22 research outputs found

    Use of a novel grammatical inference approach in classification of amyloidogenic hexapeptides

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    The present paper is a novel contribution to the field of bioinformatics by using grammatical inference in the analysis of data. We developed an algorithm for generating star-free regular expressions which turned out to be good recommendation tools, as they are characterized by a relatively high correlation coefficient between the observed and predicted binary classifications. The experiments have been performed for three datasets of amyloidogenic hexapeptides, and our results are compared with those obtained using the graph approaches, the current state-of-the-art methods in heuristic automata induction, and the support vector machine. The results showed the superior performance of the new grammatical inference algorithm on fixed-length amyloid datasets

    Languages Generated by Iterated Idempotencies.

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    The rewrite relation with parameters m and n and with the possible length limit = k or :::; k we denote by w~, =kW~· or ::;kw~ respectively. The idempotency languages generated from a starting word w by the respective operations are wDAlso other special cases of idempotency languages besides duplication have come up in different contexts. The investigations of Ito et al. about insertion and deletion, Le., operations that are also observed in DNA molecules, have established that w5 and w~ both preserve regularity.Our investigations about idempotency relations and languages start out from the case of a uniform length bound. For these relations =kW~ the conditions for confluence are characterized completely. Also the question of regularity is -k n answered for aH the languages w- D 1 are more complicated and belong to the class of context-free languages.For a generallength bound, i.e."for the relations :"::kW~, confluence does not hold so frequently. This complicatedness of the relations results also in more complicated languages, which are often non-regular, as for example the languages WWithout any length bound, idempotency relations have a very complicated structure. Over alphabets of one or two letters we still characterize the conditions for confluence. Over three or more letters, in contrast, only a few cases are solved. We determine the combinations of parameters that result in the regularity of wDIn a second chapter sorne more involved questions are solved for the special case of duplication. First we shed sorne light on the reasons why it is so difficult to determine the context-freeness ofduplication languages. We show that they fulfiH aH pumping properties and that they are very dense. Therefore aH the standard tools to prove non-context-freness do not apply here.The concept of root in Formal Language ·Theory is frequently used to describe the reduction of a word to another one, which is in sorne sense elementary.For example, there are primitive roots, periodicity roots, etc. Elementary in connection with duplication are square-free words, Le., words that do not contain any repetition. Thus we define the duplication root of w to consist of aH the square-free words, from which w can be reached via the relation w~.Besides sorne general observations we prove the decidability of the question, whether the duplication root of a language is finite.Then we devise acode, which is robust under duplication of its code words.This would keep the result of a computation from being destroyed by dupli cations in the code words. We determine the exact conditions, under which infinite such codes exist: over an alphabet of two letters they exist for a length bound of 2, over three letters already for a length bound of 1.Also we apply duplication to entire languages rather than to single words; then it is interesting to determine, whether regular and context-free languages are closed under this operation. We show that the regular languages are closed under uniformly bounded duplication, while they are not closed under duplication with a generallength bound. The context-free languages are closed under both operations.The thesis concludes with a list of open problems related with the thesis' topics

    On some modifications and applications of the post correspondence problem

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    The Post Correspondence Problem was introduced by Emil Post in 1946. The problem considers pairs of lists of sequences of symbols, or words, where each word has its place on the list determined by its index. The Post Correspondence Problem asks does there exist a sequence of indices so that, when we write the words in the order of the sequence as single words from both lists, the two resulting words are equal. Post proved the problem to be undecidable, that is, no algorithm deciding it can exist. A variety of restrictions and modifications have been introduced to the original formulation of the problem, that have then been shown to be either decidable or undecidable. Both the original Post Correspondence Problem and its modifications have been widely used in proving other decision problems undecidable. In this thesis we consider some modifications of the Post Correspondence Problem as well as some applications of it in undecidability proofs. We consider a modification for sequences of indices that are infinite to two directions. We also consider a modification to the original Post Correspondence Problem where instead of the words being equal for a sequence of indices, we take two sequences that are conjugates of each other. Two words are conjugates if we can write one word by taking the other and moving some part of that word from the end to the beginning. Both modifications are shown to be undecidable. We also use the Post Correspondence Problem and its modification for injective morphisms in proving two problems from formal language theory to be undecidable; the first problem is on special shuffling of words and the second problem on fixed points of rational functions

