270 research outputs found
Computational Approaches to Drug Profiling and Drug-Protein Interactions
Despite substantial increases in R&D spending within the pharmaceutical industry, denovo drug design has become a time-consuming endeavour. High attrition rates led to a
long period of stagnation in drug approvals. Due to the extreme costs associated with
introducing a drug to the market, locating and understanding the reasons for clinical failure
is key to future productivity. As part of this PhD, three main contributions were made in
this respect. First, the web platform, LigNFam enables users to interactively explore
similarity relationships between ‘drug like’ molecules and the proteins they bind. Secondly,
two deep-learning-based binding site comparison tools were developed, competing with
the state-of-the-art over benchmark datasets. The models have the ability to predict offtarget interactions and potential candidates for target-based drug repurposing. Finally, the
open-source ScaffoldGraph software was presented for the analysis of hierarchical scaffold
relationships and has already been used in multiple projects, including integration into a
virtual screening pipeline to increase the tractability of ultra-large screening experiments.
Together, and with existing tools, the contributions made will aid in the understanding of
drug-protein relationships, particularly in the fields of off-target prediction and drug
repurposing, helping to design better drugs faster
a literature review
Fonseca, J., & Bacao, F. (2023). Tabular and latent space synthetic data generation: a literature review. Journal of Big Data, 10, 1-37. [115]. https://doi.org/10.1186/s40537-023-00792-7 --- This research was supported by two research grants of the Portuguese Foundation for Science and Technology (“Fundação para a Ciência e a Tecnologia”), references SFRH/BD/151473/2021 and DSAIPA/DS/0116/2019, and by project UIDB/04152/2020 - Centro de Investigação em Gestão de Informação (MagIC).The generation of synthetic data can be used for anonymization, regularization, oversampling, semi-supervised learning, self-supervised learning, and several other tasks. Such broad potential motivated the development of new algorithms, specialized in data generation for specific data formats and Machine Learning (ML) tasks. However, one of the most common data formats used in industrial applications, tabular data, is generally overlooked; Literature analyses are scarce, state-of-the-art methods are spread across domains or ML tasks and there is little to no distinction among the main types of mechanism underlying synthetic data generation algorithms. In this paper, we analyze tabular and latent space synthetic data generation algorithms. Specifically, we propose a unified taxonomy as an extension and generalization of previous taxonomies, review 70 generation algorithms across six ML problems, distinguish the main generation mechanisms identified into six categories, describe each type of generation mechanism, discuss metrics to evaluate the quality of synthetic data and provide recommendations for future research. We expect this study to assist researchers and practitioners identify relevant gaps in the literature and design better and more informed practices with synthetic data.publishersversionpublishe
The Role of Synthetic Data in Improving Supervised Learning Methods: The Case of Land Use/Land Cover Classification
A thesis submitted in partial fulfillment of the requirements for the degree of Doctor in Information ManagementIn remote sensing, Land Use/Land Cover (LULC) maps constitute important assets for
various applications, promoting environmental sustainability and good resource management.
Although, their production continues to be a challenging task. There are various factors
that contribute towards the difficulty of generating accurate, timely updated LULC maps,
both via automatic or photo-interpreted LULC mapping. Data preprocessing, being a
crucial step for any Machine Learning task, is particularly important in the remote sensing
domain due to the overwhelming amount of raw, unlabeled data continuously gathered
from multiple remote sensing missions. However a significant part of the state-of-the-art
focuses on scenarios with full access to labeled training data with relatively balanced class
distributions. This thesis focuses on the challenges found in automatic LULC classification
tasks, specifically in data preprocessing tasks. We focus on the development of novel
Active Learning (AL) and imbalanced learning techniques, to improve ML performance in
situations with limited training data and/or the existence of rare classes. We also show
that much of the contributions presented are not only successful in remote sensing problems,
but also in various other multidisciplinary classification problems. The work presented
in this thesis used open access datasets to test the contributions made in imbalanced
learning and AL. All the data pulling, preprocessing and experiments are made available at
https://github.com/joaopfonseca/publications. The algorithmic implementations are made
available in the Python package ml-research at https://github.com/joaopfonseca/ml-research
Proceedings of the 8th Workshop on Detection and Classification of Acoustic Scenes and Events (DCASE 2023)
This volume gathers the papers presented at the Detection and Classification of Acoustic Scenes and Events 2023 Workshop (DCASE2023), Tampere, Finland, during 21–22 September 2023
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
A survey, review, and future trends of skin lesion segmentation and classification
The Computer-aided Diagnosis or Detection (CAD) approach for skin lesion analysis is an emerging field of research that has the potential to alleviate the burden and cost of skin cancer screening. Researchers have recently indicated increasing interest in developing such CAD systems, with the intention of providing a user-friendly tool to dermatologists to reduce the challenges encountered or associated with manual inspection. This article aims to provide a comprehensive literature survey and review of a total of 594 publications (356 for skin lesion segmentation and 238 for skin lesion classification) published between 2011 and 2022. These articles are analyzed and summarized in a number of different ways to contribute vital information regarding the methods for the development of CAD systems. These ways include: relevant and essential definitions and theories, input data (dataset utilization, preprocessing, augmentations, and fixing imbalance problems), method configuration (techniques, architectures, module frameworks, and losses), training tactics (hyperparameter settings), and evaluation criteria. We intend to investigate a variety of performance-enhancing approaches, including ensemble and post-processing. We also discuss these dimensions to reveal their current trends based on utilization frequencies. In addition, we highlight the primary difficulties associated with evaluating skin lesion segmentation and classification systems using minimal datasets, as well as the potential solutions to these difficulties. Findings, recommendations, and trends are disclosed to inform future research on developing an automated and robust CAD system for skin lesion analysis
