Frederic Sampedro, Sergio Escalera, Anna Domenech, & Ignasi Carrio. (2015). Automatic Tumor Volume Segmentation in Whole-Body PET/CT Scans: A Supervised Learning Approach Source. JMIHI - Journal of Medical Imaging and Health Informatics, 5(2), 192–201.
Abstract: Whole-body 3D PET/CT tumoral volume segmentation provides relevant diagnostic and prognostic information in clinical oncology and nuclear medicine. Carrying out this procedure manually by a medical expert is time consuming and suffers from inter- and intra-observer variabilities. In this paper, a completely automatic approach to this task is presented. First, the problem is stated and described both in clinical and technological terms. Then, a novel supervised learning segmentation framework is introduced. The segmentation by learning approach is defined within a Cascade of Adaboost classifiers and a 3D contextual proposal of Multiscale Stacked Sequential Learning. Segmentation accuracy results on 200 Breast Cancer whole body PET/CT volumes show mean 49% sensitivity, 99.993% specificity and 39% Jaccard overlap Index, which represent good performance results both at the clinical and technological level.
Keywords: CONTEXTUAL CLASSIFICATION; PET/CT; SUPERVISED LEARNING; TUMOR SEGMENTATION; WHOLE BODY
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Frederic Sampedro, Anna Domenech, & Sergio Escalera. (2014). Static and dynamic computational cancer spread quantification in whole body FDG-PET/CT scans. JMIHI - Journal of Medical Imaging and Health Informatics, 4(6), 825–831.
Abstract: In this work we address the computational cancer spread quantification scenario in whole body FDG-PET/CT scans. At the static level, this setting can be modeled as a clustering problem on the set of 3D connected components of the whole body PET tumoral segmentation mask carried out by nuclear medicine physicians. At the dynamic level, and ad-hoc algorithm is proposed in order to quantify the cancer spread time evolution which, when combined with other existing indicators, gives rise to the metabolic tumor volume-aggressiveness-spread time evolution chart, a novel tool that we claim that would prove useful in nuclear medicine and oncological clinical or research scenarios. Good performance results of the proposed methodologies both at the clinical and technological level are shown using a dataset of 48 segmented whole body FDG-PET/CT scans.
Keywords: CANCER SPREAD; COMPUTER AIDED DIAGNOSIS; MEDICAL IMAGING; TUMOR QUANTIFICATION
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Diana Ramirez Cifuentes, Ana Freire, Ricardo Baeza Yates, Joaquim Punti Vidal, Pilar Medina Bravo, Diego Velazquez, et al. (2020). Detection of Suicidal Ideation on Social Media: Multimodal, Relational, and Behavioral Analysis. JMIR - Journal of Medical Internet Research, 22(7), e17758.
Abstract: Background:
Suicide risk assessment usually involves an interaction between doctors and patients. However, a significant number of people with mental disorders receive no treatment for their condition due to the limited access to mental health care facilities; the reduced availability of clinicians; the lack of awareness; and stigma, neglect, and discrimination surrounding mental disorders. In contrast, internet access and social media usage have increased significantly, providing experts and patients with a means of communication that may contribute to the development of methods to detect mental health issues among social media users.
Objective:
This paper aimed to describe an approach for the suicide risk assessment of Spanish-speaking users on social media. We aimed to explore behavioral, relational, and multimodal data extracted from multiple social platforms and develop machine learning models to detect users at risk.
Methods:
We characterized users based on their writings, posting patterns, relations with other users, and images posted. We also evaluated statistical and deep learning approaches to handle multimodal data for the detection of users with signs of suicidal ideation (suicidal ideation risk group). Our methods were evaluated over a dataset of 252 users annotated by clinicians. To evaluate the performance of our models, we distinguished 2 control groups: users who make use of suicide-related vocabulary (focused control group) and generic random users (generic control group).
Results:
We identified significant statistical differences between the textual and behavioral attributes of each of the control groups compared with the suicidal ideation risk group. At a 95% CI, when comparing the suicidal ideation risk group and the focused control group, the number of friends (P=.04) and median tweet length (P=.04) were significantly different. The median number of friends for a focused control user (median 578.5) was higher than that for a user at risk (median 372.0). Similarly, the median tweet length was higher for focused control users, with 16 words against 13 words of suicidal ideation risk users. Our findings also show that the combination of textual, visual, relational, and behavioral data outperforms the accuracy of using each modality separately. We defined text-based baseline models based on bag of words and word embeddings, which were outperformed by our models, obtaining an increase in accuracy of up to 8% when distinguishing users at risk from both types of control users.
Conclusions:
The types of attributes analyzed are significant for detecting users at risk, and their combination outperforms the results provided by generic, exclusively text-based baseline models. After evaluating the contribution of image-based predictive models, we believe that our results can be improved by enhancing the models based on textual and relational features. These methods can be extended and applied to different use cases related to other mental disorders.
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Diana Ramirez Cifuentes, Ana Freire, Ricardo Baeza Yates, Nadia Sanz Lamora, Aida Alvarez, Alexandre Gonzalez, et al. (2021). Characterization of Anorexia Nervosa on Social Media: Textual, Visual, Relational, Behavioral, and Demographical Analysis. JMIR - Journal of Medical Internet Research, 23(7), e25925.
