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Publications

Publications by Hélder Filipe Oliveira

2020

Domain Adaptation for Heart Rate Extraction in the Neonatal Intensive Care Unit

Authors
Malafaya, D; Domingues, S; Oliveira, HP;

Publication
2020 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE

Abstract
Conventionally, vital sign monitoring for neonatal infants inside the Neonatal Intensive Care Unit is performed via probes affixed to their skin. However, such instruments may cause damage to the epidermis and increase the risk of infection as well as promote discomfort to the infant. As an alternative to traditional means of monitoring heart rate, remote Photoplethysmography techniques have been surging among the scientific community. These techniques have been vastly explored for adult subjects but not for neonatal infants, who would greatly benefit from such applications. This study aims at developing a regular consumer camera-based framework for continuous and contactless extraction of the heart rate in adult subjects in challenging conditions and investigating the tool's ability to adapt to a new domain which consists of newborn subjects and the real-world conditions of a Neonatal Intensive Care Unit.

2022

Multiple instance learning for lung pathophysiological findings detection using CT scans

Authors
Frade, J; Pereira, T; Morgado, J; Silva, F; Freitas, C; Mendes, J; Negrao, E; de Lima, BF; da Silva, MC; Madureira, AJ; Ramos, I; Costa, JL; Hespanhol, V; Cunha, A; Oliveira, HP;

Publication
MEDICAL & BIOLOGICAL ENGINEERING & COMPUTING

Abstract
Lung diseases affect the lives of billions of people worldwide, and 4 million people, each year, die prematurely due to this condition. These pathologies are characterized by specific imagiological findings in CT scans. The traditional Computer-Aided Diagnosis (CAD) approaches have been showing promising results to help clinicians; however, CADs normally consider a small part of the medical image for analysis, excluding possible relevant information for clinical evaluation. Multiple Instance Learning (MIL) approach takes into consideration different small pieces that are relevant for the final classification and creates a comprehensive analysis of pathophysiological changes. This study uses MIL-based approaches to identify the presence of lung pathophysiological findings in CT scans for the characterization of lung disease development. This work was focus on the detection of the following: Fibrosis, Emphysema, Satellite Nodules in Primary Lesion Lobe, Nodules in Contralateral Lung and Ground Glass, being Fibrosis and Emphysema the ones with more outstanding results, reaching an Area Under the Curve (AUC) of 0.89 and 0.72, respectively. Additionally, the MIL-based approach was used for EGFR mutation status prediction - the most relevant oncogene on lung cancer, with an AUC of 0.69. The results showed that this comprehensive approach can be a useful tool for lung pathophysiological characterization.

2025

Conditional Score-based Diffusion Models for Lung CT Scans Generation

Authors
Cardoso, AF; Sousa, P; Oliveira, HP; Pereira, T;

Publication
2025 47TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY (EMBC)

Abstract
Chest CT scans are essential in diagnosing lung abnormalities, including lung cancer, but their utility in training deep learning models is often pushed back by limited data availability, high labeling costs, and privacy concerns. To address these challenges, this study explores the use of score-based diffusion models for the conditional generation of lung CT scans slices. Two generation scenarios are explored: one limited to lung segmentation masks and another incorporating both lung and nodule segmentation mappings to guide the synthesis process. The proposed methods are custom U-Net architecture models trained to predict the scores in Variance Preserving (VP) and Variance Exploding (VE) Stochastic Differential Equations (SDEs), composing the primary ground for comparison in conditional sample generation. The results demonstrate the VP SDEs model's superiority in generating high-fidelity images, as evidenced by high SSIM (0.894) and PSNR (28.6) values, as well as low domain-specific FID (173.4), MMD (0.0133) and ECS (0.78) scores. The generated images consistently followed the conditional mapping guidance during the generation process, effectively producing realistic lung and nodule structures, highlighting their potential for data augmentation in medical imaging tasks. While the models achieved notable success in generating accurate 2D lung CT scan slices given simple conditional image region mappings, future work surrounds the extension of these methods to 3D conditional generation and the use of richer conditional mappings to account for broader anatomical variations. Nevertheless, this study holds promise for improvement in computer-aided systems through the support in deep learning model training for lung disease diagnosis and classification.

2025

Domain-Specific Data Augmentation for Lung Nodule Malignancy Classification

Authors
Gouveia, M; Araújo, J; Oliveira, HP; Pereira, T;

Publication
2025 47TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY (EMBC)

Abstract
Lung cancer is one of the leading causes of cancer-related deaths worldwide, mainly due to late diagnosis. Screening programs can benefit from Computer-Aided Diagnosis (CAD) systems that detect and classify lung nodules using Computed Tomography (CT) scans. A great proportion of the literature proposes deep learning models based on single and private datasets with no evaluation of their generalisation capability. The main goal of this work is to study and address the lack of generalisation to out-of-domain data (source domain different from the target domain). In this work, we propose using a ResNet architecture with 2.5D inputs capable of maintaining the spatial information of the nodules (3 input channels based on the anatomical planes). Secondly, we apply domain-specific data augmentation tailored for CT scans. Combined with data augmentation, using 2.5D inputs achieves the best results, both in in-domain data (LIDC-IDRI: N=1377 nodules; and LNDb: N=183 nodules) and in out-of-domain data (LUNGx: N=73 nodules). In in-domain data, an Area Under the Curve (AUC) of 0.914 was achieved in the internal test set and 0.746 in one of the external test sets. Notably, in out-of-domain data, where the ground-truth labels have been confirmed by biopsy, whereas the training data only involved radiologist annotation regarding the likelihood of malignancy, AUC improves from 0.576 to 0.695, reaching a performance close to that of radiology experts. In the future, strategies should be applied to deal with the level of uncertainty of lung nodule annotations based solely on the observation of the CT scans.

2025

Radiogenomic Insights from a Portuguese Lung Cancer Cohort: Foundations for Predictive Modeling

Authors
Neves, I; Freitas, C; Lemos, C; Oliveira, HP; Hespanhol, V; França, M; Pereira, T;

Publication
Measurement and Evaluations in Cancer Care

Abstract

2025

MYCN-Amplified Neuroblastoma Detection Radiomics Vs. Trainable Features

Authors
Malafaia, M; Silva, F; Carvalho, DC; Martins, R; Dias, SC; Torrão, H; Oliveira, HP; Pereira, T;

Publication
BIBE

Abstract
Neuroblastoma (NB) is the most common extracranial tumor in pediatric cases. The MYCN oncogene amplification (MNA) is knowingly correlated with a poor prognosis, making detecting this biomarker crucial for treatment selection and survival prediction. The current clinical protocol for MNA detection includes invasive procedures, such as biopsy. The proposed work aims to develop non-invasive techniques for predicting MNA in patients with diagnosed NB, using AI-based models and Computerized Tomography (CT) scans. Machine learning methods that use the imaging features extracted from the tumor on the CT slices were developed and compared with deep learning (DL) models. Additionally, agnostic explainable methods for imaging were applied to create explanations about the relevant information used by the DL models in the prediction. The results show a better performance for the DL approach, which achieved an AUC of 0.94 ± 0.04. The similarity in the explanations produced by the models trained with different data splits showed that feature extraction remains somewhat invariant to shifts in training data, which is relevant given the small amount of data available. Learning models were shown to have predictive potential that, with further improvements, can be integrated into predictive, explainable, and, thus, trustworthy systems to aid clinicians in the decision-making process. © 2025 IEEE.

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