@conference {cHernandez22a, title = {Contrastive and attention-based multiple instance learning for the prediction of sentinel lymph node status from histopathologies of primary melanoma tumours.}, booktitle = {Cancer Prevention through early detecTion (Caption) Workshop at 25th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2022)}, year = {2022}, month = {09/2022}, abstract = {

Sentinel lymph node status is a crucial prognosis factor for melanomas; nonetheless, the invasive surgery required to obtain it always puts the patient at risk. In this study, we develop a Deep Learning-based approach to predict lymph node metastasis from Whole Slide Images of primary tumours. Albeit very informative, these images come with complexities that hamper their use in machine learning applications, namely their large size and limited datasets. We propose a pre-training strategy based on self-supervised contrastive learning to extract better image feature representations and an attention-based Multiple Instance Learning approach to enhance the model{\textquoteright}s performance. With this work, we quantitatively demonstrate that combining both methods improves various classification metrics and qualitatively show that contrastive learning encourages the network to output higher attention scores to tumour tissue and lower scores to image artifacts.

}, author = {Carlos Hernandez and Marc Combalia and Susana Puig and Josep Malvehy and Ver{\'o}nica Vilaplana} } @conference {cHernandez22, title = {Sentinel lymph node status prediction with self-attention neural networks using histologies of primary melanoma tumours}, booktitle = {European Association of Dermato Oncology (EADO 2022)}, year = {2022}, month = {04/2022}, author = {Carlos Hernandez and Ver{\'o}nica Vilaplana and Marc Combalia and Sergio Garc{\'\i}a and Sebastian Podlipnik and Julio Burgos and Susana Puig and Josep Malvehy} } @conference {cHernandez, title = {Implementation of personalized medicine in cutaneous melanoma patients aided by artificial intelligence}, booktitle = {10th World Congress of2 Melanoma / 17th EADO Congress}, year = {2021}, month = {04/2021}, author = {Carlos Hernandez and Anil Kiroglu and Sergio Garc{\'\i}a and Joan Ficapal and Julio Burgos and Sebastian Podlipnik and Neus Calbet and Susana Puig and Josep Malvehy and Ver{\'o}nica Vilaplana and Marc Combalia} } @conference {cPodlipnik21, title = {Personalized medicine in melanoma patients aided by artificial intelligence}, booktitle = {Clinical Translation of Medical Image Computing and Computer Assisted Interventions (CLINICCAI) Workshop at MICCAI}, year = {2021}, month = {09/2021}, abstract = {

The 8th Edition of the American Joint Committee on Cancer (AJCC) staging system1 is the current standard for classifying patients into prognostic and treatment groups. This classification is used to predict the evolution of the patient, and therefore treatment actions provided to the individual. However, patients at the same stage behave differently, indicating that the current classification system is often insufficient to provide a customized prognosis for each patient2. It is, therefore, necessary to improve patient classification into prognostic groups. Furthermore, patients{\textquoteright} systemic and surgical treatments often involve significant toxicities and morbidities that impact their quality of life (i.e., sentinel node biopsy is not needed for 80\% of the melanoma patients, 50\% of patients do not benefit from adjuvant treatment)3. Therefore, melanoma patients should benefit from a more precise risk estimation.

We create a survival dataset for melanoma risk estimation and train survival XGBoost algorithms4 to predict the mortality, relapse, and metastasis risk. We compare their performance to the AJCC 2018 risk stratification system. Furthermore, we train classifiers to predict the risk of a positive lymph node biopsy and distant metastasis on melanoma patients and compare the performance of the proposed system to the clinical practice.

}, author = {Sebastian Podlipnik and Carlos Hernandez and Anil Kiroglu and Sergio Garc{\'\i}a and Joan Ficapal and Julio Burgos and Neus Calbet and Susana Puig and Josep Malvehy and Ver{\'o}nica Vilaplana and Marc Combalia} } @conference {cCombaliad, title = {Uncertainty Estimation in Deep Neural Networks for Dermoscopic Image Classification}, booktitle = {CVPR 2020, ISIC Skin Image Analysis Workshop}, year = {2020}, month = {2020}, abstract = {

The high performance of machine learning algorithms for the task of skin lesion classification has been shown over the past few years. However, real-world implementations are still scarce. One of the reasons could be that most methods do not quantify the uncertainty in the predictions and are not able to detect data that is anomalous or significantly different from that used in training, which may lead to a lack of confidence in the automated diagnosis or errors in the interpretation of results.

In this work, we explore the use of uncertainty estimation techniques and metrics for deep neural networks based on Monte-Carlo sampling and apply them to the problem of skin lesion classification on data from ISIC Challenges 2018 and 2019.

Our results show that uncertainty metrics can be successfully used to detect difficult and out-of-distribution samples.

}, author = {Marc Combalia and Ferran Hueto and Susana Puig and Josep Malvehy and Ver{\'o}nica Vilaplana} } @conference {cCombaliac, title = {BCN20000: Dermoscopic Lesions in the Wild}, booktitle = {International Skin Imaging Collaboration (ISIC) Challenge on Dermoscopic Skin Lesion Analysis 2019}, year = {2019}, month = {10/2019}, abstract = {

This article summarizes the BCN20000 dataset, composed of 19424 dermoscopic images of skin lesions captured from 2010 to 2016 in the facilities of the Hospital Cl{\'\i}nic in Barcelona. With this dataset, we aim to study the problem of unconstrained classification of dermoscopic images of skin cancer, including lesions found in hard-to-diagnose locations (nails and mucosa), large lesions which do not fit in the aperture of the dermoscopy device, and hypo-pigmented lesions. The BCN20000 will be provided to the participants of the ISIC Challenge 2019 \cite{ISIC2019}, where they will be asked to train algorithms to classify dermoscopic images of skin cancer automatically.

}, author = {Marc Combalia and Noel C. F. Codella and Veronica Rotemberg and Brian Helba and Ver{\'o}nica Vilaplana and Ofer Reiter and Cristina Carrera and Alicia Barreiro and Allan C. Halpern and Susana Puig and Josep Malvehy} } @conference {cCombaliab, title = {Digitally Stained Confocal Microscopy through Deep Learning}, booktitle = {International Conference on Medical Imaging with Deep Learning (MIDL 2019)}, year = {2019}, month = {07/2019}, address = {London}, abstract = {

Specialists have used confocal microscopy in the ex-vivo modality to identify tumors with\ an overall sensitivity of 96.6\% and specicity of 89.2\%. However, this technology hasn{\textquoteright}t\ established yet in the standard clinical practice because most pathologists lack the knowledge to interpret its output. In this paper we propose a combination of deep learning and\ computer vision techniques to digitally stain confocal microscopy images into H\&E-like\ slides, enabling pathologists to interpret these images without specic training. We use a\ fully convolutional neural network with a multiplicative residual connection to denoise the\ confocal microscopy images, and then stain them using a Cycle Consistency Generative\ Adversarial Network.

}, author = {Marc Combalia and Javiera P{\'e}rez-Anker and Adriana Garc{\'\i}a-Herrera and Ll{\'u}cia Alos and Ver{\'o}nica Vilaplana and Ferran Marques and Susana Puig and Josep Malvehy} }