We present a technique to perform dimensionality reduction on data that is subject to uncertainty. Our method is a generalization of traditional principal component analysis (PCA) to multivariate probability distributions. In comparison to non-linear methods, linear dimensionality reduction techniques have the advantage that the characteristics of such probability distributions remain intact after projection. We derive a representation of the covariance matrix that respects potential uncertainty in each of the observations, building the mathematical foundation of our new method uncertainty-aware PCA. In addition to the accuracy and performance gained by our approach over sampling-based strategies, our formulation allows us to perform sensitivity analysis with regard to the uncertainty in the data. For this, we propose factor traces as a novel visualization that enables us to better understand the influence of uncertainty on the chosen principal components. We provide multiple examples of our technique using real-world datasets and show how to propagate multivariate normal distributions through PCA in closed-form. Furthermore, we discuss extensions and limitations of our approach.
Population neural recordings with long-range temporal structure are often best understood in terms of a shared underlying low-dimensional dynamical process. Advances in recording technology provide access to an ever larger fraction of the population, but the standard computational approaches available to identify the collective dynamics scale poorly with the size of the dataset. Here we describe a new, scalable approach to discovering the low-dimensional dynamics that underlie simultaneously recorded spike trains from a neural population. Our method is based on recurrent linear models (RLMs), and relates closely to timeseries models based on recurrent neural networks. We formulate RLMs for neural data by generalising the Kalman-filter-based likelihood calculation for latent linear dynamical systems (LDS) models to incorporate a generalised-linear observation process. We show that RLMs describe motor-cortical population data better than either directly-coupled generalised-linear models or latent linear dynamical system models with generalised-linear observations. We also introduce the cascaded linear model (CLM) to capture low-dimensional instantaneous correlations in neural populations. The CLM describes the cortical recordings better than either Ising or Gaussian models and, like the RLM, can be fit exactly and quickly. The CLM can also be seen as a generalization of a low-rank Gaussian model, in this case factor analysis. The computational tractability of the RLM and CLM allow both to scale to very high-dimensional neural data.
We consider probabilistic PCA and related factor models from a Bayesian perspective. These models are in general not identifiable as the likelihood has a rotational symmetry. This gives rise to complicated posterior distributions with continuous subspaces of equal density and thus hinders efficiency of inference as well as interpretation of obtained parameters. In particular, posterior averages over factor loadings become meaningless and only model predictions are unambiguous. Here, we propose a parameterization based on Householder transformations, which remove the rotational symmetry of the posterior. Furthermore, by relying on results from random matrix theory, we establish the parameter distribution which leaves the model unchanged compared to the original rotationally symmetric formulation. In particular, we avoid the need to compute the Jacobian determinant of the parameter transformation. This allows us to efficiently implement probabilistic PCA in a rotation invariant fashion in any state of the art toolbox. Here, we implemented our model in the probabilistic programming language Stan and illustrate it on several examples.
The Information Bottleneck (IB) is a conceptual method for extracting the most compact, yet informative, representation of a set of variables, with respect to the target. It generalizes the notion of minimal sufficient statistics from classical parametric statistics to a broader information-theoretic sense. The IB curve defines the optimal trade-off between representation complexity and its predictive power. Specifically, it is achieved by minimizing the level of mutual information (MI) between the representation and the original variables, subject to a minimal level of MI between the representation and the target. This problem is shown to be in general NP hard. One important exception is the multivariate Gaussian case, for which the Gaussian IB (GIB) is known to obtain an analytical closed form solution, similar to Canonical Correlation Analysis (CCA). In this work we introduce a Gaussian lower bound to the IB curve; we find an embedding of the data which maximizes its "Gaussian part", on which we apply the GIB. This embedding provides an efficient (and practical) representation of any arbitrary data-set (in the IB sense), which in addition holds the favorable properties of a Gaussian distribution. Importantly, we show that the optimal Gaussian embedding is bounded from above by non-linear CCA. This allows a fundamental limit for our ability to Gaussianize arbitrary data-sets and solve complex problems by linear methods.
We investigate the geometrical structure of probabilistic generative dimensionality reduction models using the tools of Riemannian geometry. We explicitly define a distribution over the natural metric given by the models. We provide the necessary algorithms to compute expected metric tensors where the distribution over mappings is given by a Gaussian process. We treat the corresponding latent variable model as a Riemannian manifold and we use the expectation of the metric under the Gaussian process prior to define interpolating paths and measure distance between latent points. We show how distances that respect the expected metric lead to more appropriate generation of new data.