arXiv subjects

Christophe Guyeux

Publications and source records attributed to Christophe Guyeux.

At least 37 records · Page 2Linked to original sources

arXiv2017

Finding optimal finite biological sequences over finite alphabets: the OptiFin toolbox

In this paper, we present a toolbox for a specific optimization problem that frequently arises in bioinformatics or genomics. In this specific optimisation problem, the state space is a set of words of specified length over a finite alphabet. To each word is associated a score. The overall objective is to find the words which have the lowest possible score. This type of general optimization problem is encountered in e.g 3D conformation optimisation for protein structure prediction, or largest core genes subset discovery based on best supported phylogenetic tree for a set of species. In order to solve this problem, we propose a toolbox that can be easily launched using MPI and embeds 3 well-known metaheuristics. The toolbox is fully parametrized and well documented. It has been specifically designed to be easy modified and possibly improved by the user depending on the application, and does not require to be a computer scientist. We show that the toolbox performs very well on two difficult practical problems.

cs.AI↗

arXiv2017

One random jump and one permutation: sufficient conditions to chaotic, statistically faultless, and large throughput PRNG for FPGA

Sub-categories of mathematical topology, like the mathematical theory of chaos, offer interesting applications devoted to information security. In this research work, we have introduced a new chaos-based pseudorandom number generator implemented in FPGA, which is mainly based on the deletion of a Hamilton cycle within the $n$-cube (or on the vectorial negation), plus one single permutation. By doing so, we produce a kind of post-treatment on hardware pseudorandom generators, but the obtained generator has usually a better statistical profile than its input, while running at a similar speed. We tested 6 combinations of Boolean functions and strategies that all achieve to pass the most stringent TestU01 battery of tests. This generation can reach a throughput/latency ratio equal to 6.7 Gbps, being thus the second fastest FPGA generator that can pass TestU01.

cs.CR↗

arXiv2017

Lyapunov Exponent Evaluation of the CBC Mode of Operation

The Cipher Block Chaining (CBC) mode of encryption was invented in 1976, and it is currently one of the most commonly used mode. In our previous research works, we have proven that the CBC mode of operation exhibits, under some conditions, a chaotic behavior. The dynamics of this mode has been deeply investigated later, both qualitatively and quantitatively, using the rigorous mathematical topology field of research. In this article, which is an extension of our previous work, we intend to compute a new important quantitative property concerning our chaotic CBC mode of operation, which is the Lyapunov exponent.

cs.CR↗

arXiv2017

Design and evaluation of chaotic iterations based keyed hash function

Investigating how to construct a secure hash algorithm needs in-depth study, as various existing hash functions like the MD5 algorithm have recently exposed their security flaws. At the same time, hash function based on chaotic theory has become an emerging research in the field of nonlinear information security. As an extension of our previous research works, a new chaotic iterations keyed hash function is proposed in this article. Chaotic iterations are used both to construct strategies with pseudorandom number generator and to calculate new hash values using classical hash functions. It is shown that, by doing so, it is possible to apply a kind of post-treatment on existing hash algorithms, which preserves their security properties while adding Devaney's chaos. Security performance analysis of such a post-treatment are finally provided.

cs.CR↗

arXiv2017

Random Forests for Industrial Device Functioning Diagnostics Using Wireless Sensor Networks

In this paper, random forests are proposed for operating devices diagnostics in the presence of a variable number of features. In various contexts, like large or difficult-to-access monitored areas, wired sensor networks providing features to achieve diagnostics are either very costly to use or totally impossible to spread out. Using a wireless sensor network can solve this problem, but this latter is more subjected to flaws. Furthermore, the networks' topology often changes, leading to a variability in quality of coverage in the targeted area. Diagnostics at the sink level must take into consideration that both the number and the quality of the provided features are not constant, and that some politics like scheduling or data aggregation may be developed across the network. The aim of this article is ($1$) to show that random forests are relevant in this context, due to their flexibility and robustness, and ($2$) to provide first examples of use of this method for diagnostics based on data provided by a wireless sensor network.

cs.AI↗

arXiv2017

Relation between Insertion Sequences and Genome Rearrangements in Pseudomonas aeruginosa

During evolution of microorganisms genomes underwork have different changes in their lengths, gene orders, and gene contents. Investigating these structural rearrangements helps to understand how genomes have been modified over time. Some elements that play an important role in genome rearrangements are called insertion sequences (ISs), they are the simplest types of transposable elements (TEs) that widely spread within prokaryotic genomes. ISs can be defined as DNA segments that have the ability to move (cut and paste) themselves to another location within the same chromosome or not. Due to their ability to move around, they are often presented as responsible of some of these genomic recombination. Authors of this research work have regarded this claim, by checking if a relation between insertion sequences (ISs) and genome rearrangements can be found. To achieve this goal, a new pipeline that combines various tools have firstly been designed, for detecting the distribution of ORFs that belongs to each IS category. Secondly, links between these predicted ISs and observed rearrangements of two close genomes have been investigated, by seeing them with the naked eye, and by using computational approaches. The proposal has been tested on 18 complete bacterial genomes of Pseudomonas aeruginosa, leading to the conclusion that IS3 family of insertion sequences are related to genomic inversions.

