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A Formal Language-Based Approach in Biology

Marian Gheorghe, Victor Mitrana
<span title="">2004</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eaz5kv6drnd7hlqjuszvrhtqnm" style="color: black;">Comparative and Functional Genomics</a> </i> &nbsp;
This paper presents an overview of computational biology approaches and surveys some of the natural computing models using, in both cases, a formal language-based approach.  ...  Acknowledgement The work of the first author has been supported by EPSRC grant GR/R84221/01.  ...  Many variants of H systems have been invented and investigated (regulated H systems, distributed H systems, H systems with multisets, etc.).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cfg.364">doi:10.1002/cfg.364</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18629037">pmid:18629037</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2447320/">pmcid:PMC2447320</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hlp4rahzuzbchdxmatlokjr4rm">fatcat:hlp4rahzuzbchdxmatlokjr4rm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190505033213/http://downloads.hindawi.com/journals/ijg/2004/702415.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4c/97/4c97d30dd2b74aa668e81e222fff4cacb63b4a15.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cfg.364"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447320" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Regulated Grammars with Leftmost Derivation [chapter]

Henning Fernau
<span title="">1998</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
periodically time-variant grammars.  ...  Moreover, we get new results on leftmost derivations in conditional grammars. ? Supported by Deutsche Forschungsgemeinschaft grant DFG La 618/3-2.  ...  ways of regulation (see 7, 9, 10] ).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/3-540-49477-4_24">doi:10.1007/3-540-49477-4_24</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ie74whwaibc2veqces5bgtss6a">fatcat:ie74whwaibc2veqces5bgtss6a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190221214456/http://pdfs.semanticscholar.org/2f12/96f816fb0e3cdbd2053910d14244572185f5.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2f/12/2f1296f816fb0e3cdbd2053910d14244572185f5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/3-540-49477-4_24"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

A Note on the Generative Power of Some Simple Variants of Context-Free Grammars Regulated by Context Conditions [chapter]

Tomáš Masopust
<span title="">2009</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
This paper answers three open questions concerning the generative power of some simple variants of context-free grammars regulated by context conditions.  ...  forbidding strings) where permitting and forbidding strings of each production are of length no more than one, and of simple semi-conditional grammars where, in addition, no production has attached both  ...  The present paper discusses two simple variants of context-free grammars regulated by context conditions; both variants are special cases of so called context-free random context grammars (defined and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-00982-2_47">doi:10.1007/978-3-642-00982-2_47</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ioduiodgzndoxi4oqqyrgs2uha">fatcat:ioduiodgzndoxi4oqqyrgs2uha</a> </span>
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Page 1497 of Mathematical Reviews Vol. , Issue 87c [page]

<span title="">1987</span> <i title="American Mathematical Society"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_mathematical-reviews" style="color: black;">Mathematical Reviews </a> </i> &nbsp;
ordered variants of some regulated grammars.  ...  context, Indian parallel and scattered context grammars, as well as that of EOL and ETOL systems with an order restriction on the deriva- tion process.  ... 
<span class="external-identifiers"> </span>
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Membrane Computing — Current Results and Future Problems [chapter]

Francesco Bernardini, Marian Gheorghe, Natalio Krasnogor, German Terrazas
<span title="">2005</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
Several variants of this model have been investigated and the literature on the subject is now rapidly growing.  ...  There are variants that might be classified according to different criteria.  ...  Acknowledgments The research of FB and MG has been supported by the Engineering and Physical Science Research Council (EPSRC) of United Kingdom, Grant GR/R84221/01.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/11494645_6">doi:10.1007/11494645_6</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s2yhupsqizbb7amrpfsxyavcdu">fatcat:s2yhupsqizbb7amrpfsxyavcdu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20081002131045/http://www.dcs.shef.ac.uk/~marian/research/papers/lncs3526-1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ea/6a/ea6a01f92fec20020b8cb5f0f68b9282e084b874.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/11494645_6"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Page 5888 of Mathematical Reviews Vol. , Issue 98I [page]

