The causal assumptions, the study design and the data are the elements required for scientific inference in empirical research. The research is adequately communicated only if all of these elements and their relations are described precisely. Causal models with design describe the study design and the missing data mechanism together with the causal structure and allow the direct application of causal calculus in the estimation of the causal effects. The flow of the study is visualized by ordering the nodes of the causal diagram in two dimensions by their causal order and the time of the observation. Conclusions whether a causal or observational relationship can be estimated from the collected incomplete data can be made directly from the graph. Causal models with design offer a systematic and unifying view scientific inference and increase the clarity and speed of communication. Examples on the causal models for a case-control study, a nested case-control study, a clinical trial and a two-stage case-cohort study are presented.

Cellular regulatory dynamics is driven by large and intricate networks of interactions at the molecular scale, whose sheer size obfuscates understanding. In light of limited experimental data, many parameters of such dynamics are unknown, and thus models built on the detailed, mechanistic viewpoint overfit and are not predictive. At the other extreme, simple ad hoc models of complex processes often miss defining features of the underlying systems. Here we propose an approach that instead constructs phenomenological, coarse-grained models of network dynamics that automatically adapt their complexity to the amount of available data. Such adaptive models lead to accurate predictions even when microscopic details of the studied systems are unknown due to insufficient data. The approach is computationally tractable, even for a relatively large number of dynamical variables, allowing its software realization, named Sir Isaac, to make successful predictions even when important dynamic variables are unobserved. For example, it matches the known phase space structure for simulated planetary motion data, avoids overfitting in a complex biological signaling system, and produces accurate predictions for a yeast glycolysis model with only tens of data points and over half of the interacting species unobserved.

Central to robot exploration and mapping is the task of persistent localization in environmental fields characterized by spatially correlated measurements. This paper presents a Gaussian process localization (GP-Localize) algorithm that, in contrast to existing works, can exploit the spatially correlated field measurements taken during a robot's exploration (instead of relying on prior training data) for efficiently and scalably learning the GP observation model online through our proposed novel online sparse GP. As a result, GP-Localize is capable of achieving constant time and memory (i.e., independent of the size of the data) per filtering step, which demonstrates the practical feasibility of using GPs for persistent robot localization and autonomy. Empirical evaluation via simulated experiments with real-world datasets and a real robot experiment shows that GP-Localize outperforms existing GP localization algorithms.

This paper presents a novel approach for approximate integration over the uncertainty of noise and signal variances in Gaussian process (GP) regression. Our efficient and straightforward approach can also be applied to integration over input dependent noise variance (heteroscedasticity) and input dependent signal variance (nonstationarity) by setting independent GP priors for the noise and signal variances. We use expectation propagation (EP) for inference and compare results to Markov chain Monte Carlo in two simulated data sets and three empirical examples. The results show that EP produces comparable results with less computational burden.

Recently, there has been a growing interest in modeling planning with information constraints. Accordingly, an agent maximizes a regularized expected utility known as the free energy, where the regularizer is given by the information divergence from a prior to a posterior policy. While this approach can be justified in various ways, including from statistical mechanics and information theory, it is still unclear how it relates to decisionmaking against adversarial environments. This connection has previously been suggested in work relating the free energy to risk-sensitive control and to extensive form games. Here, we show that a single-agent free energy optimization is equivalent to a game between the agent and an imaginary adversary. The adversary can, by paying an exponential penalty, generate costs that diminish the decision maker's payoffs. It turns out that the optimal strategy of the adversary consists in choosing costs so as to render the decision maker indifferent among its choices, which is a definining property of a Nash equilibrium, thus tightening the connection between free energy optimization and game theory. Keywords: bounded rationality, free energy, game theory, Legendre-Fenchel transform.

When making decisions under uncertainty, the optimal choices are often difficult to discern, especially if not enough information has been gathered. Two key questions in this regard relate to whether one should stop the information gathering process and commit to a decision (stopping criterion), and if not, what information to gather next (selection criterion). In this paper, we show that the recently introduced notion, Same-Decision Probability (SDP), can be useful as both a stopping and a selection criterion, as it can provide additional insight and allow for robust decision making in a variety of scenarios. This query has been shown to be highly intractable, being PP^PP-complete, and is exemplary of a class of queries which correspond to the computation of certain expectations. We propose the first exact algorithm for computing the SDP, and demonstrate its effectiveness on several real and synthetic networks. Finally, we present new complexity results, such as the complexity of computing the SDP on models with a Naive Bayes structure. Additionally, we prove that computing the non-myopic value of information is complete for the same complexity class as computing the SDP.

Stable random variables are motivated by the central limit theorem for densities with (potentially) unbounded variance and can be thought of as natural generalizations of the Gaussian distribution to skewed and heavy-tailed phenomenon. In this paper, we introduce α-stable graphical (α-SG) models, a class of multivariate stable densities that can also be represented as Bayesian networks whose edges encode linear dependencies between random variables. One major hurdle to the extensive use of stable distributions is the lack of a closed-form analytical expression for their densities. This makes penalized maximumlikelihood based learning computationally demanding. We establish theoretically that the Bayesian information criterion (BIC) can asymptotically be reduced to the computationally more tractable minimum dispersion criterion (MDC) and develop StabLe, a structure learning algorithm based on MDC. We use simulated datasets for five benchmark network topologies to empirically demonstrate how StabLe improves upon ordinary least squares (OLS) regression. We also apply StabLe to microarray gene expression data for lymphoblastoid cells from 727 individuals belonging to eight global population groups. We establish that StabLe improves test set performance relative to OLS via tenfold cross-validation. Finally, we develop SGEX, a method for quantifying differential expression of genes between different population groups.

Massive Open Online Courses (MOOCs) bring together thousands of people from different geographies and demographic backgrounds -- but to date, little is known about how they learn or communicate. We introduce a new content-analysed MOOC dataset and use Bayesian Non-negative Matrix Factorization (BNMF) to extract communities of learners based on the nature of their online forum posts. We see that BNMF yields a superior probabilistic generative model for online discussions when compared to other models, and that the communities it learns are differentiated by their composite students' demographic and course performance indicators. These findings suggest that computationally efficient probabilistic generative modelling of MOOCs can reveal important insights for educational researchers and practitioners and help to develop more intelligent and responsive online learning environments.

Conventional graphical model selection algorithms are passive, i.e., they require all the measurements to have been collected before processing begins. We propose an active learning algorithm that uses junction tree representations to adapt future measurements based on the information gathered from prior measurements. We prove that, under certain conditions, our active learning algorithm requires fewer scalar measurements than any passive algorithm to reliably estimate a graph. A range of numerical results validate our theory and demonstrates the benefits of active learning.

We have observed an interesting, yet unexplained, phenomenon: Semidefinite programming (SDP) based relaxations of maximum likelihood estimators (MLE) tend to be tight in recovery problems with noisy data, even when MLE cannot exactly recover the ground truth. Several results establish tightness of SDP based relaxations in the regime where exact recovery from MLE is possible. However, to the best of our knowledge, their tightness is not understood beyond this regime. As an illustrative example, we focus on the generalized Procrustes problem.