171 research outputs found
Machine learning in solar physics
The application of machine learning in solar physics has the potential to
greatly enhance our understanding of the complex processes that take place in
the atmosphere of the Sun. By using techniques such as deep learning, we are
now in the position to analyze large amounts of data from solar observations
and identify patterns and trends that may not have been apparent using
traditional methods. This can help us improve our understanding of explosive
events like solar flares, which can have a strong effect on the Earth
environment. Predicting hazardous events on Earth becomes crucial for our
technological society. Machine learning can also improve our understanding of
the inner workings of the sun itself by allowing us to go deeper into the data
and to propose more complex models to explain them. Additionally, the use of
machine learning can help to automate the analysis of solar data, reducing the
need for manual labor and increasing the efficiency of research in this field.Comment: 100 pages, 13 figures, 286 references, accepted for publication as a
Living Review in Solar Physics (LRSP
Digital agriculture: research, development and innovation in production chains.
Digital transformation in the field towards sustainable and smart agriculture. Digital agriculture: definitions and technologies. Agroenvironmental modeling and the digital transformation of agriculture. Geotechnologies in digital agriculture. Scientific computing in agriculture. Computer vision applied to agriculture. Technologies developed in precision agriculture. Information engineering: contributions to digital agriculture. DIPN: a dictionary of the internal proteins nanoenvironments and their potential for transformation into agricultural assets. Applications of bioinformatics in agriculture. Genomics applied to climate change: biotechnology for digital agriculture. Innovation ecosystem in agriculture: Embrapa?s evolution and contributions. The law related to the digitization of agriculture. Innovating communication in the age of digital agriculture. Driving forces for Brazilian agriculture in the next decade: implications for digital agriculture. Challenges, trends and opportunities in digital agriculture in Brazil
Graphonomics and your Brain on Art, Creativity and Innovation : Proceedings of the 19th International Graphonomics Conference (IGS 2019 – Your Brain on Art)
[Italiano]: “Grafonomia e cervello su arte, creatività e innovazione”.
Un forum internazionale per discutere sui recenti progressi nell'interazione tra arti creative, neuroscienze, ingegneria, comunicazione, tecnologia, industria, istruzione, design, applicazioni forensi e mediche. I contributi hanno esaminato lo stato dell'arte, identificando sfide e opportunità, e hanno delineato le possibili linee di sviluppo di questo settore di ricerca. I temi affrontati includono: strategie integrate per la comprensione dei sistemi neurali, affettivi e cognitivi in ambienti realistici e complessi; individualità e differenziazione dal punto di vista neurale e comportamentale; neuroaesthetics (uso delle neuroscienze per spiegare e comprendere le esperienze estetiche a livello neurologico); creatività e innovazione; neuro-ingegneria e arte ispirata dal cervello, creatività e uso di dispositivi di mobile brain-body imaging (MoBI) indossabili; terapia basata su arte creativa; apprendimento informale; formazione; applicazioni forensi. / [English]: “Graphonomics and your brain on art, creativity and innovation”.
A single track, international forum for discussion on recent advances at the intersection of the creative arts, neuroscience, engineering, media, technology, industry, education, design, forensics, and medicine.
The contributions reviewed the state of the art, identified challenges and opportunities and created a roadmap for the field of graphonomics and your brain on art.
The topics addressed include: integrative strategies for understanding neural, affective and cognitive systems in realistic, complex environments; neural and behavioral individuality and variation; neuroaesthetics (the use of neuroscience to explain and understand the aesthetic experiences at the neurological level); creativity and innovation; neuroengineering and brain-inspired art, creative concepts and wearable mobile brain-body imaging (MoBI) designs; creative art therapy; informal learning; education; forensics
An uncertainty prediction approach for active learning - application to earth observation
Mapping land cover and land usage dynamics are crucial in remote sensing since farmers
are encouraged to either intensify or extend crop use due to the ongoing rise in the world’s
population. A major issue in this area is interpreting and classifying a scene captured in
high-resolution satellite imagery. Several methods have been put forth, including neural
networks which generate data-dependent models (i.e. model is biased toward data) and
static rule-based approaches with thresholds which are limited in terms of diversity(i.e.
model lacks diversity in terms of rules). However, the problem of having a machine learning
model that, given a large amount of training data, can classify multiple classes over different
geographic Sentinel-2 imagery that out scales existing approaches remains open.
