Permutation tests for nonparametric detection

In this paper, the authors provide a methodology to design nonparametric permutation tests and, in particular, nonparametric rank tests for applications in detection. In the first part of the paper, the authors develop the optimization theory of both permutation and rank tests in the Neyman?Pearson sense; in the second part of the paper, they carry out a comparative performance analysis of the permutation and rank tests (detectors) against the parametric ones in radar applications. First, a brief review of some contributions on nonparametric tests is realized. Then, the optimum permutation and rank tests are derived. Finally, a performance analysis is realized by Monte-Carlo simulations for the corresponding detectors, and the results are shown in curves of detection probability versus signal-to-noise ratio

Automatic design of Ant Colony Optimization for permutation problems

In this study, we present a framework based on ant colony optimization (ACO) for tackling combinatorial problems. ACO algorithms have been applied to many diferent problems, focusing on algorithmic variants that obtain high-quality solutions. Usually, the implementations are re-done for various problem even if they maintain the same details of the ACO algorithm. However, our goal is to generate a sustainable framework for applications on permutation problems. We concentrate on understanding the behavior of pheromone trails and specific methods that can be combined. Eventually, we will propose an automatic offline configuration tool to build an efective algorithm. ---RESUMEN---En este trabajo vamos a presentar un framework basado en la familia de algoritmos ant colony optimization (ACO), los cuales están dise~nados para enfrentarse a problemas combinacionales. Los algoritmos ACO han sido aplicados a diversos problemas, centrándose los investigadores en diversas variantes que obtienen buenas soluciones. Normalmente, las implementaciones se tienen que rehacer, inclusos si se mantienen los mismos detalles para los algoritmos ACO. Sin embargo, nuestro objetivo es generar un framework sostenible para aplicaciones sobre problemas de permutaciones. Nos centraremos en comprender el comportamiento de la sendas de feromonas y ciertos métodos con los que pueden ser combinados. Finalmente, propondremos una herramienta para la configuraron automática offline para construir algoritmos eficientes.

Random circular permutation of genes and expressed polypeptide chains: application of the method to the catalytic chains of aspartate transcarbamoylase.

Recent studies on proteins whose N and C termini are in close proximity have demonstrated that folding of polypeptide chains and assembly of oligomers can be accomplished with circularly permuted chains. As yet no methodical study has been conducted to determine how extensively new termini can be introduced and where such termini cannot be tolerated. We have devised a procedure to generate random circular permutations of the catalytic chains of Escherichia coli aspartate transcarbamoylase (ATCase; EC 2.1.3.2) and to select clones that produce active or stable holoenzyme containing permuted chains. A tandem gene construct was made, based on the desired linkage between amino acid residues in the C- and N-terminal regions of the polypeptide chain, and this DNA was treated with a suitable restriction enzyme to yield a fragment containing the rearranged coding sequence for the chain. Circularization achieved with DNA ligase, followed by linearization at random with DNase I, and incorporation of the linearized, repaired, blunt-ended, rearranged genes into a suitable plasmid permitted the expression of randomly permuted polypeptide chains. The plasmid with appropriate stop codons also contained pyrI, the gene encoding the regulatory chain of ATCase. Colonies expressing detectable amounts of ATCase-like molecules containing permuted catalytic chains were identified by an immunoblot technique or by their ability to grow in the absence of pyrimidines in the growth medium. Sequencing of positive clones revealed a variety of novel circular permutations. Some had N and C termini within helices of the wild-type enzyme as well as deletions and insertions. Permutations were concentrated in the C-terminal domain and only few were detected in the N-terminal domain. The technique, which is adaptable generally to proteins whose N and C termini are near each other, can be of value in relating in vivo folding of nascent, growing polypeptide chains to in vitro renaturation of complete chains and determining the role of protein sequence in folding kinetics.

Critical properties of the four-state commutative random permutation glassy Potts model in three and four dimensions

We investigate the critical properties of the four-state commutative random permutation glassy Potts model in three and four dimensions by means of Monte Carlo simulations and a finite-size scaling analysis. By using a field programmable gate array, we have been able to thermalize a large number of samples of systems with large volume. This has allowed us to observe a spin-glass ordered phase in d=4 and to study the critical properties of the transition. In d=3, our results are consistent with the presence of a Kosterlitz-Thouless transition, but also with different scenarios: transient effects due to a value of the lower critical dimension slightly below 3 could be very important.

Structure and folding of potato type II proteinase inhibitors: Circular permutation and intramolecular domain swapping

Potato type II serine proteinase inhibitors are proteins that consist of multiple sequence repeats, and exhibit a multidomain structure. The structural domains are circular permutations of the repeat sequence.. as a result or intramolecular domain swapping. Structural studies give indications for the origins of this folding behaviour, and the evolution of the inhibitor family.

Genetic Algorithm for Finding the Key’s Length and Cryptanalysis of the Permutation Cipher

In this article we discuss a possibility to use genetic algorithms in cryptanalysis. We developed and described the genetic algorithm for finding the secret key of a block permutation cipher. In this case key is a permutation of some first natural numbers. Our algorithm finds the exact key’s length and the key with controlled accuracy. Evaluation of conducted experiment’s results shows that the almost automatic cryptanalysis is possible.

