Multi-Entity Bayesian Network (MEBN) is a knowledge representation formalism combining Bayesian Networks (BN) with First-Order Logic (FOL). MEBN has sufficient expressive power for general-purpose knowledge representation and reasoning. Developing a MEBN model to support a given application is a challenge, requiring definition of entities, relationships, random variables, conditional dependence relationships, and probability distributions. When available, data can be invaluable both to improve performance and to streamline development. By far the most common format for available data is the relational database (RDB). Relational databases describe and organize data according to the Relational Model (RM). Developing a MEBN model from data stored in an RDB therefore requires mapping between the two formalisms. This paper presents MEBN-RM, a set of mapping rules between key elements of MEBN and RM. We identify links between the two languages (RM and MEBN) and define four levels of mapping from elements of RM to elements of MEBN. These definitions are implemented in the MEBN-RM algorithm, which converts a relational schema in RM to a partial MEBN model. Through this research, the software has been released as a MEBN-RM open-source software tool. The method is illustrated through two example use cases using MEBN-RM to develop MEBN models: a Critical Infrastructure Defense System and a Smart Manufacturing System.

The Gaussian mechanism is an essential building block used in multitude of differentially private data analysis algorithms. In this paper we revisit the Gaussian mechanism and show that the original analysis has several important limitations. Our analysis reveals that the variance formula for the original mechanism is far from tight in the high privacy regime ($\varepsilon \to 0$) and it cannot be extended to the low privacy regime ($\varepsilon \to \infty$). We address these limitations by developing an optimal Gaussian mechanism whose variance is calibrated directly using the Gaussian cumulative density function instead of a tail bound approximation. We also propose to equip the Gaussian mechanism with a post-processing step based on adaptive estimation techniques by leveraging that the distribution of the perturbation is known. Our experiments show that analytical calibration removes at least a third of the variance of the noise compared to the classical Gaussian mechanism, and that denoising dramatically improves the accuracy of the Gaussian mechanism in the high-dimensional regime.

Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs," which are communities of bacteria administered to patients for specific therapeutic applications. Central to the design of such therapeutics is an understanding of the causal microbial interaction network and the population dynamics of the organisms. In this work we present a Bayesian nonparametric model and associated efficient inference algorithm that addresses the key conceptual and practical challenges of learning microbial dynamics from time series microbe abundance data. These challenges include high-dimensional (300+ strains of bacteria in the gut) but temporally sparse and non-uniformly sampled data; high measurement noise; and, nonlinear and physically non-negative dynamics. Our contributions include a new type of dynamical systems model for microbial dynamics based on what we term interaction modules, or learned clusters of latent variables with redundant interaction structure (reducing the expected number of interaction coefficients from $O(n^2)$ to $O((\log n)^2)$); a fully Bayesian formulation of the stochastic dynamical systems model that propagates measurement and latent state uncertainty throughout the model; and introduction of a temporally varying auxiliary variable technique to enable efficient inference by relaxing the hard non-negativity constraint on states. We apply our method to simulated and real data, and demonstrate the utility of our technique for system identification from limited data and gaining new biological insights into bacteriotherapy design.

Networks, which represent agents and interactions between them, arise in myriad applications throughout the sciences, engineering, and even the humanities. To understand large-scale structure in a network, a common task is to cluster a network's nodes into sets called "communities" such that there are dense connections within communities but sparse connections between them. A popular and statistically principled method to perform such clustering is to use a family of generative models known as stochastic block models (SBMs). In this paper, we show that maximum likelihood estimation in an SBM is a network analog of a well-known continuum surface-tension problem that arises from an application in metallurgy. To illustrate the utility of this bridge, we implement network analogs of three surface-tension algorithms, with which we successfully recover planted community structure in synthetic networks and which yield fascinating insights on empirical networks from the field of hyperspectral video segmentation.

Bandit is a framework for designing sequential experiments. In each experiment, a learner selects an arm $A \in \mathcal{A}$ and obtains an observation corresponding to $A$. Theoretically, the tight regret lower-bound for the general bandit is polynomial with respect to the number of arms $|\mathcal{A}|$. This makes bandit incapable of handling an exponentially large number of arms, hence the bandit problem with side-information is often considered to overcome this lower bound. Recently, a bandit framework over a causal graph was introduced, where the structure of the causal graph is available as side-information. A causal graph is a fundamental model that is frequently used with a variety of real problems. In this setting, the arms are identified with interventions on a given causal graph, and the effect of an intervention propagates throughout all over the causal graph. The task is to find the best intervention that maximizes the expected value on a target node. Existing algorithms for causal bandit overcame the $\Omega(\sqrt{|\mathcal{A}|/T})$ simple-regret lower-bound; however, their algorithms work only when the interventions $\mathcal{A}$ are localized around a single node (i.e., an intervention propagates only to its neighbors). We propose a novel causal bandit algorithm for an arbitrary set of interventions, which can propagate throughout the causal graph. We also show that it achieves $O(\sqrt{ \gamma^*\log(|\mathcal{A}|T) / T})$ regret bound, where $\gamma^*$ is determined by using a causal graph structure. In particular, if the in-degree of the causal graph is bounded, then $\gamma^* = O(N^2)$, where $N$ is the number $N$ of nodes.

