@article{PereiraPereiraSilvaetal., author = {Pereira, Clayton R. and Pereira, Danilo R. and Silva, Francisco A. and Masieiro, Joao P. and Weber, Silke A. T. and Hook, Christian and Papa, Jo{\~a}o Paulo}, title = {A new computer vision-based approach to aid the diagnosis of Parkinson's disease}, series = {Computer Methods and Programs in Biomedicine}, volume = {136}, journal = {Computer Methods and Programs in Biomedicine}, publisher = {Elsevier}, doi = {10.1016/j.cmpb.2016.08.005}, pages = {79 -- 88}, abstract = {Background and Objective: Even today, pointing out an exam that can diagnose a patient with Parkinson's disease (PD) accurately enough is not an easy task. Although a number of techniques have been used in search for a more precise method, detecting such illness and measuring its level of severity early enough to postpone its side effects are not straightforward. In this work, after reviewing a considerable number of works, we conclude that only a few techniques address the problem of PD recognition by means of micrography using computer vision techniques. Therefore, we consider the problem of aiding automatic PD diagnosis by means of spirals and meanders filled out in forms, which are then compared with the template for feature extraction. Methods: In our work, both the template and the drawings are identified and separated automatically using image processing techniques, thus needing no user intervention. Since we have no registered images, the idea is to obtain a suitable representation of both template and drawings using the very same approach for all images in a fast and accurate approach. Results: The results have shown that we can obtain very reasonable recognition rates (around approximate to 67\%), with the most accurate class being the one represented by the patients, which outnumbered the control individuals in the proposed dataset. Conclusions: The proposed approach seemed to be suitable for aiding in automatic PD diagnosis by means of computer vision and machine learning techniques. Also, meander images play an important role, leading to higher accuracies than spiral images. We also observed that the main problem in detecting PD is the patients in the early stages, who can draw near-perfect objects, which are very similar to the ones made by control patients. (C) 2016 Elsevier Ireland Ltd. All rights reserved.}, language = {en} } @incollection{PereiraPassosLopesetal., author = {Pereira, Clayton R. and Passos, Leandro A. and Lopes, Ricardo R. and Weber, Silke A. T. and Hook, Christian and Papa, Joao Paulo}, title = {Parkinson's Disease Identification Using Restricted Boltzmann Machines}, series = {Computer Analysis of Images and Patterns, 17th International Conference, CAIP 2017, Ystad, Sweden, August 22-24, 2017, Proceedings, Part II}, volume = {10425}, booktitle = {Computer Analysis of Images and Patterns, 17th International Conference, CAIP 2017, Ystad, Sweden, August 22-24, 2017, Proceedings, Part II}, publisher = {Springer}, isbn = {978-3-319-64697-8}, doi = {10.1007/978-3-319-64698-5_7}, pages = {70 -- 80}, abstract = {Currently, Parkinson's Disease (PD) has no cure or accurate diagnosis, reaching approximately 60, 000 new cases yearly and worldwide, being more often in the elderly population. Its main symptoms can not be easily uncorrelated with other illness, being way more difficult to be identified at the early stages. As such, computer-aided tools have been recently used to assist in this task, but the challenge in the automatic identification of Parkinson's Disease still persists. In order to cope with this problem, we propose to employ Restricted Boltzmann Machines (RBMs) to learn features in an unsupervised fashion by analyzing images from handwriting exams, which aim at assessing the writing skills of potential individuals. These are one of the main symptoms of PD-prone people, since such kind of ability ends up being severely affected. We show that RBMs can learn proper features that help supervised classifiers in the task of automatic identification of PD patients, as well as one can obtain a more compact representation of the exam for the sake of storage and computational load purposes.