Monadic second order finite satisfiability and unbounded tree-width

The finite satisfiability problem of monadic second order logic is decidable only on classes of structures of bounded tree-width by the classic result of Seese (1991). We prove the following problem is decidable: Input: (i) A monadic second order logic sentence $\alpha$, and (ii) a sentence $\beta$ in the two-variable fragment of first order logic extended with counting quantifiers. The vocabularies of $\alpha$ and $\beta$ may intersect. Output: Is there a finite structure which satisfies $\alpha\land\beta$ such that the restriction of the structure to the vocabulary of $\alpha$ has bounded tree-width? (The tree-width of the desired structure is not bounded.) As a consequence, we prove the decidability of the satisfiability problem by a finite structure of bounded tree-width of a logic extending monadic second order logic with linear cardinality constraints of the form $|X_{1}|+\cdots+|X_{r}|<|Y_{1}|+\cdots+|Y_{s}|$, where the $X_{i}$ and $Y_{j}$ are monadic second order variables. We prove the decidability of a similar extension of WS1S

Automated Clustering and Program Repair for Introductory Programming Assignments

Providing feedback on programming assignments is a tedious task for the instructor, and even impossible in large Massive Open Online Courses with thousands of students. Previous research has suggested that program repair techniques can be used to generate feedback in programming education. In this paper, we present a novel fully automated program repair algorithm for introductory programming assignments. The key idea of the technique, which enables automation and scalability, is to use the existing correct student solutions to repair the incorrect attempts. We evaluate the approach in two experiments: (I) We evaluate the number, size and quality of the generated repairs on 4,293 incorrect student attempts from an existing MOOC. We find that our approach can repair 97% of student attempts, while 81% of those are small repairs of good quality. (II) We conduct a preliminary user study on performance and repair usefulness in an interactive teaching setting. We obtain promising initial results (the average usefulness grade 3.4 on a scale from 1 to 5), and conclude that our approach can be used in an interactive setting.Comment: Extended version of the PLDI paper of the same nam

Feedback Generation for Performance Problems in Introductory Programming Assignments

Providing feedback on programming assignments manually is a tedious, error prone, and time-consuming task. In this paper, we motivate and address the problem of generating feedback on performance aspects in introductory programming assignments. We studied a large number of functionally correct student solutions to introductory programming assignments and observed: (1) There are different algorithmic strategies, with varying levels of efficiency, for solving a given problem. These different strategies merit different feedback. (2) The same algorithmic strategy can be implemented in countless different ways, which are not relevant for reporting feedback on the student program. We propose a light-weight programming language extension that allows a teacher to define an algorithmic strategy by specifying certain key values that should occur during the execution of an implementation. We describe a dynamic analysis based approach to test whether a student's program matches a teacher's specification. Our experimental results illustrate the effectiveness of both our specification language and our dynamic analysis. On one of our benchmarks consisting of 2316 functionally correct implementations to 3 programming problems, we identified 16 strategies that we were able to describe using our specification language (in 95 minutes after inspecting 66, i.e., around 3%, implementations). Our dynamic analysis correctly matched each implementation with its corresponding specification, thereby automatically producing the intended feedback.Comment: Tech report/extended version of FSE 2014 pape

On the Concept of Variable Roles and its Use in Software Analysis

Human written source code in imperative programming languages exhibits typical patterns for variable use such as flags, loop iterators, counters, indices, bitvectors etc. Although it is widely understood by practitioners that these variable roles are important for automated software analysis tools, they are not systematically studied by the formal methods community, and not well documented in the research literature. In this paper, we study the notion of variable roles on the example of basic types (int, float, char) in C. We propose a classification of the variables in a program by variable roles, and demonstrate that classical data flow analysis lends itself naturally both as a specification formalism and an analysis paradigm for this classification problem. We demonstrate the practical applicability of our method by predicting membership of source files to the different categories of the software verification competition SVCOMP 2013

A Simple and Scalable Static Analysis for Bound Analysis and Amortized Complexity Analysis

We present the first scalable bound analysis that achieves amortized complexity analysis. In contrast to earlier work, our bound analysis is not based on general purpose reasoners such as abstract interpreters, software model checkers or computer algebra tools. Rather, we derive bounds directly from abstract program models, which we obtain from programs by comparatively simple invariant generation and symbolic execution techniques. As a result, we obtain an analysis that is more predictable and more scalable than earlier approaches. Our experiments demonstrate that our analysis is fast and at the same time able to compute bounds for challenging loops in a large real-world benchmark. Technically, our approach is based on lossy vector addition systems (VASS). Our bound analysis first computes a lexicographic ranking function that proves the termination of a VASS, and then derives a bound from this ranking function. Our methodology achieves amortized analysis based on a new insight how lexicographic ranking functions can be used for bound analysis

