When software developers modify one or more files in a large code base, they must also identify and update other related files. Many file dependencies can be detected by mining the development history of the code base: in essence, groups of related files are revealed by the logs of previous workflows. From data of this form, we show how to detect dependent files by solving a problem in binary matrix completion. We explore different latent variable models (LVMs) for this problem, including Bernoulli mixture models, exponential family PCA, restricted Boltzmann machines, and fully Bayesian approaches. We evaluate these models on the development histories of three large, open-source software systems: Mozilla Firefox, Eclipse Subversive, and Gimp. In all of these applications, we find that LVMs improve the performance of related file prediction over current leading methods.

A method for computing the rarity of latent fingerprints represented by minutiae is given. It allows determining the probability of finding a match for an evidence print in a database of n known prints. The probability of random correspondence between evidence and database is determined in three procedural steps. In the registration step the latent print is aligned by finding its core point; which is done using a procedure based on a machine learning approach based on Gaussian processes. In the evidence probability evaluation step a generative model based on Bayesian networks is used to determine the probability of the evidence; it takes into account both the dependency of each minutia on nearby minutiae and the confidence of their presence in the evidence. In the specific probability of random correspondence step the evidence probability is used to determine the probability of match among n for a given tolerance; the last evaluation is similar to the birthday correspondence probability for a specific birthday. The generative model is validated using a goodness-of-fit test evaluated with a standard database of fingerprints. The probability of random correspondence for several latent fingerprints are evaluated for varying numbers of minutiae.

Straightforward application of Deep Belief Nets (DBNs) to acoustic modeling produces a rich distributed representation of speech data that is useful for recognition and yields impressive results on the speaker-independent TIMIT phone recognition task. However, the first-layer Gaussian-Bernoulli Restricted Boltzmann Machine (GRBM) has an important limitation, shared with mixtures of diagonal-covariance Gaussians: GRBMs treat different components of the acoustic input vector as conditionally independent given the hidden state. The mean-covariance restricted Boltzmann machine (mcRBM), first introduced for modeling natural images, is a much more representationally efficient and powerful way of modeling the covariance structure of speech data. Every configuration of the precision units of the mcRBM specifies a different precision matrix for the conditional distribution over the acoustic space. In this work, we use the mcRBM to learn features of speech data that serve as input into a standard DBN. The mcRBM features combined with DBNs allow us to achieve a phone error rate of 20.5\%, which is superior to all published results on speaker-independent TIMIT to date.

The Charles Bonnet Syndrome (CBS) is characterized by complex vivid visual hallucinations in people with, primarily, eye diseases and no other neurological pathology. We present a Deep Boltzmann Machine model of CBS, exploring two core hypotheses: First, that the visual cortex learns a generative or predictive model of sensory input, thus explaining its capability to generate internal imagery. And second, that homeostatic mechanisms stabilize neuronal activity levels, leading to hallucinations being formed when input is lacking. We reproduce a variety of qualitative findings in CBS. We also introduce a modification to the DBM that allows us to model a possible role of acetylcholine in CBS as mediating the balance of feed-forward and feed-back processing. Our model might provide new insights into CBS and also demonstrates that generative frameworks are promising as hypothetical models of cortical learning and perception.

Layered models are a powerful way of describing natural scenes containing smooth surfaces that may overlap and occlude each other. For image motion estimation, such models have a long history but have not achieved the wide use or accuracy of non-layered methods. We present a new probabilistic model of optical flow in layers that addresses many of the shortcomings of previous approaches. In particular, we define a probabilistic graphical model that explicitly captures: 1) occlusions and disocclusions; 2) depth ordering of the layers; 3) temporal consistency of the layer segmentation. Additionally the optical flow in each layer is modeled by a combination of a parametric model and a smooth deviation based on an MRF with a robust spatial prior; the resulting model allows roughness in layers. Finally, a key contribution is the formulation of the layers using an image-dependent hidden field prior based on recent models for static scene segmentation. The method achieves state-of-the-art results on the Middlebury benchmark and produces meaningful scene segmentations as well as detected occlusion regions.

In this paper we propose an approximated learning framework for large scale graphical models and derive message passing algorithms for learning their parameters efficiently. We first relate CRFs and structured SVMs and show that in the CRF's primal a variant of the log-partition function, known as soft-max, smoothly approximates the hinge loss function of structured SVMs. We then propose an intuitive approximation for structured prediction problems using Fenchel duality based on a local entropy approximation that computes the exact gradients of the approximated problem and is guaranteed to converge. Unlike existing approaches, this allow us to learn graphical models with cycles and very large number of parameters efficiently. We demonstrate the effectiveness of our approach in an image denoising task. This task was previously solved by sharing parameters across cliques. In contrast, our algorithm is able to efficiently learn large number of parameters resulting in orders of magnitude better prediction.

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.

Automatic speech recognition has gradually improved over the years, but the reliable recognition of unconstrained speech is still not within reach. In order to achieve a breakthrough, many research groups are now investigating new methodologies that have potential to outperform the Hidden Markov Model technology that is at the core of all present commercial systems. In this paper, it is shown that the recently introduced concept of Reservoir Computing might form the basis of such a methodology. In a limited amount of time, a reservoir system that can recognize the elementary sounds of continuous speech has been built. The system already achieves a state-of-the-art performance, and there is evidence that the margin for further improvements is still significant.

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.

To cope with concept drift, we placed a probability distribution over the location of the most-recent drift point. We used Bayesian model comparison to update this distribution from the predictions of models trained on blocks of consecutive observations and pruned potential drift points with low probability. We compare our approach to a non-probabilistic method for drift and a probabilistic method for change-point detection. In our experiments, our approach generally yielded improved accuracy and/or speed over these other methods.