We propose a multivariate online dictionary-learning method for obtaining decompositions of brain images with structured and sparse components (aka atoms). Sparsity is to be understood in the usual sense: the dictionary atoms are constrained to contain mostly zeros. This is imposed via an $\ell_1$-norm constraint. By structured, we mean that the atoms are piece-wise smooth and compact, thus making up blobs, as opposed to scattered patterns of activation. We propose to use a Sobolev (Laplacian) penalty to impose this type of structure. Combining the two penalties, we obtain decompositions that properly delineate brain structures from functional images. This non-trivially extends the online dictionary-learning work of Mairal et al. (2010), at the price of only a factor of 2 or 3 on the overall running time. Just like the Mairal et al. (2010) reference method, the online nature of our proposed algorithm allows it to scale to arbitrarily sized datasets. Experiments on brain data show that our proposed method extracts structured and denoised dictionaries that are more intepretable and better capture inter-subject variability in small medium, and large-scale regimes alike, compared to state-of-the-art models.

New silicon technology is enabling large-scale electrophysiological recordings in vivo from hundreds to thousands of channels. Interpreting these recordings requires scalable and accurate automated methods for spike sorting, which should minimize the time required for manual curation of the results. Here we introduce KiloSort, a new integrated spike sorting framework that uses template matching both during spike detection and during spike clustering. KiloSort models the electrical voltage as a sum of template waveforms triggered on the spike times, which allows overlapping spikes to be identified and resolved. Unlike previous algorithms that compress the data with PCA, KiloSort operates on the raw data which allows it to construct a more accurate model of the waveforms. Processing times are faster than in previous algorithms thanks to batch-based optimization on GPUs. We compare KiloSort to an established algorithm and show favorable performance, at much reduced processing times. A novel post-clustering merging step based on the continuity of the templates further reduced substantially the number of manual operations required on this data, for the neurons with near-zero error rates, paving the way for fully automated spike sorting of multichannel electrode recordings.

Accurately measuring the similarity between text documents lies at the core of many real world applications of machine learning. These include web-search ranking, document recommendation, multi-lingual document matching, and article categorization. Recently, a new document metric, the word mover's distance (WMD), has been proposed with unprecedented results on kNN-based document classification. The WMD elevates high quality word embeddings to document metrics by formulating the distance between two documents as an optimal transport problem between the embedded words. However, the document distances are entirely unsupervised and lack a mechanism to incorporate supervision when available. In this paper we propose an efficient technique to learn a supervised metric, which we call the Supervised WMD (S-WMD) metric. Our algorithm learns document distances that measure the underlying semantic differences between documents by leveraging semantic differences between individual words discovered during supervised training. This is achieved with an linear transformation of the underlying word embedding space and tailored word-specific weights, learned to minimize the stochastic leave-one-out nearest neighbor classification error on a per-document level. We evaluate our metric on eight real-world text classification tasks on which S-WMD consistently outperforms almost all of our 26 competitive baselines.

Decision tree (and its extensions such as Gradient Boosting Decision Trees and Random Forest) is a widely used machine learning algorithm, due to its practical effectiveness and model interpretability. With the emergence of big data, there is an increasing need to parallelize the training process of decision tree. However, most existing attempts along this line suffer from high communication costs. In this paper, we propose a new algorithm, called \emph{Parallel Voting Decision Tree (PV-Tree)}, to tackle this challenge. After partitioning the training data onto a number of (e.g., $M$) machines, this algorithm performs both local voting and global voting in each iteration.

Even in state-spaces of modest size, planning is plagued by the "curse of dimensionality". This problem is particularly acute in human and animal cognition given the limited capacity of working memory, and the time pressures under which planning often occurs in the natural environment. Hierarchically organized modular representations have long been suggested to underlie the capacity of biological systems to efficiently and flexibly plan in complex environments. However, the principles underlying efficient modularization remain obscure, making it difficult to identify its behavioral and neural signatures. Here, we develop a normative theory of efficient state-space representations which partitions an environment into distinct modules by minimizing the average (information theoretic) description length of planning within the environment, thereby optimally trading off the complexity of planning across and within modules. We show that such optimal representations provide a unifying account for a diverse range of hitherto unrelated phenomena at multiple levels of behavior and neural representation.

