4,318 research outputs found
UMSL Bulletin 2023-2024
The 2023-2024 Bulletin and Course Catalog for the University of Missouri St. Louis.https://irl.umsl.edu/bulletin/1088/thumbnail.jp
Beam scanning by liquid-crystal biasing in a modified SIW structure
A fixed-frequency beam-scanning 1D antenna based on Liquid Crystals (LCs) is designed for application in 2D scanning with lateral alignment. The 2D array environment imposes full decoupling of adjacent 1D antennas, which often conflicts with the LC requirement of DC biasing: the proposed design accommodates both. The LC medium is placed inside a Substrate Integrated Waveguide (SIW) modified to work as a Groove Gap Waveguide, with radiating slots etched on the upper broad wall, that radiates as a Leaky-Wave Antenna (LWA). This allows effective application of the DC bias voltage needed for tuning the LCs. At the same time, the RF field remains laterally confined, enabling the possibility to lay several antennas in parallel and achieve 2D beam scanning. The design is validated by simulation employing the actual properties of a commercial LC medium
Using machine learning to predict pathogenicity of genomic variants throughout the human genome
Geschätzt mehr als 6.000 Erkrankungen werden durch Veränderungen im Genom verursacht. Ursachen gibt es viele: Eine genomische Variante kann die Translation eines Proteins stoppen, die Genregulation stören oder das Spleißen der mRNA in eine andere Isoform begünstigen. All diese Prozesse müssen überprüft werden, um die zum beschriebenen Phänotyp passende Variante zu ermitteln. Eine Automatisierung dieses Prozesses sind Varianteneffektmodelle. Mittels maschinellem Lernen und Annotationen aus verschiedenen Quellen bewerten diese Modelle genomische Varianten hinsichtlich ihrer Pathogenität.
Die Entwicklung eines Varianteneffektmodells erfordert eine Reihe von Schritten: Annotation der Trainingsdaten, Auswahl von Features, Training verschiedener Modelle und Selektion eines Modells. Hier präsentiere ich ein allgemeines Workflow dieses Prozesses. Dieses ermöglicht es den Prozess zu konfigurieren, Modellmerkmale zu bearbeiten, und verschiedene Annotationen zu testen. Der Workflow umfasst außerdem die Optimierung von Hyperparametern, Validierung und letztlich die Anwendung des Modells durch genomweites Berechnen von Varianten-Scores.
Der Workflow wird in der Entwicklung von Combined Annotation Dependent Depletion (CADD), einem Varianteneffektmodell zur genomweiten Bewertung von SNVs und InDels, verwendet. Durch Etablierung des ersten Varianteneffektmodells für das humane Referenzgenome GRCh38 demonstriere ich die gewonnenen Möglichkeiten Annotationen aufzugreifen und neue Modelle zu trainieren. Außerdem zeige ich, wie Deep-Learning-Scores als Feature in einem CADD-Modell die Vorhersage von RNA-Spleißing verbessern. Außerdem werden Varianteneffektmodelle aufgrund eines neuen, auf Allelhäufigkeit basierten, Trainingsdatensatz entwickelt.
Diese Ergebnisse zeigen, dass der entwickelte Workflow eine skalierbare und flexible Möglichkeit ist, um Varianteneffektmodelle zu entwickeln. Alle entstandenen Scores sind unter cadd.gs.washington.edu und cadd.bihealth.org frei verfügbar.More than 6,000 diseases are estimated to be caused by genomic variants. This can happen in many possible ways: a variant may stop the translation of a protein, interfere with gene regulation, or alter splicing of the transcribed mRNA into an unwanted isoform. It is necessary to investigate all of these processes in order to evaluate which variant may be causal for the deleterious phenotype. A great help in this regard are variant effect scores. Implemented as machine learning classifiers, they integrate annotations from different resources to rank genomic variants in terms of pathogenicity.
Developing a variant effect score requires multiple steps: annotation of the training data, feature selection, model training, benchmarking, and finally deployment for the model's application. Here, I present a generalized workflow of this process. It makes it simple to configure how information is converted into model features, enabling the rapid exploration of different annotations. The workflow further implements hyperparameter optimization, model validation and ultimately deployment of a selected model via genome-wide scoring of genomic variants.
