Learning cover context-free grammars from structural data

We consider the problem of learning an unknown context-free grammar when the only knowledge available and of interest to the learner is about its structural descriptions with depth at most $\ell.$ The goal is to learn a cover context-free grammar (CCFG) with respect to $\ell$, that is, a CFG whose structural descriptions with depth at most $\ell$ agree with those of the unknown CFG. We propose an algorithm, called $LA^\ell$, that efficiently learns a CCFG using two types of queries: structural equivalence and structural membership. We show that $LA^\ell$ runs in time polynomial in the number of states of a minimal deterministic finite cover tree automaton (DCTA) with respect to $\ell$. This number is often much smaller than the number of states of a minimum deterministic finite tree automaton for the structural descriptions of the unknown grammar

Analog Property Checkers: A Ddr2 Case Study

The formal specification component of verification can be exported to simulation through the idea of property checkers. The essence of this approach is the automatic construction of an observer from the specification in the form of a program that can be interfaced with a simulator and alert the user if the property is violated by a simulation trace. Although not complete, this lighter approach to formal verification has been effectively used in software and digital hardware to detect errors. Recently, the idea of property checkers has been extended to analog and mixed-signal systems. In this paper, we apply the property-based checking methodology to an industrial and realistic example of a DDR2 memory interface. The properties describing the DDR2 analog behavior are expressed in the formal specification language stl/psl in form of assertions. The simulation traces generated from an actual DDR2 interface design are checked with respect to the stl/psl assertions using the amt tool. The focus of this paper is on the translation of the official (informal and descriptive) specification of two non-trivial DDR2 properties into stl/psl assertions. We study both the benefits and the current limits of such approach

Runtime Verification of Temporal Properties over Out-of-order Data Streams

We present a monitoring approach for verifying systems at runtime. Our approach targets systems whose components communicate with the monitors over unreliable channels, where messages can be delayed or lost. In contrast to prior works, whose property specification languages are limited to propositional temporal logics, our approach handles an extension of the real-time logic MTL with freeze quantifiers for reasoning about data values. We present its underlying theory based on a new three-valued semantics that is well suited to soundly and completely reason online about event streams in the presence of message delay or loss. We also evaluate our approach experimentally. Our prototype implementation processes hundreds of events per second in settings where messages are received out of order.Comment: long version of the CAV 2017 pape

Robust Online Monitoring of Signal Temporal Logic

Signal Temporal Logic (STL) is a formalism used to rigorously specify requirements of cyberphysical systems (CPS), i.e., systems mixing digital or discrete components in interaction with a continuous environment or analog com- ponents. STL is naturally equipped with a quantitative semantics which can be used for various purposes: from assessing the robustness of a specification to guiding searches over the input and parameter space with the goal of falsifying the given property over system behaviors. Algorithms have been proposed and implemented for offline computation of such quantitative semantics, but only few methods exist for an online setting, where one would want to monitor the satisfaction of a formula during simulation. In this paper, we formalize a semantics for robust online monitoring of partial traces, i.e., traces for which there might not be enough data to decide the Boolean satisfaction (and to compute its quantitative counterpart). We propose an efficient algorithm to compute it and demonstrate its usage on two large scale real-world case studies coming from the automotive domain and from CPS education in a Massively Open Online Course (MOOC) setting. We show that savings in computationally expensive simulations far outweigh any overheads incurred by an online approach

HySIA: Tool for Simulating and Monitoring Hybrid Automata Based on Interval Analysis

We present HySIA: a reliable runtime verification tool for nonlinear hybrid automata (HA) and signal temporal logic (STL) properties. HySIA simulates an HA with interval analysis techniques so that a trajectory is enclosed sharply within a set of intervals. Then, HySIA computes whether the simulated trajectory satisfies a given STL property; the computation is performed again with interval analysis to achieve reliability. Simulation and verification using HySIA are demonstrated through several example HA and STL formulas.Comment: Appeared in RV'17; the final publication is available at Springe

Alternative RNA Splicing of the NMDA Receptor NR1 mRNA in the Neurons of the Teleost Electrosensory System