Abstract: Background: Eating disorders are psychological conditions characterized by unhealthy eating habits. Anorexia nervosa (AN) is defined as the belief of being overweight despite being dangerously underweight. The psychological signs involve emotional and behavioral issues. There is evidence that signs and symptoms can manifest on social media, wherein both harmful and beneficial content is shared daily.
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Patrick Brandao, O. Zisimopoulos, E. Mazomenos, G. Ciutib, Jorge Bernal, M. Visentini-Scarzanell, et al. (2018). Towards a computed-aided diagnosis system in colonoscopy: Automatic polyp segmentation using convolution neural networks. JMRR - Journal of Medical Robotics Research.
Abstract: Early diagnosis is essential for the successful treatment of bowel cancers including colorectal cancer (CRC) and capsule endoscopic imaging with robotic actuation can be a valuable diagnostic tool when combined with automated image analysis. We present a deep learning rooted detection and segmentation framework for recognizing lesions in colonoscopy and capsule endoscopy images. We restructure established convolution architectures, such as VGG and ResNets, by converting them into fully-connected convolution networks (FCNs), ne-tune them and study their capabilities for polyp segmentation and detection. We additionally use Shape-from-Shading (SfS) to recover depth and provide a richer representation of the tissue's structure in colonoscopy images. Depth is
incorporated into our network models as an additional input channel to the RGB information and we demonstrate that the resulting network yields improved performance. Our networks are tested on publicly available datasets and the most accurate segmentation model achieved a mean segmentation IU of 47.78% and 56.95% on the ETIS-Larib and CVC-Colon datasets, respectively. For polyp
detection, the top performing models we propose surpass the current state of the art with detection recalls superior to 90% for all datasets tested. To our knowledge, we present the rst work to use FCNs for polyp segmentation in addition to proposing a novel combination of SfS and RGB that boosts performance.
Keywords: convolutional neural networks; colonoscopy; computer aided diagnosis
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Tadashi Araki, Sumit K. Banchhor, Narendra D. Londhe, Nobutaka Ikeda, Petia Radeva, Devarshi Shukla, et al. (2016). Reliable and Accurate Calcium Volume Measurement in Coronary Artery Using Intravascular Ultrasound Videos. JMS - Journal of Medical Systems, 40(3), 51:1–51:20.
Abstract: Quantitative assessment of calcified atherosclerotic volume within the coronary artery wall is vital for cardiac interventional procedures. The goal of this study is to automatically measure the calcium volume, given the borders of coronary vessel wall for all the frames of the intravascular ultrasound (IVUS) video. Three soft computing fuzzy classification techniques were adapted namely Fuzzy c-Means (FCM), K-means, and Hidden Markov Random Field (HMRF) for automated segmentation of calcium regions and volume computation. These methods were benchmarked against previously developed threshold-based method. IVUS image data sets (around 30,600 IVUS frames) from 15 patients were collected using 40 MHz IVUS catheter (Atlantis® SR Pro, Boston Scientific®, pullback speed of 0.5 mm/s). Calcium mean volume for FCM, K-means, HMRF and threshold-based method were 37.84 ± 17.38 mm3, 27.79 ± 10.94 mm3, 46.44 ± 19.13 mm3 and 35.92 ± 16.44 mm3 respectively. Cross-correlation, Jaccard Index and Dice Similarity were highest between FCM and threshold-based method: 0.99, 0.92 ± 0.02 and 0.95 + 0.02 respectively. Student’s t-test, z-test and Wilcoxon-test are also performed to demonstrate consistency, reliability and accuracy of the results. Given the vessel wall region, the system reliably and automatically measures the calcium volume in IVUS videos. Further, we validated our system against a trained expert using scoring: K-means showed the best performance with an accuracy of 92.80 %. Out procedure and protocol is along the line with method previously published clinically.
Keywords: Interventional cardiology; Atherosclerosis; Coronary arteries; IVUS; calcium volume; Soft computing; Performance Reliability; Accuracy
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Agata Lapedriza, David Masip, & Jordi Vitria. (2006). On the Use of External Face Features for Identity Verification. Journal of Multimedia, 1(4): 11–20, 11–20.
Abstract: In general automatic face classification applications images are captured in natural environments. In these cases, the performance is affected by variations in facial images related to illumination, pose, occlusion or expressions. Most of the existing face classification systems use only the internal features information, composed by eyes, nose and mouth, since they are more difficult to imitate. Nevertheless, nowadays a lot of applications not related to security are developed, and in these cases the information located at head, chin or ears zones (external features) can be useful to improve the current accuracies. However, the lack of a natural alignment in these areas makes difficult to extract these features applying classic Bottom-Up methods. In this paper, we propose a complete scheme based on a Top-Down reconstruction algorithm to extract external features of face images. To test our system we have performed face verification experiments using public databases, given that identity verification is a general task that has many real life applications. We have considered images uniformly illuminated, images with occlusions and images with high local changes in the illumination, and the obtained results show that the information contributed by the external features can be useful for verification purposes, specially significant when faces are partially occluded.