On the other hand, supervised machine learning has evolved into an essential part of many
areas due to the increasing number of labeled datasets. Examples include creating classifiers
for applications that recognize images and voices, anticipate traffic, propose products, act
as a virtual personal assistant and detect online fraud, among many more. Since these
classifiers are highly dependent from the training datasets, without human interaction or
accurate labels, the performance of these generated classifiers with unseen observations
is uncertain. Thus, researchers attempted to evaluate a number of independent models
using a statistical distance. However, the problem of, given a train-test split and classifiers
modeled over the train set, identifying a prediction error using the relation between train
and test sets remains open.
Moreover, while some training data is essential for supervised machine learning, what
happens if there is insufficient labeled data? After all, assigning labels to unlabeled datasets
is a time-consuming process that may need significant expert human involvement. When
there aren’t enough expert manual labels accessible for the vast amount of openly available
data, active learning becomes crucial. However, given a large amount of training and
unlabeled datasets, having an active learning model that can reduce the training cost of
the classifier and at the same time assist in labeling new data points remains an open
problem.
From the experimental approaches and findings, the main research contributions, which
concentrate on the issue of optical satellite image scene classification include: building
labeled Sentinel-2 datasets with surface reflectance values; proposal of machine learning
models for pixel-based image scene classification; proposal of a statistical distance based
Evidence Function Model (EFM) to detect ML models misclassification; and proposal of
a generalised sampling approach for active learning that, together with the EFM enables
a way of determining the most informative examples.
Firstly, using a manually annotated Sentinel-2 dataset, Machine Learning (ML) models
for scene classification were developed and their performance was compared to Sen2Cor the reference package from the European Space Agency – a micro-F1 value of 84%
was attained by the ML model, which is a significant improvement over the corresponding
Sen2Cor performance of 59%. Secondly, to quantify the misclassification of the ML models,
the Mahalanobis distance-based EFM was devised. This model achieved, for the labeled
Sentinel-2 dataset, a micro-F1 of 67.89% for misclassification detection. Lastly, EFM was
engineered as a sampling strategy for active learning leading to an approach that attains
the same level of accuracy with only 0.02% of the total training samples when compared
to a classifier trained with the full training set.
With the help of the above-mentioned research contributions, we were able to provide
an open-source Sentinel-2 image scene classification package which consists of ready-touse
Python scripts and a ML model that classifies Sentinel-2 L1C images generating a
20m-resolution RGB image with the six studied classes (Cloud, Cirrus, Shadow, Snow,
Water, and Other) giving academics a straightforward method for rapidly and effectively
classifying Sentinel-2 scene images. Additionally, an active learning approach that uses, as
sampling strategy, the observed prediction uncertainty given by EFM, will allow labeling
only the most informative points to be used as input to build classifiers; Sumário:
Uma Abordagem de Previsão de Incerteza para
Aprendizagem Ativa – Aplicação à Observação da Terra
O mapeamento da cobertura do solo e a dinâmica da utilização do solo são cruciais na
deteção remota uma vez que os agricultores são incentivados a intensificar ou estender as
culturas devido ao aumento contínuo da população mundial. Uma questão importante
nesta área é interpretar e classificar cenas capturadas em imagens de satélite de alta resolução.
Várias aproximações têm sido propostas incluindo a utilização de redes neuronais
que produzem modelos dependentes dos dados (ou seja, o modelo é tendencioso em relação
aos dados) e aproximações baseadas em regras que apresentam restrições de diversidade
(ou seja, o modelo carece de diversidade em termos de regras). No entanto, a criação de
um modelo de aprendizagem automática que, dada uma uma grande quantidade de dados
de treino, é capaz de classificar, com desempenho superior, as imagens do Sentinel-2 em
diferentes áreas geográficas permanece um problema em aberto.
Por outro lado, têm sido utilizadas técnicas de aprendizagem supervisionada na resolução
de problemas nas mais diversas áreas de devido à proliferação de conjuntos de dados etiquetados.
