Derivation of Context-free Stochastic L-Grammar Rules for Promoter Sequence Modeling Using Support Vector Machine

Formal grammars can used for describing complex repeatable structures such as DNA sequences. In this paper, we describe the structural composition of DNA sequences using a context-free stochastic L-grammar. L-grammars are a special class of parallel grammars that can model the growth of living organisms, e.g. plant development, and model the morphology of a variety of organisms. We believe that parallel grammars also can be used for modeling genetic mechanisms and sequences such as promoters. Promoters are short regulatory DNA sequences located upstream of a gene. Detection of promoters in DNA sequences is important for successful gene prediction. Promoters can be recognized by certain patterns that are conserved within a species, but there are many exceptions which makes the promoter recognition a complex problem. We replace the problem of promoter recognition by induction of context-free stochastic L-grammar rules, which are later used for the structural analysis of promoter sequences. L-grammar rules are derived automatically from the drosophila and vertebrate promoter datasets using a genetic programming technique and their fitness is evaluated using a Support Vector Machine (SVM) classifier. The artificial promoter sequences generated using the derived L- grammar rules are analyzed and compared with natural promoter sequences.

Experimental Support of Argument-based Syntactic Computation

Linguistic theory, cognitive, information, and mathematical modeling are all useful while we attempt to achieve a better understanding of the Language Faculty (LF). This cross-disciplinary approach will eventually lead to the identification of the key principles applicable in the systems of Natural Language Processing. The present work concentrates on the syntax-semantics interface. We start from recursive definitions and application of optimization principles, and gradually develop a formal model of syntactic operations. The result – a Fibonacci- like syntactic tree – is in fact an argument-based variant of the natural language syntax. This representation (argument-centered model, ACM) is derived by a recursive calculus that generates a mode which connects arguments and expresses relations between them. The reiterative operation assigns primary role to entities as the key components of syntactic structure. We provide experimental evidence in support of the argument-based model. We also show that mental computation of syntax is influenced by the inter-conceptual relations between the images of entities in a semantic space.