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Publicações

Publicações por HASLab

2024

GLITCH: Polyglot Code Smell Detection in Infrastructure as Code

Autores
Saavedra, N; Ferreira, JF; Mendes, A;

Publicação
ERCIM NEWS

Abstract
GLITCH is a versatile tool designed for detecting code smells in Infrastructure as Code (IaC) scripts across multiple technologies. Developed by researchers from INESC-ID (Lisbon), INESC TEC (Porto), Instituto Superior T & eacute;cnico / University of Lisbon, and the Faculty of Engineering / University of Porto, GLITCH automates the detection of both security and design flaws in scripts written in Ansible, Chef, Docker, Puppet, and Terraform. By using a technology-agnostic framework, GLITCH aims to improve the consistency and efficiency of code smell detection, making it valuable resource for DevOps engineers and researchers focused on software quality.

2024

Patient-Centric Health Data Sovereignty: An Approach Using Proxy Re-Encryption

Autores
Rodrigues, B; Amorim, I; Silva, I; Mendes, A;

Publicação
COMPUTER SECURITY. ESORICS 2023 INTERNATIONAL WORKSHOPS, PT I

Abstract
The exponential growth in the digitisation of services implies the handling and storage of large volumes of data. Businesses and services see data sharing and crossing as an opportunity to improve and produce new business opportunities. The health sector is one area where this proves to be true, enabling better and more innovative treatments. Notwithstanding, this raises concerns regarding personal data being treated and processed. In this paper, we present a patient-centric platform for the secure sharing of health records by shifting the control over the data to the patient, therefore, providing a step further towards data sovereignty. Data sharing is performed only with the consent of the patient, allowing it to revoke access at any given time. Furthermore, we also provide a break-glass approach, resorting to Proxy Re-encryption (PRE) and the concept of a centralised trusted entity that possesses instant access to patients' medical records. Lastly, an analysis is made to assess the performance of the platform's key operations, and the impact that a PRE scheme has on those operations.

2024

Mastering Artifact Correction in Neuroimaging Analysis: A Retrospective Approach

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

Publicação

Abstract
The correction of artifacts in Magnetic Resonance Imaging (MRI) is increasingly relevant as voluntary and involuntary artifacts can hinder data acquisition. 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 propose MOANA, a novel DL-based solution to correct artifacts in multi-contrast brain MRI scans. MOANA offers 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. MOANA achieved 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. With this, the MOANA model can correct large volumes of images in less time and adapt to different levels of artifact severity, allowing for better diagnosis.

2024

Mastering Artifact Correction in Neuroimaging Analysis: A Retrospective Approach

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

Publicação

Abstract
The correction of artifacts in Magnetic Resonance Imaging (MRI) is increasingly relevant as voluntary and involuntary artifacts can hinder data acquisition. 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 propose MOANA, a novel DL-based solution to correct artifacts in multi-contrast brain MRI scans. MOANA offers 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. MOANA achieved 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. With this, the MOANA model can correct large volumes of images in less time and adapt to different levels of artifact severity, allowing for better diagnosis.

2024

A Distributed Computing Solution for Privacy-Preserving Genome-Wide Association Studies

Autores
Brito, C; Ferreira, P; Paulo, J;

Publicação

Abstract
AbstractBreakthroughs in sequencing technologies led to an exponential growth of genomic data, providing unprecedented biological in-sights and new therapeutic applications. However, analyzing such large amounts of sensitive data raises key concerns regarding data privacy, specifically when the information is outsourced to third-party infrastructures for data storage and processing (e.g., cloud computing). Current solutions for data privacy protection resort to centralized designs or cryptographic primitives that impose considerable computational overheads, limiting their applicability to large-scale genomic analysis.We introduce Gyosa, a secure and privacy-preserving distributed genomic analysis solution. Unlike in previous work, Gyosafollows a distributed processing design that enables handling larger amounts of genomic data in a scalable and efficient fashion. Further, by leveraging trusted execution environments (TEEs), namely Intel SGX, Gyosaallows users to confidentially delegate their GWAS analysis to untrusted third-party infrastructures. To overcome the memory limitations of SGX, we implement a computation partitioning scheme within Gyosa. This scheme reduces the number of operations done inside the TEEs while safeguarding the users’ genomic data privacy. By integrating this security scheme inGlow, Gyosaprovides a secure and distributed environment that facilitates diverse GWAS studies. The experimental evaluation validates the applicability and scalability of Gyosa, reinforcing its ability to provide enhanced security guarantees. Further, the results show that, by distributing GWASes computations, one can achieve a practical and usable privacy-preserving solution.

2024

Berry: A code for the differentiation of Bloch wavefunctions from DFT calculations

Autores
Reascos, L; Carneiro, F; Pereira, A; Castro, NF; Ribeiro, RM;

Publicação
COMPUTER PHYSICS COMMUNICATIONS

Abstract
Density functional calculation of electronic structures of materials is one of the most used techniques in theoretical solid state physics. These calculations retrieve single electron wavefunctions and their eigenenergies. The berry suite of programs amplifies the usefulness of DFT by ordering the eigenstates in analytic bands, allowing the differentiation of the wavefunctions in reciprocal space. It can then calculate Berry connections and curvatures and the second harmonic generation conductivity. The berry software is implemented for two dimensional materials and was tested in hBN and InSe. In the near future, more properties and functionalities are expected to be added.Program summary Program Title: berry CPC Library link to program files: https://doi .org /10 .17632 /mpbbksz2t7 .1 Developer's repository link: https://github .com /ricardoribeiro -2020 /berry Licensing provisions: MIT Programming language: Python3 Nature of problem: Differentiation of Bloch wavefunctions in reciprocal space, numerically obtained from a DFT software, applied to two dimensional materials. This enables the numeric calculation of material's properties such as Berry geometries and Second Harmonic conductivity. Solution method: Extracts Kohn-Sham functions from a DFT calculation, orders them by analytic bands using graph and AI methods and calculates the gradient of the wavefunctions along an electronic band. Additional comments including restrictions and unusual features: Applies only to two dimensional materials, and only imports Kohn-Sham functions from Quantum Espresso package.

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