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

Maximum Entropy Production Principle for Stock Returns

In our previous studies we have investigated the structural complexity of time series describing stock returns on New York's and Warsaw's stock exchanges, by employing two estimators of Shannon's entropy rate based on Lempel-Ziv and Context Tree Weighting algorithms, which were originally used for data compression. Such structural complexity of the time series describing logarithmic stock returns can be used as a measure of the inherent (model-free) predictability of the underlying price formation processes, testing the Efficient-Market Hypothesis in practice. We have also correlated the estimated predictability with the profitability of standard trading algorithms, and found that these do not use the structure inherent in the stock returns to any significant degree. To find a way to use the structural complexity of the stock returns for the purpose of predictions we propose the Maximum Entropy Production Principle as applied to stock returns, and test it on the two mentioned markets, inquiring into whether it is possible to enhance prediction of stock returns based on the structural complexity of these and the mentioned principle.Comment: 14 pages, 5 figure

Statistical Complexity of Simple 1D Spin Systems

We present exact results for two complementary measures of spatial structure generated by 1D spin systems with finite-range interactions. The first, excess entropy, measures the apparent spatial memory stored in configurations. The second, statistical complexity, measures the amount of memory needed to optimally predict the chain of spin values. These statistics capture distinct properties and are different from existing thermodynamic quantities.Comment: 4 pages with 2 eps Figures. Uses RevTeX macros. Also available at http://www.santafe.edu/projects/CompMech/papers/CompMechCommun.htm

The Thermodynamics of Network Coding, and an Algorithmic Refinement of the Principle of Maximum Entropy

The principle of maximum entropy (Maxent) is often used to obtain prior probability distributions as a method to obtain a Gibbs measure under some restriction giving the probability that a system will be in a certain state compared to the rest of the elements in the distribution. Because classical entropy-based Maxent collapses cases confounding all distinct degrees of randomness and pseudo-randomness, here we take into consideration the generative mechanism of the systems considered in the ensemble to separate objects that may comply with the principle under some restriction and whose entropy is maximal but may be generated recursively from those that are actually algorithmically random offering a refinement to classical Maxent. We take advantage of a causal algorithmic calculus to derive a thermodynamic-like result based on how difficult it is to reprogram a computer code. Using the distinction between computable and algorithmic randomness we quantify the cost in information loss associated with reprogramming. To illustrate this we apply the algorithmic refinement to Maxent on graphs and introduce a Maximal Algorithmic Randomness Preferential Attachment (MARPA) Algorithm, a generalisation over previous approaches. We discuss practical implications of evaluation of network randomness. Our analysis provides insight in that the reprogrammability asymmetry appears to originate from a non-monotonic relationship to algorithmic probability. Our analysis motivates further analysis of the origin and consequences of the aforementioned asymmetries, reprogrammability, and computation.Comment: 30 page