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Publications

Publications by LIAAD

2022

Association between co-morbidities and prescribed drugs in obstructive sleep apnea suspected patients: an inductive rule learning approach (Preprint)

Authors
Ferreira-Santos, D; Pereira Rodrigues, P;

Publication
Journal of Medical Internet Research

Abstract

2022

Effectiveness of Secondary Risk–Reducing Strategies in Patients with Unilateral Breast Cancer with Pathogenic Variants of BRCA1 and BRCA2 Subjected to Breast-Conserving Surgery: Evidence-Based Simulation Study

Authors
Maksimenko, J; Rodrigues, PP; Nakazawa Miklaševica, M; Pinto, D; Miklaševics, E; Trofimovics, G; Gardovskis, J; Cardoso, F; Cardoso, MJ;

Publication
JMIR Formative Research

Abstract
Background: Approximately 62% of patients with breast cancer with a pathogenic variant (BRCA1 or BRCA2) undergo primary breast-conserving therapy. Objective: The study aims to develop a personalized risk management decision support tool for carriers of a pathogenic variant (BRCA1 or BRCA2) who underwent breast-conserving therapy for unilateral early-stage breast cancer. Methods: We developed a Bayesian network model of a hypothetical cohort of carriers of BRCA1 or BRCA2 diagnosed with stage I/II unilateral breast cancer and treated with breast-conserving treatment who underwent subsequent second primary cancer risk–reducing strategies. Using event dependencies structured according to expert knowledge and conditional probabilities obtained from published evidence, we predicted the 40-year overall survival rate of different risk-reducing strategies for 144 cohorts of women defined by the type of pathogenic variants (BRCA1 or BRCA2), age at primary breast cancer diagnosis, breast cancer subtype, stage of primary breast cancer, and presence or absence of adjuvant chemotherapy. Results: Absence of adjuvant chemotherapy was the most powerful factor that was linked to a dramatic decline in survival. There was a negligible decline in the mortality in patients with triple-negative breast cancer, who received no chemotherapy and underwent any secondary risk–reducing strategy, compared with surveillance. The potential survival benefit from any risk-reducing strategy was more modest in patients with triple-negative breast cancer who received chemotherapy compared with patients with luminal breast cancer. However, most patients with triple-negative breast cancer in stage I benefited from bilateral risk-reducing mastectomy and risk-reducing salpingo-oophorectomy or just risk-reducing salpingo-oophorectomy. Most patients with luminal stage I/II unilateral breast cancer benefited from bilateral risk-reducing mastectomy and risk-reducing salpingo-oophorectomy. The impact of risk-reducing salpingo-oophorectomy in patients with luminal breast cancer in stage I/II increased with age. Most older patients with the BRCA1 and BRCA2 pathogenic variants in exons 12-24/25 with luminal breast cancer may gain a similar survival benefit from other risk-reducing strategies or surveillance. Conclusions: Our study showed that it is mandatory to consider the complex interplay between the types of BRCA1 and BRCA2 pathogenic variants, age at primary breast cancer diagnosis, breast cancer subtype and stage, and received systemic treatment. As no prospective study results are available at the moment, our simulation model, which will integrate a decision support system in the near future, could facilitate the conversation between the health care provider and patient and help to weigh all the options for risk-reducing strategies leading to a more balanced decision. ©Jelena Maksimenko, Pedro Pereira Rodrigues, Miki Nakazawa-Miklaševica, David Pinto, Edvins Miklaševics, Genadijs Trofimovics, Janis Gardovskis, Fatima Cardoso, Maria João Cardoso.

2022

Helping early obstructive sleep apnea diagnosis with machine learning: A systematic review (Preprint)

Authors
Ferreira-Santos, D; Amorim, P; Silva Martins, T; Monteiro-Soares, M; Pereira Rodrigues, P;

Publication

Abstract
BACKGROUND

American Academy of Sleep Medicine guidelines suggests that clinical prediction algorithms can be used to screen obstructive sleep apnea (OSA) patients without replacing polysomnography (PSG) – the gold standard.

OBJECTIVE

We aimed to identify, gather, and analyze existing machine learning approaches that are being used for disease screening in adult patients suspected of OSA.

METHODS

We searched MEDLINE, Scopus and ISI Web of Knowledge databases for evaluating the validity of different machine learning techniques, with PSG as the gold standard outcome measures. This systematic review was registered in PROSPERO under reference CRD42021221339.

RESULTS

Our search retrieved 5479 articles, of which 63 articles were included. We found 23 studies performing diagnostic models’ development alone, 26 with added internal validation, and 14 applying the clinical prediction algorithm to an independent sample (although not all reporting the most common discrimination metrics - sensitivity and/or specificity). Logistic regression was applied in 35 studies, linear regression in 16, support vector machine in 9, neural networks in 8, decision trees in 6, and Bayesian networks in 4. Random forest, discriminant analysis, classification and regression tree, and nomogram were each performed in 2 studies, while Pearson correlation, adaptative neuro-fuzzy inference system, artificial immune recognition system, genetic algorithm, supersparse linear integer models, and k-nearest neighbors’ algorithm each in 1 study. The best AUC was .98 [.96-.99] for age, waist circumference, Epworth somnolence, and oxygen saturation as predictors in a logistic regression.

