arXiv subjects

Arlindo L. Oliveira

Publications and source records attributed to Arlindo L. Oliveira.

33 records · Page 2Linked to original sources

arXiv2024

QUBIQ: Uncertainty Quantification for Biomedical Image Segmentation Challenge

Uncertainty in medical image segmentation tasks, especially inter-rater variability, arising from differences in interpretations and annotations by various experts, presents a significant challenge in achieving consistent and reliable image segmentation. This variability not only reflects the inherent complexity and subjective nature of medical image interpretation but also directly impacts the development and evaluation of automated segmentation algorithms. Accurately modeling and quantifying this variability is essential for enhancing the robustness and clinical applicability of these algorithms. We report the set-up and summarize the benchmark results of the Quantification of Uncertainties in Biomedical Image Quantification Challenge (QUBIQ), which was organized in conjunction with International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2020 and 2021. The challenge focuses on the uncertainty quantification of medical image segmentation which considers the omnipresence of inter-rater variability in imaging datasets. The large collection of images with multi-rater annotations features various modalities such as MRI and CT; various organs such as the brain, prostate, kidney, and pancreas; and different image dimensions 2D-vs-3D. A total of 24 teams submitted different solutions to the problem, combining various baseline models, Bayesian neural networks, and ensemble model techniques. The obtained results indicate the importance of the ensemble models, as well as the need for further research to develop efficient 3D methods for uncertainty quantification methods in 3D segmentation tasks.

eess.IV↗

arXiv2024

Finding Regions of Interest in Whole Slide Images Using Multiple Instance Learning

Whole Slide Images (WSI), obtained by high-resolution digital scanning of microscope slides at multiple scales, are the cornerstone of modern Digital Pathology. However, they represent a particular challenge to AI-based/AI-mediated analysis because pathology labeling is typically done at slide-level, instead of tile-level. It is not just that medical diagnostics is recorded at the specimen level, the detection of oncogene mutation is also experimentally obtained, and recorded by initiatives like The Cancer Genome Atlas (TCGA), at the slide level. This configures a dual challenge: a) accurately predicting the overall cancer phenotype and b) finding out what cellular morphologies are associated with it at the tile level. To address these challenges, a weakly supervised Multiple Instance Learning (MIL) approach was explored for two prevalent cancer types, Invasive Breast Carcinoma (TCGA-BRCA) and Lung Squamous Cell Carcinoma (TCGA-LUSC). This approach was explored for tumor detection at low magnification levels and TP53 mutations at various levels. Our results show that a novel additive implementation of MIL matched the performance of reference implementation (AUC 0.96), and was only slightly outperformed by Attention MIL (AUC 0.97). More interestingly from the perspective of the molecular pathologist, these different AI architectures identify distinct sensitivities to morphological features (through the detection of Regions of Interest, RoI) at different amplification levels. Tellingly, TP53 mutation was most sensitive to features at the higher applications where cellular morphology is resolved.

cs.CV↗

arXiv2023

DeepThought: An Architecture for Autonomous Self-motivated Systems

The ability of large language models (LLMs) to engage in credible dialogues with humans, taking into account the training data and the context of the conversation, has raised discussions about their ability to exhibit intrinsic motivations, agency, or even some degree of consciousness. We argue that the internal architecture of LLMs and their finite and volatile state cannot support any of these properties. By combining insights from complementary learning systems, global neuronal workspace, and attention schema theories, we propose to integrate LLMs and other deep learning systems into an architecture for cognitive language agents able to exhibit properties akin to agency, self-motivation, even some features of meta-cognition.

cs.AI↗

arXiv2023

Matching the Neuronal Representations of V1 is Necessary to Improve Robustness in CNNs with V1-like Front-ends

While some convolutional neural networks (CNNs) have achieved great success in object recognition, they struggle to identify objects in images corrupted with different types of common noise patterns. Recently, it was shown that simulating computations in early visual areas at the front of CNNs leads to improvements in robustness to image corruptions. Here, we further explore this result and show that the neuronal representations that emerge from precisely matching the distribution of RF properties found in primate V1 is key for this improvement in robustness. We built two variants of a model with a front-end modeling the primate primary visual cortex (V1): one sampling RF properties uniformly and the other sampling from empirical biological distributions. The model with the biological sampling has a considerably higher robustness to image corruptions that the uniform variant (relative difference of 8.72%). While similar neuronal sub-populations across the two variants have similar response properties and learn similar downstream weights, the impact on downstream processing is strikingly different. This result sheds light on the origin of the improvements in robustness observed in some biologically-inspired models, pointing to the need of precisely mimicking the neuronal representations found in the primate brain.