Exemplos disto incluem classificadores para aplicações que reconhecem imagem
e voz, antecipam tráfego, propõem produtos, atuam como assistentes pessoais virtuais e
detetam fraudes online, entre muitos outros. Uma vez que estes classificadores são fortemente
dependente do conjunto de dados de treino, sem interação humana ou etiquetas
precisas, o seu desempenho sobre novos dados é incerta. Neste sentido existem propostas
para avaliar modelos independentes usando uma distância estatística. No entanto, o problema
de, dada uma divisão de treino-teste e um classificador, identificar o erro de previsão
usando a relação entre aqueles conjuntos, permanece aberto.
Mais ainda, embora alguns dados de treino sejam essenciais para a aprendizagem supervisionada,
o que acontece quando a quantidade de dados etiquetados é insuficiente? Afinal,
atribuir etiquetas é um processo demorado e que exige perícia, o que se traduz num envolvimento
humano significativo. Quando a quantidade de dados etiquetados manualmente por
peritos é insuficiente a aprendizagem ativa torna-se crucial. No entanto, dada uma grande
quantidade dados de treino não etiquetados, ter um modelo de aprendizagem ativa que
reduz o custo de treino do classificador e, ao mesmo tempo, auxilia a etiquetagem de novas
observações permanece um problema em aberto.
A partir das abordagens e estudos experimentais, as principais contribuições deste trabalho,
que se concentra na classificação de cenas de imagens de satélite óptico incluem:
criação de conjuntos de dados Sentinel-2 etiquetados, com valores de refletância de superfície;
proposta de modelos de aprendizagem automática baseados em pixels para classificação de cenas de imagens de satétite; proposta de um Modelo de Função de Evidência (EFM)
baseado numa distância estatística para detetar erros de classificação de modelos de aprendizagem;
e proposta de uma abordagem de amostragem generalizada para aprendizagem
ativa que, em conjunto com o EFM, possibilita uma forma de determinar os exemplos mais
informativos.
Em primeiro lugar, usando um conjunto de dados Sentinel-2 etiquetado manualmente,
foram desenvolvidos modelos de Aprendizagem Automática (AA) para classificação de cenas
e seu desempenho foi comparado com o do Sen2Cor – o produto de referência da
Agência Espacial Europeia – tendo sido alcançado um valor de micro-F1 de 84% pelo classificador,
o que representa uma melhoria significativa em relação ao desempenho Sen2Cor
correspondente, de 59%. Em segundo lugar, para quantificar o erro de classificação dos
modelos de AA, foi concebido o Modelo de Função de Evidência baseado na distância de
Mahalanobis. Este modelo conseguiu, para o conjunto de dados etiquetado do Sentinel-2
um micro-F1 de 67,89% na deteção de classificação incorreta. Por fim, o EFM foi utilizado
como uma estratégia de amostragem para a aprendizagem ativa, uma abordagem
que permitiu atingir o mesmo nível de desempenho com apenas 0,02% do total de exemplos
de treino quando comparado com um classificador treinado com o conjunto de treino
completo.
Com a ajuda das contribuições acima mencionadas, foi possível desenvolver um pacote
de código aberto para classificação de cenas de imagens Sentinel-2 que, utilizando num
conjunto de scripts Python, um modelo de classificação, e uma imagem Sentinel-2 L1C,
gera a imagem RGB correspondente (com resolução de 20m) com as seis classes estudadas
(Cloud, Cirrus, Shadow, Snow, Water e Other), disponibilizando à academia um método
direto para a classificação de cenas de imagens do Sentinel-2 rápida e eficaz. Além disso, a
abordagem de aprendizagem ativa que usa, como estratégia de amostragem, a deteção de
classificacão incorreta dada pelo EFM, permite etiquetar apenas os pontos mais informativos
a serem usados como entrada na construção de classificadores
Digital agriculture: research, development and innovation in production chains.