Specific nuclear envelope transmembrane proteins can promote the location of chromosomes to and from the nuclear periphery

BACKGROUND: Different cell types have distinctive patterns of chromosome positioning in the nucleus. Although ectopic affinity-tethering of specific loci can be used to relocate chromosomes to the nuclear periphery, endogenous nuclear envelope proteins that control such a mechanism in mammalian cells have yet to be widely identified. RESULTS: To search for such proteins twenty three nuclear envelope transmembrane proteins were screened for their ability to promote peripheral localization of human chromosomes in HT1080 fibroblasts. Five of these proteins had strong effects on chromosome 5, but individual proteins affected different subsets of chromosomes. The repositioning effects were reversible and the proteins with effects all exhibited highly tissue-restricted patterns of expression. Depletion of two nuclear envelope transmembrane proteins that were preferentially expressed in liver each reduced the normal peripheral positioning of chromosome 5 in liver cells. CONCLUSIONS: The discovery of nuclear envelope transmembrane proteins that can modulate chromosome position and have restricted patterns of expression may enable dissection of the functional relevance of tissue-specific patterns of radial chromosome positioning.Publisher PDFPeer reviewe

Results of the REIMEP-17 and NUSIMEP-8 inter-laboratory comparisons

Confidence in measurement results is established via reference materials, reference measurements and inter-laboratory comparisons. The Institute for Reference Materials and Measurements of the Joint Research Centre of the European Commission (EC-JRC-IRMM) has a long time experience in the development of nuclear isotopic reference materials and in the organisation of inter-laboratory comparisons (ILCs) in compliance with the respective international ISO guides. The Regular European Inter-laboratory measurement Evaluation Programme (REIMEP) was established at IRMM in 1982 for carrying out external quality control of the measurements for the elements characteristic of the nuclear fuel cycle, while the Nuclear Signatures Inter-laboratory Measurement Evaluation Programme (NUSIMEP) aims to provide test samples for the measurement of trace amounts of nuclear material in environmental matrices. Participants in REIMEP/NUSIMEP can benchmark their measurement results against independent and traceable reference values, assessing their measurement capabilities in line with international or national quality goals. The REIMEP-17 and NUSIMEP-8 certified test samples were prepared from dissolution of mixed oxide fuel in nitric acid and addition of natural uranium. In REIMEP-17 laboratories received two test samples with undisclosed values of the U, Pu amount content and U and Pu isotope amount ratios. The certified test sample REIMEP-17A had a concentration typical for undiluted input solution whereas REIMEP 17B was a diluted fraction thereof. The NUSIMEP-8 certified test sample was prepared by further gravimetrical dilution of REIMEP-17B. Measurement of the n(235U)/n(238U) and n(240Pu)/n(239Pu) ratios were obligatory while the measurement of other ratios were optional. Laboratories were asked to apply their routine analytical procedures and report the results with associated measurement uncertainty. The participant results have been evaluated against the independent certified reference value by means of z and zeta scores in compliance with ISO 13528:2005. In general, the REIMEP-17 results were satisfactory and in compliance with the International Target Values for Measurement Uncertainties in Safeguarding Nuclear Materials (ITV2010). The NUSIMEP-8 results were overall satisfactory and met the International Atomic Energy Agency Measurement Quality Goals (IAEA-SGAS-QC) for the analysis of bulk environmental samples.JRC.D.4-Standards for Nuclear Safety, Security and Safeguard

REIMEP-17: Plutonium and uranium amount content, and isotope amount ratios in synthetic input solution - Inter-laboratory comparison, Report to participants

