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Reusing Code in Genetic Programming [chapter]

Edgar Galván López, Riccardo Poli, Carlos A. Coello Coello
2004 Lecture Notes in Computer Science  
In this paper we propose an approach to Genetic Programming based on code reuse and we test it in the design of combinational logic circuits at the gate-level.  ...  The circuits evolved by our algorithm are compared with circuits produced by human designers, by Particle Swarm Optimization, by an n-cardinality GA and by Cartesian Genetic Programming.  ...  Finally, the Essex authors would like to thank the members of the NEC (Natural and Evolutionary Computation) group for helpful comments and discussion.  ... 
doi:10.1007/978-3-540-24650-3_34 fatcat:72kahmrifrdynkkocguqtimafm

The genetic code, 8-dimensional hypercomplex numbers and dyadic shifts [article]

Sergey V. Petoukhov
2016 arXiv   pre-print
The diversity of known dialects of the genetic code is analyzed from the viewpoint of the genetic algebras. An algebraic analogy with Punnett squares for inherited traits is shown.  ...  The statement about existence of the geno-logic code in DNA and epigenetics on the base of the spectral logic of systems of Boolean functions is put forward.  ...  Special thanks to my collaborators Stepanyan I.V. and Svirin V.I for their softwares for calculations in the field of matrix genetics.  ... 
arXiv:1102.3596v11 fatcat:aposxvlq2neibcj7eeicjxe4ve

Symmetries in Genetic Systems and the Concept of Geno-Logical Coding

Sergey Petoukhov, Elena Petukhova
2016 Information  
To be able to model these phenomena, the concept of geno-logical coding, which is connected with logical functions and Boolean algebra, is put forward.  ...  Our results reveal structural connections of the genetic systems with dyadic groups of binary numbers, Walsh functions, Hadamard matrices, logical holography, and spectral analysis of systems of Boolean  ...  Petoukhov is the author of the concept of the geno-logical code and its argumentation; Elena S. Petukhova helps in computer analysis of the genetic data and in the preparation of the paper.  ... 
doi:10.3390/info8010002 fatcat:gqjumbipw5czdikqw7nmxvvnly

Topological Nature of the Genetic Code

V.A. KARASEV, V.E. STEFANOV
2001 Journal of Theoretical Biology  
The model provides an insight into the topological nature of the genetic code and can be used for development of algorithms for the prediction of the protein structure.  ...  the genetic code.  ...  The work was "nancially supported by the research grants from Russian Foundation for Basic Research (RFFI) code 99-04-49836 and GR/CMID No. 50 from Ministry of Education of Russian Federation.  ... 
doi:10.1006/jtbi.2001.2265 pmid:11312591 fatcat:zx27m7yg4vhldprxxvhavksiwa

The degeneracy of the genetic code and Hadamard matrices [article]

Sergey V. Petoukhov
2010 arXiv   pre-print
The matrix form of the presentation of the genetic code is described as the cognitive form to analyze structures of the genetic code.  ...  Peculiarities of the degeneracy of the vertebrate mitochondria genetic code are reflected in the symmetrical black-and-white mosaic of this genetic (8*8)-matrix.  ...  Acknowledgments: Described researches were made by the author in the frame of a long-term cooperation between Russian and Hungarian Academies of Sciences and in the frames of programs of "International  ... 
arXiv:0802.3366v4 fatcat:4vfcx2rlcbhw3n474tn4idmc3u

The structural analysis of protein sequences based on the quasi-amino acids code

Zhu Ping, Tang Xu-Qing, Xu Zhen-Yuan
2009 Chinese Physics B  
According to the characteristics of (Σ , +, * ), a novel quasi-amino acids code classification method is introduced and the corresponding algebraic operation table over the set ZU of the 16 kinds of quasi-amino  ...  In fact, in the mitochondrion from human and ox genomic codon, tga is just tryptophane, is not the stop codon like in other genetic code, it is the case of the Chen W C et al (2002 Acta Biophysica Sinica  ...  Here, it is possible to infer a different codon order and a different algebraic structure of the genetic code by using the same basic properties.  ... 
doi:10.1088/1674-1056/18/1/059 fatcat:cl4wonim5rgp7arus23hrvqme4

Gene algebra from a genetic code algebraic structure

R. Sanchez, E. Morgado, R. Grau
2005 Journal of Mathematical Biology  
in the genetic code analysis.  ...  Now, these properties have allowed us to build a Genetic Code ring isomorphic to the ring (Z64, +,*) of the integer module 64.  ...  [30, 31] proposed a Boolean structure of the genetic code in which the partial order of the codon set and the Boolean deductions between codons are connected to the physico-chemical properties of amino  ... 
doi:10.1007/s00285-005-0332-8 pmid:16012800 fatcat:cli27m3qsnejlixdyrik56juti

