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	Author	Debora Gil; Rosa Maria Ortiz; Carles Sanchez; Antoni Rosell
	Title	Objective endoscopic measurements of central airway stenosis. A pilot study			Type	Journal Article
	Year	2018	Publication	Respiration	Abbreviated Journal	RES
	Volume	95	Issue		Pages	63–69
	Keywords	Bronchoscopy; Tracheal stenosis; Airway stenosis; Computer-assisted analysis
	Abstract	Endoscopic estimation of the degree of stenosis in central airway obstruction is subjective and highly variable. Objective: To determine the benefits of using SENSA (System for Endoscopic Stenosis Assessment), an image-based computational software, for obtaining objective stenosis index (SI) measurements among a group of expert bronchoscopists and general pulmonologists. Methods: A total of 7 expert bronchoscopists and 7 general pulmonologists were enrolled to validate SENSA usage. The SI obtained by the physicians and by SENSA were compared with a reference SI to set their precision in SI computation. We used SENSA to efficiently obtain this reference SI in 11 selected cases of benign stenosis. A Web platform with three user-friendly microtasks was designed to gather the data. The users had to visually estimate the SI from videos with and without contours of the normal and the obstructed area provided by SENSA. The users were able to modify the SENSA contours to define the reference SI using morphometric bronchoscopy. Results: Visual SI estimation accuracy was associated with neither bronchoscopic experience (p = 0.71) nor the contours of the normal and the obstructed area provided by the system (p = 0.13). The precision of the SI by SENSA was 97.7% (95% CI: 92.4-103.7), which is significantly better than the precision of the SI by visual estimation (p < 0.001), with an improvement by at least 15%. Conclusion: SENSA provides objective SI measurements with a precision of up to 99.5%, which can be calculated from any bronchoscope using an affordable scalable interface. Providing normal and obstructed contours on bronchoscopic videos does not improve physicians' visual estimation of the SI.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	IAM; 600.075; 600.096; 600.145			Approved	no
	Call Number	Admin @ si @ GOS2018			Serial	3043
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	Author	Rosa Maria Ortiz; Debora Gil; Elisa Minchole; Marta Diez-Ferrer; Noelia Cubero de Frutos
	Title	Classification of Confolcal Endomicroscopy Patterns for Diagnosis of Lung Cancer			Type	Conference Article
	Year	2017	Publication	18th World Conference on Lung Cancer	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	Abstract	Confocal Laser Endomicroscopy (CLE) is an emerging imaging technique that allows the in-vivo acquisition of cell patterns of potentially malignant lesions. Such patterns could discriminate between inflammatory and neoplastic lesions and, thus, serve as a first in-vivo biopsy to discard cases that do not actually require a cell biopsy. The goal of this work is to explore whether CLE images obtained during videobronchoscopy contain enough visual information to discriminate between benign and malign peripheral lesions for lung cancer diagnosis. To do so, we have performed a pilot comparative study with 12 patients (6 adenocarcinoma and 6 benign-inflammatory) using 2 different methods for CLE pattern analysis: visual analysis by 3 experts and a novel methodology that uses graph methods to find patterns in pre-trained feature spaces. Our preliminary results indicate that although visual analysis can only achieve a 60.2% of accuracy, the accuracy of the proposed unsupervised image pattern classification raises to 84.6%. We conclude that CLE images visual information allow in-vivo detection of neoplastic lesions and graph structural analysis applied to deep-learning feature spaces can achieve competitive results.