Digital transformation in the field towards sustainable and smart agriculture. Digital agriculture: definitions and technologies. Agroenvironmental modeling and the digital transformation of agriculture. Geotechnologies in digital agriculture. Scientific computing in agriculture. Computer vision applied to agriculture. Technologies developed in precision agriculture. Information engineering: contributions to digital agriculture. DIPN: a dictionary of the internal proteins nanoenvironments and their potential for transformation into agricultural assets. Applications of bioinformatics in agriculture. Genomics applied to climate change: biotechnology for digital agriculture. Innovation ecosystem in agriculture: Embrapa?s evolution and contributions. The law related to the digitization of agriculture. Innovating communication in the age of digital agriculture. Driving forces for Brazilian agriculture in the next decade: implications for digital agriculture. Challenges, trends and opportunities in digital agriculture in Brazil.Translated by Beverly Victoria Young and Karl Stephan Mokross
Making Presentation Math Computable
This Open-Access-book addresses the issue of translating mathematical expressions from LaTeX to the syntax of Computer Algebra Systems (CAS). Over the past decades, especially in the domain of Sciences, Technology, Engineering, and Mathematics (STEM), LaTeX has become the de-facto standard to typeset mathematical formulae in publications. Since scientists are generally required to publish their work, LaTeX has become an integral part of today's publishing workflow. On the other hand, modern research increasingly relies on CAS to simplify, manipulate, compute, and visualize mathematics. However, existing LaTeX import functions in CAS are limited to simple arithmetic expressions and are, therefore, insufficient for most use cases. Consequently, the workflow of experimenting and publishing in the Sciences often includes time-consuming and error-prone manual conversions between presentational LaTeX and computational CAS formats. To address the lack of a reliable and comprehensive translation tool between LaTeX and CAS, this thesis makes the following three contributions. First, it provides an approach to semantically enhance LaTeX expressions with sufficient semantic information for translations into CAS syntaxes. Second, it demonstrates the first context-aware LaTeX to CAS translation framework LaCASt. Third, the thesis provides a novel approach to evaluate the performance for LaTeX to CAS translations on large-scaled datasets with an automatic verification of equations in digital mathematical libraries. This is an open access book
Machine Learning for Kinase Drug Discovery
Cancer is one of the major public health issues, causing several million losses every year. Although anti-cancer drugs have been developed and are globally administered, mild to severe side effects are known to occur during treatment. Computer-aided drug discovery has become a cornerstone for unveiling treatments of existing as well as emerging diseases. Computational methods aim to not only speed up the drug design process, but to also reduce time-consuming, costly experiments, as well as in vivo animal testing. In this context, over the last decade especially, deep learning began to play a prominent role in the prediction of molecular activity, property and toxicity.
However, there are still major challenges when applying deep learning models in drug discovery. Those challenges include data scarcity for physicochemical tasks, the difficulty of interpreting the prediction made by deep neural networks, and the necessity of open-source and robust workflows to ensure reproducibility and reusability.
In this thesis, after reviewing the state-of-the-art in deep learning applied to virtual screening, we address the previously mentioned challenges as follows: Regarding data scarcity in the context of deep learning applied to small molecules, we developed data augmentation techniques based on the SMILES encoding. This linear string notation enumerates the atoms present in a compound by following a path along the molecule graph. Multiplicity of SMILES for a single compound can be reached by traversing the graph using different paths. We applied the developed augmentation techniques to three different deep learning models, including convolutional and recurrent neural networks, and to four property and activity data sets. The results show that augmentation improves the model accuracy independently of the deep learning model, as well as of the data set size. Moreover, we computed the uncertainty of a model by using augmentation at inference time. In this regard, we have shown that the more confident the model is in its prediction, the smaller is the error, implying that a given prediction can be trusted and is close to the target value. The software and associated documentation allows making predictions for novel compounds and have been made freely available.
Trusting predictions blindly from algorithms may have serious consequences in areas of healthcare. In this context, better understanding how a neural network classifies a compound based on its input features is highly beneficial by helping to de-risk and optimize compounds. In this research project, we decomposed the inner layers of a deep neural network to identify the toxic substructures, the toxicophores, of a compound that led to the toxicity classification. Using molecular fingerprints —vectors that indicate the presence or absence of a particular atomic environment —we were able to map a toxicity score to each of these substructures. Moreover, we developed a method to visualize in 2D the toxicophores within a compound, the so- called cytotoxicity maps, which could be of great use to medicinal chemists in identifying ways to modify molecules to eliminate toxicity. Not only does the deep learning model reach state-of-the-art results, but the identified toxicophores confirm known toxic substructures, as well as expand new potential candidates.
