66,946 research outputs found
Machine Learning and Integrative Analysis of Biomedical Big Data.
Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues
Cortical spatio-temporal dimensionality reduction for visual grouping
The visual systems of many mammals, including humans, is able to integrate
the geometric information of visual stimuli and to perform cognitive tasks
already at the first stages of the cortical processing. This is thought to be
the result of a combination of mechanisms, which include feature extraction at
single cell level and geometric processing by means of cells connectivity. We
present a geometric model of such connectivities in the space of detected
features associated to spatio-temporal visual stimuli, and show how they can be
used to obtain low-level object segmentation. The main idea is that of defining
a spectral clustering procedure with anisotropic affinities over datasets
consisting of embeddings of the visual stimuli into higher dimensional spaces.
Neural plausibility of the proposed arguments will be discussed
Local and global gestalt laws: A neurally based spectral approach
A mathematical model of figure-ground articulation is presented, taking into
account both local and global gestalt laws. The model is compatible with the
functional architecture of the primary visual cortex (V1). Particularly the
local gestalt law of good continuity is described by means of suitable
connectivity kernels, that are derived from Lie group theory and are neurally
implemented in long range connectivity in V1. Different kernels are compatible
with the geometric structure of cortical connectivity and they are derived as
the fundamental solutions of the Fokker Planck, the Sub-Riemannian Laplacian
and the isotropic Laplacian equations. The kernels are used to construct
matrices of connectivity among the features present in a visual stimulus.
Global gestalt constraints are then introduced in terms of spectral analysis of
the connectivity matrix, showing that this processing can be cortically
implemented in V1 by mean field neural equations. This analysis performs
grouping of local features and individuates perceptual units with the highest
saliency. Numerical simulations are performed and results are obtained applying
the technique to a number of stimuli.Comment: submitted to Neural Computatio
Digital implementation of the cellular sensor-computers
Two different kinds of cellular sensor-processor architectures are used nowadays in various
applications. The first is the traditional sensor-processor architecture, where the sensor and the
processor arrays are mapped into each other. The second is the foveal architecture, in which a
small active fovea is navigating in a large sensor array. This second architecture is introduced
and compared here. Both of these architectures can be implemented with analog and digital
processor arrays. The efficiency of the different implementation types, depending on the used
CMOS technology, is analyzed. It turned out, that the finer the technology is, the better to use
digital implementation rather than analog
Point pattern analysis: an application to the loyalty networks of chain-stores
At the 41th congress of ERSA., Staufer-Steinnocher (2001) proved that kernel density estimation, a technique of spatial analysis belonging to the point pattern methods, can be usefully applied to geomarketing. Following this point of view, the aim of this paper is to show that other point pattern techniques (center-grahic statistics, global and local autocorrelation indexes, clustering methods, 'nearest neighbour index', 'Ripley's K statistic', etc.) are able to suggest important considerations in marketing researches, making explicit the "geographical knowledge" embedded in available informations. Namely this argument is demonstrated, analysing spatial distributions of big stores chained in a promotional network, finalised to improve fidelity in the consumers.
From receptive profiles to a metric model of V1
In this work we show how to construct connectivity kernels induced by the
receptive profiles of simple cells of the primary visual cortex (V1). These
kernels are directly defined by the shape of such profiles: this provides a
metric model for the functional architecture of V1, whose global geometry is
determined by the reciprocal interactions between local elements. Our
construction adapts to any bank of filters chosen to represent a set of
receptive profiles, since it does not require any structure on the
parameterization of the family. The connectivity kernel that we define carries
a geometrical structure consistent with the well-known properties of long-range
horizontal connections in V1, and it is compatible with the perceptual rules
synthesized by the concept of association field. These characteristics are
still present when the kernel is constructed from a bank of filters arising
from an unsupervised learning algorithm.Comment: 25 pages, 18 figures. Added acknowledgement
Numerical Approaches for Linear Left-invariant Diffusions on SE(2), their Comparison to Exact Solutions, and their Applications in Retinal Imaging
Left-invariant PDE-evolutions on the roto-translation group (and
their resolvent equations) have been widely studied in the fields of cortical
modeling and image analysis. They include hypo-elliptic diffusion (for contour
enhancement) proposed by Citti & Sarti, and Petitot, and they include the
direction process (for contour completion) proposed by Mumford. This paper
presents a thorough study and comparison of the many numerical approaches,
which, remarkably, is missing in the literature. Existing numerical approaches
can be classified into 3 categories: Finite difference methods, Fourier based
methods (equivalent to -Fourier methods), and stochastic methods (Monte
Carlo simulations). There are also 3 types of exact solutions to the
PDE-evolutions that were derived explicitly (in the spatial Fourier domain) in
previous works by Duits and van Almsick in 2005. Here we provide an overview of
these 3 types of exact solutions and explain how they relate to each of the 3
numerical approaches. We compute relative errors of all numerical approaches to
the exact solutions, and the Fourier based methods show us the best performance
with smallest relative errors. We also provide an improvement of Mathematica
algorithms for evaluating Mathieu-functions, crucial in implementations of the
exact solutions. Furthermore, we include an asymptotical analysis of the
singularities within the kernels and we propose a probabilistic extension of
underlying stochastic processes that overcomes the singular behavior in the
origin of time-integrated kernels. Finally, we show retinal imaging
applications of combining left-invariant PDE-evolutions with invertible
orientation scores.Comment: A final and corrected version of the manuscript is Published in
Numerical Mathematics: Theory, Methods and Applications (NM-TMA), vol. (9),
p.1-50, 201
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