	Address	Yokohama; Japan; October 2017
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference	IASLC WCLC
	Notes	IAM; 600.096; 600.075; 600.145			Approved	no
	Call Number	Admin @ si @ OGM2017			Serial	3044
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	Author	Debora Gil; Aura Hernandez-Sabate; David Castells; Jordi Carrabina
	Title	CYBERH: Cyber-Physical Systems in Health for Personalized Assistance			Type	Conference Article
	Year	2017	Publication	International Symposium on Symbolic and Numeric Algorithms for Scientific Computing	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	Abstract	Assistance systems for e-Health applications have some specific requirements that demand of new methods for data gathering, analysis and modeling able to deal with SmallData: 1) systems should dynamically collect data from, both, the environment and the user to issue personalized recommendations; 2) data analysis should be able to tackle a limited number of samples prone to include non-informative data and possibly evolving in time due to changes in patient condition; 3) algorithms should run in real time with possibly limited computational resources and fluctuant internet access. Electronic medical devices (and CyberPhysical devices in general) can enhance the process of data gathering and analysis in several ways: (i) acquiring simultaneously multiple sensors data instead of single magnitudes (ii) filtering data; (iii) providing real-time implementations condition by isolating tasks in individual processors of multiprocessors Systems-on-chip (MPSoC) platforms and (iv) combining information through sensor fusion techniques. Our approach focus on both aspects of the complementary role of CyberPhysical devices and analysis of SmallData in the process of personalized models building for e-Health applications. In particular, we will address the design of Cyber-Physical Systems in Health for Personalized Assistance (CyberHealth) in two specific application cases: 1) A Smart Assisted Driving System (SADs) for dynamical assessment of the driving capabilities of Mild Cognitive Impaired (MCI) people; 2) An Intelligent Operating Room (iOR) for improving the yield of bronchoscopic interventions for in-vivo lung cancer diagnosis.
	Address	Timisoara; Rumania; September 2017
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference	SYNASC
	Notes	IAM; 600.085; 600.096; 600.075; 600.145			Approved	no
	Call Number	Admin @ si @ GHC2017			Serial	3045
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	Author	Katerine Diaz; Jesus Martinez del Rincon; Aura Hernandez-Sabate; Debora Gil
	Title	Continuous head pose estimation using manifold subspace embedding and multivariate regression			Type	Journal Article
	Year	2018	Publication	IEEE Access	Abbreviated Journal	ACCESS
	Volume	6	Issue		Pages	18325 - 18334
	Keywords	Head Pose estimation; HOG features; Generalized Discriminative Common Vectors; B-splines; Multiple linear regression
	Abstract	In this paper, a continuous head pose estimation system is proposed to estimate yaw and pitch head angles from raw facial images. Our approach is based on manifold learningbased methods, due to their promising generalization properties shown for face modelling from images. The method combines histograms of oriented gradients, generalized discriminative common vectors and continuous local regression to achieve successful performance. Our proposal was tested on multiple standard face datasets, as well as in a realistic scenario. Results show a considerable performance improvement and a higher consistence of our model in comparison with other state-of-art methods, with angular errors varying between 9 and 17 degrees.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2169-3536	ISBN		Medium
	Area		Expedition		Conference
	Notes	ADAS; 600.118			Approved	no
	Call Number	Admin @ si @ DMH2018b			Serial	3091
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	Author	Esmitt Ramirez; Carles Sanchez; Agnes Borras; Marta Diez-Ferrer; Antoni Rosell; Debora Gil
	Title	Image-Based Bronchial Anatomy Codification for Biopsy Guiding in Video Bronchoscopy			Type	Conference Article
	Year	2018	Publication	OR 2.0 Context-Aware Operating Theaters, Computer Assisted Robotic Endoscopy, Clinical Image-Based Procedures, and Skin Image Analysis	Abbreviated Journal
	Volume	11041	Issue		Pages
	Keywords	Biopsy guiding; Bronchoscopy; Lung biopsy; Intervention guiding; Airway codification
	Abstract	Bronchoscopy examinations allow biopsy of pulmonary nodules with minimum risk for the patient. Even for experienced bronchoscopists, it is difficult to guide the bronchoscope to most distal lesions and obtain an accurate diagnosis. This paper presents an image-based codification of the bronchial anatomy for bronchoscopy biopsy guiding. The 3D anatomy of each patient is codified as a binary tree with nodes representing bronchial levels and edges labeled using their position on images projecting the 3D anatomy from a set of branching points. The paths from the root to leaves provide a codification of navigation routes with spatially consistent labels according to the anatomy observes in video bronchoscopy explorations. We evaluate our labeling approach as a guiding system in terms of the number of bronchial levels correctly codified, also in the number of labels-based instructions correctly supplied, using generalized mixed models and computer-generated data. Results obtained for three independent observers prove the consistency and reproducibility of our guiding system. We trust that our codification based on viewer’s projection might be used as a foundation for the navigation process in Virtual Bronchoscopy systems.