<span title="">1998</span> <i title="American Mathematical Society"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_mathematical-reviews" style="color: black;">Mathematical Reviews </a> </i> &nbsp;
More- over, we present interrelations between the LBA problem on the one hand and the relationship between the families of languages described by A-free programmed grammars with degree of non- regulation  ...  gram- mars, random context grammars, ordered grammars, Indian paral- lel grammars, k-grammars, scattered context grammars, k-simple matrix grammars and indexed grammars.  ... 
<span class="external-identifiers"> </span>
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Structurally and Arithmetically Controlled Grammars

S Ashaari, SHERZOD TURAEV, A Okhunov
<span title="2016-11-24">2016</span> <i title="IIUM Press"> International Journal on Perceptive and Cognitive Computing </i> &nbsp;
Over the quarter century, it is gratifying to note that the significance of regulated or controlledgrammars (i.e. grammars with regulated rewriting) has been recognized by many parties where it has beenused  ...  Given the extensive literature on issues related to controlledgrammars, this research focused on arithmetically controlled grammars and tree controlled grammars,which are practically important.  ...  Since then, a lot of variants of grammars with regulated rewriting have been investigated and studied in formal language field where mostly are based on context-free grammar with the aim to increase their  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.31436/ijpcc.v2i2.39">doi:10.31436/ijpcc.v2i2.39</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jwoix3ktnvbvfnv6ihpbedbuda">fatcat:jwoix3ktnvbvfnv6ihpbedbuda</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429032840/https://journals.iium.edu.my/kict/index.php/IJPCC/article/download/39/33" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/75/92/7592ce4972a8fd2b746add986b26cfb1d7a0ec12.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.31436/ijpcc.v2i2.39"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Tree Valence Controlled Grammars

Salbiah Ashaari, SHERZOD TURAEV, Abdurahim Okhunov
<span title="2017-07-20">2017</span> <i title="IIUM Press"> International Journal on Perceptive and Cognitive Computing </i> &nbsp;
Our paper is a continuing of studyingof this kind of grammars, where we introduce a new variant of tree controlled grammar called a treevalence controlled grammar, which replaces regular sets with valences  ...  as demonstrated in a number of publications on this subject for the past forty five years.In principle, these grammars generate their languages as an ordinary context-free grammar except theirderivation  ...  ACKNOWLEDGMENT This research has been supported by the grants RIGS16-368-0532 and FRGS13-074-0315 of Ministry of Education, Malaysia through International Islamic University Malaysia.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.31436/ijpcc.v3i1.48">doi:10.31436/ijpcc.v3i1.48</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ukm64cef2ndlbn5pxyxz6cbb34">fatcat:ukm64cef2ndlbn5pxyxz6cbb34</a> </span>
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Binary Context-Free Grammars

Sherzod Turaev, Rawad Abdulghafor, Ali Amer Alwan, Ali Abd Almisreb, Yonis Gulzar
<span title="2020-07-24">2020</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nzoj5rayr5hutlurimhzyjlory" style="color: black;">Symmetry</a> </i> &nbsp;
This paper investigates the binary context-free grammars as mutually controlled grammars: two context-free grammars generate strings imposing restrictions on selecting production rules to be applied in  ...  A binary grammar is a relational grammar with two nonterminal alphabets, two terminal alphabets, a set of pairs of productions and the pair of the initial nonterminals that generates the binary relation  ...  Conflicts of Interest: The authors declare no conflict of interest. The funders had no role in the design of the study and in the writing of the manuscript, or in the decision to publish the results.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/sym12081209">doi:10.3390/sym12081209</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uifgbbpqbrhvjd4kaopcexeyje">fatcat:uifgbbpqbrhvjd4kaopcexeyje</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200806205424/https://res.mdpi.com/d_attachment/symmetry/symmetry-12-01209/article_deploy/symmetry-12-01209.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/00/4a/004ad01a74f0b3fdc2e485556508fb49cbd494ce.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/sym12081209"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a>

