Probabilistic Inference on Multiple Normalized Genome-Wide Signal Profiles With Model Regularization.

Probabilistic relational models (PRMs) extend Bayesian networks (BNs) to a relational data mining context. Even though a panoply of works have focused, separately, on Bayesian networks and relational databases random generation, no work has been identified for PRMs on that track. This paper provides an algorithmic approach allowing to generate random PRMs from scratch to cover the absence of generation process. The proposed method allows to generate PRMs as well as synthetic relational data from a randomly generated relational schema and a random set of probabilistic dependencies. This can be of interest for machine learning researchers to evaluate their proposals in a common framework, as for databases designers to evaluate the effectiveness of the components of a database management system.

Most asset deterioration tools are designed for a specific application, as a consequence, a small change of the specification may result in a complete change of the tool. Inspired by the model-based approach of separating problem specification from analysis technique, we propose a model-based asset deterioration assessment framework using probabilistic relational models. The probabilistic relational models express abstract probabilistic dependency covers a range of deterioration modelling assumptions. An expert in the domain of asset deterioration can then use his knowledge of the factors that affect deterioration to customise the abstract models to a specific application, without requiring a detailed understanding the underlying computational framework. We illustrate the use of the framework with multiple variants of deterioration models.

A Unified Recommendation Framework Based on Probabilistic Relational Models

This paper proposes the use of Probabilistic Relational Models (PRM) for analyzing dependencies between Information Security Governance (ISG) components and its impact on process capability of mitigating information security vulnerabilities. Using the PRM enables inference between different ISG components expressed in probabilities, and also inference on the process capability. A concrete PRM which exemplifies how to assess the capability of the access control process is further presented, and thus showing how the PRM can be adapted to fit the analysis of a specific process in an organizational environment.

Probabilistic relational models (PRMs) extend Bayesian networks to multi-relational domains and represent the dependencies between attributes within a table and across multiple tables. This paper presents a method of integrating and learning with concept hierarchies with PRMs, in order to retrieve richer object and relational information from multi-relational databases. A concept hierarchy defines a partially ordered sequence of mappings from a set of concepts to their higher-level correspondences. Natural concept hierarchies are often associated with some attributes in databases and can be used to discover knowledge. We first introduce concept hierarchies to PRMs by using background knowledge. A score-based search algorithm is then investigated for learning with concept hierarchies in PRMs parameter estimation procedure. The method can learn the most appropriate concepts from the data and use them to update the parameters. Experimental results on both real and synthetic data are discussed.KeywordsMinimum Description LengthConcept HierarchyStatistical Relational LearningProbabilistic Relational ModelAggregate RuleThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

A Personalized Recommender System from Probabilistic Relational Model and Users’ Preferences

In chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) and other short-read sequencing experiments, a considerable fraction of the short reads align to multiple locations on the reference genome (multi-reads). Inferring the origin of multi-reads is critical for accurately mapping reads to repetitive regions. Current state-of-the-art multi-read allocation algorithms rely on the read counts in the local neighborhood of the alignment locations and ignore the variation in the copy numbers of these regions. Copy-number variation (CNV) can directly affect the read densities and, therefore, bias allocation of multi-reads. We propose cnvCSEM (CNV-guided ChIP-Seq by expectation-maximization algorithm), a flexible framework that incorporates CNV in multi-read allocation. cnvCSEM eliminates the CNV bias in multi-read allocation by initializing the read allocation algorithm with CNV-aware initial values. Our data-driven simulations illustrate that cnvCSEM leads to higher read coverage with satisfactory accuracy and lower loss in read-depth recovery (estimation). We evaluate the biological relevance of the cnvCSEM-allocated reads and the resultant peaks with the analysis of several ENCODE ChIP-seq datasets. Available at http://www.stat.wisc.edu/∼qizhang/ : qizhang@stat.wisc.edu or keles@stat.wisc.edu Supplementary data are available at Bioinformatics online.

In this paper, a probabilistic relational model is presented which combines relational algebra with probabilistic retrieval. Based on certain independence assumptions, the operators of the relational algebra are redefined such that the probabilistic algebra is a generalization of the standard relational algebra. Furthermore, a special join operator implementing probabilistic retrieval is proposed. When applied to typical document databases, queries can not only ask for documents, but for any kind of object in the database. In addition, an implicit ranking of these objects is provided in case the query relates to probabilistic indexing or uses the probabilistic join operator. The proposed algebra is intended as a standard interface to combined database and IR systems, as a basis for implementing user-friendly interfaces.

This paper presents a workflow for the design of transformation processes using different kinds of expert’s knowledge. It introduces POND (Process and observation ONtology Discovery), a workflow dedicated to answer expert’s questions about processes. It addresses two main issues: (1) how to represent the processes inner complexity, and (2) how to reason about processes taking into account uncertainty and causality. First, we show how to use a semantic model, an ontology, and its associated data to answer some of the expert’s questions concerning the processes, using semantic web languages and technologies. Then, we describe how to learn a predictive model, to discover new knowledge and provide explicative models by integrating the semantic model into a probabilistic relational model. The result is a complete workflow able to extensively analyze transformation processes through all their granularity levels and answer expert’s questions about their domains. An example of this workflow is given on biocomposites manufacturing for food packaging.