cs.CV↗

arXiv2023

Pretraining the Vision Transformer using self-supervised methods for vision based Deep Reinforcement Learning

The Vision Transformer architecture has shown to be competitive in the computer vision (CV) space where it has dethroned convolution-based networks in several benchmarks. Nevertheless, convolutional neural networks (CNN) remain the preferential architecture for the representation module in reinforcement learning. In this work, we study pretraining a Vision Transformer using several state-of-the-art self-supervised methods and assess the quality of the learned representations. To show the importance of the temporal dimension in this context we propose an extension of VICReg to better capture temporal relations between observations by adding a temporal order verification task. Our results show that all methods are effective in learning useful representations and avoiding representational collapse for observations from Atari Learning Environment (ALE) which leads to improvements in data efficiency when we evaluated in reinforcement learning (RL). Moreover, the encoder pretrained with the temporal order verification task shows the best results across all experiments, with richer representations, more focused attention maps and sparser representation vectors throughout the layers of the encoder, which shows the importance of exploring such similarity dimension. With this work, we hope to provide some insights into the representations learned by ViT during a self-supervised pretraining with observations from RL environments and which properties arise in the representations that lead to the best-performing agents. The source code will be available at: https://github.com/mgoulao/TOV-VICReg

cs.LG↗

arXiv2023

Improving Address Matching using Siamese Transformer Networks

Matching addresses is a critical task for companies and post offices involved in the processing and delivery of packages. The ramifications of incorrectly delivering a package to the wrong recipient are numerous, ranging from harm to the company's reputation to economic and environmental costs. This research introduces a deep learning-based model designed to increase the efficiency of address matching for Portuguese addresses. The model comprises two parts: (i) a bi-encoder, which is fine-tuned to create meaningful embeddings of Portuguese postal addresses, utilized to retrieve the top 10 likely matches of the un-normalized target address from a normalized database, and (ii) a cross-encoder, which is fine-tuned to accurately rerank the 10 addresses obtained by the bi-encoder. The model has been tested on a real-case scenario of Portuguese addresses and exhibits a high degree of accuracy, exceeding 95% at the door level. When utilized with GPU computations, the inference speed is about 4.5 times quicker than other traditional approaches such as BM25. An implementation of this system in a real-world scenario would substantially increase the effectiveness of the distribution process. Such an implementation is currently under investigation.

cs.LG↗

arXiv2023

Connecting metrics for shape-texture knowledge in computer vision

Modern artificial neural networks, including convolutional neural networks and vision transformers, have mastered several computer vision tasks, including object recognition. However, there are many significant differences between the behavior and robustness of these systems and of the human visual system. Deep neural networks remain brittle and susceptible to many changes in the image that do not cause humans to misclassify images. Part of this different behavior may be explained by the type of features humans and deep neural networks use in vision tasks. Humans tend to classify objects according to their shape while deep neural networks seem to rely mostly on texture. Exploring this question is relevant, since it may lead to better performing neural network architectures and to a better understanding of the workings of the vision system of primates. In this work, we advance the state of the art in our understanding of this phenomenon, by extending previous analyses to a much larger set of deep neural network architectures. We found that the performance of models in image classification tasks is highly correlated with their shape bias measured at the output and penultimate layer. Furthermore, our results showed that the number of neurons that represent shape and texture are strongly anti-correlated, thus providing evidence that there is competition between these two types of features. Finally, we observed that while in general there is a correlation between performance and shape bias, there are significant variations between architecture families.

cs.CV↗

arXiv2022

Assessing Policy, Loss and Planning Combinations in Reinforcement Learning using a New Modular Architecture

The model-based reinforcement learning paradigm, which uses planning algorithms and neural network models, has recently achieved unprecedented results in diverse applications, leading to what is now known as deep reinforcement learning. These agents are quite complex and involve multiple components, factors that can create challenges for research. In this work, we propose a new modular software architecture suited for these types of agents, and a set of building blocks that can be easily reused and assembled to construct new model-based reinforcement learning agents. These building blocks include planning algorithms, policies, and loss functions. We illustrate the use of this architecture by combining several of these building blocks to implement and test agents that are optimized to three different test environments: Cartpole, Minigrid, and Tictactoe. One particular planning algorithm, made available in our implementation and not previously used in reinforcement learning, which we called averaged minimax, achieved good results in the three tested environments. Experiments performed with this architecture have shown that the best combination of planning algorithm, policy, and loss function is heavily problem dependent. This result provides evidence that the proposed architecture, which is modular and reusable, is useful for reinforcement learning researchers who want to study new environments and techniques.