q-bio.GN↗

arXiv2017

Dependability of Sensor Networks for Industrial Prognostics and Health Management

Maintenance is an important activity in industry. It is performed either to revive a machine/component or to prevent it from breaking down. Different strategies have evolved through time, bringing maintenance to its current state: condition-based and predictive maintenances. This evolution was due to the increasing demand of reliability in industry. The key process of condition-based and predictive maintenances is prognostics and health management, and it is a tool to predict the remaining useful life of engineering assets. Nowadays, plants are required to avoid shutdowns while offering safety and reliability. Nevertheless, planning a maintenance activity requires accurate information about the system/component health state. Such information is usually gathered by means of independent sensor nodes. In this study, we consider the case where the nodes are interconnected and form a wireless sensor network. As far as we know, no research work has considered such a case of study for prognostics. Regarding the importance of data accuracy, a good prognostics requires reliable sources of information. This is why, in this paper, we will first discuss the dependability of wireless sensor networks, and then present a state of the art in prognostic and health management activities.

cs.SE↗

arXiv2017

A Security Framework for Wireless Sensor Networks: Theory and Practice

Wireless sensor networks are often deployed in public or otherwise untrusted and even hostile environments, which prompts a number of security issues. Although security is a necessity in other types of networks, it is much more so in sensor networks due to the resource-constraint, susceptibility to physical capture, and wireless nature. In this work we emphasize two security issues: (1) secure communication infrastructure and (2) secure nodes scheduling algorithm. Due to resource constraints, specific strategies are often necessary to preserve the network's lifetime and its quality of service. For instance, to reduce communication costs nodes can go to sleep mode periodically (nodes scheduling). These strategies must be proven as secure, but protocols used to guarantee this security must be compatible with the resource preservation requirement. To achieve this goal, secure communications in such networks will be defined, together with the notions of secure scheduling. Finally, some of these security properties will be evaluated in concrete case studies.

cs.DC↗

arXiv2017

On the usefulness of information hiding techniques for wireless sensor networks security

A wireless sensor network (WSN) typically consists of base stations and a large number of wireless sensors. The sensory data gathered from the whole network at a certain time snapshot can be visualized as an image. As a result, information hiding techniques can be applied to this "sensory data image". Steganography refers to the technology of hiding data into digital media without drawing any suspicion, while steganalysis is the art of detecting the presence of steganography. This article provides a brief review of steganography and steganalysis applications for wireless sensor networks (WSNs). Then we show that the steganographic techniques are both related to sensed data authentication in wireless sensor networks, and when considering the attacker point of view, which has not yet been investigated in the literature. Our simulation results show that the sink level is unable to detect an attack carried out by the nsF5 algorithm on sensed data.

cs.MM↗

arXiv2017

Well-supported phylogenies using largest subsets of core-genes by discrete particle swarm optimization

The number of complete chloroplastic genomes increases day after day, making it possible to rethink plants phylogeny at the biomolecular era. Given a set of close plants sharing in the order of one hundred of core chloroplastic genes, this article focuses on how to extract the largest subset of sequences in order to obtain the most supported species tree. Due to computational complexity, a discrete and distributed Particle Swarm Optimization (DPSO) is proposed. It is finally applied to the core genes of Rosales order.

q-bio.PE↗

arXiv2017

Introducing the truly chaotic finite state machines and their applications in security field

The truly chaotic finite machines introduced by authors in previous research papers are presented here. A state of the art in this discipline, encompassing all previous mathematical investigations, is provided, explaining how finite state machines can behave chaotically regarding the slight alteration of their inputs. This behavior is explained using Turing machines and formalized thanks to a special family of discrete dynamical systems called chaotic iterations. An illustrative example is finally given in the field of hash functions.

cs.CR↗

arXiv2017

On the ability to reconstruct ancestral genomes from Mycobacterium genus

Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and essential questions in Evolution. However, reconstructing evolution of DNA sequences requires models, algorithms, statistical and computational methods of ever increasing complexity. Since most dramatic genomic changes are caused by genome rearrangements (gene duplications, gain/loss events), it becomes crucial to understand their mechanisms and reconstruct ancestors of the given genomes. This problem is known to be NP-complete even in the "simplest" case of three genomes. Heuristic algorithms are usually executed to provide approximations of the exact solution. We state that, even if the ancestral reconstruction problem is NP-hard in theory, its exact resolution is feasible in various situations, encompassing organelles and some bacteria. Such accurate reconstruction, which identifies too some highly homoplasic mutations whose ancestral status is undecidable, will be initiated in this work-in-progress, to reconstruct ancestral genomes of two Mycobacterium pathogenetic bacterias. By mixing automatic reconstruction of obvious situations with human interventions on signaled problematic cases, we will indicate that it should be possible to achieve a concrete, complete, and really accurate reconstruction of lineages of the Mycobacterium tuberculosis complex. Thus, it is possible to investigate how these genomes have evolved from their last common ancestors.

