4,561 research outputs found
Inverse Design of Metamaterials for Tailored Linear and Nonlinear Optical Responses Using Deep Learning
The conventional process for developing an optimal design for nonlinear optical responses is based on a trial-and-error approach that is largely inefficient and does not necessarily lead to an ideal result. Deep learning can automate this process and widen the realm of nonlinear geometries and devices. This research illustrates a deep learning framework used to create an optimal plasmonic design for metamaterials with specific desired optical responses, both linear and nonlinear. The algorithm can produce plasmonic patterns that can maximize second-harmonic nonlinear effects of a nonlinear metamaterial. A nanolaminate metamaterial is used as a nonlinear material, and a plasmonic patterns are fabricated on the prepared nanolaminate to demonstrate the validity and efficacy of the deep learning algorithm for second-harmonic generation. Photonic upconversion from the infrared regime to the visible spectrum can occur through sum-frequency generation. The deep learning algorithm was improved to optimize a nonlinear plasmonic metamaterial for sum-frequency generation. The framework was then further expanded using transfer learning to lessen computation resources required to optimize metamaterials for new design parameters. The deep learning architecture applied in this research can be expanded to other optical responses and drive the innovation of novel optical applications.Ph.D
The present and future status of heavy neutral leptons
ArtÃculo escrito por un elevado número de autores, solo se referencian el que aparece en primer lugar, los autores pertenecientes a la UAM y el nombre del grupo de colaboración, si lo hubiereThe existence of nonzero neutrino masses points to the likely existence of multiple Standard Model neutral fermions. When such states are heavy enough that they cannot be produced in oscillations, they are referred to as heavy neutral leptons (HNLs). In this white paper, we discuss the present experimental status of HNLs including colliders, beta decay, accelerators, as well as astrophysical and cosmological impacts. We discuss the importance of continuing to search for HNLs, and its potential impact on our understanding of key fundamental questions, and additionally we outline the future prospects for next-generation future experiments or upcoming accelerator run scenario
Satellite remote sensing of surface winds, waves, and currents: Where are we now?
This review paper reports on the state-of-the-art concerning observations of surface winds, waves, and currents from space and their use for scientific research and subsequent applications. The development of observations of sea state parameters from space dates back to the 1970s, with a significant increase in the number and diversity of space missions since the 1990s. Sensors used to monitor the sea-state parameters from space are mainly based on microwave techniques. They are either specifically designed to monitor surface parameters or are used for their abilities to provide opportunistic measurements complementary to their primary purpose. The principles on which is based on the estimation of the sea surface parameters are first described, including the performance and limitations of each method. Numerous examples and references on the use of these observations for scientific and operational applications are then given. The richness and diversity of these applications are linked to the importance of knowledge of the sea state in many fields. Firstly, surface wind, waves, and currents are significant factors influencing exchanges at the air/sea interface, impacting oceanic and atmospheric boundary layers, contributing to sea level rise at the coasts, and interacting with the sea-ice formation or destruction in the polar zones. Secondly, ocean surface currents combined with wind- and wave- induced drift contribute to the transport of heat, salt, and pollutants. Waves and surface currents also impact sediment transport and erosion in coastal areas. For operational applications, observations of surface parameters are necessary on the one hand to constrain the numerical solutions of predictive models (numerical wave, oceanic, or atmospheric models), and on the other hand to validate their results. In turn, these predictive models are used to guarantee safe, efficient, and successful offshore operations, including the commercial shipping and energy sector, as well as tourism and coastal activities. Long-time series of global sea-state observations are also becoming increasingly important to analyze the impact of climate change on our environment. All these aspects are recalled in the article, relating to both historical and contemporary activities in these fields
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
Irish Ocean Climate and Ecosystem Status Report
Summary report for Irish Ocean Climate & Ecosystem Status Report also published here. This Irish Ocean Climate & Ecosystem Status
Summary for Policymakers brings together the
latest evidence of ocean change in Irish waters.
The report is intended to summarise the current
trends in atmospheric patterns, ocean warming,
sea level rise, ocean acidification, plankton and
fish distributions and abundance, and seabird
population trends. The report represents a
collaboration between marine researchers within
the Marine Institute and others based in Ireland’s
higher education institutes and public bodies. It
includes authors from Met Éireann, Maynooth
University, the University of Galway, the Atlantic
Technological University, National Parks and
Wildlife, Birdwatch Ireland, Trinity College Dublin,
University College Dublin, Inland Fisheries Ireland,
The National Water Forum, the Environmental
Protection Agency, and the Dundalk Institute of
Technology.This report is intended to summarise the
current trends in Ireland’s ocean climate. Use
has been made of archived marine data held by
a range of organisations to elucidate some of
the key trends observed in phenomena such as
atmospheric changes, ocean warming, sea level
rise, acidification, plankton and fish distributions
and abundance, and seabirds. The report aims to
summarise the key findings and recommendations
in each of these areas as a guide to climate
adaptation policy and for the public. It builds on the
previous Ocean Climate & Ecosystem Status Report
published in 2010.
