Infinite string block matching features for DNA classification

Author(s):  
Daniel Ashlock ◽  
Sierra Gillis ◽  
Wendy Ashlock
2021 ◽  
Vol 13 (1) ◽  
pp. 1-25
Author(s):  
Dmitry Itsykson ◽  
Alexander Okhotin ◽  
Vsevolod Oparin

The partial string avoidability problem is stated as follows: given a finite set of strings with possible “holes” (wildcard symbols), determine whether there exists a two-sided infinite string containing no substrings from this set, assuming that a hole matches every symbol. The problem is known to be NP-hard and in PSPACE, and this article establishes its PSPACE-completeness. Next, string avoidability over the binary alphabet is interpreted as a version of conjunctive normal form satisfiability problem, where each clause has infinitely many shifted variants. Non-satisfiability of these formulas can be proved using variants of classical propositional proof systems, augmented with derivation rules for shifting proof lines (such as clauses, inequalities, polynomials, etc.). First, it is proved that there is a particular formula that has a short refutation in Resolution with a shift rule but requires classical proofs of exponential size. At the same time, it is shown that exponential lower bounds for classical proof systems can be translated for their shifted versions. Finally, it is shown that superpolynomial lower bounds on the size of shifted proofs would separate NP from PSPACE; a connection to lower bounds on circuit complexity is also established.


Sign in / Sign up

Export Citation Format

Share Document