Probabilistic Logic Programming with Beta-Distributed Random Variables

We enable aProbLog---a probabilistic logical programming approach---to reason in presence of uncertain probabilities represented as Beta-distributed random variables. We achieve the same performance of state-of-the-art algorithms for highly specified and engineered domains, while simultaneously we maintain the flexibility offered by aProbLog in handling complex relational domains. Our motivation is that faithfully capturing the distribution of probabilities is necessary to compute an expected utility for effective decision making under uncertainty: unfortunately, these probability distributions can be highly uncertain due to sparse data. To understand and accurately manipulate such probability distributions we need a well-defined theoretical framework that is provided by the Beta distribution, which specifies a distribution of probabilities representing all the possible values of a probability when the exact value is unknown.Comment: Accepted for presentation at AAAI 201

Secure Cloud-Edge Deployments, with Trust

Assessing the security level of IoT applications to be deployed to heterogeneous Cloud-Edge infrastructures operated by different providers is a non-trivial task. In this article, we present a methodology that permits to express security requirements for IoT applications, as well as infrastructure security capabilities, in a simple and declarative manner, and to automatically obtain an explainable assessment of the security level of the possible application deployments. The methodology also considers the impact of trust relations among different stakeholders using or managing Cloud-Edge infrastructures. A lifelike example is used to showcase the prototyped implementation of the methodology

DeepProbLog: Neural Probabilistic Logic Programming

We introduce DeepProbLog, a probabilistic logic programming language that incorporates deep learning by means of neural predicates. We show how existing inference and learning techniques can be adapted for the new language. Our experiments demonstrate that DeepProbLog supports both symbolic and subsymbolic representations and inference, 1) program induction, 2) probabilistic (logic) programming, and 3) (deep) learning from examples. To the best of our knowledge, this work is the first to propose a framework where general-purpose neural networks and expressive probabilistic-logical modeling and reasoning are integrated in a way that exploits the full expressiveness and strengths of both worlds and can be trained end-to-end based on examples.Comment: Accepted for spotlight at NeurIPS 201

Algebraic model counting

Weighted model counting (WMC) is a well-known inference task on knowledge bases, and the basis for some of the most efficient techniques for probabilistic inference in graphical models. We introduce algebraic model counting (AMC), a generalization of WMC to a semiring structure that provides a unified view on a range of tasks and existing results. We show that AMC generalizes many well-known tasks in a variety of domains such as probabilistic inference, soft constraints and network and database analysis. Furthermore, we investigate AMC from a knowledge compilation perspective and show that all AMC tasks can be evaluated using sd-DNNF circuits, which are strictly more succinct, and thus more efficient to evaluate, than direct representations of sets of models. We identify further characteristics of AMC instances that allow for evaluation on even more succinct circuits

Network-based analysis of eQTL data to prioritize driver mutations

In clonal systems, interpreting driver genes in terms of molecular networks helps understanding how these drivers elicit an adaptive phenotype. Obtaining such a network-based understanding depends on the correct identification of driver genes. In clonal systems, independent evolved lines can acquire a similar adaptive phenotype by affecting the same molecular pathways, a phenomenon referred to as parallelism at the molecular pathway level. This implies that successful driver identification depends on interpreting mutated genes in terms of molecular networks. Driver identification and obtaining a network-based understanding of the adaptive phenotype are thus confounded problems that ideally should be solved simultaneously. In this study, a network-based eQTL method is presented that solves both the driver identification and the network-based interpretation problem. As input the method uses coupled genotype-expression phenotype data (eQTL data) of independently evolved lines with similar adaptive phenotypes and an organism-specific genome-wide interaction network. The search for mutational consistency at pathway level is defined as a subnetwork inference problem, which consists of inferring a subnetwork from the genome-wide interaction network that best connects the genes containing mutations to differentially expressed genes. Based on their connectivity with the differentially expressed genes, mutated genes are prioritized as driver genes. Based on semisynthetic data and two publicly available data sets, we illustrate the potential of the network-based eQTL method to prioritize driver genes and to gain insights in the molecular mechanisms underlying an adaptive phenotype. The method is available at http://bioinformatics.intec.ugent.be/phenetic_eqtl/index.htm

Probabilistic Programming Concepts

A multitude of different probabilistic programming languages exists today, all extending a traditional programming language with primitives to support modeling of complex, structured probability distributions. Each of these languages employs its own probabilistic primitives, and comes with a particular syntax, semantics and inference procedure. This makes it hard to understand the underlying programming concepts and appreciate the differences between the different languages. To obtain a better understanding of probabilistic programming, we identify a number of core programming concepts underlying the primitives used by various probabilistic languages, discuss the execution mechanisms that they require and use these to position state-of-the-art probabilistic languages and their implementation. While doing so, we focus on probabilistic extensions of logic programming languages such as Prolog, which have been developed since more than 20 years