Simulation of Two-Way Pushdown Automata Revisited

The linear-time simulation of 2-way deterministic pushdown automata (2DPDA) by the Cook and Jones constructions is revisited. Following the semantics-based approach by Jones, an interpreter is given which, when extended with random-access memory, performs a linear-time simulation of 2DPDA. The recursive interpreter works without the dump list of the original constructions, which makes Cook's insight into linear-time simulation of exponential-time automata more intuitive and the complexity argument clearer. The simulation is then extended to 2-way nondeterministic pushdown automata (2NPDA) to provide for a cubic-time recognition of context-free languages. The time required to run the final construction depends on the degree of nondeterminism. The key mechanism that enables the polynomial-time simulations is the sharing of computations by memoization.Comment: In Proceedings Festschrift for Dave Schmidt, arXiv:1309.455

Transductions Computed by One-Dimensional Cellular Automata

Cellular automata are investigated towards their ability to compute transductions, that is, to transform inputs into outputs. The families of transductions computed are classified with regard to the time allowed to process the input and to compute the output. Since there is a particular interest in fast transductions, we mainly focus on the time complexities real time and linear time. We first investigate the computational capabilities of cellular automaton transducers by comparing them to iterative array transducers, that is, we compare parallel input/output mode to sequential input/output mode of massively parallel machines. By direct simulations, it turns out that the parallel mode is not weaker than the sequential one. Moreover, with regard to certain time complexities cellular automaton transducers are even more powerful than iterative arrays. In the second part of the paper, the model in question is compared with the sequential devices single-valued finite state transducers and deterministic pushdown transducers. It turns out that both models can be simulated by cellular automaton transducers faster than by iterative array transducers.Comment: In Proceedings AUTOMATA&JAC 2012, arXiv:1208.249

On non-recursive trade-offs between finite-turn pushdown automata

It is shown that between one-turn pushdown automata (1-turn PDAs) and deterministic finite automata (DFAs) there will be savings concerning the size of description not bounded by any recursive function, so-called non-recursive tradeoffs. Considering the number of turns of the stack height as a consumable resource of PDAs, we can show the existence of non-recursive trade-offs between PDAs performing k+ 1 turns and k turns for k >= 1. Furthermore, non-recursive trade-offs are shown between arbitrary PDAs and PDAs which perform only a finite number of turns. Finally, several decidability questions are shown to be undecidable and not semidecidable

On the descriptional complexity of iterative arrays

The descriptional complexity of iterative arrays (lAs) is studied. Iterative arrays are a parallel computational model with a sequential processing of the input. It is shown that lAs when compared to deterministic finite automata or pushdown automata may provide savings in size which are not bounded by any recursive function, so-called non-recursive trade-offs. Additional non-recursive trade-offs are proven to exist between lAs working in linear time and lAs working in real time. Furthermore, the descriptional complexity of lAs is compared with cellular automata (CAs) and non-recursive trade-offs are proven between two restricted classes. Finally, it is shown that many decidability questions for lAs are undecidable and not semidecidable

Higher-Order Operator Precedence Languages

Floyd's Operator Precedence (OP) languages are a deterministic context-free family having many desirable properties. They are locally and parallely parsable, and languages having a compatible structure are closed under Boolean operations, concatenation and star; they properly include the family of Visibly Pushdown (or Input Driven) languages. OP languages are based on three relations between any two consecutive terminal symbols, which assign syntax structure to words. We extend such relations to k-tuples of consecutive terminal symbols, by using the model of strictly locally testable regular languages of order k at least 3. The new corresponding class of Higher-order Operator Precedence languages (HOP) properly includes the OP languages, and it is still included in the deterministic (also in reverse) context free family. We prove Boolean closure for each subfamily of structurally compatible HOP languages. In each subfamily, the top language is called max-language. We show that such languages are defined by a simple cancellation rule and we prove several properties, in particular that max-languages make an infinite hierarchy ordered by parameter k. HOP languages are a candidate for replacing OP languages in the various applications where they have have been successful though sometimes too restrictive.Comment: In Proceedings AFL 2017, arXiv:1708.0622

Flexible RNA design under structure and sequence constraints using formal languages

The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical applications in biology, additional constraints must be taken into account, such as the presence/absence of regulatory motifs, either at a specific location or anywhere in the sequence. In this study, we investigate the design of RNA sequences from their targeted secondary structure, given these additional sequence constraints. To this purpose, we develop a general framework based on concepts of language theory, namely context-free grammars and finite automata. We efficiently combine a comprehensive set of constraints into a unifying context-free grammar of moderate size. From there, we use generic generic algorithms to perform a (weighted) random generation, or an exhaustive enumeration, of candidate sequences. The resulting method, whose complexity scales linearly with the length of the RNA, was implemented as a standalone program. The resulting software was embedded into a publicly available dedicated web server. The applicability demonstrated of the method on a concrete case study dedicated to Exon Splicing Enhancers, in which our approach was successfully used in the design of \emph{in vitro} experiments.Comment: ACM BCB 2013 - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (2013

Pushdown Compression

The pressing need for eficient compression schemes for XML documents has recently been focused on stack computation [6, 9], and in particular calls for a formulation of information-lossless stack or pushdown compressors that allows a formal analysis of their performance and a more ambitious use of the stack in XML compression, where so far it is mainly connected to parsing mechanisms. In this paper we introduce the model of pushdown compressor, based on pushdown transducers that compute a single injective function while keeping the widest generality regarding stack computation. The celebrated Lempel-Ziv algorithm LZ78 [10] was introduced as a general purpose compression algorithm that outperforms finite-state compressors on all sequences. We compare the performance of the Lempel-Ziv algorithm with that of the pushdown compressors, or compression algorithms that can be implemented with a pushdown transducer. This comparison is made without any a priori assumption on the data's source and considering the asymptotic compression ratio for infinite sequences. We prove that Lempel-Ziv is incomparable with pushdown compressors