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Publications

Publications by Hélder Filipe Oliveira

2023

Machine learning-based approaches for cancer prediction using microbiome data

Authors
Freitas, P; Silva, F; Sousa, JV; Ferreira, RM; Figueiredo, C; Pereira, T; Oliveira, HP;

Publication
SCIENTIFIC REPORTS

Abstract
Emerging evidence of the relationship between the microbiome composition and the development of numerous diseases, including cancer, has led to an increasing interest in the study of the human microbiome. Technological breakthroughs regarding DNA sequencing methods propelled microbiome studies with a large number of samples, which called for the necessity of more sophisticated data-analytical tools to analyze this complex relationship. The aim of this work was to develop a machine learning-based approach to distinguish the type of cancer based on the analysis of the tissue-specific microbial information, assessing the human microbiome as valuable predictive information for cancer identification. For this purpose, Random Forest algorithms were trained for the classification of five types of cancer-head and neck, esophageal, stomach, colon, and rectum cancers-with samples provided by The Cancer Microbiome Atlas database. One versus all and multi-class classification studies were conducted to evaluate the discriminative capability of the microbial data across increasing levels of cancer site specificity, with results showing a progressive rise in difficulty for accurate sample classification. Random Forest models achieved promising performances when predicting head and neck, stomach, and colon cancer cases, with the latter returning accuracy scores above 90% across the different studies conducted. However, there was also an increased difficulty when discriminating esophageal and rectum cancers, failing to differentiate with adequate results rectum from colon cancer cases, and esophageal from head and neck and stomach cancers. These results point to the fact that anatomically adjacent cancers can be more complex to identify due to microbial similarities. Despite the limitations, microbiome data analysis using machine learning may advance novel strategies to improve cancer detection and prevention, and decrease disease burden.

2023

Transformers for Energy Forecast

Authors
Oliveira, HS; Oliveira, HP;

Publication
SENSORS

Abstract
Forecasting energy consumption models allow for improvements in building performance and reduce energy consumption. Energy efficiency has become a pressing concern in recent years due to the increasing energy demand and concerns over climate change. This paper addresses the energy consumption forecast as a crucial ingredient in the technology to optimize building system operations and identifies energy efficiency upgrades. The work proposes a modified multi-head transformer model focused on multi-variable time series through a learnable weighting feature attention matrix to combine all input variables and forecast building energy consumption properly. The proposed multivariate transformer-based model is compared with two other recurrent neural network models, showing a robust performance while exhibiting a lower mean absolute percentage error. Overall, this paper highlights the superior performance of the modified transformer-based model for the energy consumption forecast in a multivariate step, allowing it to be incorporated in future forecasting tasks, allowing for the tracing of future energy consumption scenarios according to the current building usage, playing a significant role in creating a more sustainable and energy-efficient building usage.

2023

Evaluating the ability of an artificial-intelligence cloud-based platform designed to provide information prior to locoregional therapy for breast cancer in improving patient's satisfaction with therapy: The CINDERELLA trial

Authors
Kaidar Person, O; Antunes, M; Cardoso, S; Ciani, O; Cruz, H; Di Micco, R; Gentilini, D; Gonçalves, T; Gouveia, P; Heil, J; Kabata, P; Lopes, D; Martinho, M; Martins, H; Mavioso, C; Mika, M; Montenegro, H; Oliveira, P; Pfob, A; Rotmensz, N; Schinköthe, T; Silva, G; Tarricone, R; Cardoso, M;