q-bio.GN↗

arXiv2017

Taenia Biomolecular Phylogeny and the Impact of Mitochondrial Genes on this Latter

Variations in mitochondrial genes are usually considered to infer phylogenies. However some of these genes are lesser constraint than other ones, and thus may blur the phylogenetic signals shared by the majority of the mitochondrial DNA sequences. To investigate such effects, in this research work, the molecular phylogeny of the genus Taenia is studied using 14 coding sequences extracted from mitochondrial genomes of 17 species. We constructed 16,384 trees, using a combination of 1 up to 14 genes. We obtained 131 topologies, and we showed that only four particular instances were relevant. Using further statistical investigations, we then extracted a particular topology, which displays more robustness properties.

q-bio.PE↗

arXiv2017

Hash functions using chaotic iterations

In this paper, a novel formulation of discrete chaotic iterations in the field of dynamical systems is given. Their topological properties are studied: it is mathematically proved that, under some conditions, these iterations have a chaotic behavior in the meaning of Devaney. This chaotic behavior allows us to propose a way to generate new hash functions. An illustration example is detailed in order to show how to use our theoretical study in practice.

cs.CR↗

arXiv2017

Low Cost Monitoring and Intruders Detection using Wireless Video Sensor Networks

There is a growing interest in the use of video sensor networks in surveillance applications in order to detect intruders with low cost. The essential concern of such networks is whether or not a specified target can pass or intrude the monitored region without being detected. This concern forms a serious challenge to wireless video sensor networks of weak computation and battery power. In this paper, our aim is to prolong the whole network lifetime while fulfilling the surveillance application needs. We present a novel scheduling algorithm where only a subset of video nodes contribute significantly to detect intruders and prevent malicious attacker to predict the behavior of the network prior to intrusion. Our approach is chaos-based, where every node based on its last detection, a hash value and some pseudo-random numbers easily computes a decision function to go to sleep or active mode. We validate the efficiency of our approach through theoretical analysis and demonstrate the benefits of our scheduling algorithm by simulations. Results show that in addition of being able to increase the whole network lifetime and to present comparable results against random attacks (low stealth time), our scheme is also able to withstand malicious attacks due to its fully unpredictable behavior.

cs.CR↗

arXiv2017

Predicting the Evolution of Gene $ura3$ in the Yeast Saccharomyces Cerevisiae

Since the late `60s, various genome evolutionary models have been proposed to predict the evolution of a DNA sequence as the generations pass. Most of these models are based on nucleotides evolution, so they use a mutation matrix of size 4x4. They encompass for instance the well-known models of Jukes and Cantor, Kimura, and Tamura. By essence, all of these models relate the evolution of DNA sequences to the computation of the successive powers of a mutation matrix. To make this computation possible, particular forms for the mutation matrix are assumed, which are not compatible with mutation rates that have been recently obtained experimentally on gene ura3 of the Yeast Saccharomyces cerevisiae. Using this experimental study, authors of this paper have deduced a simple mutation matrice, compute the future evolution of the rate purine/pyrimidine for ura3, investigate the particular behavior of cytosines and thymines compared to purines, and simulate the evolution of each nucleotide.

q-bio.PE↗

arXiv2017

Random Walk in a N-cube Without Hamiltonian Cycle to Chaotic Pseudorandom Number Generation: Theoretical and Practical Considerations

Designing a pseudorandom number generator (PRNG) is a difficult and complex task. Many recent works have considered chaotic functions as the basis of built PRNGs: the quality of the output would indeed be an obvious consequence of some chaos properties. However, there is no direct reasoning that goes from chaotic functions to uniform distribution of the output. Moreover, embedding such kind of functions into a PRNG does not necessarily allow to get a chaotic output, which could be required for simulating some chaotic behaviors. In a previous work, some of the authors have proposed the idea of walking into a $\mathsf{N}$-cube where a balanced Hamiltonian cycle has been removed as the basis of a chaotic PRNG. In this article, all the difficult issues observed in the previous work have been tackled. The chaotic behavior of the whole PRNG is proven. The construction of the balanced Hamiltonian cycle is theoretically and practically solved. An upper bound of the expected length of the walk to obtain a uniform distribution is calculated. Finally practical experiments show that the generators successfully pass the classical statistical tests.

cs.CR↗

arXiv2016

A Second Order Derivatives based Approach for Steganography

Steganography schemes are designed with the objective of minimizing a defined distortion function. In most existing state of the art approaches, this distortion function is based on image feature preservation. Since smooth regions or clean edges define image core, even a small modification in these areas largely modifies image features and is thus easily detectable. On the contrary, textures, noisy or chaotic regions are so difficult to model that the features having been modified inside these areas are similar to the initial ones. These regions are characterized by disturbed level curves. This work presents a new distortion function for steganography that is based on second order derivatives, which are mathematical tools that usually evaluate level curves. Two methods are explained to compute these partial derivatives and have been completely implemented. The first experiments show that these approaches are promising.

cs.MM↗