@conference {cCombaliae, title = {Artificial intelligence to predict positivity of sentinel lymph node biopsy in melanoma patients}, booktitle = {European Association of Dermato Oncology (EADO 2022)}, year = {2022}, month = {04/2022}, author = {Marc Combalia and Sebastian Podlipnik and Carlos Hernandez and Sergio Garc{\'\i}a and Joan Ficapal and Julio Burgos and Ver{\'o}nica Vilaplana and Josep Malvehy} } @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 {cHernandeza, title = {Sentinel lymph node status prediction using self-attention networks and contrastive learning from routine histology images of primary tumours}, booktitle = {Medical Imaging with Deep Learning MIDL 2022}, year = {2022}, month = {07/2022}, abstract = {

Deep learning-based computational pathology approaches are becoming increasingly prominent in histopathology image analysis. However, these images typically come with drawbacks that hamper automatic analysis, which include: labeled sample scarcity or the extremely large size of the images (ranging from\ \ to\ \ pixels). Nonetheless, they have proven to be a powerful tool for diagnosis and risk prevention. One such prevention is reducing the number of patients who undergo surgeries that do not benefit them. This study develops a pipeline for predicting sentinel lymph node (SLN) metastasis non-invasively from digitised Whole Slide Images (WSI) of primary melanoma tumours. Furthermore, we combine the use of a weakly supervised architecture with self-supervised contrastive pre-training. We experimentally demonstrate that 1) the use of self-attention improves sentinel lymph node status prediction and 2) self-supervised contrastive learning improves the quality of the learned representations compared to a standard ImageNet pre-training, which boosts the model{\textquoteright}s performance.

}, author = {Carlos Hernandez and Marc Combalia 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} } @mastersthesis {xTarres19, title = {Clasificaci{\'o}n de lesiones de piel con un ensemble de redes neuronales residuales}, year = {2019}, abstract = {

Convolutional Neural Networks have gained popularity in the recent years due to their performance regarding image analysis, both in classification and segmentation. Especially in the medical field, it is increasingly common to use automatic techniques to help specialists with the diagnosis.

In this thesis, the problem of skin lesion classification is studied. The study is based on the ISIC Challenges, given the collaboration with Hospital Cl{\'\i}nic de Barcelona, and we help in the development of the database for the ISIC Challenge 2019.

One of the key points of the development is obtaining a model that manages to classify with accuracy a database provided. To do so, we study residual neural networks and an ensemble of them to further improve the results.

The purpose of this project, therefore is the study, analysis and evaluation of the variants and modifications of residual neural networks so that it adapts to our problem using an ensemble of them. In the process, the neural network will have to tackle the problem of class imbalance

}, author = {Laia Tarr{\'e}s}, editor = {Ver{\'o}nica Vilaplana and Marc Combalia} } @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} } @inbook {bCasamitjana18, title = {Cascaded V-Net Using ROI Masks for Brain Tumor Segmentation}, booktitle = {Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. BrainLes 2017}, volume = { 10670}, number = {Lecture Notes in Computer Science}, year = {2018}, pages = {381-391}, publisher = {Springer}, organization = {Springer}, edition = {Crimi A., Bakas S., Kuijf H., Menze B., Reyes M. (eds)}, address = {Cham}, abstract = {

In this work we approach the brain tumor segmentation problem with a cascade of two CNNs inspired in the V-Net architecture, reformulating residual connections and making use of ROI masks to constrain the networks to train only on relevant voxels. This architecture allows dense training on problems with highly skewed class distributions, such as brain tumor segmentation, by focusing training only on the vecinity of the tumor area. We report results on BraTS2017 Training and Validation sets.

}, isbn = {978-3-319-75238-9}, issn = {978-3-319-75237-2}, doi = {https://doi.org/10.1007/978-3-319-75238-9_33}, url = {https://link.springer.com/chapter/10.1007/978-3-319-75238-9_33}, author = {Adri{\`a} Casamitjana and Marcel Cat{\`a} and Irina S{\'a}nchez and Marc Combalia and Ver{\'o}nica Vilaplana} } @mastersthesis {xPelegri18, title = {Clasificaci{\'o}n de im{\'a}genes histol{\'o}gicas mediante redes neuronales convolucionales}, year = {2018}, author = {Joel Bustos Pelegr{\'\i}}, editor = {Marc Combalia and Ver{\'o}nica Vilaplana} } @inbook {bCombalia18, title = {Monte-Carlo Sampling Applied to Multiple Instance Learning for Histological Image Classification}, booktitle = {Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support}, number = {11045}, year = {2018}, pages = {274-281}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, abstract = {

We propose a patch sampling strategy based on a sequential Monte-Carlo method for high resolution image classification in the context of Multiple Instance Learning. When compared with grid sampling and uniform sampling techniques, it achieves higher generalization performance. We validate the strategy on two artificial datasets and two histological datasets for breast cancer and sun exposure classification.

}, isbn = {978-3-030-00889-5}, issn = {10.1007/978-3-030-00889-5}, doi = {10.1007/978-3-030-00889-5}, author = {Marc Combalia and Ver{\'o}nica Vilaplana} } @conference {cCombaliaa, title = {Monte-Carlo Sampling applied to Multiple Instance Learning for Histological Image Classification}, booktitle = {Workshop on Deep Learning in Medical Image Analysis, MICCAI}, year = {2018}, month = {2018}, address = {Granada, Spain}, abstract = {

We propose a patch sampling strategy based on a sequential Monte-Carlo method for high resolution image classification in the context of Multiple Instance Learning. When compared with grid sampling and uniform sampling techniques, it achieves higher generalization performance. We validate the strategy on two artificial datasets and two histological datasets for breast cancer and sun exposure classification.\ 

}, author = {Marc Combalia and Ver{\'o}nica Vilaplana} } @conference {cCombalia, title = {Monte-Carlo Sampling applied to Multiple Instance Learning for Whole Slide Image Classification}, booktitle = {International Conference on Medical Imaging with Deep Learning}, year = {2018}, month = {07/2018}, address = {Amsterdam, The Netherlands}, author = {Marc Combalia and Ver{\'o}nica Vilaplana} } @conference {cCasamitjanaa, title = {Augmented V-Net for infant brain segmentation}, booktitle = {MICCAI Grand Challenge on 6-month Infant Brain MRI Segmentation, MICCAI 2017}, year = {2017}, month = {09/2017}, author = {Adri{\`a} Casamitjana and Irina S{\'a}nchez and Marc Combalia and Ver{\'o}nica Vilaplana} } @conference {cCasamitjana, title = {Augmented V-Net for White Matter Hyperintensities segmentation}, booktitle = {WMH Segmentation Challenge, Brain-lesion Workshop, MICCAI 2017 }, year = {2017}, month = {09/2017}, author = {Adri{\`a} Casamitjana and Irina S{\'a}nchez and Marc Combalia and Ver{\'o}nica Vilaplana} } @conference {cCata, title = {Masked V-Net: an approach to brain tumor segmentation}, booktitle = {Multimodal Brain Tumor Segmentation Benchmark, Brain-lesion Workshop, MICCAI 2017 }, year = {2017}, month = {09/2017}, author = {Marcel Cat{\`a} and Adri{\`a} Casamitjana and Irina S{\'a}nchez and Marc Combalia and Ver{\'o}nica Vilaplana} }