developed for CS inversion, constituting an additional contribution of this paper. Extensive results on both simulation data and real data captured by the lensless camera demonstrate the efficacy of the proposed algorithm. Furthermore, we compare the CS reconstruction results using our algorithm with the JPEG compression. Simulation results demonstrate that when limited bandwidth is available (a small number of measurements), our algorithm can achieve comparable results as JPEG.

We present two new statistical machine learning methods designed to learn on fully homomorphic encrypted (FHE) data. The introduction of FHE schemes following Gentry (2009) opens up the prospect of privacy preserving statistical machine learning analysis and modelling of encrypted data without compromising security constraints. We propose tailored algorithms for applying extremely random forests, involving a new cryptographic stochastic fraction estimator, and na\"{i}ve Bayes, involving a semi-parametric model for the class decision boundary, and show how they can be used to learn and predict from encrypted data. We demonstrate that these techniques perform competitively on a variety of classification data sets and provide detailed information about the computational practicalities of these and other FHE methods.

Dirichlet Process(DP) is a Bayesian non-parametric prior for infinite mixture modeling, where the number of mixture components grows with the number of data items. The Hierarchical Dirichlet Process (HDP), is an extension of DP for grouped data, often used for non-parametric topic modeling, where each group is a mixture over shared mixture densities. The Nested Dirichlet Process (nDP), on the other hand, is an extension of the DP for learning group level distributions from data, simultaneously clustering the groups. It allows group level distributions to be shared across groups in a non-parametric setting, leading to a non-parametric mixture of mixtures. The nCRF extends the nDP for multilevel non-parametric mixture modeling, enabling modeling topic hierarchies. However, the nDP and nCRF do not allow sharing of distributions as required in many applications, motivating the need for multi-level non-parametric admixture modeling. We address this gap by proposing multi-level nested HDPs (nHDP) where the base distribution of the HDP is itself a HDP at each level thereby leading to admixtures of admixtures at each level. Because of couplings between various HDP levels, scaling up is naturally a challenge during inference. We propose a multi-level nested Chinese Restaurant Franchise (nCRF) representation for the nested HDP, with which we outline an inference algorithm based on Gibbs Sampling. We evaluate our model with the two level nHDP for non-parametric entity topic modeling where an inner HDP creates a countably infinite set of topic mixtures and associates them with author entities, while an outer HDP associates documents with these author entities. In our experiments on two real world research corpora, the nHDP is able to generalize significantly better than existing models and detect missing author entities with a reasonable level of accuracy.

We investigate a Gaussian mixture model (GMM) with component means constrained in a pre-selected subspace. Applications to classification and clustering are explored. An EM-type estimation algorithm is derived. We prove that the subspace containing the component means of a GMM with a common covariance matrix also contains the modes of the density and the class means. This motivates us to find a subspace by applying weighted principal component analysis to the modes of a kernel density and the class means. To circumvent the difficulty of deciding the kernel bandwidth, we acquire multiple subspaces from the kernel densities based on a sequence of bandwidths. The GMM constrained by each subspace is estimated; and the model yielding the maximum likelihood is chosen. A dimension reduction property is proved in the sense of being informative for classification or clustering. Experiments on real and simulated data sets are conducted to examine several ways of determining the subspace and to compare with the reduced rank mixture discriminant analysis (MDA). Our new method with the simple technique of spanning the subspace only by class means often outperforms the reduced rank MDA when the subspace dimension is very low, making it particularly appealing for visualization.

We present a novel hybrid algorithm for Bayesian network structure learning, called Hybrid HPC (H2PC). It first reconstructs the skeleton of a Bayesian network and then performs a Bayesian-scoring greedy hill-climbing search to orient the edges. It is based on a subroutine called HPC, that combines ideas from incremental and divide-and-conquer constraint-based methods to learn the parents and children of a target variable. We conduct an experimental comparison of H2PC against Max-Min Hill-Climbing (MMHC), which is currently the most powerful state-of-the-art algorithm for Bayesian network structure learning, on several benchmarks with various data sizes. Our extensive experiments show that H2PC outperforms MMHC both in terms of goodness of fit to new data and in terms of the quality of the network structure itself, which is closer to the true dependence structure of the data. The source code (in R) of H2PC as well as all data sets used for the empirical tests are publicly available.

We are interested in solving the multiple measurement vector (MMV) problem for instances, where the underlying sparsity pattern exhibit spatio-temporal structure motivated by the electroencephalogram (EEG) source localization problem. We propose a probabilistic model that takes this structure into account by generalizing the structured spike and slab prior and the associated Expectation Propagation inference scheme. Based on numerical experiments, we demonstrate the viability of the model and the approximate inference scheme.

We present a novel approach for fully non-stationary Gaussian process regression (GPR), where all three key parameters -- noise variance, signal variance and lengthscale -- can be simultaneously input-dependent. We develop gradient-based inference methods to learn the unknown function and the non-stationary model parameters, without requiring any model approximations. We propose to infer full parameter posterior with Hamiltonian Monte Carlo (HMC), which conveniently extends the analytical gradient-based GPR learning by guiding the sampling with model gradients. We also learn the MAP solution from the posterior by gradient ascent. In experiments on several synthetic datasets and in modelling of temporal gene expression, the nonstationary GPR is shown to be necessary for modeling realistic input-dependent dynamics, while it performs comparably to conventional stationary or previous non-stationary GPR models otherwise.

We present a Bayesian non-negative tensor factorization model for count-valued tensor data, and develop scalable inference algorithms (both batch and online) for dealing with massive tensors. Our generative model can handle overdispersed counts as well as infer the rank of the decomposition. Moreover, leveraging a reparameterization of the Poisson distribution as a multinomial facilitates conjugacy in the model and enables simple and efficient Gibbs sampling and variational Bayes (VB) inference updates, with a computational cost that only depends on the number of nonzeros in the tensor. The model also provides a nice interpretability for the factors; in our model, each factor corresponds to a "topic". We develop a set of online inference algorithms that allow further scaling up the model to massive tensors, for which batch inference methods may be infeasible. We apply our framework on diverse real-world applications, such as \emph{multiway} topic modeling on a scientific publications database, analyzing a political science data set, and analyzing a massive household transactions data set.