arXiv subjects

Jacques M. Bahi

Publications and source records attributed to Jacques M. Bahi.

At least 37 records · Page 2Linked to original sources

arXiv2016

A Topological Study of Chaotic Iterations. Application to Hash Functions

Chaotic iterations, a tool formerly used in distributed computing, has recently revealed various interesting properties of disorder leading to its use in the computer science security field. In this paper, a comprehensive study of its topological behavior is proposed. It is stated that, in addition to being chaotic as defined in the Devaney's formulation, this tool possesses the property of topological mixing. Additionally, its level of sensibility, expansivity, and topological entropy are evaluated. All of these properties lead to a complete unpredictable behavior for the chaotic iterations. As it only manipulates binary digits or integers, we show that it is possible to use it to produce truly chaotic computer programs. As an application example, a truly chaotic hash function is proposed in two versions. In the second version, an artificial neural network is used, which can be stated as chaotic according to Devaney.

nlin.CD↗

arXiv2016

Quality Analysis of a Chaotic Proven Keyed Hash Function

Hash functions are cryptographic tools, which are notably involved in integrity checking and password storage. They are of primary importance to improve the security of exchanges through the Internet. However, as security flaws have been recently identified in the current standard in this domain, new ways to hash digital data must be investigated. In this document an original keyed hash function is evaluated. It is based on asynchronous iterations leading to functions that have been proven to be chaotic. It thus possesses various topological properties as uniformity and sensibility to its initial condition. These properties make our hash function satisfies established security requirements in this field. This claim is qualitatively proven and experimentally verified in this research work, among other things by realizing a large number of simulations.

cs.CR↗

arXiv2016

FPGA Design for Pseudorandom Number Generator Based on Chaotic Iteration used in Information Hiding Application

Lots of researches indicate that the inefficient generation of random numbers is a significant bottleneck for information communication applications. Therefore, Field Programmable Gate Array (FPGA) is developed to process a scalable fixed-point method for random streams generation. In our previous researches, we have proposed a technique by applying some well-defined discrete chaotic iterations that satisfy the reputed Devaney's definition of chaos, namely chaotic iterations (CI). We have formerly proven that the generator with CI can provide qualified chaotic random numbers. In this paper, this generator based on chaotic iterations is optimally redesigned for FPGA device. By doing so, the generation rate can be largely improved. Analyses show that these hardware generators can also provide good statistical chaotic random bits and can be cryptographically secure too. An application in the information hiding security field is finally given as an illustrative example.

cs.CR↗

arXiv2016

Two Security Layers for Hierarchical Data Aggregation in Sensor Networks

Due to resource restricted sensor nodes, it is important to minimize the amount of data transmission among sensor networks. To reduce the amount of sending data, an aggregation approach can be applied along the path from sensors to the sink. However, as sensor networks are often deployed in untrusted and even hostile environments, sensor nodes are prone to node compromise attacks. Hence, an end-to-end secure aggregation approach is required to ensure a healthy data reception. In this paper, we propose two layers for secure data aggregation in sensor networks. Firstly, we provide an end-to-end encryption scheme that supports operations over cypher-text. It is based on elliptic curve cryptography that exploits a smaller key size, allows the use of higher number of operations on cypher-texts, and prevents the distinction between two identical texts from their cryptograms. Secondly, we propose a new watermarking-based authentication that enables sensor nodes to ensure the identity of other nodes they are communicating with. Our experiments show that our hybrid approach of secure data aggregation enhances the security, significantly reduces computation and communication overhead, and can be practically implemented in on-the-shelf sensor platforms.

cs.DC↗

arXiv2016

Epidemiological Approach for Data Survivability in Unattended Wireless Sensor Networks

