Cookies Policy
The website need some cookies and similar means to function. If you permit us, we will use those means to collect data on your visits for aggregated statistics to improve our service. Find out More
Accept Reject
  • Menu
Publications

Publications by CTM

2024

Radiological Medical Imaging Annotation and Visualization Tool

Authors
Teiga, I; Sousa, JV; Silva, F; Pereira, T; Oliveira, HP;

Publication
UNIVERSAL ACCESS IN HUMAN-COMPUTER INTERACTION, PT III, UAHCI 2024

Abstract
Significant medical image visualization and annotation tools, tailored for clinical users, play a crucial role in disease diagnosis and treatment. Developing algorithms for annotation assistance, particularly machine learning (ML)-based ones, can be intricate, emphasizing the need for a user-friendly graphical interface for developers. Many software tools are available to meet these requirements, but there is still room for improvement, making the research for new tools highly compelling. The envisioned tool focuses on navigating sequences of DICOM images from diverse modalities, including Magnetic Resonance Imaging (MRI), Computed Tomography (CT) scans, Ultrasound (US), and X-rays. Specific requirements involve implementing manual annotation features such as freehand drawing, copying, pasting, and modifying annotations. A scripting plugin interface is essential for running Artificial Intelligence (AI)-based models and adjusting results. Additionally, adaptable surveys complement graphical annotations with textual notes, enhancing information provision. The user evaluation results pinpointed areas for improvement, including incorporating some useful functionalities, as well as enhancements to the user interface for a more intuitive and convenient experience. Despite these suggestions, participants praised the application's simplicity and consistency, highlighting its suitability for the proposed tasks. The ability to revisit annotations ensures flexibility and ease of use in this context.

2024

Deep Learning Models to Predict Brain Cancer Grade Through MRI Analysis

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

Publication
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

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

Publication
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

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

Publication
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

Causal representation learning through higher-level information extraction

Authors
Silva, F; P. Oliveira, H; Pereira, T;

Publication
ACM Computing Surveys

Abstract
The large gap between the generalization level of state-of-the-art machine learning and human learning systems calls for the development of artificial intelligence (AI) models that are truly inspired by human cognition. In tasks related to image analysis, searching for pixel-level regularities has reached a power of information extraction still far from what humans capture with image-based observations. This leads to poor generalization when even small shifts occur at the level of the observations. We explore a perspective on this problem that is directed to learning the generative process with causality-related foundations, using models capable of combining symbolic manipulation, probabilistic reasoning and pattern recognition abilities. We briefly review and explore connections of research from machine learning, cognitive science and related fields of human behavior to support our perspective for the direction to more robust and human-like artificial learning systems.

2024

Tutorial on the Use of the Photon Diffusion Approximation for Fast Calculation of Tissue Optical Properties

Authors
Pinheiro, MR; Carvalho, MI; Oliveira, LM;

Publication
JOURNAL OF BIOPHOTONICS

Abstract
Computer simulations, which are performed at a single wavelength at a time, have been traditionally used to estimate the optical properties of tissues. The results of these simulations need to be interpolated. For a broadband estimation of tissue optical properties, the use of computer simulations becomes time consuming and computer demanding. When spectral measurements are available for a tissue, the use of the photon diffusion approximation can be done to perform simple and direct calculations to obtain the broadband spectra of some optical properties. The additional estimation of the reduced scattering coefficient at a small number of discrete wavelengths allows to perform further calculations to obtain the spectra of other optical properties. This study used spectral measurements from the heart muscle to explain the calculation pipeline to obtain a complete set of the spectral optical properties and to show its versatility for use with other tissues for various biophotonics applications.

  • 6
  • 328