Publication
PLOS ONE

Abstract
BackgroundBreast cancer therapy improved significantly, allowing for different surgical approaches for the same disease stage, therefore offering patients different aesthetic outcomes with similar locoregional control. The purpose of the CINDERELLA trial is to evaluate an artificial-intelligence (AI) cloud-based platform (CINDERELLA platform) vs the standard approach for patient education prior to therapy. MethodsA prospective randomized international multicentre trial comparing two methods for patient education prior to therapy. After institutional ethics approval and a written informed consent, patients planned for locoregional treatment will be randomized to the intervention (CINDERELLA platform) or controls. The patients in the intervention arm will use the newly designed web-application (CINDERELLA platform, CINDERELLA APProach) to access the information related to surgery and/or radiotherapy. Using an AI system, the platform will provide the patient with a picture of her own aesthetic outcome resulting from the surgical procedure she chooses, and an objective evaluation of this aesthetic outcome (e.g., good/fair). The control group will have access to the standard approach. The primary objectives of the trial will be i) to examine the differences between the treatment arms with regards to patients' pre-treatment expectations and the final aesthetic outcomes and ii) in the experimental arm only, the agreement of the pre-treatment AI-evaluation (output) and patient's post-therapy self-evaluation. DiscussionThe project aims to develop an easy-to-use cost-effective AI-powered tool that improves shared decision-making processes. We assume that the CINDERELLA APProach will lead to higher satisfaction, better psychosocial status, and wellbeing of breast cancer patients, and reduce the need for additional surgeries to improve aesthetic outcome.

2023

Evaluation of Regularization Techniques for Transformers-Based Models

Authors
Oliveira, HS; Ribeiro, PP; Oliveira, HP;

Publication
Pattern Recognition and Image Analysis - 11th Iberian Conference, IbPRIA 2023, Alicante, Spain, June 27-30, 2023, Proceedings

Abstract

2023

Single Modality vs. Multimodality: What Works Best for Lung Cancer Screening?

Authors
Sousa, JV; Matos, P; Silva, F; Freitas, P; Oliveira, HP; Pereira, T;

Publication
SENSORS

Abstract
In a clinical context, physicians usually take into account information from more than one data modality when making decisions regarding cancer diagnosis and treatment planning. Artificial intelligence-based methods should mimic the clinical method and take into consideration different sources of data that allow a more comprehensive analysis of the patient and, as a consequence, a more accurate diagnosis. Lung cancer evaluation, in particular, can benefit from this approach since this pathology presents high mortality rates due to its late diagnosis. However, many related works make use of a single data source, namely imaging data. Therefore, this work aims to study the prediction of lung cancer when using more than one data modality. The National Lung Screening Trial dataset that contains data from different sources, specifically, computed tomography (CT) scans and clinical data, was used for the study, the development and comparison of single-modality and multimodality models, that may explore the predictive capability of these two types of data to their full potential. A ResNet18 network was trained to classify 3D CT nodule regions of interest (ROI), whereas a random forest algorithm was used to classify the clinical data, with the former achieving an area under the ROC curve (AUC) of 0.7897 and the latter 0.5241. Regarding the multimodality approaches, three strategies, based on intermediate and late fusion, were implemented to combine the information from the 3D CT nodule ROIs and the clinical data. From those, the best model-a fully connected layer that receives as input a combination of clinical data and deep imaging features, given by a ResNet18 inference model-presented an AUC of 0.8021. Lung cancer is a complex disease, characterized by a multitude of biological and physiological phenomena and influenced by multiple factors. It is thus imperative that the models are capable of responding to that need. The results obtained showed that the combination of different types may have the potential to produce more comprehensive analyses of the disease by the models.

2007

Synchronization software for automation in anesthesia

Authors
Bressan, N; Castro, A; Bras, S; Oliveira, HP; Ribeiro, L; Ferreira, DA; Antunes, L; Amorim, P; Nunes, CS;

Publication
2007 ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-16

Abstract
This work presents the development of a software for data acquisition and control (ASYS) on a clinical setup. Similar to the industrial Supervisory Control And Data Acquisition (SCADA) the software assembles a Target Controlled Infusion (TCI) monitoring and supervisory control data in real time from devices in a surgical room. The software is not a full controller since the TCI systems comprehend permanent interaction from the anesthesiologist Based on pharmacokinetic models, the effect-site and plasma concentrations can be related with the drug dose infused and vice versa. The software determines the infusion rates of the drug which are given as commands to the infusion pumps. This software provides the anesthesiologist with a trustworthy tool for managing a safe and balanced anesthesia. Since it also incorporates the acquisition and display of patients brain signals.

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