Unattended Wireless Sensor Networks (UWSNs) are Wireless Sensor Networks characterized by sporadic sink presence and operation in hostile settings. The absence of the sink for period of time, prevents sensor nodes to offload data in real time and offer greatly increased opportunities for attacks resulting in erasure, modification, or disclosure of sensor-collected data. In this paper, we focus on UWSNs where sensor nodes collect and store data locally and try to upload all the information once the sink becomes available. One of the most relevant issues pertaining UWSNs is to guarantee a certain level of information survivability in an unreliable network and even in presence of a powerful attackers. In this paper, we first introduce an epidemic-domain inspired approach to model the information survivability in UWSN. Next, we derive a fully distributed algorithm that supports these models and give the correctness proofs.

cs.DC↗

arXiv2016

Protein Folding in the 2D Hydrophobic-Hydrophilic (HP) Square Lattice Model is Chaotic

Among the unsolved problems in computational biology, protein folding is one of the most interesting challenges. To study this folding, tools like neural networks and genetic algorithms have received a lot of attention, mainly due to the NP-completeness of the folding process. The background idea that has given rise to the use of these algorithms is obviously that the folding process is predictable. However, this important assumption is disputable as chaotic properties of such a process have been recently highlighted. In this paper, which is an extension of a former work accepted to the 2011 International Joint Conference on Neural Networks (IJCNN11), the topological behavior of a well-known dynamical system used for protein folding prediction is evaluated. It is mathematically established that the folding dynamics in the 2D hydrophobic-hydrophilic (HP) square lattice model, simply called "the 2D model" in this document, is indeed a chaotic dynamical system as defined by Devaney. Furthermore, the chaotic behavior of this model is qualitatively and quantitatively deepened, by studying other mathematical properties of disorder, namely: the indecomposability, instability, strong transitivity, and constants of expansivity and sensitivity. Some consequences for both biological paradigms and structure prediction using this model are then discussed. In particular, it is shown that some neural networks seems to be unable to predict the evolution of this model with accuracy, due to its complex behavior.

q-bio.BM↗

arXiv2016

Chaos in DNA Evolution

In this paper, we explain why the chaotic model (CM) of Bahi and Michel (2008) accurately simulates gene mutations over time. First, we demonstrate that the CM model is a truly chaotic one, as defined by Devaney. Then, we show that mutations occurring in gene mutations have the same chaotic dynamic, thus making the use of chaotic models relevant for genome evolution.

q-bio.GN↗

arXiv2015

A new chaos-based watermarking algorithm

This paper introduces a new watermarking algorithm based on discrete chaotic iterations. After defining some coefficients deduced from the description of the carrier medium, chaotic discrete iterations are used to mix the watermark and to embed it in the carrier medium. It can be proved that this procedure generates topological chaos, which ensures that desired properties of a watermarking algorithm are satisfied.

cs.MM↗

arXiv2015

Topological chaos and chaotic iterations. Application to Hash functions

This paper introduces a new notion of chaotic algorithms. These algorithms are iterative and are based on so-called chaotic iterations. Contrary to all existing studies on chaotic iterations, we are not interested in stable states of such iterations but in their possible unpredictable behaviors. By establishing a link between chaotic iterations and the notion of Devaney's topological chaos, we give conditions ensuring that these kind of algorithms produce topological chaos. This leads to algorithms that are highly unpredictable. After presenting the theoretical foundations of our approach, we are interested in its practical aspects. We show how the theoretical algorithms give rise to computer programs that produce true topological chaos, then we propose applications in the area of information security.

cs.CR↗

arXiv2015

Chaos of Protein Folding

As protein folding is a NP-complete problem, artificial intelligence tools like neural networks and genetic algorithms are used to attempt to predict the 3D shape of an amino acids sequence. Underlying these attempts, it is supposed that this folding process is predictable. However, to the best of our knowledge, this important assumption has been neither proven, nor studied. In this paper the topological dynamic of protein folding is evaluated. It is mathematically established that protein folding in 2D hydrophobic-hydrophilic (HP) square lattice model is chaotic as defined by Devaney. Consequences for both structure prediction and biology are then outlined.

