We introduce Probabilistic Dependency Graphs (PDGs), a new class of directed graphical models. PDGs can capture inconsistent beliefs in a natural way and are more modular than Bayesian Networks (BNs), in that they make it easier to incorporate new information and restructure the representation. We show by example how PDGs are an especially natural modeling tool. We provide three semantics for PDGs, each of which can be derived from a scoring function (on joint distributions over the variables in the network) that can be viewed as representing a distribution's incompatibility with the PDG. For the PDG corresponding to a BN, this function is uniquely minimized by the distribution the BN represents, showing that PDG semantics extend BN semantics. We show further that factor graphs and their exponential families can also be faithfully represented as PDGs, while there are significant barriers to modeling a PDG with a factor graph.

In human-robot cooperation, the robot cooperates with the human to accomplish the task together. Existing approaches assume the human has a specific goal during the cooperation, and the robot infers and acts toward it. However, in real-world environments, a human usually only has a general goal (e.g., general direction or area in motion planning) at the beginning of the cooperation which needs to be clarified to a specific goal (e.g., an exact position) during cooperation. The specification process is interactive and dynamic, which depends on the environment and the behavior of the partners. The robot that does not consider the goal specification process may cause frustration to the human partner, elongate the time to come to an agreement, and compromise or fail team performance. We present Evolutionary Value Learning (EVL) approach which uses a State-based Multivariate Bayesian Inference method to model the dynamics of goal specification process in HRC, and an Evolutionary Value Updating method to actively enhance the process of goal specification and cooperation formation. This enables the robot to simultaneously help the human to specify the goal and learn a cooperative policy in a Reinforcement Learning manner. In experiments with real human subjects, the robot equipped with EVL outperforms existing methods with faster goal specification processes and better team performance.

The use of genetic variants as instrumental variables - an approach known as Mendelian randomization - is a popular epidemiological method for estimating the causal effect of an exposure (phenotype, biomarker, risk factor) on a disease or health-related outcome from observational data. Instrumental variables must satisfy strong, often untestable assumptions, which means that finding good genetic instruments among a large list of potential candidates is challenging. This difficulty is compounded by the fact that many genetic variants influence more than one phenotype through different causal pathways, a phenomenon called horizontal pleiotropy. This leads to errors not only in estimating the magnitude of the causal effect but also in inferring the direction of the putative causal link. In this paper, we propose a Bayesian approach called BayesMR that is a generalization of the Mendelian randomization technique in which we allow for pleiotropic effects and, crucially, for the possibility of reverse causation. The output of the method is a posterior distribution over the target causal effect, which provides an immediate and easily interpretable measure of the uncertainty in the estimation. More importantly, we use Bayesian model averaging to determine how much more likely the inferred direction is relative to the reverse direction.

The recent availability of huge, many-dimensional data sets, like those arising from genome-wide association studies (GWAS), provides many opportunities for strengthening causal inference. One popular approach is to utilize these many-dimensional measurements as instrumental variables (instruments) for improving the causal effect estimate between other pairs of variables. Unfortunately, searching for proper instruments in a many-dimensional set of candidates is a daunting task due to the intractable model space and the fact that we cannot directly test which of these candidates are valid, so most existing search methods either rely on overly stringent modeling assumptions or fail to capture the inherent model uncertainty in the selection process. We show that, as long as at least some of the candidates are (close to) valid, without knowing a priori which ones, they collectively still pose enough restrictions on the target interaction to obtain a reliable causal effect estimate. We propose a general and efficient causal inference algorithm that accounts for model uncertainty by performing Bayesian model averaging over the most promising many-dimensional instrumental variable models, while at the same time employing weaker assumptions regarding the data generating process. We showcase the efficiency, robustness and predictive performance of our algorithm through experimental results on both simulated and real-world data.

Bayesian optimisation presents a sample-efficient methodology for global optimisation. Within this framework, a crucial performance-determining subroutine is the maximisation of the acquisition function, a task complicated by the fact that acquisition functions tend to be non-convex and thus nontrivial to optimise. In this paper, we undertake a comprehensive empirical study of approaches to maximise the acquisition function. Additionally, by deriving novel, yet mathematically equivalent, compositional forms for popular acquisition functions, we recast the maximisation task as a compositional optimisation problem, allowing us to benefit from the extensive literature in this field. We highlight the empirical advantages of the compositional approach to acquisition function maximisation across 3958 individual experiments comprising synthetic optimisation tasks as well as tasks from Bayesmark. Given the generality of the acquisition function maximisation subroutine, we posit that the adoption of compositional optimisers has the potential to yield performance improvements across all domains in which Bayesian optimisation is currently being applied.

