A gamma process dynamic Poisson factor analysis model is proposed to factorize a dynamic count matrix, whose columns are sequentially observed count vectors. The model builds a novel Markov chain that sends the latent gamma random variables at time $(t-1)$ as the shape parameters of those at time $t$, which are linked to observed or latent counts under the Poisson likelihood. The significant challenge of inferring the gamma shape parameters is fully addressed, using unique data augmentation and marginalization techniques for the negative binomial distribution. The same nonparametric Bayesian model also applies to the factorization of a dynamic binary matrix, via a Bernoulli-Poisson link that connects a binary observation to a latent count, with closed-form conditional posteriors for the latent counts and efficient computation for sparse observations. We apply the model to text and music analysis, with state-of-the-art results.

A hierarchical gamma process infinite edge partition model is proposed to factorize the binary adjacency matrix of an unweighted undirected relational network under a Bernoulli-Poisson link. The model describes both homophily and stochastic equivalence, and is scalable to big sparse networks by focusing its computation on pairs of linked nodes. It can not only discover overlapping communities and inter-community interactions, but also predict missing edges. A simplified version omitting inter-community interactions is also provided and we reveal its interesting connections to existing models. The number of communities is automatically inferred in a nonparametric Bayesian manner, and efficient inference via Gibbs sampling is derived using novel data augmentation techniques. Experimental results on four real networks demonstrate the models' scalability and state-of-the-art performance.

In this paper we propose an extension to the Fuzzy Cognitive Maps (FCMs) that aims at aggregating a number of reasoning tasks into a one parallel run. The described approach consists in replacing real-valued activation levels of concepts (and further influence weights) by random variables. Such extension, followed by the implemented software tool, allows for determining ranges reached by concept activation levels, sensitivity analysis as well as statistical analysis of multiple reasoning results. We replace multiplication and addition operators appearing in the FCM state equation by appropriate convolutions applicable for discrete random variables. To make the model computationally feasible, it is further augmented with aggregation operations for discrete random variables. We discuss four implemented aggregators, as well as we report results of preliminary tests.

Decision making is often based on Bayesian networks. The building blocks for Bayesian networks are its conditional probability tables (CPTs). These tables are obtained by parameter estimation methods, or they are elicited from subject matter experts (SME). Some of these knowledge representations are insufficient approximations. Using knowledge fusion of cause and effect observations lead to better predictive decisions. We propose three new methods to generate CPTs, which even work when only soft evidence is provided. The first two are novel ways of mapping conditional expectations to the probability space. The third is a column extraction method, which obtains CPTs from nonlinear functions such as the multinomial logistic regression. Case studies on military effects and burnt forest desertification have demonstrated that so derived CPTs have highly reliable predictive power, including superiority over the CPTs obtained from SMEs. In this context, new quality measures for determining the goodness of a CPT and for comparing CPTs with each other have been introduced. The predictive power and enhanced reliability of decision making based on the novel CPT generation methods presented in this paper have been confirmed and validated within the context of the case studies.

Probabilistic Graphical Models (PGM) are very useful in the fields of machine learning and data mining. The crucial limitation of those models,however, is the scalability. The Bayesian Network, which is one of the most common PGMs used in machine learning and data mining, demonstrates this limitation when the training data consists of random variables, each of them has a large set of possible values. In the big data era, one would expect new extensions to the existing PGMs to handle the massive amount of data produced these days by computers, sensors and other electronic devices. With hierarchical data - data that is arranged in a treelike structure with several levels - one would expect to see hundreds of thousands or millions of values distributed over even just a small number of levels. When modeling this kind of hierarchical data across large data sets, Bayesian Networks become infeasible for representing the probability distributions. In this paper we introduce an extension to Bayesian Networks to handle massive sets of hierarchical data in a reasonable amount of time and space. The proposed model achieves perfect precision of 1.0 and high recall of 0.93 when it is used as multi-label classifier for the annotation of mass spectrometry data. On another data set of 1.5 billion search logs provided by CareerBuilder.com the model was able to predict latent semantic relationships between search keywords with accuracy up to 0.80.