}, language = {en} } @article{AfonsoPereiraWeberetal., author = {Afonso, Luis Claudio Sugi and Pereira, Clayton R. and Weber, Silke A. T. and Hook, Christian and Falc{\~a}o, Alexandre X. and Papa, Joao Paulo}, title = {Hierarchical learning using deep optimum-path forest}, series = {Journal of Visual Communication and Image Representation}, volume = {71}, journal = {Journal of Visual Communication and Image Representation}, number = {August}, publisher = {Elsevier}, doi = {10.1016/j.jvcir.2020.102823}, abstract = {Bag-of-Visual Words (BoVW) and deep learning techniques have been widely used in several domains, which include computer-assisted medical diagnoses. In this work, we are interested in developing tools for the automatic identification of Parkinson's disease using machine learning and the concept of BoVW. The proposed approach concerns a hierarchical-based learning technique to design visual dictionaries through the Deep Optimum-Path Forest classifier. The proposed method was evaluated in six datasets derived from data collected from individuals when performing handwriting exams. Experimental results showed the potential of the technique, with robust achievements.}, language = {en} } @article{AfonsoRosaPereiraetal., author = {Afonso, Luis Claudio Sugi and Rosa, Gustavo H. and Pereira, Clayton R. and Weber, Silke A. T. and Hook, Christian and Albuquerque, Victor Hugo C. and Papa, Joao Paulo}, title = {A recurrence plot-based approach for Parkinson's disease identification}, series = {Future generation computer systems - The international journal of escience}, volume = {94}, journal = {Future generation computer systems - The international journal of escience}, number = {May}, publisher = {Elsevier}, doi = {10.1016/j.future.2018.11.054}, pages = {282 -- 292}, abstract = {Parkinson's disease (PD) is a neurodegenerative disease that affects millions of people worldwide, causing mental and mainly motor dysfunctions. The negative impact on the patient's daily routine has moved the science in search of new techniques that can reduce its negative effects and also identify the disease in individuals. One of the main motor characteristics of PD is the hand tremor faced by patients, which turns out to be a crucial information to be used towards a computer-aided diagnosis. In this context, we make use of handwriting dynamics data acquired from individuals when submitted to some tasks that measure abilities related to writing skills. This work proposes the application of recurrence plots to map the signals onto the image domain, which are further used to feed a Convolutional Neural Network for learning proper information that can help the automatic identification of PD. The proposed approach was assessed in a public dataset under several scenarios that comprise different combinations of deep-based architectures, image resolutions, and training set sizes. Experimental results showed significant accuracy improvement compared to our previous work with an average accuracy of over 87\%. Moreover, it was observed an improvement in accuracy concerning the classification of patients (i.e., mean recognition rates above to 90\%). The promising results showed the potential of the proposed approach towards the automatic identification of Parkinson's disease.}, language = {en} } @article{PereiraPereiraRosaetal., author = {Pereira, Clayton R. and Pereira, Danilo R. and Rosa, Gustavo H. and Albuquerque, Victor Hugo C. and Weber, Silke A. T. and Hook, Christian and Papa, Jo{\~a}o Paulo}, title = {Handwritten dynamics assessment through convolutional neural networks}, series = {Artificial Intelligence in Medicine}, volume = {37}, journal = {Artificial Intelligence in Medicine}, number = {May}, publisher = {Elsevier}, doi = {10.1016/j.artmed.2018.04.001}, pages = {67 -- 77}, abstract = {Background and objective Parkinson's disease (PD) is considered a degenerative disorder that affects the motor system, which may cause tremors, micrography, and the freezing of gait. Although PD is related to the lack of dopamine, the triggering process of its development is not fully understood yet. Methods In this work, we introduce convolutional neural networks to learn features from images produced by handwritten dynamics, which capture different information during the individual's assessment. Additionally, we make available a dataset composed of images and signal-based data to foster the research related to computer-aided PD diagnosis. Results The proposed approach was compared against raw data and texture-based descriptors, showing suitable results, mainly in the context of early stage detection, with results nearly to 95\%. Conclusions The analysis of handwritten dynamics using deep learning techniques showed to be useful for automatic Parkinson's disease identification, as well as it can outperform handcrafted features.