Effective Complexity and its Relation to Logical Depth

Effective complexity measures the information content of the regularities of an object. It has been introduced by M. Gell-Mann and S. Lloyd to avoid some of the disadvantages of Kolmogorov complexity, also known as algorithmic information content. In this paper, we give a precise formal definition of effective complexity and rigorous proofs of its basic properties. In particular, we show that incompressible binary strings are effectively simple, and we prove the existence of strings that have effective complexity close to their lengths. Furthermore, we show that effective complexity is related to Bennett's logical depth: If the effective complexity of a string $x$ exceeds a certain explicit threshold then that string must have astronomically large depth; otherwise, the depth can be arbitrarily small.Comment: 14 pages, 2 figure

Effective complexity of stationary process realizations

The concept of effective complexity of an object as the minimal description length of its regularities has been initiated by Gell-Mann and Lloyd. The regularities are modeled by means of ensembles, that is probability distributions on finite binary strings. In our previous paper we propose a definition of effective complexity in precise terms of algorithmic information theory. Here we investigate the effective complexity of binary strings generated by stationary, in general not computable, processes. We show that under not too strong conditions long typical process realizations are effectively simple. Our results become most transparent in the context of coarse effective complexity which is a modification of the original notion of effective complexity that uses less parameters in its definition. A similar modification of the related concept of sophistication has been suggested by Antunes and Fortnow.Comment: 14 pages, no figure

Logic Meets Algebra: the Case of Regular Languages

The study of finite automata and regular languages is a privileged meeting point of algebra and logic. Since the work of Buchi, regular languages have been classified according to their descriptive complexity, i.e. the type of logical formalism required to define them. The algebraic point of view on automata is an essential complement of this classification: by providing alternative, algebraic characterizations for the classes, it often yields the only opportunity for the design of algorithms that decide expressibility in some logical fragment. We survey the existing results relating the expressibility of regular languages in logical fragments of MSO[S] with algebraic properties of their minimal automata. In particular, we show that many of the best known results in this area share the same underlying mechanics and rely on a very strong relation between logical substitutions and block-products of pseudovarieties of monoid. We also explain the impact of these connections on circuit complexity theory.Comment: 37 page

Training-free Measures Based on Algorithmic Probability Identify High Nucleosome Occupancy in DNA Sequences

We introduce and study a set of training-free methods of information-theoretic and algorithmic complexity nature applied to DNA sequences to identify their potential capabilities to determine nucleosomal binding sites. We test our measures on well-studied genomic sequences of different sizes drawn from different sources. The measures reveal the known in vivo versus in vitro predictive discrepancies and uncover their potential to pinpoint (high) nucleosome occupancy. We explore different possible signals within and beyond the nucleosome length and find that complexity indices are informative of nucleosome occupancy. We compare against the gold standard (Kaplan model) and find similar and complementary results with the main difference that our sequence complexity approach. For example, for high occupancy, complexity-based scores outperform the Kaplan model for predicting binding representing a significant advancement in predicting the highest nucleosome occupancy following a training-free approach.Comment: 8 pages main text (4 figures), 12 total with Supplementary (1 figure