New DNA Codes from Cyclic Codes over Mixed Alphabets

Hai Q. Dinh, Sachin Pathak, Ashish Kumar Upadhyay, Woraphon Yamaka
2020 Mathematics  
We discuss their generator polynomials as well as the structure of separable codes. Using the structure of separable codes, we study cyclic DNA codes.  ...  As applications, we provide examples of new cyclic DNA codes constructed by our results.  ...  The work of Sachin Pathak was supported by the University Grant Commission (UGC), Government of India.  ... 
doi:10.3390/math8111977 fatcat:o5nvqhvwi5hpnkuce6svlmkere

Coding Theory

Joachim Rosenthal, Mohammad Amin Shokrollahi
2007 Oberwolfach Reports  
The workshop on coding theory covered many facets of the recent research advances.  ...  Coding theory lies naturally at the intersection of a large number of disciplines in pure and applied mathematics: algebra and number theory, probability theory and statistics, communication theory, discrete  ...  Coding-Theoretic Problems in Genetics: Superimposed Codes for Compressed Sensing DNA Microarrays Olgica Milenkovic (joint work with Wei Dai) We consider the problem of algebraic construction of projection  ... 
doi:10.4171/owr/2007/56 fatcat:ac2rttsrn5g2rn5la72nudiyum

A brief history of the development of error correcting codes

I.S. Reed
2000 Computers and Mathematics with Applications  
It describes the history in which the author was a participant in some of the early developments of error-correcting codes and computers.  ...  Also details are given about the origins of both the Reed-Muller and Reed-Solomon codes. (~)  ...  The algebraic structure imposed on these multinomials made it possible for me to find a decoding algorithm for these codes which is now called majority-logic decoding.  ... 
doi:10.1016/s0898-1221(00)00112-7 fatcat:qcpmplrixnh3zepk4tx32pz5we

The genetic code, algebra of projection operators and problems of inherited biological ensembles [article]

Sergey Petoukhov
2017 arXiv   pre-print
This article is devoted to applications of projection operators to simulate phenomenological properties of the molecular-genetic code system.  ...  Described results can be used for developing algebraic biology, bio-technical applications and some other fields of science and technology.  ...  In author's opinion, one of many promising applications of projectors in mathematical biology and bioinformatics is the study of connections between genetic projectors and Boolean algebra.  ... 
arXiv:1307.7882v9 fatcat:qgqqxdnx45bmvgxuahc2ptaapi

Syntia: Synthesizing the Semantics of Obfuscated Code

Tim Blazytko, Moritz Contag, Cornelius Aschermann, Thorsten Holz
2017 USENIX Security Symposium  
As program synthesis can synthesize code of arbitrary code complexity, it is only limited by the complexity of the underlying code's semantic.  ...  To demonstrate the practical feasibility of our approach, we automatically learn the semantics of 489 out of 500 random expressions obfuscated via Mixed Boolean-Arithmetic.  ...  Acknowledgments We thank the reviewers for their valuable feedback.  ... 
dblp:conf/uss/BlazytkoCAH17 fatcat:2nayu7gzynf2fog4todzpbyzqa

Network Coding Theory: A Survey

Riccardo Bassoli, Hugo Marques, Jonathan Rodriguez, Kenneth W. Shum, Rahim Tafazolli
2013 IEEE Communications Surveys and Tutorials  
This article surveys all known fields of network coding theory and leads the reader through the antecedents of the network coding theory to the most recent results, considering also information theory  ...  Next to the pure theory of network coding, a branch of investigation was focusing on algorithmic implementation of network codes.  ...  of the hierarchy of some algebraic structures with their characteristics.  ... 
doi:10.1109/surv.2013.013013.00104 fatcat:jgnf4i7rczfqrcyv7tygrydtxm

Increase in Modified Condition/Decision Coverage using program code transformer

Sangharatna Godboley, G. S. Prashanth, D. P. Mohapatro, B. Majhi
2013 2013 3rd IEEE International Advance Computing Conference (IACC)  
We use code transformation techniques which consist of the following major steps: Identification of predicates, Simplification of sum of product by QUINE-McMLUSKY method, and generating empty true-false  ...  Modified Condition / Decision Coverage (MC / DC) is a white box testing criteria aiming to prove that all conditions involved in a predicate can influence the predicate value in the desired way.  ...  PCT converts each predicate in an entered program code to the standard sum-of product (SOP) form by Boolean algebra [13] .  ... 
doi:10.1109/iadcc.2013.6514432 fatcat:2ihf7qk77vb7peppi33rujr7zi

Teaching machines to understand data science code by semantic enrichment of dataflow graphs [article]

Evan Patterson, Ioana Baldini, Aleksandra Mojsilovic, Kush R. Varshney
2019 arXiv   pre-print
They deserve to have intelligent tools that reveal the connections between code and its subject matter.  ...  Throughout the paper, we focus on code written by data scientists and we locate our work within a larger movement towards collaborative, open, and reproducible science.  ...  algebraic structures like groups and monoids.  ... 
arXiv:1807.05691v2 fatcat:cmgrc2ku3jbabctmhngxtknunu
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