	Address	Granada; September 2018
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title	LNCS
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference	MICCAIW
	Notes	IAM; 600.096; 600.075; 601.323; 600.145			Approved	no
	Call Number	Admin @ si @ RSB2018b			Serial	3137
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	Author	Marta Ligero; Guillermo Torres; Carles Sanchez; Katerine Diaz; Raquel Perez; Debora Gil
	Title	Selection of Radiomics Features based on their Reproducibility			Type	Conference Article
	Year	2019	Publication	41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society	Abbreviated Journal
	Volume		Issue		Pages	403-408
	Keywords
	Abstract	Dimensionality reduction is key to alleviate machine learning artifacts in clinical applications with Small Sample Size (SSS) unbalanced datasets. Existing methods rely on either the probabilistic distribution of training data or the discriminant power of the reduced space, disregarding the impact of repeatability and uncertainty in features.In the present study is proposed the use of reproducibility of radiomics features to select features with high inter-class correlation coefficient (ICC). The reproducibility includes the variability introduced in the image acquisition, like medical scans acquisition parameters and convolution kernels, that affects intensity-based features and tumor annotations made by physicians, that influences morphological descriptors of the lesion.For the reproducibility of radiomics features three studies were conducted on cases collected at Vall Hebron Oncology Institute (VHIO) on responders to oncology treatment. The studies focused on the variability due to the convolution kernel, image acquisition parameters, and the inter-observer lesion identification. The features selected were those features with a ICC higher than 0.7 in the three studies.The selected features based on reproducibility were evaluated for lesion malignancy classification using a different database. Results show better performance compared to several state-of-the-art methods including Principal Component Analysis (PCA), Kernel Discriminant Analysis via QR decomposition (KDAQR), LASSO, and an own built Convolutional Neural Network.
	Address	Berlin; Alemanya; July 2019
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference	EMBC
	Notes	IAM; 600.139; 600.145			Approved	no
	Call Number	Admin @ si @ LTS2019			Serial	3358
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	Author	Debora Gil; Antonio Esteban Lansaque; Sebastian Stefaniga; Mihail Gaianu; Carles Sanchez
	Title	Data Augmentation from Sketch			Type	Conference Article
	Year	2019	Publication	International Workshop on Uncertainty for Safe Utilization of Machine Learning in Medical Imaging	Abbreviated Journal
	Volume	11840	Issue		Pages	155-162
	Keywords	Data augmentation; cycleGANs; Multi-objective optimization
	Abstract	State of the art machine learning methods need huge amounts of data with unambiguous annotations for their training. In the context of medical imaging this is, in general, a very difficult task due to limited access to clinical data, the time required for manual annotations and variability across experts. Simulated data could serve for data augmentation provided that its appearance was comparable to the actual appearance of intra-operative acquisitions. Generative Adversarial Networks (GANs) are a powerful tool for artistic style transfer, but lack a criteria for selecting epochs ensuring also preservation of intra-operative content. We propose a multi-objective optimization strategy for a selection of cycleGAN epochs ensuring a mapping between virtual images and the intra-operative domain preserving anatomical content. Our approach has been applied to simulate intra-operative bronchoscopic videos and chest CT scans from virtual sketches generated using simple graphical primitives.