The kernel is in the least core for permutation games

Permutation games are totally balanced transferable utility cooperative games arising from certain sequencing and re-assignment optimization problems. It is known that for permutation games the bargaining set and the core coincide, consequently, the kernel is a subset of the core. We prove that for permutation games the kernel is contained in the least core, even if the latter is a lower dimensional subset of the core. By means of a 5-player permutation game we demonstrate that, in sense of the lexicographic center procedure leading to the nucleolus, this inclusion result can not be strengthened. Our 5-player permutation game is also an example (of minimum size) for a game with a non-convex kernel.

Refined composite multiscale permutation entropy to overcome multiscale permutation entropy length dependence

International audience

An analysis of the RC4 family of stream ciphers against algebraic attacks

To date, most applications of algebraic analysis and attacks on stream ciphers are on those based on lin- ear feedback shift registers (LFSRs). In this paper, we extend algebraic analysis to non-LFSR based stream ciphers. Specifically, we perform an algebraic analysis on the RC4 family of stream ciphers, an example of stream ciphers based on dynamic tables, and inves- tigate its implications to potential algebraic attacks on the cipher. This is, to our knowledge, the first pa- per that evaluates the security of RC4 against alge- braic attacks through providing a full set of equations that describe the complex word manipulations in the system. For an arbitrary word size, we derive alge- braic representations for the three main operations used in RC4, namely state extraction, word addition and state permutation. Equations relating the inter- nal states and keystream of RC4 are then obtained from each component of the cipher based on these al- gebraic representations, and analysed in terms of their contributions to the security of RC4 against algebraic attacks. Interestingly, it is shown that each of the three main operations contained in the components has its own unique algebraic properties, and when their respective equations are combined, the resulting system becomes infeasible to solve. This results in a high level of security being achieved by RC4 against algebraic attacks. On the other hand, the removal of an operation from the cipher could compromise this security. Experiments on reduced versions of RC4 have been performed, which confirms the validity of our algebraic analysis and the conclusion that the full RC4 stream cipher seems to be immune to algebraic attacks at present.

Analysis of linear relationships in block ciphers

This thesis is devoted to the study of linear relationships in symmetric block ciphers. A block cipher is designed so that the ciphertext is produced as a nonlinear function of the plaintext and secret master key. However, linear relationships within the cipher can still exist if the texts and components of the cipher are manipulated in a number of ways, as shown in this thesis. There are four main contributions of this thesis. The first contribution is the extension of the applicability of integral attacks from word-based to bitbased block ciphers. Integral attacks exploit the linear relationship between texts at intermediate stages of encryption. This relationship can be used to recover subkey bits in a key recovery attack. In principle, integral attacks can be applied to bit-based block ciphers. However, specific tools to define the attack on these ciphers are not available. This problem is addressed in this thesis by introducing a refined set of notations to describe the attack. The bit patternbased integral attack is successfully demonstrated on reduced-round variants of the block ciphers Noekeon, Present and Serpent. The second contribution is the discovery of a very small system of equations that describe the LEX-AES stream cipher. LEX-AES is based heavily on the 128-bit-key (16-byte) Advanced Encryption Standard (AES) block cipher. In one instance, the system contains 21 equations and 17 unknown bytes. This is very close to the upper limit for an exhaustive key search, which is 16 bytes. One only needs to acquire 36 bytes of keystream to generate the equations. Therefore, the security of this cipher depends on the difficulty of solving this small system of equations. The third contribution is the proposal of an alternative method to measure diffusion in the linear transformation of Substitution-Permutation-Network (SPN) block ciphers. Currently, the branch number is widely used for this purpose. It is useful for estimating the possible success of differential and linear attacks on a particular SPN cipher. However, the measure does not give information on the number of input bits that are left unchanged by the transformation when producing the output bits. The new measure introduced in this thesis is intended to complement the current branch number technique. The measure is based on fixed points and simple linear relationships between the input and output words of the linear transformation. The measure represents the average fraction of input words to a linear diffusion transformation that are not effectively changed by the transformation. This measure is applied to the block ciphers AES, ARIA, Serpent and Present. It is shown that except for Serpent, the linear transformations used in the block ciphers examined do not behave as expected for a random linear transformation. The fourth contribution is the identification of linear paths in the nonlinear round function of the SMS4 block cipher. The SMS4 block cipher is used as a standard in the Chinese Wireless LAN Wired Authentication and Privacy Infrastructure (WAPI) and hence, the round function should exhibit a high level of nonlinearity. However, the findings in this thesis on the existence of linear relationships show that this is not the case. It is shown that in some exceptional cases, the first four rounds of SMS4 are effectively linear. In these cases, the effective number of rounds for SMS4 is reduced by four, from 32 to 28. The findings raise questions about the security provided by SMS4, and might provide clues on the existence of a flaw in the design of the cipher.