cs.LG↗

arXiv2021

Assessing the Impact of Attention and Self-Attention Mechanisms on the Classification of Skin Lesions

Attention mechanisms have raised significant interest in the research community, since they promise significant improvements in the performance of neural network architectures. However, in any specific problem, we still lack a principled way to choose specific mechanisms and hyper-parameters that lead to guaranteed improvements. More recently, self-attention has been proposed and widely used in transformer-like architectures, leading to significant breakthroughs in some applications. In this work we focus on two forms of attention mechanisms: attention modules and self-attention. Attention modules are used to reweight the features of each layer input tensor. Different modules have different ways to perform this reweighting in fully connected or convolutional layers. The attention models studied are completely modular and in this work they will be used with the popular ResNet architecture. Self-Attention, originally proposed in the area of Natural Language Processing makes it possible to relate all the items in an input sequence. Self-Attention is becoming increasingly popular in Computer Vision, where it is sometimes combined with convolutional layers, although some recent architectures do away entirely with convolutions. In this work, we study and perform an objective comparison of a number of different attention mechanisms in a specific computer vision task, the classification of samples in the widely used Skin Cancer MNIST dataset. The results show that attention modules do sometimes improve the performance of convolutional neural network architectures, but also that this improvement, although noticeable and statistically significant, is not consistent in different settings. The results obtained with self-attention mechanisms, on the other hand, show consistent and significant improvements, leading to the best results even in architectures with a reduced number of parameters.

cs.CV↗

arXiv2021

Using Soft Labels to Model Uncertainty in Medical Image Segmentation

Medical image segmentation is inherently uncertain. For a given image, there may be multiple plausible segmentation hypotheses, and physicians will often disagree on lesion and organ boundaries. To be suited to real-world application, automatic segmentation systems must be able to capture this uncertainty and variability. Thus far, this has been addressed by building deep learning models that, through dropout, multiple heads, or variational inference, can produce a set - infinite, in some cases - of plausible segmentation hypotheses for any given image. However, in clinical practice, it may not be practical to browse all hypotheses. Furthermore, recent work shows that segmentation variability plateaus after a certain number of independent annotations, suggesting that a large enough group of physicians may be able to represent the whole space of possible segmentations. Inspired by this, we propose a simple method to obtain soft labels from the annotations of multiple physicians and train models that, for each image, produce a single well-calibrated output that can be thresholded at multiple confidence levels, according to each application's precision-recall requirements. We evaluated our method on the MICCAI 2021 QUBIQ challenge, showing that it performs well across multiple medical image segmentation tasks, produces well-calibrated predictions, and, on average, performs better at matching physicians' predictions than other physicians.

cs.CV↗

arXiv2021

Modelling Neuronal Behaviour with Time Series Regression: Recurrent Neural Networks on C. Elegans Data

Given the inner complexity of the human nervous system, insight into the dynamics of brain activity can be gained from understanding smaller and simpler organisms, such as the nematode C. Elegans. The behavioural and structural biology of these organisms is well-known, making them prime candidates for benchmarking modelling and simulation techniques. In these complex neuronal collections, classical, white-box modelling techniques based on intrinsic structural or behavioural information are either unable to capture the profound nonlinearities of the neuronal response to different stimuli or generate extremely complex models, which are computationally intractable. In this paper we show how the nervous system of C. Elegans can be modelled and simulated with data-driven models using different neural network architectures. Specifically, we target the use of state of the art recurrent neural networks architectures such as LSTMs and GRUs and compare these architectures in terms of their properties and their accuracy as well as the complexity of the resulting models. We show that GRU models with a hidden layer size of 4 units are able to accurately reproduce with high accuracy the system's response to very different stimuli.

q-bio.NC↗

arXiv2021

Encoder-Decoder Architectures for Clinically Relevant Coronary Artery Segmentation