Graph grammars with string-regulated rewriting

Daniel Lobo, Francisco J. Vico, Jürgen Dassow
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/elaf5sq7lfdxfdejhkqbtz6qoq" style="color: black;">Theoretical Computer Science</a> </i> &nbsp;
We demonstrate that the power of expression increases when genetic regulation is included in the model, as compared to non-regulated grammars.  ...  Additionally, we propose a hierarchy of string-regulated graph grammars, arranged by expressive power.  ...  to an expressive-power hierarchy of variants of string-regulated graph grammars.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tcs.2011.07.004">doi:10.1016/j.tcs.2011.07.004</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xrhxtxyedngnbevzba5szoo7tm">fatcat:xrhxtxyedngnbevzba5szoo7tm</a> </span>
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Page 3201 of Mathematical Reviews Vol. , Issue 88f [page]

<span title="">1988</span> <i title="American Mathematical Society"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_mathematical-reviews" style="color: black;">Mathematical Reviews </a> </i> &nbsp;
The first one, the valence grammars in one of our earlier papers [Rev. Roumaine Math.  ...  Summary: “We discuss here three classes of regulation mechanisms for context-free grammars, all three introduced in the eighties.  ... 
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Learning metamorphic malware signatures from samples

Marco Campion, Mila Dalla Preda, Roberto Giacobazzi
<span title="2021-02-19">2021</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/th6jepbrbndhlmrilkgb4fbya4" style="color: black;">Journal in Computer Virology and Hacking Techniques</a> </i> &nbsp;
This allows us to learn the transformation rules used by the metamorphic engine to generate the considered code variants. We validate the results of MetaSign on some case studies.  ...  In particular, we formalize the language of code variants in terms of pure context-free grammars, which are similar to context-free grammars with no terminal symbols.  ...  Rather than considering the raw bytes structure of metamorphic malware variants, we specify code mutations in terms of grammar rules extracted from the analysis of some metamorphic malware samples.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11416-021-00377-z">doi:10.1007/s11416-021-00377-z</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ua7rwcb4wfdcjh2ihhk22j3id4">fatcat:ua7rwcb4wfdcjh2ihhk22j3id4</a> </span>
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One nation, one spelling, one school: writing education and the nationalisation of orthography in the Netherlands (1750–1850)

Bob Schoemaker, Gijsbert Rutten
<span title="2019-06-12">2019</span> <i title="Informa UK Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/njru42ug2fd5la23lbvgprwrjq" style="color: black;">Paedagogica Historica: International Journal of the History of Education</a> </i> &nbsp;
The orthography and the grammar constituted regulations for the written language (schrijftaalregeling), which were part of a broader effort at nationalisation.  ...  In 1804, the first official spelling of Dutch was published as part of a national language policy that had been argued for since the middle of the eighteenth century, and in 1805, an official grammar was  ...  One commentator argued that there was no need for "children of the lower social orders" to develop a noteworthy writing style, yet being able to write "with some correctness and order" was highly recommended  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1080/00309230.2019.1622573">doi:10.1080/00309230.2019.1622573</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/32bgnmkgxne53hvqpnqxlo23ri">fatcat:32bgnmkgxne53hvqpnqxlo23ri</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210427095334/https://scholarlypublications.universiteitleiden.nl/access/item%3A3076611/view" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/db/45/db452c786fa442359426c3cf56dcca0ebc718714.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1080/00309230.2019.1622573"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> tandfonline.com </button> </a>

Page 5137 of Mathematical Reviews Vol. , Issue 97H [page]

<span title="">1997</span> <i title="American Mathematical Society"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_mathematical-reviews" style="color: black;">Mathematical Reviews </a> </i> &nbsp;
Summary: “We introduce a generalized form of the shuffle op- eration, particular versions of which give rise to some previously investigated variants.  ...  For this reason the algebra SP( A) will be ordered (a definition too extensive to present here)— in the authors’ opinion this “new ordering is one of the main contributions of the paper”.  ... 
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Page 7285 of Mathematical Reviews Vol. , Issue 98K [page]

<span title="">1998</span> <i title="American Mathematical Society"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_mathematical-reviews" style="color: black;">Mathematical Reviews </a> </i> &nbsp;
We also present the relations to contextual grammars with shuffled context and some new results on such grammars, and discuss the linguistic importance of such grammars.”  ...  The au- thor establishes some inclusions, equalities and proper inclusions between families of languages generated by these types of con- trolled grammars.  ... 
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