The report examines the recently published
literature in each of the topic areas and combines
this in many cases with analysis of new data sets
including long-term time series to identify trends
in essential ocean variables in Irish waters. In
some cases, model projections of the likely future
state of the atmosphere and ocean are presented
under different climate emission scenarios.Marine Institut
Is attention all you need in medical image analysis? A review
Medical imaging is a key component in clinical diagnosis, treatment planning
and clinical trial design, accounting for almost 90% of all healthcare data.
CNNs achieved performance gains in medical image analysis (MIA) over the last
years. CNNs can efficiently model local pixel interactions and be trained on
small-scale MI data. The main disadvantage of typical CNN models is that they
ignore global pixel relationships within images, which limits their
generalisation ability to understand out-of-distribution data with different
'global' information. The recent progress of Artificial Intelligence gave rise
to Transformers, which can learn global relationships from data. However, full
Transformer models need to be trained on large-scale data and involve
tremendous computational complexity. Attention and Transformer compartments
(Transf/Attention) which can well maintain properties for modelling global
relationships, have been proposed as lighter alternatives of full Transformers.
Recently, there is an increasing trend to co-pollinate complementary
local-global properties from CNN and Transf/Attention architectures, which led
to a new era of hybrid models. The past years have witnessed substantial growth
in hybrid CNN-Transf/Attention models across diverse MIA problems. In this
systematic review, we survey existing hybrid CNN-Transf/Attention models,
review and unravel key architectural designs, analyse breakthroughs, and
evaluate current and future opportunities as well as challenges. We also
introduced a comprehensive analysis framework on generalisation opportunities
of scientific and clinical impact, based on which new data-driven domain
generalisation and adaptation methods can be stimulated
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
Synthetic Aperture Radar (SAR) Meets Deep Learning
This reprint focuses on the application of the combination of synthetic aperture radars and depth learning technology. It aims to further promote the development of SAR image intelligent interpretation technology. A synthetic aperture radar (SAR) is an important active microwave imaging sensor, whose all-day and all-weather working capacity give it an important place in the remote sensing community. Since the United States launched the first SAR satellite, SAR has received much attention in the remote sensing community, e.g., in geological exploration, topographic mapping, disaster forecast, and traffic monitoring. It is valuable and meaningful, therefore, to study SAR-based remote sensing applications. In recent years, deep learning represented by convolution neural networks has promoted significant progress in the computer vision community, e.g., in face recognition, the driverless field and Internet of things (IoT). Deep learning can enable computational models with multiple processing layers to learn data representations with multiple-level abstractions. This can greatly improve the performance of various applications. This reprint provides a platform for researchers to handle the above significant challenges and present their innovative and cutting-edge research results when applying deep learning to SAR in various manuscript types, e.g., articles, letters, reviews and technical reports
Robustness and Interpretability of Neural Networks’ Predictions under Adversarial Attacks
Le reti neurali profonde (DNNs) sono potenti modelli predittivi, che superano le capacità umane in una varietà di task. Imparano sistemi decisionali complessi e flessibili dai dati a disposizione e raggiungono prestazioni eccezionali in molteplici campi di apprendimento automatico, dalle applicazioni dell'intelligenza artificiale, come il riconoscimento di immagini, parole e testi, alle scienze più tradizionali, tra cui medicina, fisica e biologia. Nonostante i risultati eccezionali, le prestazioni elevate e l’alta precisione predittiva non sono sufficienti per le applicazioni nel mondo reale, specialmente in ambienti critici per la sicurezza, dove l'utilizzo dei DNNs è fortemente limitato dalla loro natura black-box. Vi è una crescente necessità di comprendere come vengono eseguite le predizioni, fornire stime di incertezza, garantire robustezza agli attacchi avversari e prevenire comportamenti indesiderati.
Anche le migliori architetture sono vulnerabili a piccole perturbazioni nei dati di input, note come attacchi avversari: manipolazioni malevole degli input che sono percettivamente indistinguibili dai campioni originali ma sono in grado di ingannare il modello in predizioni errate. In questo lavoro, dimostriamo che tale fragilità è correlata alla geometria del manifold dei dati ed è quindi probabile che sia una caratteristica intrinseca delle predizioni dei DNNs. Questa
condizione suggerisce una possibile direzione al fine di ottenere robustezza agli attacchi: studiamo la geometria degli attacchi avversari nel limite di un numero infinito di dati e di pesi per le reti neurali Bayesiane, dimostrando che, in questo limite, sono immuni agli attacchi avversari gradient-based. Inoltre, proponiamo alcune tecniche di training per migliorare la robustezza delle architetture deterministiche. In particolare, osserviamo sperimentalmente che ensembles di reti neurali addestrati su proiezioni casuali degli input originali in spazi basso-dimensionali sono più resistenti agli attacchi.