Level Set Estimation (LSE) is an important problem with applications in various fields such as material design, biotechnology, machine operational testing, etc. Existing techniques suffer from the scalability issue, that is, these methods do not work well with high dimensional inputs. This paper proposes novel methods to solve the high dimensional LSE problems using Bayesian Neural Networks. In particular, we consider two types of LSE problems: (1) \textit{explicit} LSE problem where the threshold level is a fixed user-specified value, and, (2) \textit{implicit} LSE problem where the threshold level is defined as a percentage of the (unknown) maximum of the objective function. For each problem, we derive the corresponding theoretic information based acquisition function to sample the data points so as to maximally increase the level set accuracy. Furthermore, we also analyse the theoretical time complexity of our proposed acquisition functions, and suggest a practical methodology to efficiently tune the network hyper-parameters to achieve high model accuracy. Numerical experiments on both synthetic and real-world datasets show that our proposed method can achieve better results compared to existing state-of-the-art approaches.

Maximum entropy (MAXENT) method has a large number of applications in theoretical and applied machine learning, since it provides a convenient non-parametric tool for estimating unknown probabilities. The method is a major contribution of statistical physics to probabilistic inference. However, a systematic approach towards its validity limits is currently missing. Here we study MAXENT in a Bayesian decision theory set-up, i.e. assuming that there exists a well-defined prior Dirichlet density for unknown probabilities, and that the average Kullback-Leibler (KL) distance can be employed for deciding on the quality and applicability of various estimators. These allow to evaluate the relevance of various MAXENT constraints, check its general applicability, and compare MAXENT with estimators having various degrees of dependence on the prior, viz. the regularized maximum likelihood (ML) and the Bayesian estimators. We show that MAXENT applies in sparse data regimes, but needs specific types of prior information. In particular, MAXENT can outperform the optimally regularized ML provided that there are prior rank correlations between the estimated random quantity and its probabilities.

L\'evy walks are found in the migratory behaviour patterns of various organisms, and the reason for this phenomenon has been much discussed. We use simulations to demonstrate that learning causes the changes in confidence level during decision-making in non-stationary environments, and results in L\'evy-walk-like patterns. One inference algorithm involving confidence is Bayesian inference. We propose an algorithm that introduces the effects of learning and forgetting into Bayesian inference, and simulate an imitation game in which two decision-making agents incorporating the algorithm estimate each other's internal models from their opponent's observational data. For forgetting without learning, agent confidence levels remained low due to a lack of information on the counterpart and Brownian walks occurred for a wide range of forgetting rates. Conversely, when learning was introduced, high confidence levels occasionally occurred even at high forgetting rates, and Brownian walks universally became L\'evy walks through a mixture of high- and low-confidence states.

A connection between the General Linear Model (GLM) in combination with classical statistical inference and the machine learning (MLE)-based inference is described in this paper. Firstly, the estimation of the GLM parameters is expressed as a Linear Regression Model (LRM) of an indicator matrix, that is, in terms of the inverse problem of regressing the observations. In other words, both approaches, i.e. GLM and LRM, apply to different domains, the observation and the label domains, and are linked by a normalization value at the least-squares solution. Subsequently, from this relationship we derive a statistical test based on a more refined predictive algorithm, i.e. the (non)linear Support Vector Machine (SVM) that maximizes the class margin of separation, within a permutation analysis. The MLE-based inference employs a residual score and includes the upper bound to compute a better estimation of the actual (real) error. Experimental results demonstrate how the parameter estimations derived from each model resulted in different classification performances in the equivalent inverse problem. Moreover, using real data the aforementioned predictive algorithms within permutation tests, including such model-free estimators, are able to provide a good trade-off between type I error and statistical power.

Detecting semantic concept of columns in tabular data is of particular interest to many applications ranging from data integration, cleaning, search to feature engineering and model building in machine learning. Recently, several works have proposed supervised learning-based or heuristic pattern-based approaches to semantic type annotation. Both have shortcomings that prevent them from generalizing over a large number of concepts or examples. Many neural network based methods also present scalability issues. Additionally, none of the known methods works well for numerical data. We propose $C^2$, a column to concept mapper that is based on a maximum likelihood estimation approach through ensembles. It is able to effectively utilize vast amounts of, albeit somewhat noisy, openly available table corpora in addition to two popular knowledge graphs to perform effective and efficient concept prediction for structured data. We demonstrate the effectiveness of $C^2$ over available techniques on 9 datasets, the most comprehensive comparison on this topic so far.