The workflow is applied to train Combined Annotation Dependent Depletion (CADD), a variant effect model that is scoring SNVs and InDels genome-wide. I show that the workflow can be quickly adapted to novel annotations by porting CADD to the genome reference GRCh38. Further, I demonstrate the integration of deep-neural network scores as features into a new CADD model, improving the annotation of RNA splicing events. Finally, I apply the workflow to train multiple variant effect models from training data that is based on variants selected by allele frequency.
In conclusion, the developed workflow presents a flexible and scalable method to train variant effect scores. All software and developed scores are freely available from cadd.gs.washington.edu and cadd.bihealth.org
Introduction to Facial Micro Expressions Analysis Using Color and Depth Images: A Matlab Coding Approach (Second Edition, 2023)
The book attempts to introduce a gentle introduction to the field of Facial
Micro Expressions Recognition (FMER) using Color and Depth images, with the aid
of MATLAB programming environment. FMER is a subset of image processing and it
is a multidisciplinary topic to analysis. So, it requires familiarity with
other topics of Artifactual Intelligence (AI) such as machine learning, digital
image processing, psychology and more. So, it is a great opportunity to write a
book which covers all of these topics for beginner to professional readers in
the field of AI and even without having background of AI. Our goal is to
provide a standalone introduction in the field of MFER analysis in the form of
theorical descriptions for readers with no background in image processing with
reproducible Matlab practical examples. Also, we describe any basic definitions
for FMER analysis and MATLAB library which is used in the text, that helps
final reader to apply the experiments in the real-world applications. We
believe that this book is suitable for students, researchers, and professionals
alike, who need to develop practical skills, along with a basic understanding
of the field. We expect that, after reading this book, the reader feels
comfortable with different key stages such as color and depth image processing,
color and depth image representation, classification, machine learning, facial
micro-expressions recognition, feature extraction and dimensionality reduction.
The book attempts to introduce a gentle introduction to the field of Facial
Micro Expressions Recognition (FMER) using Color and Depth images, with the aid
of MATLAB programming environment.Comment: This is the second edition of the boo
Sensing User's Activity, Channel, and Location with Near-Field Extra-Large-Scale MIMO
This paper proposes a grant-free massive access scheme based on the
millimeter wave (mmWave) extra-large-scale multiple-input multiple-output
(XL-MIMO) to support massive Internet-of-Things (IoT) devices with low latency,
high data rate, and high localization accuracy in the upcoming sixth-generation
(6G) networks. The XL-MIMO consists of multiple antenna subarrays that are
widely spaced over the service area to ensure line-of-sight (LoS)
transmissions. First, we establish the XL-MIMO-based massive access model
considering the near-field spatial non-stationary (SNS) property. Then, by
exploiting the block sparsity of subarrays and the SNS property, we propose a
structured block orthogonal matching pursuit algorithm for efficient active
user detection (AUD) and channel estimation (CE). Furthermore, different
sensing matrices are applied in different pilot subcarriers for exploiting the
diversity gains. Additionally, a multi-subarray collaborative localization
algorithm is designed for localization. In particular, the angle of arrival
(AoA) and time difference of arrival (TDoA) of the LoS links between active
users and related subarrays are extracted from the estimated XL-MIMO channels,
and then the coordinates of active users are acquired by jointly utilizing the
AoAs and TDoAs. Simulation results show that the proposed algorithms outperform
existing algorithms in terms of AUD and CE performance and can achieve
centimeter-level localization accuracy.Comment: Submitted to IEEE Transactions on Communications, Major revision.
Codes will be open to all on https://gaozhen16.github.io/ soo
Computational Geometry Contributions Applied to Additive Manufacturing
This Doctoral Thesis develops novel articulations of Computation Geometry for applications on Additive Manufacturing, as follows:
(1) Shape Optimization in Lattice Structures. Implementation and sensitivity analysis of the SIMP (Solid Isotropic Material with Penalization) topology optimization strategy. Implementation of a method to transform density maps, resulting from topology optimization, into surface lattice structures. Procedure to integrate material homogenization and Design of Experiments (DOE) to estimate the stress/strain response of large surface lattice domains.
