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Publications

Publications by Joana Patrícia Morgado

2021

An Interpretable Approach for Lung Cancer Prediction and Subtype Classification using Gene Expression

Authors
Ramos, B; Pereira, T; Moranguinho, J; Morgado, J; Costa, JL; Oliveira, HP;

Publication
2021 43RD ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE & BIOLOGY SOCIETY (EMBC)

Abstract
Lung cancer is the deadliest form of cancer, accounting for 20% of total cancer deaths. It represents a group of histologically and molecularly heterogeneous diseases even within the same histological subtype. Moreover, accurate histological subtype diagnosis influences the specific subtype's target genes, which will help define the treatment plan to target those genes in therapy. Deep learning (DL) models seem to set the benchmarks for the tasks of cancer prediction and subtype classification when using gene expression data; however, these methods do not provide interpretability, which is great concern from the perspective of cancer biology since the identification of the cancer driver genes in an individual provides essential information for treatment and prognosis. In this work, we identify some limitations of previous work that showed efforts to build algorithms to extract feature weights from DL models, and we propose using tree-based learning algorithms that address these limitations. Preliminary results show that our methods outperform those of related research while providing model interpretability.

2021

Attention Based Deep Multiple Instance Learning Approach for Lung Cancer Prediction using Histopathological Images

Authors
Moranguinho, J; Pereira, T; Ramos, B; Morgado, J; Costa, JL; Oliveira, HP;

Publication
2021 43RD ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE & BIOLOGY SOCIETY (EMBC)

Abstract
Deep Neural Networks using histopathological images as an input currently embody one of the gold standards in automated lung cancer diagnostic solutions, with Deep Convolutional Neural Networks achieving the state of the art values for tissue type classification. One of the main reasons for such results is the increasing availability of voluminous amounts of data, acquired through the efforts employed by extensive projects like The Cancer Genome Atlas. Nonetheless, whole slide images remain weakly annotated, as most common pathologist annotations refer to the entirety of the image and not to individual regions of interest in the patient's tissue sample. Recent works have demonstrated Multiple Instance Learning as a successful approach in classification tasks entangled with this lack of annotation, by representing images as a bag of instances where a single label is available for the whole bag. Thus, we propose a bag/embedding-level lung tissue type classifier using Multiple Instance Learning, where the automated inspection of lung biopsy whole slide images determines the presence of cancer in a given patient. Furthermore, we use a post-model interpretability algorithm to validate our model's predictions and highlight the regions of interest for such predictions.

2021

Applying Machine Learning for Traffic Forecasting in Porto, Portugal

Authors
Maia, P; Morgado, J; Goncalves, T; Albuquerque, T;

Publication
MACHINE LEARNING AND PRINCIPLES AND PRACTICE OF KNOWLEDGE DISCOVERY IN DATABASES, PT II

Abstract
Pollutant emissions from passenger cars give rise to harmful effects on human health and the environment. Predicting traffic flow is a challenging problem, but essential to understand what factors influence car traffic and what measures should be taken to reduce carbon dioxide emissions. In this work, we developed a predictive model to forecast traffic flow in several locations in the city of Porto for 24 h later, i.e., the next day at the same time. We trained a XGBoost Regressor with multi-modal data from 2018 and 2019 obtained from traffic and weather sensors of the city of Porto and the geographic location of several points of interest. The proposed model achieved a mean absolute error, mean square error, Spearman's rank correlation coefficient, and Pearson correlation coefficient equal to 80.59, 65395, 0.9162, and 0.7816, respectively, when tested on the test set. The developed model makes it possible to analyse which areas of the city of Porto will have more traffic the next day and take measures to optimise this increasing flow of cars. One of the ideas present in the literature is to develop intelligent traffic lights that change their timers according to the expected traffic in the area. This system could help decrease the levels of carbon dioxide emitted and therefore decrease its harmful effects on the health of the population and the environment.

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