Keywords: Face Verification, Computer Vision, Machine Learning
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Sergio Escalera, Oriol Pujol, J. Mauri, & Petia Radeva. (2009). Intravascular Ultrasound Tissue Characterization with Sub-class Error-Correcting Output Codes. Journal of Signal Processing Systems, 55(1-3), 35–47.
Abstract: Intravascular ultrasound (IVUS) represents a powerful imaging technique to explore coronary vessels and to study their morphology and histologic properties. In this paper, we characterize different tissues based on radial frequency, texture-based, and combined features. To deal with the classification of multiple tissues, we require the use of robust multi-class learning techniques. In this sense, error-correcting output codes (ECOC) show to robustly combine binary classifiers to solve multi-class problems. In this context, we propose a strategy to model multi-class classification tasks using sub-classes information in the ECOC framework. The new strategy splits the classes into different sub-sets according to the applied base classifier. Complex IVUS data sets containing overlapping data are learnt by splitting the original set of classes into sub-classes, and embedding the binary problems in a problem-dependent ECOC design. The method automatically characterizes different tissues, showing performance improvements over the state-of-the-art ECOC techniques for different base classifiers. Furthermore, the combination of RF and texture-based features also shows improvements over the state-of-the-art approaches.
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Mariella Dimiccoli. (2016). Fundamentals of cone regression. Journal of Statistics Surveys, 53–99.
Abstract: Cone regression is a particular case of quadratic programming that minimizes a weighted sum of squared residuals under a set of linear inequality constraints. Several important statistical problems such as isotonic, concave regression or ANOVA under partial orderings, just to name a few, can be considered as particular instances of the cone regression problem. Given its relevance in Statistics, this paper aims to address the fundamentals of cone regression from a theoretical and practical point of view. Several formulations of the cone regression problem are considered and, focusing on the particular case of concave regression as an example, several algorithms are analyzed and compared both qualitatively and quantitatively through numerical simulations. Several improvements to enhance numerical stability and bound the computational cost are proposed. For each analyzed algorithm, the pseudo-code and its corresponding code in Matlab are provided. The results from this study demonstrate that the choice of the optimization approach strongly impacts the numerical performances. It is also shown that methods are not currently available to solve efficiently cone regression problems with large dimension (more than many thousands of points). We suggest further research to fill this gap by exploiting and adapting classical multi-scale strategy to compute an approximate solution.
Keywords: cone regression; linear complementarity problems; proximal operators.
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Debora Gil, Jose Maria-Carazo, & Roberto Marabini. (2006). On the nature of 2D crystal unbending. Journal of Structural Biology, 156(3), 546–555.
Abstract: Crystal unbending, the process that aims to recover a perfect crystal from experimental data, is one of the more important steps in electron crystallography image processing. The unbending process involves three steps: estimation of the unit cell displacements from their ideal positions, extension of the deformation field to the whole image and transformation of the image in order to recover an ideal crystal. In this work, we present a systematic analysis of the second step oriented to address two issues. First, whether the unit cells remain undistorted and only the distance between them should be changed (rigid case) or should be modified with the same deformation suffered by the whole crystal (elastic case). Second, the performance of different extension algorithms (interpolation versus approximation) is explored. Our experiments show that there is no difference between elastic and rigid cases or among the extension algorithms. This implies that the deformation fields are constant over large areas. Furthermore, our results indicate that the main source of error is the transformation of the crystal image.
Keywords: Electron microscopy
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Enric Marti, J.Roncaries, Debora Gil, Aura Hernandez-Sabate, Antoni Gurgui, & Ferran Poveda. (2015). PBL On Line: A proposal for the organization, part-time monitoring and assessment of PBL group activities. JOTSE - Journal of Technology and Science Education, 87–96.
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Carles Sanchez, Oriol Ramos Terrades, Patricia Marquez, Enric Marti, J.Roncaries, & Debora Gil. (2015). Automatic evaluation of practices in Moodle for Self Learning in Engineering. JOTSE - Journal of Technology and Science Education, 97–106.
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Neus Salvatella, E Fernandez-Nofrerias, Francesco Ciompi, Oriol Rodriguez-Leor, H. Tizon, Xavier Carrillo, et al. (2010). Radial Artery Volume Changes After Administration Of Two Different Intra-arterial Drug Regimens. Assessment by Intravascular Ultrasound. JACC - Journal of the American College of Cardiology, 56(13s1), B119.
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S. Tanimoto, N. Bruining, David Rotger, Petia Radeva, J. Ligthart, R.T. van Domburg, et al. (2008). Late Stent Recoil of the Bioabsorbable Everolimus Eluting Coronary Stent and its Relationship with Stent Struts Distribution and Plaque Morphology. Journal of the American College of Cardiology, vol. 52(20):1616–1620.
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Robert Benavente, Maria Vanrell, & Ramon Baldrich. (2008). Parametric Fuzzy Sets for Automatic Color Naming. Journal of the Optical Society of America A, 2582–2593.
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