A formal-linguistic approach for solving an entertaining task is offered in this paper. The well-known task of the Hanoi towers is discussed in relation to some concepts of formal languages and grammars. A context-fre...A formal-linguistic approach for solving an entertaining task is offered in this paper. The well-known task of the Hanoi towers is discussed in relation to some concepts of formal languages and grammars. A context-free grammar which generates an algorithm for solving this task is described. A deterministic pushdown automation which in its work imitates the work of monks in solving the task of the Hanoi towers is built.展开更多
We consider context-free grammars of the form G = {f → f^b1＋b2＋1g^a1＋a2, g → f^b1 g^a1＋1},where ai and bi are integers sub ject to certain positivity conditions. Such a grammar G gives rise to triangular arrays...We consider context-free grammars of the form G = {f → f^b1＋b2＋1g^a1＋a2, g → f^b1 g^a1＋1},where ai and bi are integers sub ject to certain positivity conditions. Such a grammar G gives rise to triangular arrays {T（n, k）}0≤k≤n satisfying a three-term recurrence relation. Many combinatorial sequences can be generated in this way. Let Tn （x） =∑k=0^n T（n, k）x^k. Based on the differential operator with respect to G, we define a sequence of linear operators Pn such that Tn＋1（x） = Pn（Tn（x））. Applying the characterization of real stability preserving linear operators on the multivariate polynomials due to Borcea and Br？ndén, we obtain a necessary and sufficient condition for the operator Pn to be real stability preserving for any n. As a consequence, we are led to a sufficient condition for the real-rootedness of the polynomials defined by certain triangular arrays, obtained by Wang and Yeh.Moreover, as special cases we obtain grammars that lead to identities involving the Whitney numbers and the Bessel numbers.展开更多
Stochastic context-free grammars （SCFGs） have been applied to predicting RNA secondary structure. The prediction of RNA secondary structure can be facilitated by incorporating with comparative sequence analysis. How...Stochastic context-free grammars （SCFGs） have been applied to predicting RNA secondary structure. The prediction of RNA secondary structure can be facilitated by incorporating with comparative sequence analysis. However, most of existing SCFG-based methods lack explicit phylogenic analysis of homologous RNA sequences, which is probably the reason why these methods are not ideal in practical application. Hence, we present a new SCFG-based method by integrating phylogenic analysis with the newly defined profile SCFG. The method can be summarized as： 1） we define a new profile SCFG, M, to depict consensus secondary structure of multiple RNA sequence alignment; 2） we introduce two distinct hidden Markov models, λ and λ＇, to perform phylogenic analysis of homologous RNA sequences. Here, λ＇ is for non-structural regions of the sequence and λ＇ is for structural regions of the sequence; 3） we merge λ and λ＇ into M to devise a combined model for prediction of RNA secondary structure. We tested our method on data sets constructed from the Rfam database. The sensitivity and specificity of our method are more accurate than those of the predictions by Pfold.展开更多
文摘A formal-linguistic approach for solving an entertaining task is offered in this paper. The well-known task of the Hanoi towers is discussed in relation to some concepts of formal languages and grammars. A context-free grammar which generates an algorithm for solving this task is described. A deterministic pushdown automation which in its work imitates the work of monks in solving the task of the Hanoi towers is built.
基金Supported by the 973 Projectthe PCSIRT Project+1 种基金the Doctoral Program Fund of the Ministry of Educationthe National Science Foundation of China
文摘We consider context-free grammars of the form G = {f → f^b1＋b2＋1g^a1＋a2, g → f^b1 g^a1＋1},where ai and bi are integers sub ject to certain positivity conditions. Such a grammar G gives rise to triangular arrays {T（n, k）}0≤k≤n satisfying a three-term recurrence relation. Many combinatorial sequences can be generated in this way. Let Tn （x） =∑k=0^n T（n, k）x^k. Based on the differential operator with respect to G, we define a sequence of linear operators Pn such that Tn＋1（x） = Pn（Tn（x））. Applying the characterization of real stability preserving linear operators on the multivariate polynomials due to Borcea and Br？ndén, we obtain a necessary and sufficient condition for the operator Pn to be real stability preserving for any n. As a consequence, we are led to a sufficient condition for the real-rootedness of the polynomials defined by certain triangular arrays, obtained by Wang and Yeh.Moreover, as special cases we obtain grammars that lead to identities involving the Whitney numbers and the Bessel numbers.
基金the National Natural Science Foundation of China under Grant No.60673018
文摘Stochastic context-free grammars （SCFGs） have been applied to predicting RNA secondary structure. The prediction of RNA secondary structure can be facilitated by incorporating with comparative sequence analysis. However, most of existing SCFG-based methods lack explicit phylogenic analysis of homologous RNA sequences, which is probably the reason why these methods are not ideal in practical application. Hence, we present a new SCFG-based method by integrating phylogenic analysis with the newly defined profile SCFG. The method can be summarized as： 1） we define a new profile SCFG, M, to depict consensus secondary structure of multiple RNA sequence alignment; 2） we introduce two distinct hidden Markov models, λ and λ＇, to perform phylogenic analysis of homologous RNA sequences. Here, λ＇ is for non-structural regions of the sequence and λ＇ is for structural regions of the sequence; 3） we merge λ and λ＇ into M to devise a combined model for prediction of RNA secondary structure. We tested our method on data sets constructed from the Rfam database. The sensitivity and specificity of our method are more accurate than those of the predictions by Pfold.