    Eucharistic Paradigms in the Didache Correlated to Paradigms in the New Testament

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    Thesis Statement: We contend that it is possible to articulate a viable correlation between eucharistic accounts in the New Testament and the prayers in Didache 9 & 10, by way of the various words spoken over the elements of cup and bread. Summary Statement: This paper addresses eucharistic constructs found in Didache chapters 9 and 10. An initial chapter lays a foundation for discussion with a general treatment of the Didache as a whole. The second chapter provides a translation of the focal chapters and correlates them with broader observations from the first chapter. A third chapter engages various scholastic efforts relevant to the thesis, and the final chapter presents a speculative model as a demonstration of the thesis statement

    Eucharistic Paradigms in the Didache Correlated to Paradigms in the New Testament

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    Thesis Statement: We contend that it is possible to articulate a viable correlation between eucharistic accounts in the New Testament and the prayers in Didache 9 & 10, by way of the various words spoken over the elements of cup and bread. Summary Statement: This paper addresses eucharistic constructs found in Didache chapters 9 and 10. An initial chapter lays a foundation for discussion with a general treatment of the Didache as a whole. The second chapter provides a translation of the focal chapters and correlates them with broader observations from the first chapter. A third chapter engages various scholastic efforts relevant to the thesis, and the final chapter presents a speculative model as a demonstration of the thesis statement

    Multi-verb constructions in Eastern Indonesia

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    Constructions with multiple verbal elements have posed a long-standing challenge to linguistic analysis. Most studies of verb serialisation have been confined to single languages rather than looking at crosslinguistic patterns. This book provides the first in-depth account into the areal characteristics of multi-verb constructions (MVCs) in Eastern Indonesia. By collating published data as well as corpus data from 32 Austronesian and Papuan languages, the study traces commonalities as well as differences in MVC use across the area. Analysis takes place on two levels: first, the morpho-syntactic behaviour of MVCs is taken into account. As this plane of analysis arguably does not provide any meaningful insights into why MVCs are construed and used the way they are, a semantic account of MVCs is presented. One of the main hypotheses advanced in this book is that the crucial driving force behind multi-verb construals is semantic interaction between the verbs, leading to four principal techniques of event formation: merging, staging, modification, and free juxtaposition. The study aims at showing that while all four techniques are, to varying degrees, in use in Eastern Indonesian languages, the morpho-syntactic output does not necessarily mirror these underlying differences in event conception. Applying insights from Davidsonian event semantics as well as from predicate decomposition, the book provides a model of event interaction that helps to explain differences in MVC behaviour such as issues in constituent order or operator assignment

    Multi-verb constructions in Eastern Indonesia (Volume 28)

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    Constructions with multiple verbal elements have posed a long-standing challenge to linguistic analysis. Most studies of verb serialisation have been confined to single languages rather than looking at crosslinguistic patterns. This book provides the first in-depth account into the areal characteristics of multi-verb constructions (MVCs) in Eastern Indonesia. By collating published data as well as corpus data from 32 Austronesian and Papuan languages, the study traces commonalities as well as differences in MVC use across the area. Analysis takes place on two levels: first, the morpho-syntactic behaviour of MVCs is taken into account. As this plane of analysis arguably does not provide any meaningful insights into why MVCs are construed and used the way they are, a semantic account of MVCs is presented. One of the main hypotheses advanced in this book is that the crucial driving force behind multi-verb construals is semantic interaction between the verbs, leading to four principal techniques of event formation: merging, staging, modification, and free juxtaposition. The study aims at showing that while all four techniques are, to varying degrees, in use in Eastern Indonesian languages, the morpho-syntactic output does not necessarily mirror these underlying differences in event conception. Applying insights from Davidsonian event semantics as well as from predicate decomposition, the book provides a model of event interaction that helps to explain differences in MVC behaviour such as issues in constituent order or operator assignment

    Physical mechanisms may be as important as brain mechanisms in evolution of speech [Commentary on Ackerman, Hage, & Ziegler. Brain Mechanisms of acoustic communication in humans and nonhuman primates: an evolutionary perspective]

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    We present two arguments why physical adaptations for vocalization may be as important as neural adaptations. First, fine control over vocalization is not easy for physical reasons, and modern humans may be exceptional. Second, we present an example of a gorilla that shows rudimentary voluntary control over vocalization, indicating that some neural control is already shared with great apes
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