Deep neural networks have received a considerable attention due to the success of their training for real world machine learning applications. They are also of great interest to the understanding of sensory processing in cortical sensory hierarchies. The purpose of this work is to advance our theoretical understanding of the computational benefits of these architectures. Using a simple model of clustered noisy inputs and a simple learning rule, we provide analytically derived recursion relations describing the propagation of the signals along the deep network. By analysis of these equations, and defining performance measures, we show that these model networks have optimal depths. We further explore the dependence of the optimal architecture on the system parameters.

We propose probabilistic latent variable models for multi-view anomaly detection, which is the task of finding instances that have inconsistent views given multi-view data. With the proposed model, all views of a non-anomalous instance are assumed to be generated from a single latent vector. On the other hand, an anomalous instance is assumed to have multiple latent vectors, and its different views are generated from different latent vectors. By inferring the number of latent vectors used for each instance with Dirichlet process priors, we obtain multi-view anomaly scores. The proposed model can be seen as a robust extension of probabilistic canonical correlation analysis for noisy multi-view data. We present Bayesian inference procedures for the proposed model based on a stochastic EM algorithm. The effectiveness of the proposed model is demonstrated in terms of performance when detecting multi-view anomalies.

The success of kernel methods has initiated the design of novel positive semidefinite functions, in particular for structured data. A leading design paradigm for this is the convolution kernel, which decomposes structured objects into their parts and sums over all pairs of parts. Assignment kernels, in contrast, are obtained from an optimal bijection between parts, which can provide a more valid notion of similarity. In general however, optimal assignments yield indefinite functions, which complicates their use in kernel methods. We characterize a class of base kernels used to compare parts that guarantees positive semidefinite optimal assignment kernels. These base kernels give rise to hierarchies from which the optimal assignment kernels are computed in linear time by histogram intersection. We apply these results by developing the Weisfeiler-Lehman optimal assignment kernel for graphs. It provides high classification accuracy on widely-used benchmark data sets improving over the original Weisfeiler-Lehman kernel.

In this paper, we propose a very deep fully convolutional encoding-decoding framework for image restoration such as denoising and super-resolution. The network is composed of multiple layers of convolution and deconvolution operators, learning end-to-end mappings from corrupted images to the original ones. The convolutional layers act as the feature extractor, which capture the abstraction of image contents while eliminating noises/corruptions. Deconvolutional layers are then used to recover the image details. We propose to symmetrically link convolutional and deconvolutional layers with skip-layer connections, with which the training converges much faster and attains a higher-quality local optimum. First, the skip connections allow the signal to be back-propagated to bottom layers directly, and thus tackles the problem of gradient vanishing, making training deep networks easier and achieving restoration performance gains consequently. Second, these skip connections pass image details from convolutional layers to deconvolutional layers, which is beneficial in recovering the original image. Significantly, with the large capacity, we can handle different levels of noises using a single model. Experimental results show that our network achieves better performance than recent state-of-the-art methods.

Markov chain Monte Carlo (MCMC) is one of the main workhorses of probabilistic inference, but it is notoriously hard to measure the quality of approximate posterior samples. This challenge is particularly salient in black box inference methods, which can hide details and obscure inference failures. In this work, we extend the recently introduced bidirectional Monte Carlo technique to evaluate MCMC-based posterior inference algorithms. By running annealed importance sampling (AIS) chains both from prior to posterior and vice versa on simulated data, we upper bound in expectation the symmetrized KL divergence between the true posterior distribution and the distribution of approximate samples. We integrate our method into two probabilistic programming languages, WebPPL and Stan, and validate it on several models and datasets. As an example of how our method be used to guide the design of inference algorithms, we apply it to study the effectiveness of different model representations in WebPPL and Stan.