CONCLUSIONS

Although high values were obtained, they still lack external validation results in large cohorts and a standard OSA criteria definition.

2022

Effectiveness of Secondary Risk-Reducing Strategies in Patients With Unilateral Breast Cancer With Pathogenic Variants of BRCA1 and BRCA2 Subjected to Breast-Conserving Surgery: Evidence-Based Simulation Study

Authors
Maksimenko, J; Rodrigues, PP; Nakazawa Miklasevica, M; Pinto, D; Miklasevics, E; Trofimovics, G; Gardovskis, J; Cardoso, F; Cardoso, MJ;

Publication
JMIR FORMATIVE RESEARCH

Abstract
Background: Approximately 62% of patients with breast cancer with a pathogenic variant (BRCA1 or BRCA2) undergo primary breast-conserving therapy. Objective: The study aims to develop a personalized risk management decision support tool for carriers of a pathogenic variant (BRCA1 or BRCA2) who underwent breast-conserving therapy for unilateral early-stage breast cancer. Methods: We developed a Bayesian network model of a hypothetical cohort of carriers of BRCA1 or BRCA2 diagnosed with stage I/II unilateral breast cancer and treated with breast-conserving treatment who underwent subsequent second primary cancer risk-reducing strategies. Using event dependencies structured according to expert knowledge and conditional probabilities obtained from published evidence, we predicted the 40-year overall survival rate of different risk-reducing strategies for 144 cohorts of women defined by the type of pathogenic variants (BRCA1 or BRCA2), age at primary breast cancer diagnosis, breast cancer subtype, stage of primary breast cancer, and presence or absence of adjuvant chemotherapy. Results: Absence of adjuvant chemotherapy was the most powerful factor that was linked to a dramatic decline in survival. There was a negligible decline in the mortality in patients with triple-negative breast cancer, who received no chemotherapy and underwent any secondary risk-reducing strategy, compared with surveillance. The potential survival benefit from any risk-reducing strategy was more modest in patients with triple-negative breast cancer who received chemotherapy compared with patients with luminal breast cancer. However, most patients with triple-negative breast cancer in stage I benefited from bilateral risk-reducing mastectomy and risk-reducing salpingo-oophorectomy or just risk-reducing salpingo-oophorectomy. Most patients with luminal stage I/II unilateral breast cancer benefited from bilateral risk-reducing mastectomy and risk-reducing salpingo-oophorectomy. The impact of risk-reducing salpingo-oophorectomy in patients with luminal breast cancer in stage I/II increased with age. Most older patients with the BRCA1 and BRCA2 pathogenic variants in exons 12-24/25 with luminal breast cancer may gain a similar survival benefit from other risk-reducing strategies or surveillance. Conclusions: Our study showed that it is mandatory to consider the complex interplay between the types of BRCA1 and BRCA2 pathogenic variants, age at primary breast cancer diagnosis, breast cancer subtype and stage, and received systemic treatment. As no prospective study results are available at the moment, our simulation model, which will integrate a decision support system in the near future, could facilitate the conversation between the health care provider and patient and help to weigh all the options for risk-reducing strategies leading to a more balanced decision.

2022

Detection of Loanwords in Angolan Portuguese: A Text Mining Approach

Authors
Muhongo, TS; Brazdil, PB; Silva, F;

Publication
INTELIGENCIA ARTIFICIAL-IBEROAMERICAL JOURNAL OF ARTIFICIAL INTELLIGENCE

Abstract
Angola is characterized by many different languages and social, cultural and political realities, which had a marked effect on Angolan Portuguese (AP). Consequently, AP is characterized by diatopic variation. One of the marked effects is the loanwords imported from other Angolan languages. Our objective is to analyze different Angolan texts, analyze the lexical forms used and conduct a comparative study with European Portuguese, aiming at identifying the possible loanwords in Angolan Portuguese. This process was automated, as well as the identification of all loanwords' cotexts. In addition, we determine the lexical class of each loanword and the Angolan language of its origin. Most lexical loanwords come from the Kimbundu, although AP includes loanwords from some other Angolan languages too. Our study serves as a basis for preparing an Angolan regionalism dictionary. We noticed that more than 700 identified loanwords do not figure in the existing dictionaries.

2022

Semi-Automatic Approaches for Exploiting Shifter Patterns in Domain-Specific Sentiment Analysis

Authors
Brazdil, P; Muhammad, SH; Oliveira, F; Cordeiro, J; Silva, F; Silvano, P; Leal, A;

Publication
MATHEMATICS

Abstract
This paper describes two different approaches to sentiment analysis. The first is a form of symbolic approach that exploits a sentiment lexicon together with a set of shifter patterns and rules. The sentiment lexicon includes single words (unigrams) and is developed automatically by exploiting labeled examples. The shifter patterns include intensification, attenuation/downtoning and inversion/reversal and are developed manually. The second approach exploits a deep neural network, which uses a pre-trained language model. Both approaches were applied to texts on economics and finance domains from newspapers in European Portuguese. We show that the symbolic approach achieves virtually the same performance as the deep neural network. In addition, the symbolic approach provides understandable explanations, and the acquired knowledge can be communicated to others. We release the shifter patterns to motivate future research in this direction.

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