Complicated generative models often result in a situation where computing the likelihood of observed data is intractable, while simulating from the conditional density given a parameter value is relatively easy. Approximate Bayesian Computation (ABC) is a paradigm that enables simulation-based posterior inference in such cases by measuring the similarity between simulated and observed data in terms of a chosen set of summary statistics. However, there is no general rule to construct sufficient summary statistics for complex models. Insufficient summary statistics will "leak" information, which leads to ABC algorithms yielding samples from an incorrect (partial) posterior. In this paper, we propose a fully nonparametric ABC paradigm which circumvents the need for manually selecting summary statistics. Our approach, K2-ABC, uses maximum mean discrepancy (MMD) to construct a dissimilarity measure between the observed and simulated data. The embedding of an empirical distribution of the data into a reproducing kernel Hilbert space plays a role of the summary statistic and is sufficient whenever the corresponding kernels are characteristic. Experiments on a simulated scenario and a real-world biological problem illustrate the effectiveness of the proposed algorithm. M Park and W Jitkrittum contributed equally.

The histogram method is a powerful non-parametric approach for estimating the probability density function of a continuous variable. But the construction of a histogram, compared to the parametric approaches, demands a large number of observations to capture the underlying density function. Thus it is not suitable for analyzing a sparse data set, a collection of units with a small size of data. In this paper, by employing the probabilistic topic model, we develop a novel Bayesian approach to alleviating the sparsity problem in the conventional histogram estimation. Our method estimates a unit's density function as a mixture of basis histograms, in which the number of bins for each basis, as well as their heights, is determined automatically. The estimation procedure is performed by using the fast and easy-to-implement collapsed Gibbs sampling. We apply the proposed method to synthetic data, showing that it performs well.

The discovery of causal relationships from purely observational data is a fundamental problem in science. The most elementary form of such a causal discovery problem is to decide whether X causes Y or, alternatively, Y causes X, given joint observations of two variables X, Y. An example is to decide whether altitude causes temperature, or vice versa, given only joint measurements of both variables. Even under the simplifying assumptions of no confounding, no feedback loops, and no selection bias, such bivariate causal discovery problems are challenging. Nevertheless, several approaches for addressing those problems have been proposed in recent years. We review two families of such methods: Additive Noise Methods (ANM) and Information Geometric Causal Inference (IGCI). We present the benchmark CauseEffectPairs that consists of data for 100 different cause-effect pairs selected from 37 datasets from various domains (e.g., meteorology, biology, medicine, engineering, economy, etc.) and motivate our decisions regarding the "ground truth" causal directions of all pairs. We evaluate the performance of several bivariate causal discovery methods on these real-world benchmark data and in addition on artificially simulated data. Our empirical results on real-world data indicate that certain methods are indeed able to distinguish cause from effect using only purely observational data, although more benchmark data would be needed to obtain statistically significant conclusions. One of the best performing methods overall is the additive-noise method originally proposed by Hoyer et al. (2009), which obtains an accuracy of 63+-10 % and an AUC of 0.74+-0.05 on the real-world benchmark. As the main theoretical contribution of this work we prove the consistency of that method.

Nowadays, hospitals are ubiquitous and integral to modern society. Patients flow in and out of a veritable whirlwind of paperwork, consultations, and potential inpatient admissions, through an abstracted system that is not without flaws. One of the biggest flaws in the medical system is perhaps an unexpected one: the patient alarm system. One longitudinal study reported an 88.8% rate of false alarms, with other studies reporting numbers of similar magnitudes. These false alarm rates lead to a number of deleterious effects that manifest in a significantly lower standard of care across clinics. This paper discusses a model-based probabilistic inference approach to identifying variables at a detection level. We design a generative model that complies with an overview of human physiology and perform approximate Bayesian inference. One primary goal of this paper is to justify a Bayesian modeling approach to increasing robustness in a physiological domain. We use three data sets provided by Physionet, a research resource for complex physiological signals, in the form of the Physionet 2014 Challenge set-p1 and set-p2, as well as the MGH/MF Waveform Database. On the extended data set our algorithm is on par with the other top six submissions to the Physionet 2014 challenge.

We survey concepts at the frontier of research connecting artificial, animal and human cognition to computation and information processing---from the Turing test to Searle's Chinese Room argument, from Integrated Information Theory to computational and algorithmic complexity. We start by arguing that passing the Turing test is a trivial computational problem and that its pragmatic difficulty sheds light on the computational nature of the human mind more than it does on the challenge of artificial intelligence. We then review our proposed algorithmic information-theoretic measures for quantifying and characterizing cognition in various forms. These are capable of accounting for known biases in human behavior, thus vindicating a computational algorithmic view of cognition as first suggested by Turing, but this time rooted in the concept of algorithmic probability, which in turn is based on computational universality while being independent of computational model, and which has the virtue of being predictive and testable as a model theory of cognitive behavior.