A Framework for Reasoning on Probabilistic Description Logics

While there exist several reasoners for Description Logics, very few of them can cope with uncertainty. BUNDLE is an inference framework that can exploit several OWL (non-probabilistic) reasoners to perform inference over Probabilistic Description Logics. In this chapter, we report the latest advances implemented in BUNDLE. In particular, BUNDLE can now interface with the reasoners of the TRILL system, thus providing a uniform method to execute probabilistic queries using different settings. BUNDLE can be easily extended and can be used either as a standalone desktop application or as a library in OWL API-based applications that need to reason over Probabilistic Description Logics. The reasoning performance heavily depends on the reasoner and method used to compute the probability. We provide a comparison of the different reasoning settings on several datasets.

Learning Probabilistic Sentential Decision Diagrams by Sampling

Probabilistic circuits are deep probabilistic models with neural-network-like semantics capable of accurately and efficiently answering probabilistic queries without sacrificing expressiveness. Probabilistic Sentential Decision Diagrams (PSDDs) are a subclass of probabilistic circuits able to embed logical constraints to the circuit’s structure. In doing so, they obtain extra expressiveness with empirical optimal performance. Despite achieving competitive performance compared to other state-of-the-art competitors, there have been very few attempts at learning PSDDs from a combination of both data and knowledge in the form of logical formulae. Our work investigates sampling random PSDDs consistent with domain knowledge and evaluating against state-of-the-art probabilistic models. We propose a method of sampling that retains important structural constraints on the circuit’s graph that guarantee query tractability. Finally, we show that these samples are able to achieve competitive performance even on larger domains.

Hypothesized diprotomeric enzyme complex supported by stochastic modelling of palytoxin-induced Na/K pump channels

The sodium–potassium pump (Na + /K + pump) is crucial for cell physiology. Despite great advances in the understanding of this ionic pumping system, its mechanism is not completely understood. We propose the use of a statistical model checker to investigate palytoxin (PTX)-induced Na + /K + pump channels. We modelled a system of reactions representing transitions between the conformational substates of the channel with parameters, concentrations of the substates and reaction rates extracted from simulations reported in the literature, based on electrophysiological recordings in a whole-cell configuration. The model was implemented using the UPPAAL-SMC platform. Comparing simulations and probabilistic queries from stochastic system semantics with experimental data, it was possible to propose additional reactions to reproduce the single-channel dynamic. The probabilistic analyses and simulations suggest that the PTX-induced Na + /K + pump channel functions as a diprotomeric complex in which protein–protein interactions increase the affinity of the Na + /K + pump for PTX.

Learning Probabilistic Graphical Models

Probabilistic Graphical Models (PGM) are a class of statistical models that use a graph structure over a set of variables to encode independence relations between those variables. By augmenting the graph by local parameters, a PGM allows for a compact representation of a joint probability distribution over the variables of the graph, which allows for efficient inference algorithms. PGMs are often used for modeling physical and biological systems, and such models are then in turn used to both answer probabilistic queries concerning the variables and to represent certain causal and/or statistical relations in the domain. In this chapter, the authors give an overview of common techniques used for automatic construction of such models from a dataset of observations (usually referred to as learning), and they also review some important applications. The chapter guides the reader to the relevant literature for further study.

Interpolation Between AIS Reports: Probabilistic Inferences Over Vessel Path Space

We present a method for addressing probabilistic queries about the location of a vessel in the time interval between two position reports, such as from the Automatic Identification System (AIS). The heart of the method is the random generation of physically feasible paths connecting the two reports. The method empowers operators to answer probabilistic questions about any characteristic of the unknown true path. For illustrative purposes, we demonstrate the use of the method to identify which of several vessels is the most likely perpetrator, in a fictitious scenario in which illegal dumping of waste matter has taken place.