Interpolant tree automata and their application in Horn clause verification

This paper investigates the combination of abstract interpretation over the domain of convex polyhedra with interpolant tree automata, in an abstraction-refinement scheme for Horn clause verification. These techniques have been previously applied separately, but are combined in a new way in this paper. The role of an interpolant tree automaton is to provide a generalisation of a spurious counterexample during refinement, capturing a possibly infinite set of spurious counterexample traces. In our approach these traces are then eliminated using a transformation of the Horn clauses. We compare this approach with two other methods; one of them uses interpolant tree automata in an algorithm for trace abstraction and refinement, while the other uses abstract interpretation over the domain of convex polyhedra without the generalisation step. Evaluation of the results of experiments on a number of Horn clause verification problems indicates that the combination of interpolant tree automaton with abstract interpretation gives some increase in the power of the verification tool, while sometimes incurring a performance overhead.Comment: In Proceedings VPT 2016, arXiv:1607.0183

RAGE mediates S100A4-induced cell motility via MAPK/ERK and hypoxia signaling and is a prognostic biomarker for human colorectal cancer metastasis

Survival of colorectal cancer patients is strongly dependent on development of distant metastases. S100A4 is a prognostic biomarker and inducer for colorectal cancer metastasis. Besides exerting intracellular functions, S100A4 is secreted extracellularly. The receptor for advanced glycation end products (RAGE) is one of its interaction partners. The impact of the S100A4-RAGE interaction for cell motility and metastasis formation in colorectal cancer has not been elucidated so far. Here we demonstrate the RAGE-dependent increase in migratory and invasive capabilities of colorectal cancer cells via binding to extracellular S100A4. We show the direct interaction of S100A4 and RAGE, leading to hyperactivated MAPK/ERK and hypoxia signaling. The S100A4-RAGE axis increased cell migration (P<0.005) and invasion (P<0.005), which was counteracted with recombinant soluble RAGE and RAGE-specific antibodies. In colorectal cancer patients, not distantly metastasized at surgery, high RAGE expression in primary tumors correlated with metachronous metastasis, reduced overall (P=0.022) and metastasis-free survival (P=0.021). In summary, interaction of S100A4-RAGE mediates S100A4-induced colorectal cancer cell motility. RAGE by itself represents a biomarker for prognosis of colorectal cancer. Thus, therapeutic approaches targeting RAGE or intervening in S100A4-RAGE-dependent signaling early in tumor progression might represent alternative strategies restricting S100A4-induced colorectal cancer metastasis

Efficient Interpolation for the Theory of Arrays

Existing techniques for Craig interpolation for the quantifier-free fragment of the theory of arrays are inefficient for computing sequence and tree interpolants: the solver needs to run for every partitioning $(A, B)$ of the interpolation problem to avoid creating $AB$-mixed terms. We present a new approach using Proof Tree Preserving Interpolation and an array solver based on Weak Equivalence on Arrays. We give an interpolation algorithm for the lemmas produced by the array solver. The computed interpolants have worst-case exponential size for extensionality lemmas and worst-case quadratic size otherwise. We show that these bounds are strict in the sense that there are lemmas with no smaller interpolants. We implemented the algorithm and show that the produced interpolants are useful to prove memory safety for C programs.Comment: long version of the paper at IJCAR 201

Proving Safety with Trace Automata and Bounded Model Checking

Loop under-approximation is a technique that enriches C programs with additional branches that represent the effect of a (limited) range of loop iterations. While this technique can speed up the detection of bugs significantly, it introduces redundant execution traces which may complicate the verification of the program. This holds particularly true for verification tools based on Bounded Model Checking, which incorporate simplistic heuristics to determine whether all feasible iterations of a loop have been considered. We present a technique that uses \emph{trace automata} to eliminate redundant executions after performing loop acceleration. The method reduces the diameter of the program under analysis, which is in certain cases sufficient to allow a safety proof using Bounded Model Checking. Our transformation is precise---it does not introduce false positives, nor does it mask any errors. We have implemented the analysis as a source-to-source transformation, and present experimental results showing the applicability of the technique

Using a runway paradigm to assess the relative strength of rats' motivations for enrichment objects

Laboratory animals should be provided with enrichment objects in their cages; however, it is first necessary to test whether the proposed enrichment objects provide benefits that increase the animals’ welfare. The two main paradigms currently used to assess proposed enrichment objects are the choice test, which is limited to determining relative frequency of choice, and consumer demand studies, which can indicate the strength of a preference but are complex to design. Here, we propose a third methodology: a runway paradigm, which can be used to assess the strength of an animal’s motivation for enrichment objects, is simpler to use than consumer demand studies, and is faster to complete than typical choice tests. Time spent with objects in a standard choice test was used to rank several enrichment objects in order to compare with the ranking found in our runway paradigm. The rats ran significantly more times, ran faster, and interacted longer with objects with which they had previously spent the most time. It was concluded that this simple methodology is suitable for measuring rats’ motivation to reach enrichment objects. This can be used to assess the preference for different types of enrichment objects or to measure reward system processes

Kassiopeia: A Modern, Extensible C++ Particle Tracking Package

The Kassiopeia particle tracking framework is an object-oriented software package using modern C++ techniques, written originally to meet the needs of the KATRIN collaboration. Kassiopeia features a new algorithmic paradigm for particle tracking simulations which targets experiments containing complex geometries and electromagnetic fields, with high priority put on calculation efficiency, customizability, extensibility, and ease of use for novice programmers. To solve Kassiopeia's target physics problem the software is capable of simulating particle trajectories governed by arbitrarily complex differential equations of motion, continuous physics processes that may in part be modeled as terms perturbing that equation of motion, stochastic processes that occur in flight such as bulk scattering and decay, and stochastic surface processes occuring at interfaces, including transmission and reflection effects. This entire set of computations takes place against the backdrop of a rich geometry package which serves a variety of roles, including initialization of electromagnetic field simulations and the support of state-dependent algorithm-swapping and behavioral changes as a particle's state evolves. Thanks to the very general approach taken by Kassiopeia it can be used by other experiments facing similar challenges when calculating particle trajectories in electromagnetic fields. It is publicly available at https://github.com/KATRIN-Experiment/Kassiopei

Commissioning of the vacuum system of the KATRIN Main Spectrometer

The KATRIN experiment will probe the neutrino mass by measuring the beta-electron energy spectrum near the endpoint of tritium beta-decay. An integral energy analysis will be performed by an electro-static spectrometer (Main Spectrometer), an ultra-high vacuum vessel with a length of 23.2 m, a volume of 1240 m^3, and a complex inner electrode system with about 120000 individual parts. The strong magnetic field that guides the beta-electrons is provided by super-conducting solenoids at both ends of the spectrometer. Its influence on turbo-molecular pumps and vacuum gauges had to be considered. A system consisting of 6 turbo-molecular pumps and 3 km of non-evaporable getter strips has been deployed and was tested during the commissioning of the spectrometer. In this paper the configuration, the commissioning with bake-out at 300{\deg}C, and the performance of this system are presented in detail. The vacuum system has to maintain a pressure in the 10^{-11} mbar range. It is demonstrated that the performance of the system is already close to these stringent functional requirements for the KATRIN experiment, which will start at the end of 2016.Comment: submitted for publication in JINST, 39 pages, 15 figure