The sequence for cDNA encoding the NMDA receptor subunit 1 (aptNR1) of the weakly electric fish Apteronotus leptorhynchus has been determined. The deduced amino acid sequence is approximately 88% identical to other vertebrate NR1 proteins, with sequence homology extending to the alternatively spliced cassettes N1 and C1. The fish and mammalian N1 and C1 splice cassettes are identical at 20 of 21 and 30 of 37 amino acid positions, respectively. We did not detect a C2 splice cassette in aptNR1 mRNA, but we did find two novel C-terminal alternative splice cassettes labeled C1' and C1". The relative levels of NR1 transcripts containing the N1 and C1 splice cassettes were determined by using RNase protection and in situ hybridization analysis. N1-containing mRNAs are more abundant in caudal brain regions, similar to the patterns reported for mammalian brain. In contrast, the relative levels of transcripts containing the C1 splice cassette are much lower in fish than in mammals, averaging only 9% for the whole brain. The levels of C1 splicing increased in more rostral brain regions. In situ hybridizations with N1- and C1-specific probes demonstrated that N1 cassette splicing occurs in most neurons but that C1 splicing is heterogeneous and is restricted to a subset of neuronal types in the electrosensory system

On-Line Monitoring for Temporal Logic Robustness

In this paper, we provide a Dynamic Programming algorithm for on-line monitoring of the state robustness of Metric Temporal Logic specifications with past time operators. We compute the robustness of MTL with unbounded past and bounded future temporal operators MTL over sampled traces of Cyber-Physical Systems. We implemented our tool in Matlab as a Simulink block that can be used in any Simulink model. We experimentally demonstrate that the overhead of the MTL robustness monitoring is acceptable for certain classes of practical specifications

Efficient Online Timed Pattern Matching by Automata-Based Skipping

The timed pattern matching problem is an actively studied topic because of its relevance in monitoring of real-time systems. There one is given a log $w$ and a specification $\mathcal{A}$ (given by a timed word and a timed automaton in this paper), and one wishes to return the set of intervals for which the log $w$, when restricted to the interval, satisfies the specification $\mathcal{A}$. In our previous work we presented an efficient timed pattern matching algorithm: it adopts a skipping mechanism inspired by the classic Boyer--Moore (BM) string matching algorithm. In this work we tackle the problem of online timed pattern matching, towards embedded applications where it is vital to process a vast amount of incoming data in a timely manner. Specifically, we start with the Franek-Jennings-Smyth (FJS) string matching algorithm---a recent variant of the BM algorithm---and extend it to timed pattern matching. Our experiments indicate the efficiency of our FJS-type algorithm in online and offline timed pattern matching

Molecular biology of the apteronotus NMDA receptor NR1 subunit

The complete sequences and expression patterns of the NR1 (aptNR1) subunit of the N-methyl-d-aspartate (NMDA) receptor and its alternative splice isoforms have been determined for the weakly electric fish Apteronotus leptorhynchus. The deduced amino acid sequence of aptNR1 is approximately 88 % identical to the NR1 sequences of other vertebrate. Two of the three alternative splice cassettes previously described for mammalian NR1s, N1 and C1, are present in aptNR1, but the third cassette, C2, is not found. In addition, two teleost-specific splice cassettes occur on the N-terminal side of the C1 sequence. The cellular patterns of aptNR1 expression, including the patterns of N1 and C1 splicing, have been mapped using the in situ hybridization technique. High levels of aptNR1 mRNA were detected throughout the central nervous system including most neurons of the electrosensory system, with the highest levels in electrosensory lateral line lobe pyramidal cells. Expression of the N1 splice isoform was higher in more caudal regions of the brain, and expression of the C1 splice isoform was higher in more rostral regions. The N1 splice isoform was present in almost all NR1-positive cells, in contrast to the C1 splice isoform which was restricted to a subset of NR1-positive cells. These results demonstrate that the NR1 subunit of the NMDA receptor is evolutionarily conserved across species and that regulation of alternative RNA splicing modulates the properties of NR1 in different neurons of the central nervous system of A. leptorhynchus