62399989
Proceedings of the 8th international conference on Grammatical Inference: algorithms and applications
28066504
Multiple splicing systems and the universal computability
We propose a new extension of splicing systems, called multiple splicing systems, based on a kind of logic grammars. First, we introduce a class of Elementary formal systems, called simple H-form EFS, and show that its generative power is equivalent to the class of basic splicing systems (the original Head's splicing system) and is more adequate as representation device for formal languages. Next, we gradually extend the simple class of EFSs and get a very natural extension of splicing systems, multiple splicing systems. We show that multiple splicing systems have universal computability.
32287187
Sticker systems with complex structures
Abstract In this paper, we propose a variant of sticker systems which uses molecules with complex structures. Since the original sticker systems (Paun et al. (1998) [2, 8]) working on double strands of DNA have been studied as a formal model for self-assembly in DNA computing, we extend the sticker systems to working on more complex (higher-order) structures of DNA molecules. The advantage of sticker systems with complex structures is that augmented with weak codings we can obtain the characterization of recursively enumerable languages by using only sticking (hybridization) operations for complex molecules, while the usual sticker systems require more complicated operations such as the simultaneous use of couples of dominoes or coherent computations besides morphisms.
40461039
Learning local languages and its application to protein /spl alpha/-chain identification
Concerns an efficient algorithm for learning in the limit a special type of regular language called a locally testable language from positive data, and its application to identifying the protein /spl alpha/-chain region in amino acid sequences. First, we present a linear-time algorithm that, given a locally testable language, learns (identifies) its deterministic finite state automaton in the limit from only positive data. This provides a practical and efficient learning method for a specific domain of symbolic analysis. We then describe several experimental results using the learning algorithm. Following a theoretical observation which strongly suggests that a certain type of amino acid sequence can be expressed by a locally testable language, we apply the learning algorithm to identifying the protein /spl alpha/-chain region in amino acid sequences for hemoglobin. Experimental scores show an overall success rate of 95% correct identification for positive data and 96% for negative data.<<ETX>>
26602421
Learning Approximately Regular Languages with Reversible Languages
In this note, we consider the problem of learning approximately regular languages in the limit from positive data using the class of k-reversible languages. The class of k-reversible languages was introduced by Angluin (1982), and proved to be efficiently identifiable in the limit from positive data only. We show that Angluin's learning algorithm for the class of k-reversible languages can be readily adopted for the approximate identification of regular languages from positive data. Considering the negative result on the exact identifiability by Gold (1967), this approximation approach would be one of the best we could hope for learning the class of regular languages from positive data only.
38554897
Tree Adjoining Grammars for RNA Structure Prediction
In this paper, we are concerned with identifying a subclass of tree adjoining grammars (TAGs) that is suitable for the application to modeling and predicting RNA secondary structures. The goal of this paper is twofold: For the purpose of applying to the RNA secondary structure prediction problem, we first introduce a special subclass of TAGs and develop a fast parsing algorithm for the subclass, together with some of its language theoretic characterizations. Then, based on the algorithm, we develop a prediction system and demonstrate the effectiveness of the system by presenting some experimental results obtained from biological data, where free energy evaluation selection for parse trees is incorporated into the algorithm.
3026036
Towards a Semantic Wiki-Based Japanese Biodictionary
This paper describes an on-going project to develop and maintain a web-based Japanese Biodictionary within a Semantic Wiki environment. For the development of the dictionary, MediaWiki is extended to enable the writing of labeled links that represent RDF triples. The extension enables Semantic Wiki to provide not only collaborative environment for experts in various biol- ogy fields to create and edit the dictionary, but also the navigation support to manage relations between terms. Using a simple wiki syntax, people can de- velop and maintain the dictionary visually and easily.