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Publications

Publications by António Luís Sousa

2022

Cloud-Based Privacy-Preserving Medical Imaging System Using Machine Learning Tools

Authors
Alves, J; Soares, B; Brito, C; Sousa, A;

Publication
PROGRESS IN ARTIFICIAL INTELLIGENCE, EPIA 2022

Abstract
Healthcare environments are generating a deluge of sensitive data. Nonetheless, dealing with large amounts of data is an expensive task, and current solutions resort to the cloud environment. Additionally, the intersection of the cloud environment and healthcare data opens new challenges regarding data privacy. With this in mind, we propose MEDCLOUDCARE (MCC), a healthcare application offering medical image viewing and processing tools while integrating cloud computing and AI. Moreover, MCC provides security and privacy features, scalability and high availability. The system is intended for two user groups: health professionals and researchers. The former can remotely view, process and share medical imaging information in the DICOM format. Also, it can use pre-trained Machine Learning (ML) models to aid the analysis of medical images. The latter can remotely add, share, and deploy ML models to perform inference on DICOM images. MCC incorporates a DICOM web viewer enabling users to view and process DICOM studies, which they can also upload and store. Regarding the security and privacy of the data, all sensitive information is encrypted at rest and in transit. Furthermore, MCC is intended for cloud environments. Thus, the system is deployed using Kubernetes, increasing the efficiency, availability and scalability of the ML inference process.

2024

MAC: An Artifact Correction Framework for Brain MRI based on Deep Neural Networks

Authors
Oliveira, A; Cepa, B; Brito, C; Sousa, A;

Publication

Abstract
AbstractThe correction of artifacts in Magnetic Resonance Imaging (MRI) is crucial due to physiological phenomena and technical issues affecting diagnostic quality. Reverting from corrupted to artifact-free images is a complex task. Deep Learning (DL) models have been employed to preserve data characteristics and to identify and correct those artifacts. We proposeMAC, a novel DL-based solution to correct artifacts in multi-contrast brain MRI scans.MACoffers two models: the simulation and the correction models. The simulation model introduces perturbations similar to those occurring in an exam while preserving the original image as ground truth; this is required as publicly available datasets rarely have motion-corrupted images. It allows the addition of three types of artifacts with different degrees of severity. The DL-based correction model adds a fourth contrast to state-of-the-art solutions while improving the overall performance of the models.MACachieved the highest results in the FLAIR contrast, with a Structural Similarity Index Measure (SSIM) of 0.9803 and a Normalized Mutual Information (NMI) of 0.8030. Moreover, the model reduced training time by 63% compared to its predecessor.MACmodel can correct large volumes of images faster and adapt to different levels of artifact severity than current state-ofthe-art models, allowing for better diagnosis.

2024

To FID or not to FID: Applying GANs for MRI Image Generation in HPC

Authors
Cepa, B; Brito, C; Sousa, A;

Publication

Abstract
AbstractWith the rapid growth of Deep Learning models and neural networks, the medical data available for training – which is already significantly less than other types of data – is becoming scarce. For that purpose, Generative Adversarial Networks (GANs) have received increased attention due to their ability to synthesize new realistic images. Our preliminary work shows promising results for brain MRI images; however, there is a need to distribute the workload, which can be supported by High-Performance Computing (HPC) environments. In this paper, we generate 256×256 MRI images of the brain in a distributed setting. We obtained an FIDRadImageNetof 10.67 for the DCGAN and 23.54 for the WGAN-GP, which are consistent with results reported in several works published in this scope. This allows us to conclude that distributing the GAN generation process is a viable option to overcome the computational constraints imposed by these models and, therefore, facilitate the generation of new data for training purposes.

2023

Generative Adversarial Networks in Healthcare: A Case Study on MRI Image Generation

Authors
Cepa, B; Brito, C; Sousa, A;

Publication
2023 IEEE 7TH PORTUGUESE MEETING ON BIOENGINEERING, ENBENG

Abstract
Medical imaging, mainly Magnetic Resonance Imaging (MRI), plays a predominant role in healthcare diagnosis. Nevertheless, the diagnostic process is prone to errors and is conditioned by available medical data, which might be insufficient. A novel solution is resorting to image generation algorithms to address these challenges. Thus, this paper presents a Deep Learning model based on a Deep Convolutional Generative Adversarial Network (DCGAN) architecture. Our model generates 2D MRI images of size 256x256, containing an axial view of the brain with a tumor. The model was implemented using ChainerMN, a scalable and flexible framework that enables faster and parallel training of Deep Learning networks. The images obtained provide an overall representation of the brain structure and the tumoral area and show considerable brain-tumor separation. For this purpose, and owing to their previous state-of-the-art results in general image-generation tasks, we conclude that GAN-based models are a promising approach for medical imaging.

2012

DEDISbench: A benchmark for deduplicated storage systems

Authors
Paulo, J; Reis, P; Pereira, J; Sousa, A;

Publication
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Abstract
Deduplication is widely accepted as an effective technique for eliminating duplicated data in backup and archival systems. Nowadays, deduplication is also becoming appealing in cloud computing, where large-scale virtualized storage infrastructures hold huge data volumes with a significant share of duplicated content. There have thus been several proposals for embedding deduplication in storage appliances and file systems, providing different performance trade-offs while targeting both user and application data, as well as virtual machine images. It is however hard to determine to what extent is deduplication useful in a particular setting and what technique will provide the best results. In fact, existing disk I/O micro-benchmarks are not designed for evaluating deduplication systems, following simplistic approaches for generating data written that lead to unrealistic amounts of duplicates. We address this with DEDISbench, a novel micro-benchmark for evaluating disk I/O performance of block based deduplication systems. As the main contribution, we introduce the generation of a realistic duplicate distribution based on real datasets. Moreover, DEDISbench also allows simulating access hotspots and different load intensities for I/O operations. The usefulness of DEDISbench is shown by comparing it with Bonnie++ and IOzone open-source disk I/O micro-benchmarks on assessing two open-source deduplication systems, Opendedup and Lessfs, using Ext4 as a baseline. As a secondary contribution, our results lead to novel insight on the performance of these file systems. © 2012 Springer-Verlag.

2002

Optimistic total order in wide area networks

Authors
Sousa, A; Pereira, J; Moura, F; Oliveira, R;

Publication
21ST IEEE SYMPOSIUM ON RELIABLE DISTRIBUTED SYSTEMS, PROCEEDINGS

Abstract
Total order multicast greatly simplifies the implementation of fault-tolerant services using the replicated state machine approach. The additional latency of total ordering can be masked by taking advantage of spontaneous ordering observed in LANs: A tentative delivery allows the application to proceed in parallel with the ordering protocol. The effectiveness of the technique rests on the optimistic assumption that a large share of correctly ordered tentative deliveries offsets the cost of undoing the effect of mistakes. This paper proposes a simple technique which enables the usage of optimistic delivery also in WANs with much larger transmission delays where the optimistic assumption does not normally hold. Our proposal exploits local clocks and the stability of network delays to reduce the mistakes in the ordering of tentative deliveries. An experimental evaluation of a modified sequencer-based protocol is presented, illustrating the usefulness of the approach in fault-tolerant database management.

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