Nuclear safeguards is based on international agreements and in the EU has the rank of European law (Euratom Treaty, Chapter VII, Euratom regulation 302/2005) ensuring that materials usable in both peaceful and military applications – such as uranium and plutonium – are used for peaceful purposes only. Physical verification measurements at nuclear facilities, such as reprocessing and fuel fabrication plants, are a part of safeguards inspections. The reliability of measurement results in nuclear material accountancy and verification is indispensable for an effective safeguards system. A new external quality control campaign, REIMEP-17 on "Plutonium and uranium amount content, and isotope amount ratios in synthetic input solution" was organised by JRC-IRMM in cooperation with JRC-ITU, particularly for EURATOM safeguards (DG ENER) laboratories and the IAEA Network of Analytical Laboratories for nuclear material analysis (IAEA-NWAL), as well as for laboratories from industry and experts in the field. Participating laboratories in REIMEP-17 received two samples with undisclosed U, Pu amount content and n(238Pu)/n(239Pu), n(240Pu)/n(239Pu), n(241Pu)/n(239Pu) n(242Pu)/n(239Pu) and n(234U)/n(238U), n(235U)/n(238U), n(236U)/n(238U) amount ratio values. One of the samples, REIMEP 17A had uranium and plutonium amount contents typical for undiluted spent nuclear fuel input solution and the other sample, REIMEP-17B was a diluted fraction of it. The participants were requested to apply their standard analytical procedures and report the results with the associated uncertainties. The laboratories were also requested to complete and return a questionnaire so that an overall picture of the laboratories’ capabilities could be made. REIMEP-17 was announced to participants in April 2012. Sixteen laboratories registered for REIMEP 17. Due to delays in the shipment of the samples and problems with the transport containers, three laboratories were not able to receive the samples. Three laboratories withdrew their participation. Consequently, the deadline for submitting the results had to be extended until July 1, 2013. In the end JRC-IRMM received results from nine laboratories; one laboratory did not submit the results. The reported measurement results have been evaluated against the independent reference values by means of z-scores and zeta-scores in compliance with international guidelines. In general the REIMEP-17 participants' results were satisfactory and in compliance with the International Target Values for Measurement Uncertainties in Safeguarding Nuclear Materials (ITV2010). This report presents the REIMEP-17 participants' results; including the evaluation of the questionnaire.JRC.D.4-Standards for Nuclear Safety, Security and Safeguard

NUSIMEP-8: Uranium and plutonium isotope amount ratios in low-level synthetic nitrate solution - Inter-laboratory comparison, Report to participants

The Additional Protocol (AP) authorizes safeguards authorities to verify the absence of undeclared nuclear activities in all parts of a state’s nuclear fuel cycle as well as any other location where nuclear material is or may be present. As a part of the Additional Protocol, environmental sampling has become an important tool for the detection of non-declared nuclear activities. In environmental sampling, swipe samples are collected for bulk and particle analysis. Considering the potential consequences of the analyses, these measurements need to be subjected to a rigorous quality management system. The Nuclear Signatures Inter-laboratory Measurement Evaluation Programme (NUSIMEP) was established in 1996 to support the growing need to trace and measure the isotopic abundances of elements characteristic for the nuclear fuel cycle present in trace amounts in the environment. NUSIMEP-8 focused on measurements of low-level uranium and plutonium in synthetic nitrate solution aiming to support EURATOM safeguards (DG ENER), the IAEA Network of Analytical Laboratories (NWAL) for bulk analysis of environmental samples and laboratories in the field. The NUSIMEP-8 solution was prepared from mixed oxide fuel dissolved in nitric acid with addition of natural uranium and diluted to an environmental level. Participating laboratories in NUSIMEP-8 received one sample solution with undisclosed values of n(238Pu)/n(239Pu), n(240Pu)/n(239Pu), n(241Pu)/n(239Pu), n(242Pu)/n(239Pu) and n(234U)/n(238U), n(235U)/n(238U), n(236U)/n(238U) amount ratios. Those isotope amount ratios were measured by participating laboratories using their routine analytical procedures. Measurement of the major isotope ratios n(235U)/n(238U) and n(240Pu)/n(239Pu) were obligatory; measurement of the minor isotope ratios were optional. 25 laboratories registered for NUSIMEP-8, three withdrew the registration while one laboratory encountered problems with the shipment of the sample. Finally, 19 participants have reported measurement results using different analytical techniques, among those 10 NWAL laboratories. Two participants did not report their results due to technical problems. The participant measurement results have been evaluated against the certified reference values by means of z-scores and zeta-scores in compliance with ISO 13528:2005. The NUSIMEP-8 results were overall satisfactory and in compliance with the IAEA Measurement Quality Goals for the analysis of bulk environmental samples. This report presents the NUSIMEP-8 participant results; including the evaluation of the questionnaire. In addition feedback from the measurement communities in nuclear safeguards, nuclear security and environmental sciences was collected in view of identifying future needs for NUSIMEP inter-laboratory comparisons.JRC.D.4-Standards for Nuclear Safety, Security and Safeguard