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Publicações

Publicações por Tânia Pereira

2025

Domain-Specific Data Augmentation for Lung Nodule Malignancy Classification

Autores
Gouveia M.; Araujo J.; Oliveira H.P.; Pereira T.;

Publicação
Annual International Conference of the IEEE Engineering in Medicine and Biology Society IEEE Engineering in Medicine and Biology Society Annual International Conference

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.Clinical relevance- This work provides an automatic method for lung nodule malignancy classification based on CT scans, combined with generalisation methods that allow a good performance across different cohort populations and hospitals.

2025

Recent applications of EEG-based brain-computer-interface in the medical field

Autores
Liu, XY; Wang, WL; Liu, M; Chen, MY; Pereira, T; Doda, DY; Ke, YF; Wang, SY; Wen, D; Tong, XG; Li, WG; Yang, Y; Han, XD; Sun, YL; Song, X; Hao, CY; Zhang, ZH; Liu, XY; Li, CY; Peng, R; Song, XX; Yasi, A; Pang, MJ; Zhang, K; He, RN; Wu, L; Chen, SG; Chen, WJ; Chao, YG; Hu, CG; Zhang, H; Zhou, M; Wang, K; Liu, PF; Chen, C; Geng, XY; Qin, Y; Gao, DR; Song, EM; Cheng, LL; Chen, X; Ming, D;

Publicação
MILITARY MEDICAL RESEARCH

Abstract
Brain-computer interfaces (BCIs) represent an emerging technology that facilitates direct communication between the brain and external devices. In recent years, numerous review articles have explored various aspects of BCIs, including their fundamental principles, technical advancements, and applications in specific domains. However, these reviews often focus on signal processing, hardware development, or limited applications such as motor rehabilitation or communication. This paper aims to offer a comprehensive review of recent electroencephalogram (EEG)-based BCI applications in the medical field across 8 critical areas, encompassing rehabilitation, daily communication, epilepsy, cerebral resuscitation, sleep, neurodegenerative diseases, anesthesiology, and emotion recognition. Moreover, the current challenges and future trends of BCIs were also discussed, including personal privacy and ethical concerns, network security vulnerabilities, safety issues, and biocompatibility.

2025

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

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

Publicação
Measurement and Evaluations in Cancer Care

Abstract

2025

MYCN-Amplified Neuroblastoma Detection Radiomics Vs. Trainable Features

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

Publicação
Proceedings - 2025 IEEE 25th International Conference on Bioinformatics and Bioengineering, BIBE 2025

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.

2025

Incrementally Learning to Segment the Lungs: Similarities and Differences Across Institutions

Autores
Sousa, JV; Oliveira, P; Pereira, T;

Publicação
Proceedings - 2025 IEEE 25th International Conference on Bioinformatics and Bioengineering, BIBE 2025

Abstract
Segmentation of the lungs in Computed Tomography (CT) is very challenging due to changes in lung shape, size, and parenchyma pattern, as well as differences in imaging acquisition protocols. As a consequence, these models may not be robust and may decrease their performance when deployed in a clinical setting. The Continual Learning paradigm holds great promise since learning models continually acquire incoming knowledge, having the ability to adapt to changing environments. In this work, experience replay with random sampling of past data was implemented, using the original CT images and the corresponding ground-truths. Data from four different institutions were used to develop the experiments, and the models were evaluated on a cross-cohort dataset. Using raw data, the goal was to study how the datasets and their imaging patterns were related and what impact the training datasets have on one another. The catastrophic forgetting effect diminished for almost all datasets. For two of the in-domain test datasets there was forward and backward transfer, results that could be linked to a possible similarity between them. A mean DSC of 0.94 was obtained across all datasets. The results showed how the similarity or disparity between data from different institutions can influence the performance of learning models. © 2025 IEEE.

2025

Multi-task transformer network for subject-independent iEEG seizure detection

Autores
Sun, YL; Cheng, LL; Si, XP; He, RN; Pereira, T; Pang, MJ; Zhang, K; Song, X; Ming, D; Liu, XY;

Publicação
EXPERT SYSTEMS WITH APPLICATIONS

Abstract
Subject-independent seizure detection algorithms are typically grounded in scalp electroencephalogram (EEG) databases, due to standardized channels and locations of EEG electrodes. Intracranial EEG (iEEG) has the characteristics of low noise and high temporal resolution compared with scalp EEG. However, it is still a big challenge for seizure detection using iEEG, because of the inconsistent number and locations of implanted electrodes in different patients, which results in a lack of unified algorithms. This study introduces an innovative approach for subject-independent seizure detection using iEEG, combining channel-wise mixup, transformer networks, and multi-task learning. Channel-wise mixup enhances data utilization by effectively leveraging information from different subjects, while multi-task learning improves the generalization of the model by concurrently optimizing both the seizure detection and the subject recognition tasks. 2983 files from two well-known epilepsy databases, i.e. SWEC-ETHZ and HUP were used in our study and the result showed that our approach surpasses currently existing methods. In terms of accuracy and generalization of seizure detection, our method achieved an area under the receiver operating characteristic curve (AUC) of 0.97 and 0.95 on the two databases respectively, which are significantly higher than the result of the currently existing methods. This study proposed anew method with great potential for surgery planning of epilepsy patients.

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