BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction

A novel discrete mathematical approach is proposed as an additional tool for molecular systematics which does not require prior statistical assumptions concerning the evolutionary process. The method is based on algorithms generating mathematical representations directly from DNA/RNA or protein sequences, followed by the output of numerical (scalar or vector) and visual characteristics (graphs). The binary encoded sequence information is transformed into a compact analytical form, called the Iterative Canonical Form (or ICF) of Boolean functions, which can then be used as a generalized molecular descriptor. The method provides raw vector data for calculating different distance matrices, which in turn can be analyzed by neighbor-joining or UPGMA to derive a phylogenetic tree, or by principal coordinates analysis to get an ordination scattergram. The new method and the associated software for inferring phylogenetic trees are called the Boolean analysis or BOOL-AN

Probabilistic methods in the analysis of protein interaction networks

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Suppressors of selection

Inspired by recent works on evolutionary graph theory, an area of growing interest in mathematical and computational biology, we present the first known examples of undirected structures acting as suppressors of selection for any fitness value $r > 1$. This means that the average fixation probability of an advantageous mutant or invader individual placed at some node is strictly less than that of this individual placed in a well-mixed population. This leads the way to study more robust structures less prone to invasion, contrary to what happens with the amplifiers of selection where the fixation probability is increased on average for advantageous invader individuals. A few families of amplifiers are known, although some effort was required to prove it. Here, we use computer aided techniques to find an exact analytical expression of the fixation probability for some graphs of small order (equal to $6$, $8$ and $10$) proving that selection is effectively reduced for $r > 1$. Some numerical experiments using Monte Carlo methods are also performed for larger graphs.Comment: New title, improved presentation, and further examples. Supporting Information is also include

A System for Accessible Artificial Intelligence

While artificial intelligence (AI) has become widespread, many commercial AI systems are not yet accessible to individual researchers nor the general public due to the deep knowledge of the systems required to use them. We believe that AI has matured to the point where it should be an accessible technology for everyone. We present an ongoing project whose ultimate goal is to deliver an open source, user-friendly AI system that is specialized for machine learning analysis of complex data in the biomedical and health care domains. We discuss how genetic programming can aid in this endeavor, and highlight specific examples where genetic programming has automated machine learning analyses in previous projects.Comment: 14 pages, 5 figures, submitted to Genetic Programming Theory and Practice 2017 worksho

Evolutionary search for novel superhard materials: Methodology and applications to forms of carbon and TiO2

We have developed a method for prediction of the hardest crystal structures in a given chemical system. It is based on the evolutionary algorithm USPEX (Universal Structure Prediction: Evolutionary Xtallography) and electronegativity-based hardness model that we have augmented with bond-valence model and graph theory. These extensions enable correct description of the hardness of layered, molecular, and low-symmetry crystal structures. Applying this method to C and TiO2, we have (i) obtained a number of low-energy carbon structures with hardness slightly lower than diamond and (ii) proved that TiO2 in any of its possible polymorphs cannot be the hardest oxide, its hardness being below 17 GPa.Comment: Submitted in November 2010; revised in March 2011; resubmitted 24 June 2011; published 12 September 2011. 8 pages, 2 tables, 3 figure