Semantic processing of EHR data for clinical research

There is a growing need to semantically process and integrate clinical data from different sources for clinical research. This paper presents an approach to integrate EHRs from heterogeneous resources and generate integrated data in different data formats or semantics to support various clinical research applications. The proposed approach builds semantic data virtualization layers on top of data sources, which generate data in the requested semantics or formats on demand. This approach avoids upfront dumping to and synchronizing of the data with various representations. Data from different EHR systems are first mapped to RDF data with source semantics, and then converted to representations with harmonized domain semantics where domain ontologies and terminologies are used to improve reusability. It is also possible to further convert data to application semantics and store the converted results in clinical research databases, e.g. i2b2, OMOP, to support different clinical research settings. Semantic conversions between different representations are explicitly expressed using N3 rules and executed by an N3 Reasoner (EYE), which can also generate proofs of the conversion processes. The solution presented in this paper has been applied to real-world applications that process large scale EHR data.Comment: Accepted for publication in Journal of Biomedical Informatics, 2015, preprint versio

Programming with Algebraic Effects and Handlers

Eff is a programming language based on the algebraic approach to computational effects, in which effects are viewed as algebraic operations and effect handlers as homomorphisms from free algebras. Eff supports first-class effects and handlers through which we may easily define new computational effects, seamlessly combine existing ones, and handle them in novel ways. We give a denotational semantics of eff and discuss a prototype implementation based on it. Through examples we demonstrate how the standard effects are treated in eff, and how eff supports programming techniques that use various forms of delimited continuations, such as backtracking, breadth-first search, selection functionals, cooperative multi-threading, and others

Survey over Existing Query and Transformation Languages

A widely acknowledged obstacle for realizing the vision of the Semantic Web is the inability of many current Semantic Web approaches to cope with data available in such diverging representation formalisms as XML, RDF, or Topic Maps. A common query language is the first step to allow transparent access to data in any of these formats. To further the understanding of the requirements and approaches proposed for query languages in the conventional as well as the Semantic Web, this report surveys a large number of query languages for accessing XML, RDF, or Topic Maps. This is the first systematic survey to consider query languages from all these areas. From the detailed survey of these query languages, a common classification scheme is derived that is useful for understanding and differentiating languages within and among all three areas

RDF Querying

Reactive Web systems, Web services, and Web-based publish/ subscribe systems communicate events as XML messages, and in many cases require composite event detection: it is not sufficient to react to single event messages, but events have to be considered in relation to other events that are received over time. Emphasizing language design and formal semantics, we describe the rule-based query language XChangeEQ for detecting composite events. XChangeEQ is designed to completely cover and integrate the four complementary querying dimensions: event data, event composition, temporal relationships, and event accumulation. Semantics are provided as model and fixpoint theories; while this is an established approach for rule languages, it has not been applied for event queries before

Formalisation and Implementation of the XACML Access Control Mechanism

We propose a formal account of XACML, an OASIS standard adhering to the Policy Based Access Control model for the specifica- tion and enforcement of access control policies. To clarify all ambiguous and intricate aspects of XACML, we provide it with a more manageable alternative syntax and with a solid semantic ground. This lays the basis for developing tools and methodologies which allow software engineers to easily and precisely regulate access to resources using policies. To demonstrate feasibility and effectiveness of our approach, we provide a software tool, supporting the specification and evaluation of policies and access requests, whose implementation fully relies on our formal development

Web and Semantic Web Query Languages

A number of techniques have been developed to facilitate powerful data retrieval on the Web and Semantic Web. Three categories of Web query languages can be distinguished, according to the format of the data they can retrieve: XML, RDF and Topic Maps. This article introduces the spectrum of languages falling into these categories and summarises their salient aspects. The languages are introduced using common sample data and query types. Key aspects of the query languages considered are stressed in a conclusion

Rehearsal: A Configuration Verification Tool for Puppet

Large-scale data centers and cloud computing have turned system configuration into a challenging problem. Several widely-publicized outages have been blamed not on software bugs, but on configuration bugs. To cope, thousands of organizations use system configuration languages to manage their computing infrastructure. Of these, Puppet is the most widely used with thousands of paying customers and many more open-source users. The heart of Puppet is a domain-specific language that describes the state of a system. Puppet already performs some basic static checks, but they only prevent a narrow range of errors. Furthermore, testing is ineffective because many errors are only triggered under specific machine states that are difficult to predict and reproduce. With several examples, we show that a key problem with Puppet is that configurations can be non-deterministic. This paper presents Rehearsal, a verification tool for Puppet configurations. Rehearsal implements a sound, complete, and scalable determinacy analysis for Puppet. To develop it, we (1) present a formal semantics for Puppet, (2) use several analyses to shrink our models to a tractable size, and (3) frame determinism-checking as decidable formulas for an SMT solver. Rehearsal then leverages the determinacy analysis to check other important properties, such as idempotency. Finally, we apply Rehearsal to several real-world Puppet configurations.Comment: In proceedings of ACM SIGPLAN Conference on Programming Language Design and Implementation (PLDI) 201

Permission-Based Separation Logic for Multithreaded Java Programs

This paper presents a program logic for reasoning about multithreaded Java-like programs with dynamic thread creation, thread joining and reentrant object monitors. The logic is based on concurrent separation logic. It is the first detailed adaptation of concurrent separation logic to a multithreaded Java-like language. The program logic associates a unique static access permission with each heap location, ensuring exclusive write accesses and ruling out data races. Concurrent reads are supported through fractional permissions. Permissions can be transferred between threads upon thread starting, thread joining, initial monitor entrancies and final monitor exits. In order to distinguish between initial monitor entrancies and monitor reentrancies, auxiliary variables keep track of multisets of currently held monitors. Data abstraction and behavioral subtyping are facilitated through abstract predicates, which are also used to represent monitor invariants, preconditions for thread starting and postconditions for thread joining. Value-parametrized types allow to conveniently capture common strong global invariants, like static object ownership relations. The program logic is presented for a model language with Java-like classes and interfaces, the soundness of the program logic is proven, and a number of illustrative examples are presented

Relational Parametricity and Separation Logic

Separation logic is a recent extension of Hoare logic for reasoning about programs with references to shared mutable data structures. In this paper, we provide a new interpretation of the logic for a programming language with higher types. Our interpretation is based on Reynolds's relational parametricity, and it provides a formal connection between separation logic and data abstraction