Parea: multi-view ensemble clustering for cancer subtype discovery

Multi-view clustering methods are essential for the stratification of patients into sub-groups of similar molecular characteristics. In recent years, a wide range of methods has been developed for this purpose. However, due to the high diversity of cancer-related data, a single method may not perform sufficiently well in all cases. We present Parea, a multi-view hierarchical ensemble clustering approach for disease subtype discovery. We demonstrate its performance on several machine learning benchmark datasets. We apply and validate our methodology on real-world multi-view cancer patient data. Parea outperforms the current state-of-the-art on six out of seven analysed cancer types. We have integrated the Parea method into our developed Python package Pyrea (https://github.com/mdbloice/Pyrea), which enables the effortless and flexible design of ensemble workflows while incorporating a wide range of fusion and clustering algorithms

Representational Account of Memory: Insights from Aging and Synesthesia

The representational account of memory envisages perception and memory to be on a continuum rather than in discretely divided brain systems [Bussey, T. J., & Saksida, L. M. Memory, perception, and the ventral visual-perirhinal-hippocampal stream: Thinking outside of the boxes. Hippocampus, 17, 898–908, 2007]. We tested this account using a novel between-group design with young grapheme-color synesthetes, older adults, and young controls. We investigated how the disparate sensory-perceptual abilities between these groups translated into associative memory performance for visual stimuli that do not induce synesthesia. ROI analyses of the entire ventral visual stream showed that associative retrieval (a pair-associate retrieved in the absence of a visual stimulus) yielded enhanced activity in young and older adults' visual regions relative to synesthetes, whereas associative recognition (deciding whether a visual stimulus was the correct pair-associate) was characterized by enhanced activity in synesthetes' visual regions relative to older adults. Whole-brain analyses at associative retrieval revealed an effect of age in early visual cortex, with older adults showing enhanced activity relative to synesthetes and young adults. At associative recognition, the group effect was reversed: Synesthetes showed significantly enhanced activity relative to young and older adults in early visual regions. The inverted group effects observed between retrieval and recognition indicate that reduced sensitivity in visual cortex (as in aging) comes with increased activity during top–down retrieval and decreased activity during bottom–up recognition, whereas enhanced sensitivity (as in synesthesia) shows the opposite pattern. Our results provide novel evidence for the direct contribution of perceptual mechanisms to visual associative memory based on the examples of synesthesia and aging

A high-resolution 43-year atmospheric hindcast for South America generated with the MPI regional model

An evaluation of the present-day climate in South America simulated by the MPI atmospheric limited area model, REMO, is made. The model dataset was generated by dynamical downscaling from the ECMWF-ERA40 reanalysis and compared to in-situ observations. The model is able to reproduce the low-level summer monsoon circulation but it has some deficiencies in representing the South American Low-Level Jet structure. At upper levels, summer circulation features like the Bolivian High and the associated subtropical jet are well simulated by the model. Sea-level pressure fields are in general well represented by REMO. The model exhibits reasonable skill in representing the general features of the mean seasonal cycle of precipitation. Nevertheless, there is a systematic overestimation of precipitation in both tropical and subtropical regions. Differences between observed and modeled temperature are smaller than 1.5A degrees C over most of the continent, excepting during spring when those differences are quite large. Results also show that the dynamical downscaling performed using REMO introduces some enhancement of the global reanalysis especially in temperature at the tropical regions during the warm season and in precipitation in both the subtropics and extratropics. It is then concluded that REMO can be a useful tool for regional downscaling of global simulations of present and future climates

First order wetting of rough substrates and quantum unbinding

Replica and functional renormalization group methods show that, with short range substrate forces or in strong fluctuation regimes, wetting of a self-affine rough wall in 2D turns first-order as soon as the wall roughness exponent exceeds the anisotropy index of bulk interface fluctuations. Different thresholds apply with long range forces in mean field regimes. For bond-disordered bulk, fixed point stability suggests similar results, which ultimately rely on basic properties of quantum bound states with asymptotically power-law repulsive potentials.Comment: 11 pages, 1 figur

He Scattering from Random Adsorbates, Disordered Compact Islands and Fractal Submonolayers: Intensity Manifestations of Surface Disorder

A theoretical study is made on He scattering from three fundamental classes of disordered ad-layers: (a) Translationally random adsorbates, (b) disordered compact islands and (c) fractal submonolayers. The implications of the results to experimental studies of He scattering from disordered surfaces are discussed, and a combined experimental-theoretical study is made for Ag submonolayers on Pt(111). Some of the main theoretical findings are: (1) Structural aspects of the calculated intensities from translationally random clusters were found to be strongly correlated with those of individual clusters. (2) Low intensity Bragg interference peaks appear even for scattering from very small ad-islands, and contain information on the ad-island local electron structure. (3) For fractal islands, just as for islands with a different structure, the off-specular intensity depends on the parameters of the He/Ag interaction, and does not follow a universal power law as previously proposed in the literature. In the experimental-theoretical study of Ag on Pt(111), we use first experimental He scattering data from low-coverage (single adsorbate) systems to determine an empirical He/Ag-Pt potential of good quality. Then, we carry out He scattering calculations for high coverage and compare with experiments. The conclusions are that the actual experimental phase corresponds to small compact Ag clusters of narrow size distribution, translationally disordered on the surface.Comment: 36 double-spaced pages, 10 figures; accepted by J. Chem. Phys., scheduled to appear March 8. More info available at http://www.fh.huji.ac.il/~dani

Correlation length by measuring empty space in simulated aggregates

We examine the geometry of the spaces between particles in diffusion-limited cluster aggregation, a numerical model of aggregating suspensions. Computing the distribution of distances from each point to the nearest particle, we show that it has a scaled form independent of the concentration phi, for both two- (2D) and three-dimensional (3D) model gels at low phi. The mean remoteness is proportional to the density-density correlation length of the gel, xi, allowing a more precise measurement of xi than by other methods. A simple analytical form for the scaled remoteness distribution is developed, highlighting the geometrical information content of the data. We show that the second moment of the distribution gives a useful estimate of the permeability of porous media.Comment: 4 page

A Theory of Cheap Control in Embodied Systems

We present a framework for designing cheap control architectures for embodied agents. Our derivation is guided by the classical problem of universal approximation, whereby we explore the possibility of exploiting the agent's embodiment for a new and more efficient universal approximation of behaviors generated by sensorimotor control. This embodied universal approximation is compared with the classical non-embodied universal approximation. To exemplify our approach, we present a detailed quantitative case study for policy models defined in terms of conditional restricted Boltzmann machines. In contrast to non-embodied universal approximation, which requires an exponential number of parameters, in the embodied setting we are able to generate all possible behaviors with a drastically smaller model, thus obtaining cheap universal approximation. We test and corroborate the theory experimentally with a six-legged walking machine. The experiments show that the sufficient controller complexity predicted by our theory is tight, which means that the theory has direct practical implications. Keywords: cheap design, embodiment, sensorimotor loop, universal approximation, conditional restricted Boltzmann machineComment: 27 pages, 10 figure