}, language = {en} } @inproceedings{PereiraPereiradaSilvaetal., author = {Pereira, Clayton R. and Pereira, Danilo R. and da Silva, Francisco A. and Hook, Christian and Weber, Silke A. T. and Pereira, Luis A. M. and Papa, Jo{\~a}o Paulo}, title = {A Step Towards the Automated Diagnosis of Parkinson's Disease: Analyzing Handwriting Movements}, series = {2015 IEEE 28th International Symposium on Computer-Based Medical Systems, 22.-25.06.2015, Sao Carlos, Brazil}, booktitle = {2015 IEEE 28th International Symposium on Computer-Based Medical Systems, 22.-25.06.2015, Sao Carlos, Brazil}, publisher = {IEEE}, isbn = {978-1-4673-6775-2}, issn = {2372-9198}, doi = {10.1109/cbms.2015.34}, pages = {171 -- 176}, abstract = {Parkinson's disease (PD) has affected millions of people world-wide, being its major problem the loss of movements and, consequently, the ability of working and locomotion. Although we can find several works that attempt at dealing with this problem out there, most of them make use of datasets composed by a few subjects only. In this work, we present some results toward the automated diagnosis of PD by means of computer vision-based techniques in a dataset composed by dozens of patients, which is one of the main contributions of this work. The dataset is part of a joint research project that aims at extracting both visual and signal-based information from healthy and PD patients in order to go forward the early diagnosis of PD patients. The dataset is composed by handwriting clinical exams that are analyzed by means of image processing and machine learning techniques, being the preliminary results encouraging and promising. Additionally, a new quantitative feature to measure the amount of tremor of an individual's handwritten trace called Mean Relative Tremor is also presented.}, language = {en} } @article{MendelRauberdeSouzaJretal., author = {Mendel, Robert and Rauber, David and de Souza Jr., Luis Antonio and Papa, Jo{\~a}o Paulo and Palm, Christoph}, title = {Error-Correcting Mean-Teacher: Corrections instead of consistency-targets applied to semi-supervised medical image segmentation}, series = {Computers in Biology and Medicine}, volume = {154}, journal = {Computers in Biology and Medicine}, number = {March}, publisher = {Elsevier}, issn = {0010-4825}, doi = {10.1016/j.compbiomed.2023.106585}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:898-opus4-57790}, pages = {13}, abstract = {Semantic segmentation is an essential task in medical imaging research. Many powerful deep-learning-based approaches can be employed for this problem, but they are dependent on the availability of an expansive labeled dataset. In this work, we augment such supervised segmentation models to be suitable for learning from unlabeled data. Our semi-supervised approach, termed Error-Correcting Mean-Teacher, uses an exponential moving average model like the original Mean Teacher but introduces our new paradigm of error correction. The original segmentation network is augmented to handle this secondary correction task. Both tasks build upon the core feature extraction layers of the model. For the correction task, features detected in the input image are fused with features detected in the predicted segmentation and further processed with task-specific decoder layers. The combination of image and segmentation features allows the model to correct present mistakes in the given input pair. The correction task is trained jointly on the labeled data. On unlabeled data, the exponential moving average of the original network corrects the student's prediction. The combined outputs of the students' prediction with the teachers' correction form the basis for the semi-supervised update. We evaluate our method with the 2017 and 2018 Robotic Scene Segmentation data, the ISIC 2017 and the BraTS 2020 Challenges, a proprietary Endoscopic Submucosal Dissection dataset, Cityscapes, and Pascal VOC 2012. Additionally, we analyze the impact of the individual components and examine the behavior when the amount of labeled data varies, with experiments performed on two distinct segmentation architectures. Our method shows improvements in terms of the mean Intersection over Union over the supervised baseline and competing methods. Code is available at https://github.com/CloneRob/ECMT.