q-bio.BM↗

arXiv2015

Improved Core Genes Prediction for Constructing well-supported Phylogenetic Trees in large sets of Plant Species

The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies, many similarity based algorithms, mainly dependent on calculating sequence alignment matrices, have been proposed to find them. In these kinds of approaches, a significantly high similarity score between two coding sequences extracted from a given annotation tool means that one has the same genes. In a previous work article, we presented a quality test approach (QTA) that improves the core genes quality by combining two annotation tools (namely NCBI, a partially human-curated database, and DOGMA, an efficient annotation algorithm for chloroplasts). This method takes the advantages from both sequence similarity and gene features to guarantee that the core genome contains correct and well-clustered coding sequences (\emph{i.e.}, genes). We then show in this article how useful are such well-defined core genes for biomolecular phylogenetic reconstructions, by investigating various subsets of core genes at various family or genus levels, leading to subtrees with strong bootstraps that are finally merged in a well-supported supertree.

q-bio.GN↗

arXiv2015

Hybrid Genetic Algorithm and Lasso Test Approach for Inferring Well Supported Phylogenetic Trees based on Subsets of Chloroplastic Core Genes

The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their chloroplasts, the phylogenetic tree that can be inferred by their core genes is not necessarily well supported, due to the possible occurrence of "problematic" genes (i.e., homoplasy, incomplete lineage sorting, horizontal gene transfers, etc.) which may blur phylogenetic signal. However, a trustworthy phylogenetic tree can still be obtained if the number of problematic genes is low, the problem being to determine the largest subset of core genes that produces the best supported tree. To discard problematic genes and due to the overwhelming number of possible combinations, we propose an hybrid approach that embeds both genetic algorithms and statistical tests. Given a set of organisms, the result is a pipeline of many stages for the production of well supported phylogenetic trees. The proposal has been applied to different cases of plant families, leading to encouraging results for these families.

cs.AI↗

arXiv2014

Gene Similarity-based Approaches for Determining Core-Genes of Chloroplasts

In computational biology and bioinformatics, the manner to understand evolution processes within various related organisms paid a lot of attention these last decades. However, accurate methodologies are still needed to discover genes content evolution. In a previous work, two novel approaches based on sequence similarities and genes features have been proposed. More precisely, we proposed to use genes names, sequence similarities, or both, insured either from NCBI or from DOGMA annotation tools. Dogma has the advantage to be an up-to-date accurate automatic tool specifically designed for chloroplasts, whereas NCBI possesses high quality human curated genes (together with wrongly annotated ones). The key idea of the former proposal was to take the best from these two tools. However, the first proposal was limited by name variations and spelling errors on the NCBI side, leading to core trees of low quality. In this paper, these flaws are fixed by improving the comparison of NCBI and DOGMA results, and by relaxing constraints on gene names while adding a stage of post-validation on gene sequences. The two stages of similarity measures, on names and sequences, are thus proposed for sequence clustering. This improves results that can be obtained using either NCBI or DOGMA alone. Results obtained with this quality control test are further investigated and compared with previously released ones, on both computational and biological aspects, considering a set of 99 chloroplastic genomes.

cs.NE↗

arXiv2014

Finding the Core-Genes of Chloroplasts

Due to the recent evolution of sequencing techniques, the number of available genomes is rising steadily, leading to the possibility to make large scale genomic comparison between sets of close species. An interesting question to answer is: what is the common functionality genes of a collection of species, or conversely, to determine what is specific to a given species when compared to other ones belonging in the same genus, family, etc. Investigating such problem means to find both core and pan genomes of a collection of species, \textit{i.e.}, genes in common to all the species vs. the set of all genes in all species under consideration. However, obtaining trustworthy core and pan genomes is not an easy task, leading to a large amount of computation, and requiring a rigorous methodology. Surprisingly, as far as we know, this methodology in finding core and pan genomes has not really been deeply investigated. This research work tries to fill this gap by focusing only on chloroplastic genomes, whose reasonable sizes allow a deep study. To achieve this goal, a collection of 99 chloroplasts are considered in this article. Two methodologies have been investigated, respectively based on sequence similarities and genes names taken from annotation tools. The obtained results will finally be evaluated in terms of biological relevance.

