Efficient Monitoring of Parametric Context Free Patterns

Recent developments in runtime verification and monitoring show that parametric regular and temporal logic specifications can be efficiently monitored against large programs. However, these logics reduce to ordinary finite automata, limiting their expressivity. For example, neither can specify structured properties that refer to the call stack of the program. While context-free grammars (CFGs) are expressive and well-understood, existing techniques of monitoring CFGs generate massive runtime overhead in real-life applications. This paper shows for the first time that monitoring parametric CFGs is practical (on the order of 10% or lower for average cases, several times faster than the state-of-the-art). We present a monitor synthesis algorithm for CFGs based on an LR(1) parsing algorithm, modified with stack cloning to account for good prefix matching. In addition, a logic-independent mechanism is introduced to support partial matching, allowing patterns to be checked against fragments of execution traces

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

A K Definition of Scheme

This paper presents an executable rewriting logic semantics of R5RS Scheme using the K definitional technique [19]. We refer to this definition as K-Scheme. The presented semantics follows the K language definitional style but is almost entirely equational. It can also be regarded as a denotational specification with an initial model semantics of Scheme. Equational specifications can be executed on common rewrite engines, provided that equations are oriented into rewrite rules, typically from left-to-right. The rewriting logic semantics in this paper is the most complete formal definition of Scheme that we are aware of, in the sense that it provides definitions for more Scheme language features than any other similar attempts. The presented executable definition, K-Scheme, can serve as a platform for experimentation with variants and extensions of Scheme, for example concurrency. K-Scheme also serves to show the viability of K as a definitional framework for programming languages

A Formal Rewriting Logic Semantic Definition of Scheme

This paper presents a formal definition of Scheme (based on the informal definition given in the R5RS report R5RS. The definition is purely equational, so it can be regarded as an algebraic denotational specification with an initial model/algebra semantics of Scheme. Moreover, it is executable, in the sense that equations can be oriented from left-to-right into rewrite rules and thus giving an operational semantics of Scheme as well; this way, an interpreter for Scheme is obtained for free by just executing the presented Scheme definition on term rewrite engines. Maude is used in this paper, but other equational engines could have been used as well. The definition in this paper is the most complete formal definition of Scheme that we are aware of and can play two important roles: as a formal definition of Scheme complementary to the informal one in the R5RS report, and as a platform for experimentation with variants and extensions of Scheme, for example concurrency. This work is part of the rewriting logic semantics project, whose broad scope is to formally define languages and language features in rewriting logic, and then use the generic support provided by rewriting logic to obtain not only interpreters, but also formal analysis tools for the defined languages

Towards Categorizing and Formalizing the JDK API

Formal specification of correct library usage is extremely useful, both for software developers and for the formal analysis tools they use, such as model checkers or runtime monitoring systems. Unfortunately, the process of creating formal specifications is time consuming, and, for the most part, even the libraries in greatest use, such as the Java Development Kit (JDK) standard library, are left wholly without formal specification. This paper presents a tool-supported approach to help writing formal specifications for Java libraries and creating documentation augmented with highlighting and formal specifications. The presented approach has been applied to systematically and completely formalize the runtime properties of three core and commonly used packages of the JDK API, namely java.io, java.lang and java.util, yielding 137 formal specifications. Indirectly, this paper also brings empirical evidence that parametric specifications may be sufficiently powerful to express virtually all desirable runtime properties of the JDK API, and that its informal documentation can be formalized.published or submitted for publicationnot peer reviewe

Efficient Formalism-Independent Monitoring of Parametric Properties

Efficient monitoring of parametric properties, in spite of increasingly growing interest thanks to applications such as testing and security, imposes a highly non-trivial challenge on monitoring approaches due to the potentially huge number of parameter instances. A few solutions have been proposed, but most of them compromise their expressiveness for performance or vice versa. In this paper, we propose a generic, in terms of specification formalisms, yet efficient, solution to monitoring parametric specifications. Our approach is based on a general semantics for slicing parametric traces and makes use of knowledge about the property to monitor. The needed knowledge is not specific to the underlying formalism and can be easily computed when generating monitoring code from the property. An extensive evaluation shows that the monitoring code generated by our algorithm is still faster than other state-of-art techniques optimized for particular logics or properties

How Successful Is Data Structure Analysis in Isolating and Analyzing Linked Data Structures?

This report describes a set of experiments to evaluate qualitatively the effectiveness of Data Structure Analysis (DSA) in identifying properties of a program's data structures. We manually inspected several benchmarks to identify linked data structures and their properties, and compared these against the results produced by DSA. The properties we considered are those that were the primary goals of DSA: distinguishing different kinds of data structures, distinct instances of a particular kind, type information for objects within an LDS, and information about the lifetime of such objects (particularly, those local to a function rather than global). We define a set of metrics for the DS graphs computed by DSA that we use to summarize our results concisely for each benchmark. The results of the study are summarized in the last section

Scalable Parametric Runtime Monitoring

Runtime monitoring is an effective means to improve the reliability of systems. In recent years, parametric monitoring, which is highly suitable for object-oriented systems, has gained significant traction. Previous work on the performance of parametric runtime monitoring has focused on the performance of monitoring only one specification at a time. A realistic system, however, has numerous properties that need to be monitored simultaneously. This paper introduces scalable techniques to improve the performance of one of the fastest parametric monitoring systems, JavaMOP, in the presence of multiple simultaneous properties, resulting in average runtime overheads that are less than the summation of the overheads of the properties run in isolation. An extensive evaluation shows that these techniques, which were derived following a thorough investigation and analysis of the current bottlenecks in JavaMOP, improve its runtime performance in the presence of multiple properties by up to two times and the memory usage by 34%published or submitted for publicationnot peer reviewe