}, language = {en} } @inproceedings{DeSouzaJrAfonsoPalmetal., author = {De Souza Jr., Luis Antonio and Afonso, Luis Claudio Sugi and Palm, Christoph and Papa, Jo{\~a}o Paulo}, title = {Barrett's Esophagus Identification Using Optimum-Path Forest}, series = {Proceedings of the 30th Conference on Graphics, Patterns and Images Tutorials (SIBGRAPI-T 2017), Niter{\´o}i, Rio de Janeiro, Brazil, 2017, 17-20 October}, booktitle = {Proceedings of the 30th Conference on Graphics, Patterns and Images Tutorials (SIBGRAPI-T 2017), Niter{\´o}i, Rio de Janeiro, Brazil, 2017, 17-20 October}, doi = {10.1109/SIBGRAPI.2017.47}, pages = {308 -- 314}, abstract = {Computer-assisted analysis of endoscopic images can be helpful to the automatic diagnosis and classification of neoplastic lesions. Barrett's esophagus (BE) is a common type of reflux that is not straight forward to be detected by endoscopic surveillance, thus being way susceptible to erroneous diagnosis, which can cause cancer when not treated properly. In this work, we introduce the Optimum-Path Forest (OPF) classifier to the task of automatic identification of Barrett'sesophagus, with promising results and outperforming the well known Support Vector Machines (SVM) in the aforementioned context. We consider describing endoscopic images by means of feature extractors based on key point information, such as the Speeded up Robust Features (SURF) and Scale-Invariant Feature Transform (SIFT), for further designing a bag-of-visual-wordsthat is used to feed both OPF and SVM classifiers. The best results were obtained by means of the OPF classifier for both feature extractors, with values lying on 0.732 (SURF) - 0.735(SIFT) for sensitivity, 0.782 (SURF) - 0.806 (SIFT) for specificity, and 0.738 (SURF) - 0.732 (SIFT) for the accuracy.}, subject = {Speiser{\"o}hrenkrankheit}, language = {en} } @inproceedings{DeSouzaJrHookPapaetal., author = {De Souza Jr., Luis Antonio and Hook, Christian and Papa, Jo{\~a}o Paulo and Palm, Christoph}, title = {Barrett's Esophagus Analysis Using SURF Features}, series = {Bildverarbeitung f{\"u}r die Medizin 2017; Algorithmen - Systeme - Anwendungen. Proceedings des Workshops vom 12. bis 14. M{\"a}rz 2017 in Heidelberg}, booktitle = {Bildverarbeitung f{\"u}r die Medizin 2017; Algorithmen - Systeme - Anwendungen. Proceedings des Workshops vom 12. bis 14. M{\"a}rz 2017 in Heidelberg}, publisher = {Springer}, address = {Berlin}, doi = {10.1007/978-3-662-54345-0_34}, pages = {141 -- 146}, abstract = {The development of adenocarcinoma in Barrett's esophagus is difficult to detect by endoscopic surveillance of patients with signs of dysplasia. Computer assisted diagnosis of endoscopic images (CAD) could therefore be most helpful in the demarcation and classification of neoplastic lesions. In this study we tested the feasibility of a CAD method based on Speeded up Robust Feature Detection (SURF). A given database containing 100 images from 39 patients served as benchmark for feature based classification models. Half of the images had previously been diagnosed by five clinical experts as being "cancerous", the other half as "non-cancerous". Cancerous image regions had been visibly delineated (masked) by the clinicians. SURF features acquired from full images as well as from masked areas were utilized for the supervised training and testing of an SVM classifier. The predictive accuracy of the developed CAD system is illustrated by sensitivity and specificity values. The results based on full image matching where 0.78 (sensitivity) and 0.82 (specificity) were achieved, while the masked region approach generated results of 0.90 and 0.95, respectively.}, subject = {Speiser{\"o}hrenkrankheit}, language = {en} } @article{EbigboMendelProbstetal., author = {Ebigbo, Alanna and Mendel, Robert and Probst, Andreas and Manzeneder, Johannes and De Souza Jr., Luis Antonio and Papa, Jo{\~a}o Paulo and Palm, Christoph and Messmann, Helmut}, title = {Computer-aided diagnosis using deep learning in the evaluation of early oesophageal adenocarcinoma}, series = {GuT}, volume = {68}, journal = {GuT}, number = {7}, publisher = {British Society of Gastroenterology}, doi = {10.1136/gutjnl-2018-317573}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:898-opus4-68}, pages = {1143 -- 1145}, abstract = {Computer-aided diagnosis using deep learning (CAD-DL) may be an instrument to improve endoscopic assessment of Barrett's oesophagus (BE) and early oesophageal adenocarcinoma (EAC). Based on still images from two databases, the diagnosis of EAC by CAD-DL reached sensitivities/specificities of 97\%/88\% (Augsburg data) and 92\%/100\% (Medical Image Computing and Computer-Assisted Intervention [MICCAI] data) for white light (WL) images and 94\%/80\% for narrow band images (NBI) (Augsburg data), respectively. Tumour margins delineated by experts into images were detected satisfactorily with a Dice coefficient (D) of 0.72. This could be a first step towards CAD-DL for BE assessment. If developed further, it could become a useful adjunctive tool for patient management.}, subject = {Speiser{\"o}hrenkrebs}, language = {en} }