	Address	Shenzhen; China; October 2019
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title	LNCS
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference	CLIP
	Notes	IAM; 600.145; 601.337; 600.139; 600.145			Approved	no
	Call Number	Admin @ si @ GES2019			Serial	3359
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	Author	Carles Sanchez; Miguel Viñas; Coen Antens; Agnes Borras; Debora Gil
	Title	Back to Front Architecture for Diagnosis as a Service			Type	Conference Article
	Year	2018	Publication	20th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing	Abbreviated Journal
	Volume		Issue		Pages	343-346
	Keywords
	Abstract	Software as a Service (SaaS) is a cloud computing model in which a provider hosts applications in a server that customers use via internet. Since SaaS does not require to install applications on customers' own computers, it allows the use by multiple users of highly specialized software without extra expenses for hardware acquisition or licensing. A SaaS tailored for clinical needs not only would alleviate licensing costs, but also would facilitate easy access to new methods for diagnosis assistance. This paper presents a SaaS client-server architecture for Diagnosis as a Service (DaaS). The server is based on docker technology in order to allow execution of softwares implemented in different languages with the highest portability and scalability. The client is a content management system allowing the design of websites with multimedia content and interactive visualization of results allowing user editing. We explain a usage case that uses our DaaS as crowdsourcing platform in a multicentric pilot study carried out to evaluate the clinical benefits of a software for assessment of central airway obstruction.
	Address	Timisoara; Rumania; September 2018
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference	SYNASC
	Notes	IAM; 600.145			Approved	no
	Call Number	Admin @ si @ SVA2018			Serial	3360
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	Author	Debora Gil; Antoni Rosell
	Title	Advances in Artificial Intelligence – How Lung Cancer CT Screening Will Progress?			Type	Abstract
	Year	2019	Publication	World Lung Cancer Conference	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	Abstract	Invited speaker
	Address	Barcelona; September 2019
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference	IASLC WCLC
	Notes	IAM; 600.139; 600.145			Approved	no
	Call Number	Admin @ si @ GiR2019			Serial	3361
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	Author	Debora Gil; Antonio Esteban Lansaque; Agnes Borras; Esmitt Ramirez; Carles Sanchez
	Title	Intraoperative Extraction of Airways Anatomy in VideoBronchoscopy			Type	Journal Article
	Year	2020	Publication	IEEE Access	Abbreviated Journal	ACCESS
	Volume	8	Issue		Pages	159696 - 159704
	Keywords
	Abstract	A main bottleneck in bronchoscopic biopsy sampling is to efficiently reach the lesion navigating across bronchial levels. Any guidance system should be able to localize the scope position during the intervention with minimal costs and alteration of clinical protocols. With the final goal of an affordable image-based guidance, this work presents a novel strategy to extract and codify the anatomical structure of bronchi, as well as, the scope navigation path from videobronchoscopy. Experiments using interventional data show that our method accurately identifies the bronchial structure. Meanwhile, experiments using simulated data verify that the extracted navigation path matches the 3D route.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	IAM; 600.139; 600.145			Approved	no
	Call Number	Admin @ si @ GEB2020			Serial	3467
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	Author	Debora Gil; Guillermo Torres
	Title	A multi-shape loss function with adaptive class balancing for the segmentation of lung structures			Type	Conference Article
	Year	2020	Publication	34th International Congress and Exhibition on Computer Assisted Radiology & Surgery	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	Abstract
	Address	Virtual; June 2020
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference	CARS
	Notes	IAM; 600.139; 600.145			Approved	no
	Call Number	Admin @ si @ GiT2020			Serial	3472
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	Author	Debora Gil; Oriol Ramos Terrades; Raquel Perez
	Title	Topological Radiomics (TOPiomics): Early Detection of Genetic Abnormalities in Cancer Treatment Evolution			Type	Conference Article
	Year	2020	Publication	Women in Geometry and Topology	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	Abstract
	Address	Barcelona; September 2019
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	IAM; DAG; 600.139; 600.145; 600.121			Approved	no
	Call Number	Admin @ si @ GRP2020			Serial	3473
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	Author	Debora Gil; Katerine Diaz; Carles Sanchez; Aura Hernandez-Sabate
	Title	Early Screening of SARS-CoV-2 by Intelligent Analysis of X-Ray Images			Type	Miscellaneous