An Artificial Intelligence (AI) system is an autonomous system which emulates human mental and physical activities such as Observe, Orient, Decide, and Act, called the OODA process. An AI system performing the OODA process requires a semantically rich representation to handle a complex real world situation and ability to reason under uncertainty about the situation. Multi-Entity Bayesian Networks (MEBNs) combines First-Order Logic with Bayesian Networks for representing and reasoning about uncertainty in complex, knowledge-rich domains. MEBN goes beyond standard Bayesian networks to enable reasoning about an unknown number of entities interacting with each other in various types of relationships, a key requirement for the OODA process of an AI system. MEBN models have heretofore been constructed manually by a domain expert. However, manual MEBN modeling is labor-intensive and insufficiently agile. To address these problems, an efficient method is needed for MEBN modeling. One of the methods is to use machine learning to learn a MEBN model in whole or in part from data. In the era of Big Data, data-rich environments, characterized by uncertainty and complexity, have become ubiquitous. The larger the data sample is, the more accurate the results of the machine learning approach can be. Therefore, machine learning has potential to improve the quality of MEBN models as well as the effectiveness for MEBN modeling. In this research, we study a MEBN learning framework to develop a MEBN model from a combination of domain expert's knowledge and data. To evaluate the MEBN learning framework, we conduct an experiment to compare the MEBN learning framework and the existing manual MEBN modeling in terms of development efficiency.

Hybrid Bayesian Networks (HBNs), which contain both discrete and continuous variables, arise naturally in many application areas (e.g., image understanding, data fusion, medical diagnosis, fraud detection). This paper concerns inference in an important subclass of HBNs, the conditional Gaussian (CG) networks, in which all continuous random variables have Gaussian distributions and all children of continuous random variables must be continuous. Inference in CG networks can be NP-hard even for special-case structures, such as poly-trees, where inference in discrete Bayesian networks can be performed in polynomial time. Therefore, approximate inference is required. In approximate inference, it is often necessary to trade off accuracy against solution time. This paper presents an extension to the Hybrid Message Passing inference algorithm for general CG networks and an algorithm for optimizing its accuracy given a bound on computation time. The extended algorithm uses Gaussian mixture reduction to prevent an exponential increase in the number of Gaussian mixture components. The trade-off algorithm performs pre-processing to find optimal run-time settings for the extended algorithm. Experimental results for four CG networks compare performance of the extended algorithm with existing algorithms and show the optimal settings for these CG networks.

Shenoy and Shafer {Shenoy:90} demonstrated that both for Dempster-Shafer Theory and probability theory there exists a possibility to calculate efficiently marginals of joint belief distributions (by so-called local computations) provided that the joint distribution can be decomposed (factorized) into a belief network. A number of algorithms exists for decomposition of probabilistic joint belief distribution into a bayesian (belief) network from data. For example Spirtes, Glymour and Schein{Spirtes:90b} formulated a Conjecture that a direct dependence test and a head-to-head meeting test would suffice to construe bayesian network from data in such a way that Pearl's concept of d-separation {Geiger:90} applies. This paper is intended to transfer Spirtes, Glymour and Scheines {Spirtes:90b} approach onto the ground of the Dempster-Shafer Theory (DST). For this purpose, a frequentionistic interpretation of the DST developed in {Klopotek:93b} is exploited. A special notion of conditionality for DST is introduced and demonstrated to behave with respect to Pearl's d-separation {Geiger:90} much the same way as conditional probability (though some differences like non-uniqueness are evident). Based on this, an algorithm analogous to that from {Spirtes:90b} is developed. The notion of a partially oriented graph (pog) is introduced and within this graph the notion of p-d-separation is defined. If direct dependence test and head-to-head meeting test are used to orient the pog then its p-d-separation is shown to be equivalent to the Pearl's d-separation for any compatible dag.

During the 60s and 70s, AI researchers explored intuitions about intelligence by writing programs that displayed intelligent behavior. Many good ideas came out from this work but programs written by hand were not robust or general. After the 80s, research increasingly shifted to the development of learners capable of inferring behavior and functions from experience and data, and solvers capable of tackling well-defined but intractable models like SAT, classical planning, Bayesian networks, and POMDPs. The learning approach has achieved considerable success but results in black boxes that do not have the flexibility, transparency, and generality of their model-based counterparts. Model-based approaches, on the other hand, require models and scalable algorithms. Model-free learners and model-based solvers have close parallels with Systems 1 and 2 in current theories of the human mind: the first, a fast, opaque, and inflexible intuitive mind; the second, a slow, transparent, and flexible analytical mind. In this paper, I review developments in AI and draw on these theories to discuss the gap between model-free learners and model-based solvers, a gap that needs to be bridged in order to have intelligent systems that are robust and general.

Constrained counting and sampling are two fundamental problems in Computer Science with numerous applications, including network reliability, privacy, probabilistic reasoning, and constrained-random verification. In constrained counting, the task is to compute the total weight, subject to a given weighting function, of the set of solutions of the given constraints. In constrained sampling, the task is to sample randomly, subject to a given weighting function, from the set of solutions to a set of given constraints. Consequently, constrained counting and sampling have been subject to intense theoretical and empirical investigations over the years. Prior work, however, offered either heuristic techniques with poor guarantees of accuracy or approaches with proven guarantees but poor performance in practice. In this thesis, we introduce a novel hashing-based algorithmic framework for constrained sampling and counting that combines the classical algorithmic technique of universal hashing with the dramatic progress made in combinatorial reasoning tools, in particular, SAT and SMT, over the past two decades. The resulting frameworks for counting (ApproxMC2) and sampling (UniGen) can handle formulas with up to million variables representing a significant boost up from the prior state of the art tools' capability to handle few hundreds of variables. If the initial set of constraints is expressed as Disjunctive Normal Form (DNF), ApproxMC is the only known Fully Polynomial Randomized Approximation Scheme (FPRAS) that does not involve Monte Carlo steps. By exploiting the connection between definability of formulas and variance of the distribution of solutions in a cell defined by 3-universal hash functions, we introduced an algorithmic technique, MIS, that reduced the size of XOR constraints employed in the underlying universal hash functions by as much as two orders of magnitude.