scholarly journals Comments on universal and left universal grammars, context-sensitive languages, and context-free grammar forms

1978 ◽  
Vol 39 (2) ◽  
pp. 135-142 ◽  
Author(s):  
S.A. Greibach
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Witold Dyrka ◽  
Marlena Gąsior-Głogowska ◽  
Monika Szefczyk ◽  
Natalia Szulc

Abstract Background Amyloid signaling motifs are a class of protein motifs which share basic structural and functional features despite the lack of clear sequence homology. They are hard to detect in large sequence databases either with the alignment-based profile methods (due to short length and diversity) or with generic amyloid- and prion-finding tools (due to insufficient discriminative power). We propose to address the challenge with a machine learning grammatical model capable of generalizing over diverse collections of unaligned yet related motifs. Results First, we introduce and test improvements to our probabilistic context-free grammar framework for protein sequences that allow for inferring more sophisticated models achieving high sensitivity at low false positive rates. Then, we infer universal grammars for a collection of recently identified bacterial amyloid signaling motifs and demonstrate that the method is capable of generalizing by successfully searching for related motifs in fungi. The results are compared to available alternative methods. Finally, we conduct spectroscopy and staining analyses of selected peptides to verify their structural and functional relationship. Conclusions While the profile HMMs remain the method of choice for modeling homologous sets of sequences, PCFGs seem more suitable for building meta-family descriptors and extrapolating beyond the seed sample.


1975 ◽  
Vol 4 (43) ◽  
Author(s):  
Grzegorz Rozenberg ◽  
Arto Salomaa

It is shown that every context-sensitive language can be generated by a context-free grammar with graph control over sets of productions. This can be done in two different ways, corresponding to unconditional transfer programmed grammars and programmed grammars with empty failure fields. Also some results concerning ordinary programmed grammars are established.


2012 ◽  
Vol 367 (1598) ◽  
pp. 1956-1970 ◽  
Author(s):  
Gerhard Jäger ◽  
James Rogers

The first part of this article gives a brief overview of the four levels of the Chomsky hierarchy, with a special emphasis on context-free and regular languages. It then recapitulates the arguments why neither regular nor context-free grammar is sufficiently expressive to capture all phenomena in the natural language syntax. In the second part, two refinements of the Chomsky hierarchy are reviewed, which are both relevant to the extant research in cognitive science: the mildly context-sensitive languages (which are located between context-free and context-sensitive languages), and the sub-regular hierarchy (which distinguishes several levels of complexity within the class of regular languages).


2018 ◽  
Vol 47 (1) ◽  
pp. 25-44 ◽  
Author(s):  
Qingyu Gong ◽  
Jingzhu Li ◽  
Tong Liu ◽  
Na Wang

Urban designers find it virtually impossible to (re)construct self-organising urban fabric formed by a synthesis of various builders. Here we show how generic, bottom-up grammars represent historic urban fabric in a unique context, and how shape rules are embedded in the evolutionary context. This paper generalises and formalises a context-free grammar and a context-sensitive grammar to describe and design two broadly categorised (i.e. orthogonal and non-orthogonal) urban patterns. Both grammars are constructive and employ morphological parameters to govern the patterning towards a desired form. The context-free grammar describes the density and aggregation of built forms while the context-sensitive grammar represents the interactions between streets and plots. Both grammars were applied to preserve the figure-ground relationship and proved effective in designing complex urban fabric.


1982 ◽  
Vol 11 (155) ◽  
Author(s):  
Bent Bruun Kristensen ◽  
Ole Lehrmann Madsen ◽  
Birger Møller-Pedersen ◽  
Kristen Nygaard

<p>The intent of this paper is to illustrate the following general ideas:</p><p>-- Use of the context free grammar of a programming language as an integrated part of its programming system.</p><p>-- Reconsideration of the border line between language and system.</p><p>-- Systematic modularization of programs for the various translation phases.</p><p>The specific ideas presented in this paper are language independent methods for handling:</p><p>-- Modularization of programs.</p><p>-- Separate translation in the form of context sensitive parsing (type checking) of modules.</p><p>-- Protection of part of a module, e.g. protection of the representation of an abstract data type.</p><p>The mechanism for modularization is unusual as it is based on the context-free syntax of the language. A module may be a sentential form generated by any nonterminal of the grammar.</p>


2021 ◽  
Author(s):  
Witold Dyrka ◽  
Marlena Gąsior-Głogowska ◽  
Monika Szefczyk

AbstractBackgroundAmyloid signaling motifs are a class of protein motifs which share basic structural and functional features despite lack of apparent sequence homology. They are hard to detect in large sequence databases either with the alignment-based profile methods (due to short length and diversity) or with generic amyloid- and prion-finding tools (due to insufficient discriminative power). We propose to address the challenge with a machine learning grammatical model capable of generalizing over diverse collections of unaligned yet related motifs.ResultsFirst, we introduce and test improvements to our probabilistic context-free grammar framework for protein sequences that allow for inferring more sophisticated models achieving high sensitivity at low false positive rates. Then, we infer universal grammars for a collection of recently identified bacterial amyloid signaling motifs and demonstrate that the method is capable of generalizing by successfully searching for related motifs in fungi. The results are compared to available alternative methods. Finally, we conduct spectroscopy analyses of selected peptides to verify their structural and functional relationship.ConclusionsWhile the profile HMMs remain the method of choice for modeling homologous sets of sequences, PCFGs seem more suitable for building meta-family descriptors and extrapolating beyond the seed sample.


2020 ◽  
Vol 39 (6) ◽  
pp. 8463-8475
Author(s):  
Palanivel Srinivasan ◽  
Manivannan Doraipandian

Rare event detections are performed using spatial domain and frequency domain-based procedures. Omnipresent surveillance camera footages are increasing exponentially due course the time. Monitoring all the events manually is an insignificant and more time-consuming process. Therefore, an automated rare event detection contrivance is required to make this process manageable. In this work, a Context-Free Grammar (CFG) is developed for detecting rare events from a video stream and Artificial Neural Network (ANN) is used to train CFG. A set of dedicated algorithms are used to perform frame split process, edge detection, background subtraction and convert the processed data into CFG. The developed CFG is converted into nodes and edges to form a graph. The graph is given to the input layer of an ANN to classify normal and rare event classes. Graph derived from CFG using input video stream is used to train ANN Further the performance of developed Artificial Neural Network Based Context-Free Grammar – Rare Event Detection (ACFG-RED) is compared with other existing techniques and performance metrics such as accuracy, precision, sensitivity, recall, average processing time and average processing power are used for performance estimation and analyzed. Better performance metrics values have been observed for the ANN-CFG model compared with other techniques. The developed model will provide a better solution in detecting rare events using video streams.


Cybernetics ◽  
1974 ◽  
Vol 8 (3) ◽  
pp. 349-351
Author(s):  
A. A. Letichevskii

2013 ◽  
Vol 39 (1) ◽  
pp. 57-85 ◽  
Author(s):  
Alexander Fraser ◽  
Helmut Schmid ◽  
Richárd Farkas ◽  
Renjing Wang ◽  
Hinrich Schütze

We study constituent parsing of German, a morphologically rich and less-configurational language. We use a probabilistic context-free grammar treebank grammar that has been adapted to the morphologically rich properties of German by markovization and special features added to its productions. We evaluate the impact of adding lexical knowledge. Then we examine both monolingual and bilingual approaches to parse reranking. Our reranking parser is the new state of the art in constituency parsing of the TIGER Treebank. We perform an analysis, concluding with lessons learned, which apply to parsing other morphologically rich and less-configurational languages.


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