cs.CE↗

arXiv2013

Topological study and Lyapunov exponent of a secure steganographic scheme

CIS2 is a steganographic scheme proposed in the information hiding literature, belonging into the small category of algorithms being both stego and topologically secure. Due to its stego-security, this scheme is able to face attacks that take place into the "watermark only attack" framework. Its topological security reinforce its capability to face attacks in other frameworks as "known message attack" or "known original attack", in the Simmons' prisoner problem. In this research work, the study of topological properties of C I S 2 is enlarged by describing this scheme as iterations over the real line, and investigating other security properties of topological nature as the Lyapunov exponent. Results show that this scheme is able to withdraw a malicious attacker in the "estimated original attack" context too.

cs.CR↗

arXiv2013

Computational investigations of folded self-avoiding walks related to protein folding

Various subsets of self-avoiding walks naturally appear when investigating existing methods designed to predict the 3D conformation of a protein of interest. Two such subsets, namely the folded and the unfoldable self-avoiding walks, are studied computationally in this article. We show that these two sets are equal and correspond to the whole $n$-step self-avoiding walks for $n\leqslant 14$, but that they are different for numerous $n \geqslant 108$, which are common protein lengths. Concrete counterexamples are provided and the computational methods used to discover them are completely detailed. A tool for studying these subsets of walks related to both pivot moves and proteins conformations is finally presented.

q-bio.BM↗

arXiv2013

Is protein folding problem really a NP-complete one ? First investigations

To determine the 3D conformation of proteins is a necessity to understand their functions or interactions with other molecules. It is commonly admitted that, when proteins fold from their primary linear structures to their final 3D conformations, they tend to choose the ones that minimize their free energy. To find the 3D conformation of a protein knowing its amino acid sequence, bioinformaticians use various models of different resolutions and artificial intelligence tools, as the protein folding prediction problem is a NP complete one. More precisely, to determine the backbone structure of the protein using the low resolution models (2D HP square and 3D HP cubic), by finding the conformation that minimize free energy, is intractable exactly. Both the proof of NP-completeness and the 2D prediction consider that acceptable conformations have to satisfy a self-avoiding walk (SAW) requirement, as two different amino acids cannot occupy a same position in the lattice. It is shown in this document that the SAW requirement considered when proving NP-completeness is different from the SAW requirement used in various prediction programs, and that they are different from the real biological requirement. Indeed, the proof of NP completeness and the predictions in silico consider conformations that are not possible in practice. Consequences of this fact are investigated in this research work.

q-bio.BM↗

arXiv2013

Protein structure prediction software generate two different sets of conformations. Or the study of unfolded self-avoiding walks

Self-avoiding walks (SAW) are the source of very difficult problems in probabilities and enumerative combinatorics. They are also of great interest as they are, for instance, the basis of protein structure prediction in bioinformatics. Authors of this article have previously shown that, depending on the prediction algorithm, the sets of obtained conformations differ: all the self-avoiding walks can be reached using stretching-based algorithms whereas only the folded SAWs can be attained with methods that iteratively fold the straight line. A first study of (un)folded self-avoiding walks is presented in this article. The contribution is majorly a survey of what is currently known about these sets. In particular we provide clear definitions of various subsets of self-avoiding walks related to pivot moves (folded or unfoldable SAWs, etc.) and the first results we have obtained, theoretically or computationally, on these sets. A list of open questions is provided too, and the consequences on the protein structure prediction problem is finally investigated.

q-bio.BM↗