A comparative study of algorithms for the flowshop scheduling problem

In this paper, we propose three meta-heuristic algorithms for the permutation flowshop (PFS) and the general flowshop (GFS) problems. Two different neighborhood structures are used for these two types of flowshop problem. For the PFS problem, an insertion neighborhood structure is used, while for the GFS problem, a critical-path neighborhood structure is adopted. To evaluate the performance of the proposed algorithms, two sets of problem instances are tested against the algorithms for both types of flowshop problems. The computational results show that the proposed meta-heuristic algorithms with insertion neighborhood for the PFS problem perform slightly better than the corresponding algorithms with critical-path neighborhood for the GFS problem. But in terms of computation time, the GFS algorithms are faster than the corresponding PFS algorithms.

‘Wide Atlantic Ocean’ : acting methods and cultural translation in mainstream theatre

A recent production of Nicholson’s Shadowlands at the Brisbane Powerhouse could have included two advertising lines: “Outspoken American-Jewish poet meets conservative British Oxford scholar” and “Emotive American Method trained actor meets contained British trained actor.” While the fusion of acting methodologies in intercultural acting has been discussed at length, little discussion has focussed on the juxtaposition of diverse acting styles in production in mainstream theatre. This paper explores how the permutation of American Method acting and a more traditional British conservatory acting in Crossbow’s August 2010 production of Shadowlands worked to add extra layers of meaning to the performance text. This sometimes inimical relationship between two acting styles had its beginnings in the rehearsal room and continued onstage. Audience reception to the play in post-performance discussions revealed the audience’s acute awareness of the transatlantic cultural tensions on stage. On one occasion, this resulted in a heated debate on cultural expression, continuing well after the event, during which audience members became co-performers in the cultural discourses of the play.

An ensemble method for predicting subnuclear localizations from primary protein structures

Background Predicting protein subnuclear localization is a challenging problem. Some previous works based on non-sequence information including Gene Ontology annotations and kernel fusion have respective limitations. The aim of this work is twofold: one is to propose a novel individual feature extraction method; another is to develop an ensemble method to improve prediction performance using comprehensive information represented in the form of high dimensional feature vector obtained by 11 feature extraction methods. Methodology/Principal Findings A novel two-stage multiclass support vector machine is proposed to predict protein subnuclear localizations. It only considers those feature extraction methods based on amino acid classifications and physicochemical properties. In order to speed up our system, an automatic search method for the kernel parameter is used. The prediction performance of our method is evaluated on four datasets: Lei dataset, multi-localization dataset, SNL9 dataset and a new independent dataset. The overall accuracy of prediction for 6 localizations on Lei dataset is 75.2% and that for 9 localizations on SNL9 dataset is 72.1% in the leave-one-out cross validation, 71.7% for the multi-localization dataset and 69.8% for the new independent dataset, respectively. Comparisons with those existing methods show that our method performs better for both single-localization and multi-localization proteins and achieves more balanced sensitivities and specificities on large-size and small-size subcellular localizations. The overall accuracy improvements are 4.0% and 4.7% for single-localization proteins and 6.5% for multi-localization proteins. The reliability and stability of our classification model are further confirmed by permutation analysis. Conclusions It can be concluded that our method is effective and valuable for predicting protein subnuclear localizations. A web server has been designed to implement the proposed method. It is freely available at http://bioinformatics.awowshop.com/snlpr​ed_page.php.

Known and chosen key differential distinguishers for block ciphers

In this paper we investigate the differential properties of block ciphers in hash function modes of operation. First we show the impact of differential trails for block ciphers on collision attacks for various hash function constructions based on block ciphers. Further, we prove the lower bound for finding a pair that follows some truncated differential in case of a random permutation. Then we present open-key differential distinguishers for some well known round-reduced block ciphers.

RPAS integration within an Australian ATM system : what equipment and which airspace

The Australian Civil Aviation Safety Authority (CASA) currently lists more than 100 separate entities or organisations which maintain a UAS Operator Certificate (UOC) [1]. Approved operations are overwhelmingly a permutation of aerial photography, surveillance, survey or spotting and predominantly, are restricted to Visual Line of Sight (VLOS) operations, below 400 feet, and not within 3 NM of an aerodrome. However, demand is increasing for a Remote Piloted Aerial System (RPAS) regulatory regime which facilitates more expansive operations, in particular unsegregated, Beyond Visual Line of Sight (BVLOS) operations. Despite this demand, there is national and international apprehension regarding the necessary levels of airworthiness and operational regulation required to maintain safety and minimise the risk associated with unsegregated operations. Fundamental to addressing these legitimate concerns will be the mechanisms that underpin safe separation and collision avoidance. Whilst a large body of research has been dedicated to investigating on-board, Sense and Avoid (SAA) technology necessary to meet this challenge, this paper focuses on the contribution of the NAS to separation assurance, and how it will support, as well as complicate RPAS integration. The paper collates and presents key, but historically disparate, threads of Australian RPAS and NAS related information, and distils it with a filter focused on minimising RPAS collision risk. Our ongoing effort is motivated by the need to better understand the separation assurance contribution provided by the NAS layers, in the first instance, and subsequently employ this information to identify scenarios where the coincident collision risk is demonstrably low, providing legitimate substantiation for concessions on equipage and airworthiness standards.