In order to speed up the drug discovery process, the accessibility to robust and modular workflows is extremely advantageous. In this context, the fully open-source TeachOpenCADD project was developed. Significant tasks in both cheminformatics and bioinformatics are implemented in a pedagogical fashion, allowing the material to be used for teaching as well as the starting point for novel research. In this framework, a special pipeline is dedicated to kinases, a family of proteins which are known to be involved in diseases such as cancer. The aim is to gain insights into off-targets, i.e. proteins that are unintentionally affected by a compound, and that can cause adverse effects in treatments. Four measures of kinase similarity are implemented, taking into account sequence, and structural information, as well as protein-ligand interaction, and ligand profiling data. The workflow provides clustering of a set of kinases, which can be further analyzed to understand off-target effects of inhibitors. Results show that analyzing kinases using several perspectives is crucial for the insight into off-target prediction, and gaining a global perspective of the kinome.
These novel methods can be exploited in the discovery of new drugs, and more specifically diseases involved in the dysregulation of kinases, such as cancer
CAPTCHA Types and Breaking Techniques: Design Issues, Challenges, and Future Research Directions
The proliferation of the Internet and mobile devices has resulted in
malicious bots access to genuine resources and data. Bots may instigate
phishing, unauthorized access, denial-of-service, and spoofing attacks to
mention a few. Authentication and testing mechanisms to verify the end-users
and prohibit malicious programs from infiltrating the services and data are
strong defense systems against malicious bots. Completely Automated Public
Turing test to tell Computers and Humans Apart (CAPTCHA) is an authentication
process to confirm that the user is a human hence, access is granted. This
paper provides an in-depth survey on CAPTCHAs and focuses on two main things:
(1) a detailed discussion on various CAPTCHA types along with their advantages,
disadvantages, and design recommendations, and (2) an in-depth analysis of
different CAPTCHA breaking techniques. The survey is based on over two hundred
studies on the subject matter conducted since 2003 to date. The analysis
reinforces the need to design more attack-resistant CAPTCHAs while keeping
their usability intact. The paper also highlights the design challenges and
open issues related to CAPTCHAs. Furthermore, it also provides useful
recommendations for breaking CAPTCHAs
Aesthetic choices: Defining the range of aesthetic views in interactive digital media including games and 3D virtual environments (3D VEs)
Defining aesthetic choices for interactive digital media such as games is a challenging task. Objective and subjective factors such as colour, symmetry, order and complexity, and statistical features among others play an important role for defining the aesthetic properties of interactive digital artifacts. Computational approaches developed in this regard also consider objective factors such as statistical image features for the assessment of aesthetic qualities. However, aesthetics for interactive digital media, such as games, requires more nuanced consideration than simple objective and subjective factors, for choosing a range of aesthetic features.
From the study it was found that the there is no one single optimum position or viewpoint with a corresponding relationship to the aesthetic considerations that influence interactive digital media. Instead, the incorporation of aesthetic features demonstrates the need to consider each component within interactive digital media as part of a range of possible features, and therefore within a range of possible camera positions. A framework, named as PCAWF, emphasized that combination of features and factors demonstrated the need to define a range of aesthetic viewpoints. This is important for improved user experience. From the framework it has been found that factors including the storyline, user state, gameplay, and application type are critical to defining the reasons associated with making aesthetic choices. The selection of a range of aesthetic features and characteristics is influenced by four main factors and sub-factors associated with the main factors.
This study informs the future of interactive digital media interaction by providing clarity and reasoning behind the aesthetic decision-making inclusions that are integrated into automatically generated vision by providing a framework for choosing a range of aesthetic viewpoints in a 3D virtual environment of a game. The study identifies critical juxtapositions between photographic and cinema-based media aesthetics by incorporating qualitative rationales from experts within the interactive digital media field. This research will change the way Artificial Intelligence (AI) generated interactive digital media in the way that it chooses visual outputs in terms of camera positions, field-view, orientation, contextual considerations, and user experiences. It will impact across all automated systems to ensure that human-values, rich variations, and extensive complexity are integrated in the AI-dominated development and design of future interactive digital media production
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