Conventional dynamic Bayesian networks (DBNs) are based on the homogeneous Markov assumption, which is too restrictive in many practical applications. Various approaches to relax the homogeneity assumption have therefore been proposed in the last few years. The present paper aims to improve the flexibility of two recent versions of non-homogeneous DBNs, which either (i) suffer from the need for data discretization, or (ii) assume a time-invariant network structure. Allowing the network structure to be fully flexible leads to the risk of overfitting and inflated inference uncertainty though, especially in the highly topical field of systems biology, where independent measurements tend to be sparse. In the present paper we investigate three conceptually different regularization schemes based on inter-segment information sharing. We assess the performance in a comparative evaluation study based on simulated data. We compare the predicted segmentation of gene expression time series obtained during embryogenesis in Drosophila melanogaster with other state-of-the-art techniques. We conclude our evaluation with an application to synthetic biology, where the objective is to predict a known regulatory network of five genes in Saccharomyces cerevisiae.

We propose a novel method for inferring whether X causes Y or vice versa from joint observations of X and Y . The basic idea is to model the observed data using probabilistic latent variable models, which incorporate the effects of unobserved noise. To this end, we consider the hypothetical effect variable to be a function of the hypothetical cause variable and an independent noise term (not necessarily additive). An important novel aspect of our work is that we do not restrict the model class, but instead put general nonparametric priors on this function and on the distribution of the cause. The causal direction can then be inferred by using standard Bayesian model selection. We evaluate our approach on synthetic data and real-world data and report encouraging results.

We develop an online variational Bayes (VB) algorithm for Latent Dirichlet Allocation (LDA). Online LDA is based on online stochastic optimization with a natural gradient step, which we show converges to a local optimum of the VB objective function. It can handily analyze massive document collections, including those arriving in a stream. We study the performance of online LDA in several ways, including by fitting a 100-topic topic model to 3.3M articles from Wikipedia in a single pass. We demonstrate that online LDA finds topic models as good or better than those found with batch VB, and in a fraction of the time.

We consider the problem of reinforcement learning in high-dimensional spaces when the number of features is bigger than the number of samples. In particular, we study the least-squares temporal difference (LSTD) learning algorithm when a space of low dimension is generated with a random projection from a high-dimensional space. We provide a thorough theoretical analysis of the LSTD with random projections and derive performance bounds for the resulting algorithm. We also show how the error of LSTD with random projections is propagated through the iterations of a policy iteration algorithm and provide a performance bound for the resulting least-squares policy iteration (LSPI) algorithm.

Many problems in machine learning and statistics can be formulated as (generalized) eigenproblems. In terms of the associated optimization problem, computing linear eigenvectors amounts to finding critical points of a quadratic function subject to quadratic constraints. In this paper we show that a certain class of constrained optimization problems with nonquadratic objective and constraints can be understood as nonlinear eigenproblems. We derive a generalization of the inverse power method which is guaranteed to converge to a nonlinear eigenvector. We apply the inverse power method to 1-spectral clustering and sparse PCA which can naturally be formulated as nonlinear eigenproblems. In both applications we achieve state-of-the-art results in terms of solution quality and runtime. Moving beyond the standard eigenproblem should be useful also in many other applications and our inverse power method can be easily adapted to new problems.

We extend logistic regression by using t-exponential families which were introduced recently in statistical physics. This gives rise to a regularized risk minimization problem with a non-convex loss function. An efficient block coordinate descent optimization scheme can be derived for estimating the parameters. Because of the nature of the loss function, our algorithm is tolerant to label noise. Furthermore, unlike other algorithms which employ non-convex loss functions, our algorithm is fairly robust to the choice of initial values. We verify both these observations empirically on a number of synthetic and real datasets.

Recent experimental work has suggested that the neural firing rate can be interpreted as a fractional derivative, at least when signal variation induces neural adaptation. Here, we show that the actual neural spike-train itself can be considered as the fractional derivative, provided that the neural signal is approximated by a sum of power-law kernels. A simple standard thresholding spiking neuron suffices to carry out such an approximation, given a suitable refractory response. Empirically, we find that the online approximation of signals with a sum of power-law kernels is beneficial for encoding signals with slowly varying components, like long-memory self-similar signals. For such signals, the online power-law kernel approximation typically required less than half the number of spikes for similar SNR as compared to sums of similar but exponentially decaying kernels. As power-law kernels can be accurately approximated using sums or cascades of weighted exponentials, we demonstrate that the corresponding decoding of spike-trains by a receiving neuron allows for natural and transparent temporal signal filtering by tuning the weights of the decoding kernel.

In some stochastic environments the well-known reinforcement learning algorithm Q-learning performs very poorly. This poor performance is caused by large overestimations of action values. These overestimations result from a positive bias that is introduced because Q-learning uses the maximum action value as an approximation for the maximum expected action value. We introduce an alternative way to approximate the maximum expected value for any set of random variables. The obtained double estimator method is shown to sometimes underestimate rather than overestimate the maximum expected value. We apply the double estimator to Q-learning to construct Double Q-learning, a new off-policy reinforcement learning algorithm. We show the new algorithm converges to the optimal policy and that it performs well in some settings in which Q-learning performs poorly due to its overestimation.

During the last years support vector machines (SVMs) have been successfully applied even in situations where the input space $X$ is not necessarily a subset of $R^d$. Examples include SVMs using probability measures to analyse e.g. histograms or coloured images, SVMs for text classification and web mining, and SVMs for applications from computational biology using, e.g., kernels for trees and graphs. Moreover, SVMs are known to be consistent to the Bayes risk, if either the input space is a complete separable metric space and the reproducing kernel Hilbert space (RKHS) $H\subset L_p(P_X)$ is dense, or if the SVM is based on a universal kernel $k$. So far, however, there are no RKHSs of practical interest known that satisfy these assumptions on $\cH$ or $k$ if $X \not\subset R^d$. We close this gap by providing a general technique based on Taylor-type kernels to explicitly construct universal kernels on compact metric spaces which are not subset of $R^d$. We apply this technique for the following special cases: universal kernels on the set of probability measures, universal kernels based on Fourier transforms, and universal kernels for signal processing.

We address the problem of estimating the F-measure of a given model as accurately as possible on a fixed labeling budget. This problem occurs whenever an estimate cannot be obtained from held-out training data; for instance, when data that have been used to train the model are held back for reasons of privacy or do not reflect the test distribution. In this case, new test instances have to be drawn and labeled at a cost. An active estimation procedure selects instances according to an instrumental sampling distribution. An analysis of the sources of estimation error leads to an optimal sampling distribution that minimizes estimator variance. We explore conditions under which active estimates of F-measures are more accurate than estimates based on instances sampled from the test distribution.