There is currently a large interest in relational probabilistic models. While the concept of context-specific independence (CSI) has been well-studied for models such as Bayesian networks, this is not the case for relational probabilistic models. In this paper we show that directed relational probabilistic models often exhibit CSI by identifying three different sources of CSI in such models (two of which are inherent to the relational character of the models).

Identity verification is essential in our mission to identify potential terrorists and criminals. It is not a trivial task because terrorists reportedly assume multiple identities using either fraudulent or legitimate means. A national identification card and biometrics technologies have been proposed as solutions to the identity problem. However, several studies show their inability to tackle the complex problem. We aim to develop data mining alternatives that can match identities referring to the same individual. Existing identity matching techniques based on data mining primarily rely on personal identity features. In this research, we propose a new identity matching technique that considers both personal identity features and social identity features. We define two groups of social identity features including social activities and social relations. The proposed technique is built upon a probabilistic relational model that utilizes a relational database structure to extract social identity features. Experiments show that the social activity features significantly improve the matching performance while the social relation features effectively reduce false positive and false negative decisions.

: Natural language (supplemented with diagrams and some mathematical notations) is convenient for succinct communication of technical descriptions between the various stakeholders (e.g., customers, designers, implementers) involved in the design of software systems. However, natural language descriptions can be informal, incomplete, imprecise and ambiguous, and cannot be processed easily by design and analysis tools. Formal languages, on the other hand, formulate design requirements in a precise and unambiguous mathematical notation, but are more difficult to master and use. We propose a methodology for connecting semi-formal requirements with formal descriptions through an intermediate representation. We have implemented this methodology in a research prototype called Automatic Requirements Specification Extraction from Natural Language (ARSENAL). The main novelty of ARSENAL lies in its ability to generate a fully-specified complete formal model automatically from natural language requirements. ARSENAL extracts relations from text using semantic parsing and progressively refines them over multiple stages to create a final composite model. Currently, ARSENAL generates formal models in linear-time temporal logic (LTL), but the approach can be adapted for other models, e.g., probabilistic relational models like Markov Logic Networks (MLN). The formal models of the requirements can be used to check important design and system properties, e.g., consistency, satisfiability, realizability. ARSENAL has a modular and flexible architecture that facilitates porting it from one domain to another. We evaluated ARSENAL on complex requirements from two real-world case studies: the Time-Triggered Ethernet (TTEthernet) communication platform used in space, and FAA-Isolette infant incubators used in NICU. We systematically evaluated various aspects of ARSENAL -- the accuracy of the natural language processing stage, the degree of automation, and robustness to noise.

Students’ performance and motivation are influenced by their emotions. Game-based learning (GBL) environments comprise elements that facilitate learning and the creation of an emotional connection with students. GBL environments include Intelligent Tutoring Systems (ITSs) to ensure personalized learning. ITSs reason about students’ needs and characteristics (student modeling) to provide suitable instruction (tutor modeling). The authors’ research is focused on the design and implementation of an emotional student model for GBL environments based on the Control-Value Theory of achievement emotions by Pekrun et al. (2007). The model reasons about answers to questions in game dialogues and contextual variables related to student behavior acquired through students’ interaction with PlayPhysics. The authors’ model is implemented using Dynamic Bayesian Networks (DBNs), which are derived using Probabilistic Relational Models (PRMs), machine learning techniques, and statistical methods. This work compares an earlier approach that uses Multinomial Logistic Regression (MLR) and cross-tabulation for learning the structure and conditional probability tables with an approach that employs Necessary Path Condition and Expectation Maximization algorithms. Results showed that the latter approach is more effective at classifying the control of outcome-prospective emotions. Future work will focus on applying this approach to classification of activity and outcome-retrospective emotions.

Probabilistic Relational Models (PRMs) extend Bayesian networks (BNs) with the notion of class of relational databases. Because of their richness, learning them is a difficult task. In this paper, we propose a method that learns a PRM from data using the semantic knowledge of an ontology describing these data in order to make the learning easier. To present our approach, we describe an implementation based on an ontology of transformation processes and compare its performance to that of a method that learns a PRM directly from data. We show that, even with small datasets, our approach of learning a PRM using an ontology is more efficient.

We have developed an intelligent tutoring system coupled with a virtual laboratory, which constitute a semi-open learning environment. This environment provides the student with the opportunity to learn through exploration within a virtual laboratory, while achieving the expected learning objectives. The key element of this environment is a novel representation for the student model based on probabilistic relational models. This student model has several advantages: flexibility, user adaptability, high modularity and facilities for model construction for different scenarios. The model keeps track of the students' knowledge at different levels of granularity, combining the performance and exploration behavior in several experiments, to decide the best way to guide the student in following experiments, and to re-categorize the students based on the results. We have implemented a tutor for a virtual robotics laboratory, and evaluated the system with an initial group of 20 students. The results show that students who explore the virtual environment with the help of the tutor have a better academic skills, and also that the predictions of the student model are generally accurate.