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Publications

Publications by Jaime Cardoso

2018

Supervised deep learning embeddings for the prediction of cervical cancer diagnosis

Authors
Fernandes, K; Chicco, D; Cardoso, JS; Fernandes, J;

Publication
PEERJ COMPUTER SCIENCE

Abstract
Cervical cancer remains a significant cause of mortality all around the world, even if it can be prevented and cured by removing affected tissues in early stages. Providing universal and efficient access to cervical screening programs is a challenge that requires identifying vulnerable individuals in the population, among other steps. In this work, we present a computationally automated strategy for predicting the outcome of the patient biopsy, given risk patterns from individual medical records. We propose a machine learning technique that allows a joint and fully supervised optimization of dimensionality reduction and classification models. We also build a model able to highlight relevant properties in the low dimensional space, to ease the classification of patients. We instantiated the proposed approach with deep learning architectures, and achieved accurate prediction results (top area under the curve AUC = 0.6875) which outperform previously developed methods, such as denoising autoencoders. Additionally, we explored some clinical findings from the embedding spaces, and we validated them through the medical literature, making them reliable for physicians and biomedical researchers.

2018

A Class Imbalance Ordinal Method for Alzheimer's Disease Classification

Authors
Cruz, R; Silveira, M; Cardoso, JS;

Publication
2018 International Workshop on Pattern Recognition in Neuroimaging, PRNI 2018, Singapore, Singapore, June 12-14, 2018

Abstract
The majority of computer-Aided diagnosis methods for Alzheimer's disease (AD) from brain images either address only two stages of the disease at a time (and reduce the problem to binary classification) or do not exploit the ordinal nature of the different classes. An exception is the work by Fan et al. [1], which proposed an ordinal method that obtained better performance than traditional multiclass classification. Still, special care should be taken when data is class imbalanced, i.e. when some classes are overly represented when compared to others. Building on top of [1], this work makes use of a recently published ordinal classifier, which transforms the problem into sets of pairwise ranking problems, in order to address the class imbalance in the data [2]. Several methods were experimented with, using a Support Vector Machine as the underlying estimator. The pairwise ranking approach has shown promising results, both for traditional and imbalance metrics. © 2018 IEEE.

2018

The value of 3D images in the aesthetic evaluation of breast cancer conservative treatment. Results from a prospective multicentric clinical trial

Authors
Cardoso, MJ; Vrieling, C; Cardoso, JS; Oliveira, HP; Williams, NR; Dixon, JM; Gouveia, P; Keshtgar, M; Mosahebi, A; Bishop, D; Lacher, R; Liefers, GJ; Molenkamp, B; Van de Velde, C; Azevedo, I; Canny, R; Christie, D; Evans, A; Fitzal, F; Graham, P; Hamdi, M; Joahensen, J; Laws, S; Merck, B; Reece, G; Sacchini, V; Vrancken, MJ; Wilkinson, L; Matthes, GZ;

Publication
BREAST

Abstract
Purpose: BCCT.core (Breast Cancer Conservative Treatment. cosmetic results) is a software created for the objective evaluation of aesthetic result of breast cancer conservative treatment using a single patient frontal photography. The lack of volume information has been one criticism, as the use of 3D information might improve accuracy in aesthetic evaluation. In this study, we have evaluated the added value of 3D information to two methods of aesthetic evaluation: a panel of experts; and an augmented version of the computational model - BCCT.core3d. Material and methods: Within the scope of EU Seventh Framework Programme Project PICTURE, 2D and 3D images from 106 patients from three clinical centres were evaluated by a panel of 17 experts and the BCCT.core. Agreement between all methods was calculated using the kappa (K) and weighted kappa (wK) statistics. Results: Subjective agreement between 2D and 3D individual evaluation was fair to moderate. The agreement between the expert classification and the BCCT.core software with both 2D and 3D features was also fair to moderate. Conclusions: The inclusion of 3D images did not add significant information to the aesthetic evaluation either by the panel or the software. Evaluation of aesthetic outcome can be performed using of the BCCT.core software, with a single frontal image.

2018

Binary ranking for ordinal class imbalance

Authors
Cruz, R; Fernandes, K; Costa, JFP; Ortiz, MP; Cardoso, JS;

Publication
PATTERN ANALYSIS AND APPLICATIONS

Abstract
Imbalanced classification has been extensively researched in the last years due to its prevalence in real-world datasets, ranging from very different topics such as health care or fraud detection. This literature has long been dominated by variations of the same family of solutions (e.g. mainly resampling and cost-sensitive learning). Recently, a new and promising way of tackling this problem has been introduced: learning with scoring pairwise ranking so that each pair of classes contribute in tandem to the decision boundary. In this sense, the paper addresses the problem of class imbalance in the context of ordinal regression, proposing two novel contributions: (a) approaching the imbalance by binary pairwise ranking using a well-known label decomposition ensemble, and (b) introducing a regularization into this ensemble so that parallel decision boundaries are favored. These are two independent contributions that synergize well. Our model is tested using linear Support Vector Machines and our results are compared against state-of-the-art models. Both approaches show promising performance in ordinal class imbalance, with an overall 15% improvement relative to the state-of-the-art, as evaluated by a balanced metric.

2018

A Uniform Performance Index for Ordinal Classification with Imbalanced Classes

Authors
Silva, W; Pinto, JR; Cardoso, JS;

Publication
2018 INTERNATIONAL JOINT CONFERENCE ON NEURAL NETWORKS (IJCNN)

Abstract
Ordinal classification is a specific and demanding task, where the aim is not only to increase accuracy, but to also capture the natural order between the classes, and penalize incorrect predictions by how much they deviate from this ranking. If an ordinal classifier must be able to comply with all these requirements, a suitable ordinal metric must be able to accurately measure its degree of compliance. However, the current metrics are unable to completely capture these considerations when assessing classification performance. Moreover, most suffer from sensitivity to imbalanced classes, very common in ordinal classification. In this paper, we propose two variants of a novel performance index that accounts for both accuracy and ranking in the performance assessment of ordinal classification, and is robust against imbalanced classes. © 2018 IEEE.

2018

Deep Image Segmentation by Quality Inference

Authors
Fernandes, K; Cruz, R; Cardoso, JS;

Publication
2018 INTERNATIONAL JOINT CONFERENCE ON NEURAL NETWORKS (IJCNN)

Abstract
Traditionally, convolutional neural networks are trained for semantic segmentation by having an image given as input and the segmented mask as output. In this work, we propose a neural network trained by being given an image and mask pair, with the output being the quality of that pairing. The segmentation is then created afterwards through backpropagation on the mask. This allows enriching training with semi-supervised synthetic variations on the ground-truth. The proposed iterative segmentation technique allows improving an existing segmentation or creating one from scratch. We compare the performance of the proposed methodology with state-of-the-art deep architectures for image segmentation and achieve competitive results, being able to improve their segmentations. © 2018 IEEE.

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