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Publicações

Publicações por Tânia Pereira

2023

A Machine Learning Approach for Predicting Microsatellite Instability using RNA-seq

Autores
Simões, M; Pereira, T; Silva, F; Machado, JMF; Oliveira, HP;

Publicação
IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023, Istanbul, Turkiye, December 5-8, 2023

Abstract
Microsatellite Instability (MSI) is an important biomarker in cancer patients, showing a defective DNA mismatch repair system. Its detection allows the use of immunotherapy to treat cancer, an approach that is revolutionizing cancer treatment. MSI is especially relevant for three types of cancer: Colon Adenocarcinoma (COAD), Stomach Adenocarcinoma (STAD), and Uterus corpus endometrial cancer (UCEC). In this work, learning algorithms were employed to predict MSI using RNA-seq data from The Cancer Genome Atlas (TCGA) database, with a focus on the selection of the most informative genomic features. The Multi-Layer Perceptron (MLP) obtained the best score (AUC = 98.44%), showing that it is possible to exploit information from RNA-seq data to find relevant relationships with the instability levels of microsatellites (MS). The accurate prediction of MSI with transcription data from cancer patients will help with the correct determination of MSI status and adequate prescription of immunotherapy, creating more precise and personalized patient care. At the genetic level, the study revealed a high expression of genes related to cell regulation functions, and a low expression of genes responsible for Mismatch Repair functions, in patients with high instability.

2023

The 2023 wearable photoplethysmography roadmap

Autores
Charlton, PH; Allen, J; Bailon, R; Baker, S; Behar, JA; Chen, F; Clifford, GD; Clifton, DA; Davies, HJ; Ding, C; Ding, XR; Dunn, J; Elgendi, M; Ferdoushi, M; Franklin, D; Gil, E; Hassan, MF; Hernesniemi, J; Hu, X; Ji, N; Khan, Y; Kontaxis, S; Korhonen, I; Kyriacou, PA; Laguna, P; Lazaro, J; Lee, CK; Levy, J; Li, YM; Liu, CY; Liu, J; Lu, L; Mandic, DP; Marozas, V; Mejía-Mejía, E; Mukkamala, R; Nitzan, M; Pereira, T; Poon, CCY; Ramella-Roman, JC; Saarinen, H; Shandhi, MMH; Shin, H; Stansby, G; Tamura, T; Vehkaoja, A; Wang, WK; Zhang, YT; Zhao, N; Zheng, DC; Zhu, TT;

Publicação
PHYSIOLOGICAL MEASUREMENT

Abstract
Photoplethysmography is a key sensing technology which is used in wearable devices such as smartwatches and fitness trackers. Currently, photoplethysmography sensors are used to monitor physiological parameters including heart rate and heart rhythm, and to track activities like sleep and exercise. Yet, wearable photoplethysmography has potential to provide much more information on health and wellbeing, which could inform clinical decision making. This Roadmap outlines directions for research and development to realise the full potential of wearable photoplethysmography. Experts discuss key topics within the areas of sensor design, signal processing, clinical applications, and research directions. Their perspectives provide valuable guidance to researchers developing wearable photoplethysmography technology.

2024

Deep Learning Models to Predict Brain Cancer Grade Through MRI Analysis

Autores
Vale, P; Boer, J; Oliveira, HP; Pereira, T;

Publicação
2024 IEEE 37TH INTERNATIONAL SYMPOSIUM ON COMPUTER-BASED MEDICAL SYSTEMS, CBMS 2024

Abstract
The early and accurate detection and the grading characterization of brain cancer will generate a positive impact on the treatment plan of those patients. AI-based models can help analyze the Magnetic Resonance Imaging (MRI) to make an initial assessment of the tumor grading. The objective of this work was to develop an Al-based model to classify the grading of the tumor using the MRI. Two regions of interest were explored, with several levels of complexity for the neural network architecture, and Iwo strategies to deal with Unbalanced data. The best results were obtained for the most complex architecture (Resnet50) with a combination of weighted random sampler and data augmentation achieving a balanced accuracy of 62.26%. This work confirmed that complex problems required a more dense neural network and strategies to deal with the unbalanced data.

2024

A review of machine learning methods for cancer characterization from microbiome data

Autores
Teixeira, M; Silva, F; Ferreira, RM; Pereira, T; Figueiredo, C; Oliveira, HP;

Publicação
NPJ PRECISION ONCOLOGY

Abstract
Recent studies have shown that the microbiome can impact cancer development, progression, and response to therapies suggesting microbiome-based approaches for cancer characterization. As cancer-related signatures are complex and implicate many taxa, their discovery often requires Machine Learning approaches. This review discusses Machine Learning methods for cancer characterization from microbiome data. It focuses on the implications of choices undertaken during sample collection, feature selection and pre-processing. It also discusses ML model selection, guiding how to choose an ML model, and model validation. Finally, it enumerates current limitations and how these may be surpassed. Proposed methods, often based on Random Forests, show promising results, however insufficient for widespread clinical usage. Studies often report conflicting results mainly due to ML models with poor generalizability. We expect that evaluating models with expanded, hold-out datasets, removing technical artifacts, exploring representations of the microbiome other than taxonomical profiles, leveraging advances in deep learning, and developing ML models better adapted to the characteristics of microbiome data will improve the performance and generalizability of models and enable their usage in the clinic.

2024

CNN-based Methods for Survival Prediction using CT images for Lung Cancer Patients

Autores
Amaro, M; Oliveira, HP; Pereira, T;

Publicação
2024 IEEE 37TH INTERNATIONAL SYMPOSIUM ON COMPUTER-BASED MEDICAL SYSTEMS, CBMS 2024

Abstract
Lung Cancer (LC) is still among the top main causes of death worldwide, and it is the leading death number among other cancers. Several AI-based methods have been developed for the early detection of LC, trying to use Computed Tomography (CT) images to identify the initial signs of the disease. The survival prediction could help the clinicians to adequate the treatment plan and all the proceedings, by the identification of the most severe cases that need more attention. In this study, several deep learning models were compared to predict the survival of LC patients using CT images. The best performing model, a CNN with 3 layers, achieved an AUC value of 0.80, a Precision value of 0.56 and a Recall of 0.64. The obtained results showed that CT images carry information that can be used to assess the survival of LC.

2024

Exploring the differences between Multi-task and Single-task with the use of hxplainable AI for lung nodule classification

Autores
Fernandes, L; Pereira, T; Oliveira, HP;

Publicação
2024 IEEE 37TH INTERNATIONAL SYMPOSIUM ON COMPUTER-BASED MEDICAL SYSTEMS, CBMS 2024

Abstract
Currently, lung cancer is one of the deadliest diseases that affects millions of people globally. However, Artificial Intelligence is being increasingly integrated with healthcare practices, with the goal to aid in the early diagnosis of lung cancer. Although such methods have shown very promising results, they still lack transparency to the user, which consequently could make their generalised adoption a challenging task. Therefore, in this work we explore the use of post-hoc explainable methods, to better understand the inner-workings of an already established multitasking framework that executes the segmentation and the classification task of lung nodules simultaneously. The idea behind such study is to understand how a multitasking approach impacts the model's performance in the lung nodule classification task when compared to single-task models. Our results show that the multitasking approach works as an attention mechanism by aiding the model to learn more meaningful features. Furthermore, the multitasking framework was able to achieve a better performance in regard to the explainability metric, with an increase of 7% when compared to our baseline, and also during the classification and segmentation task, with an increase of 4.84% and 15.03%; for each task respectively, when also compared to the studied baselines.

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