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Understanding the three-dimensional (3D) structure of the genome is essential for elucidating vital biological processes and their links to human disease. To determine how the genome folds within the nucleus, chromosome conformation capture methods such as HiC have recently been employed. However, computational methods that exploit the resulting high-throughput, high-resolution data are still suffering from important limitations. In this work, we explore the idea of manifold learning for the 3D chromatin structure inference and present a novel method, REcurrent Autoencoders for CHromatin 3D structure prediction (REACH-3D). Our framework employs autoencoders with recurrent neural units to reconstruct the chromatin structure. In comparison to existing methods, REACH-3D makes no transfer function assumption and permits dynamic analysis. Evaluating REACH-3D on synthetic data indicated high agreement with the ground truth. When tested on real experimental HiC data, REACH-3D recovered most faithfully the expected biological properties and obtained the highest correlation coefficient with microscopy measurements. Last, REACH-3D was applied to dynamic HiC data, where it successfully modeled chromatin conformation during the cell cycle., Comment: 10 pages, 7 figures, 1 algorithm. Neural Information Processing Systems, Machine Learning for Molecules and Materials, 2018

In this paper we show that a radial oscillating bubble in a liquid behaves like a convergent acoustic lens., Comment: 5 pages

Using the formula found by Noorbala and Sepehrinia, the wave deviation in an inhomogeneous medium with continuous variation of propagation velocity is deduced. For electromagnetic waves (light) that propagate in the gravitational field, the deduced deviation is identical to that calculated from General Relativity. The method and its consequences are a good example that verifies the Noorbala-Sepehrinia's formula as well as the mecano-optics analogy (Hamilton's principle / principle of stationary action and Fermat's principle) for the bodies movement in the gravitational field., Comment: 9 pages, 1 figure

Modern stochastic optimization methods often rely on uniform sampling which is agnostic to the underlying characteristics of the data. This might degrade the convergence by yielding estimates that suffer from a high variance. A possible remedy is to employ non-uniform importance sampling techniques, which take the structure of the dataset into account. In this work, we investigate a recently proposed setting which poses variance reduction as an online optimization problem with bandit feedback. We devise a novel and efficient algorithm for this setting that finds a sequence of importance sampling distributions competitive with the best fixed distribution in hindsight, the first result of this kind. While we present our method for sampling datapoints, it naturally extends to selecting coordinates or even blocks of thereof. Empirical validations underline the benefits of our method in several settings., Comment: COLT 2018

The analysis of the secondary Bjerknes force between two bubbles suggests that this force is analogous to the electrostatic forces. The same analogy is suggested by the existence of a scattering cross section of an acoustic wave on a bubble. Our paper brings new arguments in support of this analogy. The study which we perform is dedicated to the acoustic force and to the scattering cross section at resonance in order to highlight their angular frequency independence of the inductor wave. Also, our study reveals that the angular frequency and the amplitude of the induction pressure wave are not related. Highlighting this analogy will allow us a better understanding of the electrostatic interaction if the electron is modeled as an oscillating bubble in the vacuum., Comment: 18 pages

The present paper aims to complete an earlier paper where the acoustic world was introduced. This is accomplished by analyzing the interactions which occur between the inhomogeneities of the acoustic medium, which are induced by the acoustic vibrations traveling in the medium. When a wave packet travels in a medium, the medium becomes inhomogeneous. The spherical wave packet behaves like an acoustic spherical lens for the acoustic plane waves. According to the principle of causality, there is an interaction between the wave and plane wave packet. In specific conditions the wave packet behaves as an acoustic black hole., Comment: 10 pages

In this paper we prove, by expressing the energy as a function of the wave propagation speed, it is highlighted the existence of an equivalent mass of the wave, as well as of an Einstein type relations between the energy and this mass. Also, we establish a relation between angular frequency and energy similar to that of the Planck relation. For the propagating wave, there is a de Broglie type relationship between the linear momentum and the action variable (the angular momentum), i.e. the wave linear momentum is proportional to the wave number, the proportionality coefficient being the action., Comment: 11 pages

In this paper we study the relations of Planck-Einstein-de Broglie type for the wave packets. We assume that the wave packet is a possible model of particle . When studying the behaviour of the wave packet for standing waves, in relation to an accelerated observer (i.e. Rindler observer), there can be demonstrated that the equivalent mass of the packet is the inertial mass. In our scenario, the waves and of the wave packets are depicted by the strain induced/produced in the medium. The properties of the waves, of the wave packet and, generally, of the perturbations in a material medium suggest the existence of an acoustic world. The acoustic world has mechanical and thermodynamical properties. The perturbations that are generated and propagated in the medium are correlated by means of acoustic waves with maximum speed. The observers of this world of disturbances (namely the acoustic world) have senses that are based on the perception of mechanical waves (disturbance of any kind) and apparatus for detecting and acquiring information by means of the same type of wave. Time and length measurements (and other parameters) are correlated by Lorentz type transformations, where the maximum speed is the speed of the sound waves. By applying these transformations to the packet of standing waves, there results that the energy, mass, linear momentum and the action variable/variable action undergo relativistic changes. We highlight the fact that the dynamic relativist relationship between energy and momentum is a consequence of the wave packet model for a particle. We have also emphasized the existence of certain limits for the energy of the disturbance and the corresponding action variable., Comment: 18 pages

Game theory provides a general mathematical background to study the effect of pair interactions and evolutionary rules on the macroscopic behavior of multi-player games where players with a finite number of strategies may represent a wide scale of biological objects, human individuals, or even their associations. In these systems the interactions are characterized by matrices that can be decomposed into elementary matrices (games) and classified into four types. The concept of decomposition helps the identification of potential games and also the evaluation of the potential that plays a crucial role in the determination of the preferred Nash equilibrium, and defines the Boltzmann distribution towards which these systems evolve for suitable types of dynamical rules. This survey draws parallel between the potential games and the kinetic Ising type models which are investigated for a wide scale of connectivity structures. We discuss briefly the applicability of the tools and concepts of statistical physics and thermodynamics. Additionally the general features of ordering phenomena, phase transitions and slow relaxations are outlined and applied to evolutionary games. The discussion extends to games with three or more strategies. Finally we discuss what happens when the system is weakly driven out of the "equilibrium state" by switching on non-potential components representing games of cyclic dominance., Comment: review, 77 pages, 39 figures, to be published in Phys. Rep. (2016)

Formation and competition of associations are studied in a six-species ecological model where each species has two predators and two prey. Each site of a square lattice is occupied by an individual belonging to one of the six species. The evolution of the spatial distribution of species is governed by iterated invasions between the neighboring predator-prey pairs with species specific rates and by site exchange between the neutral pairs with a probability $X$. This dynamical rule yields the formation of five associations composed of two or three species with proper spatiotemporal patterns. For large $X$ a cyclic dominance can occur between the three two-species associations whereas one of the two three-species associations prevails in the whole system for low values of $X$ in the final state. Within an intermediate range of $X$ all the five associations coexist due to the fact that cyclic invasions between the two-species associations reduce their resistance temporarily against the invasion of three-species associations., Comment: 6 pages, 8 figures

Instead of the homogeneous ordered particle distributions characteristic to equilibrium systems a self-organizing polydomain structure is found to be stable at low temperatures in a square lattice-gas model with repulsive nearest neighbor interaction when the particle jumps are biased by a uniform electric field. We have performed Monte Carlo simulations to study the domain structure varying the temperatures, fields and system sizes. Revision of the traditional picture on this system raises interesting problems as discussed., Comment: 4 pages (REVTEX) including 5 PS figures (uuencoded)