Automatic Abstraction for Congruences

One approach to verifying bit-twiddling algorithms is to derive invariants between the bits that constitute the variables of a program. Such invariants can often be described with systems of congruences where in each equation $\vec{c} \cdot \vec{x} = d \mod m$, (unknown variable m)$is a power of two,$\vec{c}$is a vector of integer coefficients, and$\vec{x}$ is a vector of propositional variables (bits). Because of the low-level nature of these invariants and the large number of bits that are involved, it is important that the transfer functions can be derived automatically. We address this problem, showing how an analysis for bit-level congruence relationships can be decoupled into two parts: (1) a SAT-based abstraction (compilation) step which can be automated, and (2) an interpretation step that requires no SAT-solving. We exploit triangular matrix forms to derive transfer functions efficiently, even in the presence of large numbers of bits. Finally we propose program transformations that improve the analysis results

Unusual development of light-reflecting pigment cells in intact and regenerating tail in the periodic albino mutant of Xenopus laevis

Unusual light-reflecting pigment cells, “white pigment cells”, specifically appear in the periodic albino mutant (ap/ap) of Xenopus laevis and localize in the same place where melanophores normally differentiate in the wild-type. The mechanism responsible for the development of unusual pigment cells is unclear. In this study, white pigment cells in the periodic albino were compared with melanophores in the wild-type, using a cell culture system and a tail-regenerating system. Observations of both intact and cultured cells demonstrate that white pigment cells are unique in (1) showing characteristics of melanophore precursors at various stages of development, (2) accumulating reflecting platelets characteristic of iridophores, and (3) exhibiting pigment dispersion in response to α-melanocyte stimulating hormone (α-MSH) in the same way that melanophores do. When a tadpole tail is amputated, a functionally competent new tail is regenerated. White pigment cells appear in the mutant regenerating tail, whereas melanophores differentiate in the wild-type regenerating tail. White pigment cells in the mutant regenerating tail are essentially similar to melanophores in the wild-type regenerating tail with respect to their localization, number, and response to α-MSH. In addition to white pigment cells, iridophores which are never present in the intact tadpole tail appear specifically in the somites near the amputation level in the mutant regenerating tail. Iridophores are distinct from white pigment cells in size, shape, blue light-induced fluorescence, and response to α-MSH. These findings strongly suggest that white pigment cells in the mutant arise from melanophore precursors and accumulate reflecting platelets characteristic of iridophores

LTL Parameter Synthesis of Parametric Timed Automata

The parameter synthesis problem for parametric timed automata is undecidable in general even for very simple reachability properties. In this paper we introduce restrictions on parameter valuations under which the parameter synthesis problem is decidable for LTL properties. The investigated bounded integer parameter synthesis problem could be solved using an explicit enumeration of all possible parameter valuations. We propose an alternative symbolic zone-based method for this problem which results in a faster computation. Our technique extends the ideas of the automata-based approach to LTL model checking of timed automata. To justify the usefulness of our approach, we provide experimental evaluation and compare our method with explicit enumeration technique.Comment: 23 pages, extended versio

Polyhedral Analysis using Parametric Objectives

The abstract domain of polyhedra lies at the heart of many program analysis techniques. However, its operations can be expensive, precluding their application to polyhedra that involve many variables. This paper describes a new approach to computing polyhedral domain operations. The core of this approach is an algorithm to calculate variable elimination (projection) based on parametric linear programming. The algorithm enumerates only non-redundant inequalities of the projection space, hence permits anytime approximation of the output

Verifying parameterized timed security protocols

Quantitative timing is often explicitly used in systems for better security, e.g., the credentials for automatic website logon often has limited lifetime. Verifying timing relevant security protocols in these systems is very challenging as timing adds another dimension of complexity compared with the untimed protocol verification. In our previous work, we proposed an approach to check the correctness of the timed authentication in security protocols with fixed timing constraints. However, a more difficult question persists, i.e., given a particular protocol design, whether the protocol has security flaws in its design or it can be configured secure with proper parameter values? In this work, we answer this question by proposing a parameterized verification framework, where the quantitative parameters in the protocols can be intuitively specified as well as automatically analyzed. Given a security protocol, our verification algorithm either produces the secure constraints of the parameters, or constructs an attack that works for any parameter values. The correctness of our algorithm is formally proved. We implement our method into a tool called PTAuth and evaluate it with several security protocols. Using PTAuth, we have successfully found a timing attack in Kerberos V which is unreported before.No Full Tex

LNCS

We present two algorithmic approaches for synthesizing linear hybrid automata from experimental data. Unlike previous approaches, our algorithms work without a template and generate an automaton with nondeterministic guards and invariants, and with an arbitrary number and topology of modes. They thus construct a succinct model from the data and provide formal guarantees. In particular, (1) the generated automaton can reproduce the data up to a specified tolerance and (2) the automaton is tight, given the first guarantee. Our first approach encodes the synthesis problem as a logical formula in the theory of linear arithmetic, which can then be solved by an SMT solver. This approach minimizes the number of modes in the resulting model but is only feasible for limited data sets. To address scalability, we propose a second approach that does not enforce to find a minimal model. The algorithm constructs an initial automaton and then iteratively extends the automaton based on processing new data. Therefore the algorithm is well-suited for online and synthesis-in-the-loop applications. The core of the algorithm is a membership query that checks whether, within the specified tolerance, a given data set can result from the execution of a given automaton. We solve this membership problem for linear hybrid automata by repeated reachability computations. We demonstrate the effectiveness of the algorithm on synthetic data sets and on cardiac-cell measurements

Resolving Stellar Populations outside the Local Group: MAD observations of UKS2323-326

We present a study aimed at deriving constraints on star formation at intermediate ages from the evolved stellar populations in the dwarf irregular galaxy UKS2323-326. These observations were also intended to demonstrate the scientific capabilities of the multi-conjugated adaptive optics demonstrator (MAD) implemented at the ESO Very Large Telescope as a test-bench of adaptive optics (AO) techniques. We perform accurate, deep photometry of the field using J and Ks band AO images of the central region of the galaxy. The near-infrared (IR) colour-magnitude diagrams clearly show the sequences of asymptotic giant branch (AGB) stars, red supergiants, and red giant branch (RGB) stars down to ~1 mag below the RGB tip. Optical-near-IR diagrams, obtained by combining our data with Hubble Space Telescope observations, provide the best separation of stars in the various evolutionary stages. The counts of AGB stars brighter than the RGB tip allow us to estimate the star formation at intermediate ages. Assuming a Salpeter initial mass function, we find that the star formation episode at intermediate ages produced ~6x10^5 M_sun of stars in the observed region.Comment: 4 pages, 4 figures, Accepted for publication in A&A Letter

Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling

Use of adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread, providing new insights into the immune system with potential broad clinical and diagnostic applications. However, like many high-throughput technologies, it comes with several problems, and the AIRR Community was established to understand and help solve them. We, the AIRR Community's Biological Resources Working Group, have surveyed scientists about the need for standards and controls in generating and annotating AIRR-seq data. Here, we review the current status of AIRR-seq, provide the results of our survey, and based on them, offer recommendations for developing AIRR-seq standards and controls, including future work. Keywords: B-cell Receptor (BCR); IG; T-cell Receptor (TCR); TR; antibody; immunoglobulin; immunology; inflammation; next generation sequencing (NGS)