Simultaneous recordings of the activity of large neural populations are extremely valuable as they can be used to infer the dynamics and interactions of neurons in a local circuit, shedding light on the computations performed. It is now possible to measure the activity of hundreds of neurons using 2-photon calcium imaging. However, many computations are thought to involve circuits consisting of thousands of neurons, such as cortical barrels in rodent somatosensory cortex. Here we contribute a statistical method for stitching" together sequentially imaged sets of neurons into one model by phrasing the problem as fitting a latent dynamical system with missing observations. This method allows us to substantially expand the population-sizes for which population dynamics can be characterized---beyond the number of simultaneously imaged neurons. In particular, we demonstrate using recordings in mouse somatosensory cortex that this method makes it possible to predict noise correlations between non-simultaneously recorded neuron pairs."

Distance-based approaches to outlier detection are popular in data mining, as they do not require to model the underlying probability distribution, which is particularly challenging for high-dimensional data. We present an empirical comparison of various approaches to distance-based outlier detection across a large number of datasets. We report the surprising observation that a simple, sampling-based scheme outperforms state-of-the-art techniques in terms of both efficiency and effectiveness. To better understand this phenomenon, we provide a theoretical analysis why the sampling-based approach outperforms alternative methods based on k-nearest neighbor search.

This paper presents Correlated Nystrom Views (XNV), a fast semi-supervised algorithm for regression and classification. The algorithm draws on two main ideas. First, it generates two views consisting of computationally inexpensive random features. Second, multiview regression, using Canonical Correlation Analysis (CCA) on unlabeled data, biases the regression towards useful features. It has been shown that CCA regression can substantially reduce variance with a minimal increase in bias if the views contains accurate estimators. Recent theoretical and empirical work shows that regression with random features closely approximates kernel regression, implying that the accuracy requirement holds for random views. We show that XNV consistently outperforms a state-of-the-art algorithm for semi-supervised learning: substantially improving predictive performance and reducing the variability of performance on a wide variety of real-world datasets, whilst also reducing runtime by orders of magnitude.

We present a novel non-parametric method for finding a subspace of stimulus features that contains all information about the response of a system. Our method generalizes similar approaches to this problem such as spike triggered average, spike triggered covariance, or maximally informative dimensions. Instead of maximizing the mutual information between features and responses directly, we use integral probability metrics in kernel Hilbert spaces to minimize the information between uninformative features and the combination of informative features and responses. Since estimators of these metrics access the data via kernels, are easy to compute, and exhibit good theoretical convergence properties, our method can easily be generalized to populations of neurons or spike patterns. By using a particular expansion of the mutual information, we can show that the informative features must contain all information if we can make the uninformative features independent of the rest.

The Bayesian online change point detection (BOCPD) algorithm provides an efficient way to do exact inference when the parameters of an underlying model may suddenly change over time. BOCPD requires computation of the underlying model's posterior predictives, which can only be computed online in $O(1)$ time and memory for exponential family models. We develop variational approximations to the posterior on change point times (formulated as run lengths) for efficient inference when the underlying model is not in the exponential family, and does not have tractable posterior predictive distributions. In doing so, we develop improvements to online variational inference. We apply our methodology to a tracking problem using radar data with a signal-to-noise feature that is Rice distributed. We also develop a variational method for inferring the parameters of the (non-exponential family) Rice distribution.

It has long been recognised that statistical dependencies in neuronal activity need to be taken into account when decoding stimuli encoded in a neural population. Less studied, though equally pernicious, is the need to take account of dependencies between synaptic weights when decoding patterns previously encoded in an auto-associative memory. We show that activity-dependent learning generically produces such correlations, and failing to take them into account in the dynamics of memory retrieval leads to catastrophically poor recall. We derive optimal network dynamics for recall in the face of synaptic correlations caused by a range of synaptic plasticity rules. These dynamics involve well-studied circuit motifs, such as forms of feedback inhibition and experimentally observed dendritic nonlinearities. We therefore show how addressing the problem of synaptic correlations leads to a novel functional account of key biophysical features of the neural substrate.

Infinite mixture models are commonly used for clustering. One can sample from the posterior of mixture assignments by Monte Carlo methods or find its maximum a posteriori solution by optimization. However, in some problems the posterior is diffuse and it is hard to interpret the sampled partitionings. In this paper, we introduce novel statistics based on block sizes for representing sample sets of partitionings and feature allocations. We develop an element-based definition of entropy to quantify segmentation among their elements. Then we propose a simple algorithm called entropy agglomeration (EA) to summarize and visualize this information. Experiments on various infinite mixture posteriors as well as a feature allocation dataset demonstrate that the proposed statistics are useful in practice.

We study optimal image encoding based on a generative approach with non-linear feature combinations and explicit position encoding. By far most approaches to unsupervised learning learning of visual features, such as sparse coding or ICA, account for translations by representing the same features at different positions. Some earlier models used a separate encoding of features and their positions to facilitate invariant data encoding and recognition. All probabilistic generative models with explicit position encoding have so far assumed a linear superposition of components to encode image patches. Here, we for the first time apply a model with non-linear feature superposition and explicit position encoding. By avoiding linear superpositions, the studied model represents a closer match to component occlusions which are ubiquitous in natural images. In order to account for occlusions, the non-linear model encodes patches qualitatively very different from linear models by using component representations separated into mask and feature parameters. We first investigated encodings learned by the model using artificial data with mutually occluding components. We find that the model extracts the components, and that it can correctly identify the occlusive components with the hidden variables of the model. On natural image patches, the model learns component masks and features for typical image components. By using reverse correlation, we estimate the receptive fields associated with the model's hidden units. We find many Gabor-like or globular receptive fields as well as fields sensitive to more complex structures. Our results show that probabilistic models that capture occlusions and invariances can be trained efficiently on image patches, and that the resulting encoding represents an alternative model for the neural encoding of images in the primary visual cortex.

While graphs with continuous node attributes arise in many applications, state-of-the-art graph kernels for comparing continuous-attributed graphs suffer from a high runtime complexity; for instance, the popular shortest path kernel scales as $\mathcal{O}(n^4)$, where $n$ is the number of nodes. In this paper, we present a class of path kernels with computational complexity $\mathcal{O}(n^2 (m + \delta^2))$, where $\delta$ is the graph diameter and $m$ the number of edges. Due to the sparsity and small diameter of real-world graphs, these kernels scale comfortably to large graphs. In our experiments, the presented kernels outperform state-of-the-art kernels in terms of speed and accuracy on classification benchmark datasets.

Causal inference uses observational data to infer the causal structure of the data generating system. We study a class of restricted Structural Equation Models for time series that we call Time Series Models with Independent Noise (TiMINo). These models require independent residual time series, whereas traditional methods like Granger causality exploit the variance of residuals. This work contains two main contributions: (1) Theoretical: By restricting the model class (e.g. to additive noise) we provide more general identifiability results than existing ones. The results cover lagged and instantaneous effects that can be nonlinear and unfaithful, and non-instantaneous feedbacks between the time series. (2) Practical: If there are no feedback loops between time series, we propose an algorithm based on non-linear independence tests of time series. When the data are causally insufficient, or the data generating process does not satisfy the model assumptions, this algorithm may still give partial results, but mostly avoids incorrect answers. The Structural Equation Model point of view allows us to extend both the theoretical and the algorithmic part to situations in which the time series have been measured with different time delays (as may happen for fMRI data, for example). TiMINo outperforms existing methods on artificial and real data. Code is provided.