	Year	2020	Publication	Arxiv	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	Abstract	Future SARS-CoV-2 virus outbreak COVID-XX might possibly occur during the next years. However the pathology in humans is so recent that many clinical aspects, like early detection of complications, side effects after recovery or early screening, are currently unknown. In spite of the number of cases of COVID-19, its rapid spread putting many sanitary systems in the edge of collapse has hindered proper collection and analysis of the data related to COVID-19 clinical aspects. We describe an interdisciplinary initiative that integrates clinical research, with image diagnostics and the use of new technologies such as artificial intelligence and radiomics with the aim of clarifying some of SARS-CoV-2 open questions. The whole initiative addresses 3 main points: 1) collection of standardize data including images, clinical data and analytics; 2) COVID-19 screening for its early diagnosis at primary care centers; 3) define radiomic signatures of COVID-19 evolution and associated pathologies for the early treatment of complications. In particular, in this paper we present a general overview of the project, the experimental design and first results of X-ray COVID-19 detection using a classic approach based on HoG and feature selection. Our experiments include a comparison to some recent methods for COVID-19 screening in X-Ray and an exploratory analysis of the feasibility of X-Ray COVID-19 screening. Results show that classic approaches can outperform deep-learning methods in this experimental setting, indicate the feasibility of early COVID-19 screening and that non-COVID infiltration is the group of patients most similar to COVID-19 in terms of radiological description of X-ray. Therefore, an efficient COVID-19 screening should be complemented with other clinical data to better discriminate these cases.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	IAM; 600.139; 600.145; 601.337			Approved	no
	Call Number	Admin @ si @ GDS2020			Serial	3474
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	Author	Oriol Ramos Terrades; Albert Berenguel; Debora Gil
	Title	A flexible outlier detector based on a topology given by graph communities			Type	Miscellaneous
	Year	2020	Publication	Arxiv	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	Abstract	Outlier, or anomaly, detection is essential for optimal performance of machine learning methods and statistical predictive models. It is not just a technical step in a data cleaning process but a key topic in many fields such as fraudulent document detection, in medical applications and assisted diagnosis systems or detecting security threats. In contrast to population-based methods, neighborhood based local approaches are simple flexible methods that have the potential to perform well in small sample size unbalanced problems. However, a main concern of local approaches is the impact that the computation of each sample neighborhood has on the method performance. Most approaches use a distance in the feature space to define a single neighborhood that requires careful selection of several parameters. This work presents a local approach based on a local measure of the heterogeneity of sample labels in the feature space considered as a topological manifold. Topology is computed using the communities of a weighted graph codifying mutual nearest neighbors in the feature space. This way, we provide with a set of multiple neighborhoods able to describe the structure of complex spaces without parameter fine tuning. The extensive experiments on real-world data sets show that our approach overall outperforms, both, local and global strategies in multi and single view settings.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	IAM; DAG; 600.139; 600.145; 600.140; 600.121			Approved	no
	Call Number	Admin @ si @ RBG2020			Serial	3475
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	Author	Esmitt Ramirez; Carles Sanchez; Debora Gil
	Title	Localizing Pulmonary Lesions Using Fuzzy Deep Learning			Type	Conference Article
	Year	2019	Publication	21st International Symposium on Symbolic and Numeric Algorithms for Scientific Computing	Abbreviated Journal
	Volume		Issue		Pages	290-294
	Keywords
	Abstract	The usage of medical images is part of the clinical daily in several healthcare centers around the world. Particularly, Computer Tomography (CT) images are an important key in the early detection of suspicious lung lesions. The CT image exploration allows the detection of lung lesions before any invasive procedure (e.g. bronchoscopy, biopsy). The effective localization of lesions is performed using different image processing and computer vision techniques. Lately, the usage of deep learning models into medical imaging from detection to prediction shown that is a powerful tool for Computer-aided software. In this paper, we present an approach to localize pulmonary lung lesion using fuzzy deep learning. Our approach uses a simple convolutional neural network based using the LIDC-IDRI dataset. Each image is divided into patches associated a probability vector (fuzzy) according their belonging to anatomical structures on a CT. We showcase our approach as part of a full CAD system to exploration, planning, guiding and detection of pulmonary lesions.
	Address	Timisoara; Rumania; September 2019
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference	SYNASC
	Notes	IAM; 600.145; 600.140; 601.337; 601.323			Approved	no
	Call Number	Admin @ si @ RSG2019			Serial	3531
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