155,860 research outputs found
Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires
The adaptive immune system recognizes antigens via an immense array of
antigen-binding antibodies and T-cell receptors, the immune repertoire. The
interrogation of immune repertoires is of high relevance for understanding the
adaptive immune response in disease and infection (e.g., autoimmunity, cancer,
HIV). Adaptive immune receptor repertoire sequencing (AIRR-seq) has driven the
quantitative and molecular-level profiling of immune repertoires thereby
revealing the high-dimensional complexity of the immune receptor sequence
landscape. Several methods for the computational and statistical analysis of
large-scale AIRR-seq data have been developed to resolve immune repertoire
complexity in order to understand the dynamics of adaptive immunity. Here, we
review the current research on (i) diversity, (ii) clustering and network,
(iii) phylogenetic and (iv) machine learning methods applied to dissect,
quantify and compare the architecture, evolution, and specificity of immune
repertoires. We summarize outstanding questions in computational immunology and
propose future directions for systems immunology towards coupling AIRR-seq with
the computational discovery of immunotherapeutics, vaccines, and
immunodiagnostics.Comment: 27 pages, 2 figure
Observer-biased bearing condition monitoring: from fault detection to multi-fault classification
Bearings are simultaneously a fundamental component and one of the principal causes of failure in rotary machinery. The work focuses on the employment of fuzzy clustering for bearing condition monitoring, i.e., fault detection and classification. The output of a clustering algorithm is a data partition (a set of clusters) which is merely a hypothesis on the structure of the data. This hypothesis requires validation by domain experts. In general, clustering algorithms allow a limited usage of domain knowledge on the cluster formation process. In this study, a novel method allowing for interactive clustering in bearing fault diagnosis is proposed. The method resorts to shrinkage to generalize an otherwise unbiased clustering algorithm into a biased one. In this way, the method provides a natural and intuitive way to control the cluster formation process, allowing for the employment of domain knowledge to guiding it. The domain expert can select a desirable level of granularity ranging from fault detection to classification of a variable number of faults and can select a specific region of the feature space for detailed analysis. Moreover, experimental results under realistic conditions show that the adopted algorithm outperforms the corresponding unbiased algorithm (fuzzy c-means) which is being widely used in this type of problems. (C) 2016 Elsevier Ltd. All rights reserved.Grant number: 145602
A Collection of Challenging Optimization Problems in Science, Engineering and Economics
Function optimization and finding simultaneous solutions of a system of
nonlinear equations (SNE) are two closely related and important optimization
problems. However, unlike in the case of function optimization in which one is
required to find the global minimum and sometimes local minima, a database of
challenging SNEs where one is required to find stationary points (extrama and
saddle points) is not readily available. In this article, we initiate building
such a database of important SNE (which also includes related function
optimization problems), arising from Science, Engineering and Economics. After
providing a short review of the most commonly used mathematical and
computational approaches to find solutions of such systems, we provide a
preliminary list of challenging problems by writing the Mathematical
formulation down, briefly explaning the origin and importance of the problem
and giving a short account on the currently known results, for each of the
problems. We anticipate that this database will not only help benchmarking
novel numerical methods for solving SNEs and function optimization problems but
also will help advancing the corresponding research areas.Comment: Accepted as an invited contribution to the special session on
Evolutionary Computation for Nonlinear Equation Systems at the 2015 IEEE
Congress on Evolutionary Computation (at Sendai International Center, Sendai,
Japan, from 25th to 28th May, 2015.
Delay Parameter Selection in Permutation Entropy Using Topological Data Analysis
Permutation Entropy (PE) is a powerful tool for quantifying the
predictability of a sequence which includes measuring the regularity of a time
series. Despite its successful application in a variety of scientific domains,
PE requires a judicious choice of the delay parameter . While another
parameter of interest in PE is the motif dimension , Typically is
selected between and with or giving optimal results for the
majority of systems. Therefore, in this work we focus solely on choosing the
delay parameter. Selecting is often accomplished using trial and error
guided by the expertise of domain scientists. However, in this paper, we show
that persistent homology, the flag ship tool from Topological Data Analysis
(TDA) toolset, provides an approach for the automatic selection of . We
evaluate the successful identification of a suitable from our TDA-based
approach by comparing our results to a variety of examples in published
literature
3D printing of optical materials: an investigation of the microscopic properties
3D printing technologies are currently enabling the fabrication of objects
with complex architectures and tailored properties. In such framework, the
production of 3D optical structures, which are typically based on optical
transparent matrices, optionally doped with active molecular compounds and
nanoparticles, is still limited by the poor uniformity of the printed
structures. Both bulk inhomogeneities and surface roughness of the printed
structures can negatively affect the propagation of light in 3D printed optical
components. Here we investigate photopolymerization-based printing processes by
laser confocal microscopy. The experimental method we developed allows the
printing process to be investigated in-situ, with microscale spatial
resolution, and in real-time. The modelling of the photo-polymerization
kinetics allows the different polymerization regimes to be investigated and the
influence of process variables to be rationalized. In addition, the origin of
the factors limiting light propagation in printed materials are rationalized,
with the aim of envisaging effective experimental strategies to improve optical
properties of printed materials.Comment: 8 pages, 3 figure
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