Deep learning in food category recognition
Integrating artificial intelligence with food category recognition has been a field of interest for research for the
past few decades. It is potentially one of the next steps in revolutionizing human interaction with food. The
modern advent of big data and the development of data-oriented fields like deep learning have provided advancements
in food category recognition. With increasing computational power and ever-larger food datasets,
the approach’s potential has yet to be realized. This survey provides an overview of methods that can be applied
to various food category recognition tasks, including detecting type, ingredients, quality, and quantity. We
survey the core components for constructing a machine learning system for food category recognition, including
datasets, data augmentation, hand-crafted feature extraction, and machine learning algorithms. We place a
particular focus on the field of deep learning, including the utilization of convolutional neural networks, transfer
learning, and semi-supervised learning. We provide an overview of relevant studies to promote further developments
in food category recognition for research and industrial applicationsMRC (MC_PC_17171)Royal Society (RP202G0230)BHF (AA/18/3/34220)Hope Foundation for Cancer Research (RM60G0680)GCRF (P202PF11)Sino-UK Industrial
Fund (RP202G0289)LIAS (P202ED10Data Science
Enhancement Fund (P202RE237)Fight for Sight (24NN201);Sino-UK
Education Fund (OP202006)BBSRC (RM32G0178B8
One Shot Learning with class partitioning and cross validation voting (CP-CVV)
Producción CientíficaOne Shot Learning includes all those techniques that make it possible to classify images using a single image per category. One of its possible applications is the identification of food products. For a grocery store, it is interesting to record a single image of each product and be able to recognise it again from other images, such as photos taken by customers. Within deep learning, Siamese neural networks are able to verify whether two images belong to the same category or not. In this paper, a new Siamese network training technique, called CP-CVV, is presented. It uses the combination of different models trained with different classes. The separation of validation classes has been done in such a way that each of the combined models is different in order to avoid overfitting with respect to the validation. Unlike normal training, the test images belong to classes that have not previously been used in training, allowing the model to work on new categories, of which only one image exists. Different backbones have been evaluated in the Siamese composition, but also the integration of multiple models with different backbones. The results show that the model improves on previous works and allows the classification problem to be solved, an additional step towards the use of Siamese networks. To the best of our knowledge, there is no existing work that has proposed integrating Siamese neural networks using a class-based validation set separation technique so as to be better at generalising for unknown classes. Additionally, we have applied Cross-Validation-Voting with ConvNeXt to improve the existing classification results of a well-known Grocery Store Dataset.The Centre for the Development of Industrial Technology (CDTI) and by the Instituto para la Competitividad Empresarial de Castilla y León - FEDER (Project CCTT3/20/VA/0003
Towards Deep Learning with Competing Generalisation Objectives
The unreasonable effectiveness of Deep Learning continues to deliver unprecedented Artificial Intelligence capabilities to billions of people. Growing datasets and technological advances keep extending the reach of expressive model architectures trained through efficient optimisations. Thus, deep learning approaches continue to provide increasingly proficient subroutines for, among others, computer vision and natural interaction through speech and text. Due to their scalable learning and inference priors, higher performance is often gained cost-effectively through largely automatic training. As a result, new and improved capabilities empower more people while the costs of access drop.
The arising opportunities and challenges have profoundly influenced research. Quality attributes of scalable software became central desiderata of deep learning paradigms, including reusability, efficiency, robustness and safety. Ongoing research into continual, meta- and robust learning aims to maximise such scalability metrics in addition to multiple generalisation criteria, despite possible conflicts. A significant challenge is to satisfy competing criteria automatically and cost-effectively.
In this thesis, we introduce a unifying perspective on learning with competing generalisation objectives and make three additional contributions. When autonomous learning through multi-criteria optimisation is impractical, it is reasonable to ask whether knowledge of appropriate trade-offs could make it simultaneously effective and efficient. Informed by explicit trade-offs of interest to particular applications, we developed and evaluated bespoke model architecture priors. We introduced a novel architecture for sim-to-real transfer of robotic control policies by learning progressively to generalise anew. Competing desiderata of continual learning were balanced through disjoint capacity and hierarchical reuse of previously learnt representations. A new state-of-the-art meta-learning approach is then proposed. We showed that meta-trained hypernetworks efficiently store and flexibly reuse knowledge for new generalisation criteria through few-shot gradient-based optimisation. Finally, we characterised empirical trade-offs between the many desiderata of adversarial robustness and demonstrated a novel defensive capability of implicit neural networks to hinder many attacks simultaneously
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