(2) Simulation of Laser Metal Deposition. Finite Element Method implementation of a 2D nonlinear thermal model of the Laser Metal Deposition (LMD) process considering temperaturedependent material properties, phase change and radiation. Finite Element Method implementation of a 2D linear transient thermal model for a metal substrate that is heated by the action of a laser.
(3) Process Planning for Laser Metal Deposition. Implementation of a 2.5D path planning method for Laser Metal Deposition. Conceptualization of a workflow for the synthesis of the Reeb Graph for a solid region in â„ť" denoted by its Boundary Representation (B-Rep). Implementation of a voxel-based geometric simulator for LMD process. Conceptualization, implementation, and validation of a tool for the minimization of the material over-deposition at corners in LMD. Implementation of a 3D (non-planar) slicing and path planning method for the LMD-manufacturing of overhanging features in revolute workpieces.
The aforementioned contributions have been screened by the international scientific community via Journal and Conference submissions and publications
Modelling, Monitoring, Control and Optimization for Complex Industrial Processes
This reprint includes 22 research papers and an editorial, collected from the Special Issue "Modelling, Monitoring, Control and Optimization for Complex Industrial Processes", highlighting recent research advances and emerging research directions in complex industrial processes. This reprint aims to promote the research field and benefit the readers from both academic communities and industrial sectors
Exploring QCD matter in extreme conditions with Machine Learning
In recent years, machine learning has emerged as a powerful computational
tool and novel problem-solving perspective for physics, offering new avenues
for studying strongly interacting QCD matter properties under extreme
conditions. This review article aims to provide an overview of the current
state of this intersection of fields, focusing on the application of machine
learning to theoretical studies in high energy nuclear physics. It covers
diverse aspects, including heavy ion collisions, lattice field theory, and
neutron stars, and discuss how machine learning can be used to explore and
facilitate the physics goals of understanding QCD matter. The review also
provides a commonality overview from a methodology perspective, from
data-driven perspective to physics-driven perspective. We conclude by
discussing the challenges and future prospects of machine learning applications
in high energy nuclear physics, also underscoring the importance of
incorporating physics priors into the purely data-driven learning toolbox. This
review highlights the critical role of machine learning as a valuable
computational paradigm for advancing physics exploration in high energy nuclear
physics.Comment: 146 pages,53 figure
Reformulating aircraft routing algorithms to reduce fuel burn and thus CO2 emissions
During the UN Climate Change Conference (COP26), in November 2021, the international
aviation community agreed to advance actions to reduce CO2 emissions. Adopting more
fuel efficient routes, now that full global satellite coverage is available, could achieve this
quickly and economically. Here flights between New York and London, from 1st December, 2019 to 29th February, 2020 are considered. Trajectories through wind fields from a
global atmospheric re-analysis dataset are found using optimal control theory. Initially,
time minimal routes are obtained by applying Pontryagin’s Minimum Principle. Minimum
time air distances are compared with actual Air Traffic Management tracks. Potential air
distance savings range from 0.7 to 16.4%, depending on direction and track efficiency.
To gauge the potential for longer duration time minimal round trips in the future, due
to climate change, trajectories are considered for historic and future time periods, using
an ensemble of climate models. Next, fixed-time, fuel-minimal routes are sought. Fuel
consumption is modelled with a new physics-driven fuel burn function, which is aircraft
model specific. Control variables of position-dependent aircraft headings and airspeeds or
just headings are used. The importance of airspeed in finding trajectories is established,
by comparing fuel burn found from a global search of optimised results for the discretised approximation of each formulation. Finally, dynamic programming is applied to find
free-time, fuel-optimal routes. Results show that significant fuel reductions are possible,
compared with estimates of fuel use from actual flights, without significant changes to
flight duration. Fuel use for winter 2019–2020 could have been reduced by 4.6% eastbound and 3.9% westbound on flights between Heathrow and John F Kennedy Airports.
This equates to a 16.6 million kg reduction in CO2 emissions. Thus large reductions in
fuel consumption and emissions are possible immediately, without waiting decades for
incremental improvements in fuel-efficiency through technological advances
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