1,001 research outputs found
icet - A Python library for constructing and sampling alloy cluster expansions
Alloy cluster expansions (CEs) provide an accurate and computationally
efficient mapping of the potential energy surface of multi-component systems
that enables comprehensive sampling of the many-dimensional configuration
space. Here, we introduce \textsc{icet}, a flexible, extensible, and
computationally efficient software package for the construction and sampling of
CEs. \textsc{icet} is largely written in Python for easy integration in
comprehensive workflows, including first-principles calculations for the
generation of reference data and machine learning libraries for training and
validation. The package enables training using a variety of linear regression
algorithms with and without regularization, Bayesian regression, feature
selection, and cross-validation. It also provides complementary functionality
for structure enumeration and mapping as well as data management and analysis.
Potential applications are illustrated by two examples, including the
computation of the phase diagram of a prototypical metallic alloy and the
analysis of chemical ordering in an inorganic semiconductor.Comment: 10 page
Inferring Multiple Graphical Structures
Gaussian Graphical Models provide a convenient framework for representing
dependencies between variables. Recently, this tool has received a high
interest for the discovery of biological networks. The literature focuses on
the case where a single network is inferred from a set of measurements, but, as
wetlab data is typically scarce, several assays, where the experimental
conditions affect interactions, are usually merged to infer a single network.
In this paper, we propose two approaches for estimating multiple related
graphs, by rendering the closeness assumption into an empirical prior or group
penalties. We provide quantitative results demonstrating the benefits of the
proposed approaches. The methods presented in this paper are embeded in the R
package 'simone' from version 1.0-0 and later
Towards a Multi-Subject Analysis of Neural Connectivity
Directed acyclic graphs (DAGs) and associated probability models are widely
used to model neural connectivity and communication channels. In many
experiments, data are collected from multiple subjects whose connectivities may
differ but are likely to share many features. In such circumstances it is
natural to leverage similarity between subjects to improve statistical
efficiency. The first exact algorithm for estimation of multiple related DAGs
was recently proposed by Oates et al. 2014; in this letter we present examples
and discuss implications of the methodology as applied to the analysis of fMRI
data from a multi-subject experiment. Elicitation of tuning parameters requires
care and we illustrate how this may proceed retrospectively based on technical
replicate data. In addition to joint learning of subject-specific connectivity,
we allow for heterogeneous collections of subjects and simultaneously estimate
relationships between the subjects themselves. This letter aims to highlight
the potential for exact estimation in the multi-subject setting.Comment: to appear in Neural Computation 27:1-2
Classification of Humans into Ayurvedic Prakruti Types using Computer Vision
Ayurveda, a 5000 years old Indian medical science, believes that the universe and hence humans are made up of five elements namely ether, fire, water, earth, and air. The three Doshas (Tridosha) Vata, Pitta, and Kapha originated from the combinations of these elements. Every person has a unique combination of Tridosha elements contributing to a person’s ‘Prakruti’. Prakruti governs the physiological and psychological tendencies in all living beings as well as the way they interact with the environment. This balance influences their physiological features like the texture and colour of skin, hair, eyes, length of fingers, the shape of the palm, body frame, strength of digestion and many more as well as the psychological features like their nature (introverted, extroverted, calm, excitable, intense, laidback), and their reaction to stress and diseases. All these features are coded in the constituents at the time of a person’s creation and do not change throughout their lifetime. Ayurvedic doctors analyze the Prakruti of a person either by assessing the physical features manually and/or by examining the nature of their heartbeat (pulse). Based on this analysis, they diagnose, prevent and cure the disease in patients by prescribing precision medicine.
This project focuses on identifying Prakruti of a person by analysing his facial features like hair, eyes, nose, lips and skin colour using facial recognition techniques in computer vision. This is the first of its kind research in this problem area that attempts to bring image processing into the domain of Ayurveda
Sparse Coding on Symmetric Positive Definite Manifolds using Bregman Divergences
This paper introduces sparse coding and dictionary learning for Symmetric
Positive Definite (SPD) matrices, which are often used in machine learning,
computer vision and related areas. Unlike traditional sparse coding schemes
that work in vector spaces, in this paper we discuss how SPD matrices can be
described by sparse combination of dictionary atoms, where the atoms are also
SPD matrices. We propose to seek sparse coding by embedding the space of SPD
matrices into Hilbert spaces through two types of Bregman matrix divergences.
This not only leads to an efficient way of performing sparse coding, but also
an online and iterative scheme for dictionary learning. We apply the proposed
methods to several computer vision tasks where images are represented by region
covariance matrices. Our proposed algorithms outperform state-of-the-art
methods on a wide range of classification tasks, including face recognition,
action recognition, material classification and texture categorization
Hybrid High-order Functional Connectivity Networks Using Resting-state Functional MRI for Mild Cognitive Impairment Diagnosis
Conventional functional connectivity (FC), referred to as low-order FC, estimates temporal correlation of the resting-state functional magnetic resonance imaging (rs-fMRI) time series between any pair of brain regions, simply ignoring the potentially high-level relationship among these brain regions. A high-order FC based on "correlation's correlation" has emerged as a new approach for abnormality detection of brain disease. However, separate construction of the low- and high-order FC networks overlooks information exchange between the two FC levels. Such a higher-level relationship could be more important for brain diseases study. In this paper, we propose a novel framework, namely "hybrid high-order FC networks" by exploiting the higher-level dynamic interaction among brain regions for early mild cognitive impairment (eMCI) diagnosis. For each sliding window-based rs-fMRI sub-series, we construct a whole-brain associated high-order network, by estimating the correlations between the topographical information of the high-order FC sub-network from one brain region and that of the low-order FC sub-network from another brain region. With multi-kernel learning, complementary features from multiple time-varying FC networks constructed at different levels are fused for eMCI classification. Compared with other state-of-the-art methods, the proposed framework achieves superior diagnosis accuracy, and hence could be promising for understanding pathological changes of brain connectome
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