Successivamente, ci concentriamo sul problema dell'interpretabilità delle predizioni delle reti nel contesto delle saliency-based explanations. Analizziamo la stabilità delle explanations soggette ad attacchi avversari e dimostriamo che, nel limite di un numero infinito di dati e di pesi, le interpretazioni Bayesiane sono più stabili di quelle fornite dalle reti deterministiche. Confermiamo questo comportamento in modo sperimentale nel regime di un numero finito di dati.
Infine, introduciamo il concetto di attacco avversario alle sequenze di amminoacidi per protein Language Models (LM). I modelli di Deep Learning per la predizione della struttura delle proteine, come AlphaFold2, sfruttano le architetture Transformer e il loro meccanismo di attention per catturare le proprietà strutturali e funzionali delle sequenze di amminoacidi. Nonostante l'elevata precisione delle predizioni, perturbazioni biologicamente piccole delle sequenze di input, o anche mutazioni di un singolo amminoacido, possono portare a strutture 3D sostanzialmente diverse. Al contempo, i protein LMs sono insensibili alle mutazioni che inducono misfolding o disfunzione (ad esempio le missense mutations). In particolare, le predizioni delle coordinate 3D non rivelano l'effetto di unfolding indotto da queste mutazioni. Pertanto, esiste un'evidente incoerenza tra l'importanza biologica delle mutazioni e il conseguente cambiamento nella predizione strutturale. Ispirati da questo problema, introduciamo il concetto di perturbazione avversaria delle sequenze proteiche negli embedding continui dei protein LMs. Il nostro metodo utilizza i valori di attention per rilevare le posizioni degli amminoacidi più vulnerabili nelle sequenze di input. Le mutazioni avversarie sono biologicamente diverse dalle sequenze di riferimento e sono in grado di alterare in modo significativo le strutture 3D.Deep Neural Networks (DNNs) are powerful predictive models, exceeding human capabilities in a variety of tasks. They learn complex and flexible decision systems from the available data and achieve exceptional performances in multiple machine learning fields, spanning from applications in artificial intelligence, such as image, speech and text recognition, to the more traditional sciences, including medicine, physics and biology. Despite the outstanding achievements, high performance and high predictive accuracy are not sufficient for real-world applications, especially in safety-critical settings, where the usage of DNNs is severely limited by their black-box nature. There is an increasing need to understand how predictions are performed, to provide uncertainty estimates, to guarantee robustness to malicious attacks and to prevent unwanted behaviours.
State-of-the-art DNNs are vulnerable to small perturbations in the input data, known as adversarial attacks: maliciously crafted manipulations of the inputs that are perceptually indistinguishable from the original samples but are capable of fooling the model into incorrect predictions. In this work, we prove that such brittleness is related to the geometry of the data manifold and is therefore likely to be an intrinsic feature of DNNs’ predictions. This negative
condition suggests a possible direction to overcome such limitation: we study the geometry of adversarial attacks in the large-data, overparameterized limit for Bayesian Neural Networks and prove that, in this limit, they are immune to gradient-based adversarial attacks. Furthermore, we propose some training techniques to improve the adversarial robustness of deterministic architectures. In particular, we experimentally observe that ensembles of NNs trained on random projections of the original inputs into lower dimensional spaces are more resilient to the attacks.
Next, we focus on the problem of interpretability of NNs’ predictions in the setting of saliency-based explanations. We analyze the stability of the explanations under adversarial attacks on the inputs and we prove that, in the large-data and overparameterized limit, Bayesian interpretations are more stable than those provided by deterministic networks. We validate this behaviour in multiple experimental settings in the finite data regime.
Finally, we introduce the concept of adversarial perturbations of amino acid sequences for protein Language Models (LMs). Deep Learning models for protein structure prediction, such as AlphaFold2, leverage Transformer architectures and their attention mechanism to capture structural and functional properties of amino acid sequences. Despite the high accuracy of predictions, biologically small perturbations of the input sequences, or even single point mutations, can lead to substantially different 3d structures. On the other hand, protein language models are insensitive to mutations that induce misfolding or dysfunction (e.g. missense mutations). Precisely, predictions of the 3d coordinates do not reveal the structure-disruptive effect of these mutations. Therefore, there is an evident inconsistency between the biological importance of mutations and the resulting change in structural prediction. Inspired by this problem, we introduce the concept of adversarial perturbation of protein sequences in continuous embedding spaces of protein language models. Our method relies on attention scores to detect the most vulnerable amino acid positions in the input sequences. Adversarial mutations are biologically diverse from their references and are able to significantly alter the resulting 3D structures
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