Coronary X-ray angiography is a crucial clinical procedure for the diagnosis and treatment of coronary artery disease, which accounts for roughly 16% of global deaths every year. However, the images acquired in these procedures have low resolution and poor contrast, making lesion detection and assessment challenging. Accurate coronary artery segmentation not only helps mitigate these problems, but also allows the extraction of relevant anatomical features for further analysis by quantitative methods. Although automated segmentation of coronary arteries has been proposed before, previous approaches have used non-optimal segmentation criteria, leading to less useful results. Most methods either segment only the major vessel, discarding important information from the remaining ones, or segment the whole coronary tree based mostly on contrast information, producing a noisy output that includes vessels that are not relevant for diagnosis. We adopt a better-suited clinical criterion and segment vessels according to their clinical relevance. Additionally, we simultaneously perform catheter segmentation, which may be useful for diagnosis due to the scale factor provided by the catheter's known diameter, and is a task that has not yet been performed with good results. To derive the optimal approach, we conducted an extensive comparative study of encoder-decoder architectures trained on a combination of focal loss and a variant of generalized dice loss. Based on the EfficientNet and the UNet++ architectures, we propose a line of efficient and high-performance segmentation models using a new decoder architecture, the EfficientUNet++, whose best-performing version achieved average dice scores of 0.8904 and 0.7526 for the artery and catheter classes, respectively, and an average generalized dice score of 0.9234.

eess.IV↗

arXiv2021

Modeling the geospatial evolution of COVID-19 using spatio-temporal convolutional sequence-to-sequence neural networks

Europe was hit hard by the COVID-19 pandemic and Portugal was one of the most affected countries, having suffered three waves in the first twelve months. Approximately between Jan 19th and Feb 5th 2021 Portugal was the country in the world with the largest incidence rate, with 14-days incidence rates per 100,000 inhabitants in excess of 1000. Despite its importance, accurate prediction of the geospatial evolution of COVID-19 remains a challenge, since existing analytical methods fail to capture the complex dynamics that result from both the contagion within a region and the spreading of the infection from infected neighboring regions. We use a previously developed methodology and official municipality level data from the Portuguese Directorate-General for Health (DGS), relative to the first twelve months of the pandemic, to compute an estimate of the incidence rate in each location of mainland Portugal. The resulting sequence of incidence rate maps was then used as a gold standard to test the effectiveness of different approaches in the prediction of the spatial-temporal evolution of the incidence rate. Four different methods were tested: a simple cell level autoregressive moving average (ARMA) model, a cell level vector autoregressive (VAR) model, a municipality-by-municipality compartmental SIRD model followed by direct block sequential simulation and a convolutional sequence-to-sequence neural network model based on the STConvS2S architecture. We conclude that the convolutional sequence-to-sequence neural network is the best performing method, when predicting the medium-term future incidence rate, using the available information.

cs.LG↗

arXiv2021

Automated Detection of Coronary Artery Stenosis in X-ray Angiography using Deep Neural Networks

Coronary artery disease leading up to stenosis, the partial or total blocking of coronary arteries, is a severe condition that affects millions of patients each year. Automated identification and classification of stenosis severity from minimally invasive procedures would be of great clinical value, but existing methods do not match the accuracy of experienced cardiologists, due to the complexity of the task. Although a number of computational approaches for quantitative assessment of stenosis have been proposed to date, the performance of these methods is still far from the required levels for clinical applications. In this paper, we propose a two-step deep-learning framework to partially automate the detection of stenosis from X-ray coronary angiography images. In the two steps, we used two distinct convolutional neural network architectures, one to automatically identify and classify the angle of view, and another to determine the bounding boxes of the regions of interest in frames where stenosis is visible. Transfer learning and data augmentation techniques were used to boost the performance of the system in both tasks. We achieved a 0.97 accuracy on the task of classifying the Left/Right Coronary Artery (LCA/RCA) angle view and 0.68/0.73 recall on the determination of the regions of interest, for LCA and RCA, respectively. These results compare favorably with previous results obtained using related approaches, and open the way to a fully automated method for the identification of stenosis severity from X-ray angiographies.

eess.IV↗

arXiv2018

Conditional Random Fields as Recurrent Neural Networks for 3D Medical Imaging Segmentation

The Conditional Random Field as a Recurrent Neural Network layer is a recently proposed algorithm meant to be placed on top of an existing Fully-Convolutional Neural Network to improve the quality of semantic segmentation. In this paper, we test whether this algorithm, which was shown to improve semantic segmentation for 2D RGB images, is able to improve segmentation quality for 3D multi-modal medical images. We developed an implementation of the algorithm which works for any number of spatial dimensions, input/output image channels, and reference image channels. As far as we know this is the first publicly available implementation of this sort. We tested the algorithm with two distinct 3D medical imaging datasets, we concluded that the performance differences observed were not statistically significant. Finally, in the discussion section of the paper, we go into the reasons as to why this technique transfers poorly from natural images to medical images.

cs.CV↗