This paper proposes Deep Hyperalignment (DHA) as a regularized, deep extension, scalable Hyperalignment (HA) method, which is well-suited for applying functional alignment to fMRI datasets with nonlinearity, high-dimensionality (broad ROI), and a large number of subjects. Unlink previous methods, DHA is not limited by a restricted fixed kernel function. Further, it uses a parametric approach, rank-m Singular Value Decomposition (SVD), and stochastic gradient descent for optimization. Therefore, DHA has a suitable time complexity for large datasets, and DHA does not require the training data when it computes the functional alignment for a new subject. Experimental studies on multi-subject fMRI analysis confirm that the DHA method achieves superior performance to other state-of-the-art HA algorithms.

Word embeddings are a powerful approach to capturing semantic similarity among terms in a vocabulary. In this paper, we develop exponential family embeddings, which extends the idea of word embeddings to other types of high-dimensional data. As examples, we studied several types of data: neural data with real-valued observations, count data from a market basket analysis, and ratings data from a movie recommendation system. The main idea is that each observation is modeled conditioned on a set of latent embeddings and other observations, called the context, where the way the context is defined depends on the problem. In language the context is the surrounding words; in neuroscience the context is close-by neurons; in market basket data the context is other items in the shopping cart. Each instance of an embedding defines the context, the exponential family of conditional distributions, and how the embedding vectors are shared across data. We infer the embeddings with stochastic gradient descent, with an algorithm that connects closely to generalized linear models. On all three of our applications--neural activity of zebrafish, users' shopping behavior, and movie ratings--we found that exponential family embedding models are more effective than other dimension reduction methods. They better reconstruct held-out data and find interesting qualitative structure.

Due to their simplicity and excellent performance, parallel asynchronous variants of stochastic gradient descent have become popular methods to solve a wide range of large-scale optimization problems on multi-core architectures. Yet, despite their practical success, support for nonsmooth objectives is still lacking, making them unsuitable for many problems of interest in machine learning, such as the Lasso, group Lasso or empirical risk minimization with convex constraints. In this work, we propose and analyze ProxASAGA, a fully asynchronous sparse method inspired by SAGA, a variance reduced incremental gradient algorithm. The proposed method is easy to implement and significantly outperforms the state of the art on several nonsmooth, large-scale problems. We prove that our method achieves a theoretical linear speedup with respect to the sequential version under assumptions on the sparsity of gradients and block-separability of the proximal term. Empirical benchmarks on a multi-core architecture illustrate practical speedups of up to 12x on a 20-core machine.

Stochastic Gradient Markov Chain Monte Carlo (SG-MCMC) algorithms have become increasingly popular for Bayesian inference in large-scale applications. Even though these methods have proved useful in several scenarios, their performance is often limited by their bias. In this study, we propose a novel sampling algorithm that aims to reduce the bias of SG-MCMC while keeping the variance at a reasonable level. Our approach is based on a numerical sequence acceleration method, namely the Richardson-Romberg extrapolation, which simply boils down to running almost the same SG-MCMC algorithm twice in parallel with different step sizes. We illustrate our framework on the popular Stochastic Gradient Langevin Dynamics (SGLD) algorithm and propose a novel SG-MCMC algorithm referred to as Stochastic Gradient Richardson-Romberg Langevin Dynamics (SGRRLD). We provide formal theoretical analysis and show that SGRRLD is asymptotically consistent, satisfies a central limit theorem, and its non-asymptotic bias and the mean squared-error can be bounded. Our results show that SGRRLD attains higher rates of convergence than SGLD in both finite-time and asymptotically, and it achieves the theoretical accuracy of the methods that are based on higher-order integrators. We support our findings using both synthetic and real data experiments.

Deep neural networks (DNNs) and probabilistic graphical models (PGMs) are the two main tools for statistical modeling. While DNNs provide the ability to model rich and complex relationships between input and output variables, PGMs provide the ability to encode dependencies among the output variables themselves. End-to-end training methods for models with structured graphical dependencies on top of neural predictions have recently emerged as a principled way of combining these two paradigms. While these models have proven to be powerful in discriminative settings with discrete outputs, extensions to structured continuous spaces, as well as performing efficient inference in these spaces, are lacking. We propose non-parametric structured output networks (NSON), a modular approach that cleanly separates a non-parametric, structured posterior representation from a discriminative inference scheme but allows joint end-to-end training of both components. Our experiments evaluate the ability of NSONs to capture structured posterior densities (modeling) and to compute complex statistics of those densities (inference). We compare our model to output spaces of varying expressiveness and popular variational and sampling-based inference algorithms.

Neural Information Processing Systems http://nips.cc/

In this paper, we aim to answer three key open questions: (i) whether and how brain networks are cross-correlated at different time scales with long-range dependencies ("long-memory" process,

As datasets grow richer, an important challenge is to leverage the full features in the data to maximize the number of useful discoveries while controlling for false positives. We address this problem in the context of multiple hypotheses testing, where for each hypothesis, we observe a p-value along with a set of features specific to that hypothesis. For example, in genetic association studies, each hypothesis tests the correlation between a variant and the trait.

Neural Information Processing Systems http://nips.cc/

There are numerous examples where accounting for the predictors' interactions is of interest, including problems of identifying epistasis (gene-gene) and gene-environment interactions in genetics