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Katerine Diaz; Francesc J. Ferri; Aura Hernandez-Sabate |
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Title |
An overview of incremental feature extraction methods based on linear subspaces |
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Journal Article |
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2018 |
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Knowledge-Based Systems |
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KBS |
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145 |
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219-235 |
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With the massive explosion of machine learning in our day-to-day life, incremental and adaptive learning has become a major topic, crucial to keep up-to-date and improve classification models and their corresponding feature extraction processes. This paper presents a categorized overview of incremental feature extraction based on linear subspace methods which aim at incorporating new information to the already acquired knowledge without accessing previous data. Specifically, this paper focuses on those linear dimensionality reduction methods with orthogonal matrix constraints based on global loss function, due to the extensive use of their batch approaches versus other linear alternatives. Thus, we cover the approaches derived from Principal Components Analysis, Linear Discriminative Analysis and Discriminative Common Vector methods. For each basic method, its incremental approaches are differentiated according to the subspace model and matrix decomposition involved in the updating process. Besides this categorization, several updating strategies are distinguished according to the amount of data used to update and to the fact of considering a static or dynamic number of classes. Moreover, the specific role of the size/dimension ratio in each method is considered. Finally, computational complexity, experimental setup and the accuracy rates according to published results are compiled and analyzed, and an empirical evaluation is done to compare the best approach of each kind. |
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0950-7051 |
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ADAS; 600.118;IAM |
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Admin @ si @ DFH2018 |
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3090 |
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Katerine Diaz; Jesus Martinez del Rincon; Aura Hernandez-Sabate; Debora Gil |
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Title |
Continuous head pose estimation using manifold subspace embedding and multivariate regression |
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Journal Article |
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Year |
2018 |
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IEEE Access |
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ACCESS |
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6 |
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18325 - 18334 |
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Head Pose estimation; HOG features; Generalized Discriminative Common Vectors; B-splines; Multiple linear regression |
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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. |
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2169-3536 |
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ADAS; 600.118;IAM |
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Admin @ si @ DMH2018b |
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3091 |
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Marta Diez-Ferrer; Debora Gil; Elena Carreño; Susana Padrones; Samantha Aso; Vanesa Vicens; Cubero Noelia; Rosa Lopez Lisbona; Carles Sanchez; Agnes Borras; Antoni Rosell |
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Positive Airway Pressure-Enhanced CT to Improve Virtual Bronchoscopic Navigation |
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2016 |
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Chest Journal |
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CHEST |
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150 |
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4 |
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1003A |
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IAM; 600.096; 600.075 |
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Admin @ si @ DGC2016 |
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3099 |
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Esmitt Ramirez; Carles Sanchez; Agnes Borras; Marta Diez-Ferrer; Antoni Rosell; Debora Gil |
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BronchoX: bronchoscopy exploration software for biopsy intervention planning |
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2018 |
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Healthcare Technology Letters |
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HTL |
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5 |
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5 |
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177–182 |
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Virtual bronchoscopy (VB) is a non-invasive exploration tool for intervention planning and navigation of possible pulmonary lesions (PLs). A VB software involves the location of a PL and the calculation of a route, starting from the trachea, to reach it. The selection of a VB software might be a complex process, and there is no consensus in the community of medical software developers in which is the best-suited system to use or framework to choose. The authors present Bronchoscopy Exploration (BronchoX), a VB software to plan biopsy interventions that generate physician-readable instructions to reach the PLs. The authors’ solution is open source, multiplatform, and extensible for future functionalities, designed by their multidisciplinary research and development group. BronchoX is a compound of different algorithms for segmentation, visualisation, and navigation of the respiratory tract. Performed results are a focus on the test the effectiveness of their proposal as an exploration software, also to measure its accuracy as a guiding system to reach PLs. Then, 40 different virtual planning paths were created to guide physicians until distal bronchioles. These results provide a functional software for BronchoX and demonstrate how following simple instructions is possible to reach distal lesions from the trachea. |
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IAM; 600.096; 600.075; 601.323; 601.337; 600.145 |
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Admin @ si @ RSB2018a |
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3132 |
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Debora Gil; Ruth Aris; Agnes Borras; Esmitt Ramirez; Rafael Sebastian; Mariano Vazquez |
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Title |
Influence of fiber connectivity in simulations of cardiac biomechanics |
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Journal Article |
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Year |
2019 |
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International Journal of Computer Assisted Radiology and Surgery |
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IJCAR |
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14 |
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1 |
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63–72 |
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Cardiac electromechanical simulations; Diffusion tensor imaging; Fiber connectivity |
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PURPOSE:
Personalized computational simulations of the heart could open up new improved approaches to diagnosis and surgery assistance systems. While it is fully recognized that myocardial fiber orientation is central for the construction of realistic computational models of cardiac electromechanics, the role of its overall architecture and connectivity remains unclear. Morphological studies show that the distribution of cardiac muscular fibers at the basal ring connects epicardium and endocardium. However, computational models simplify their distribution and disregard the basal loop. This work explores the influence in computational simulations of fiber distribution at different short-axis cuts.
METHODS:
We have used a highly parallelized computational solver to test different fiber models of ventricular muscular connectivity. We have considered two rule-based mathematical models and an own-designed method preserving basal connectivity as observed in experimental data. Simulated cardiac functional scores (rotation, torsion and longitudinal shortening) were compared to experimental healthy ranges using generalized models (rotation) and Mahalanobis distances (shortening, torsion).
RESULTS:
The probability of rotation was significantly lower for ruled-based models [95% CI (0.13, 0.20)] in comparison with experimental data [95% CI (0.23, 0.31)]. The Mahalanobis distance for experimental data was in the edge of the region enclosing 99% of the healthy population.
CONCLUSIONS:
Cardiac electromechanical simulations of the heart with fibers extracted from experimental data produce functional scores closer to healthy ranges than rule-based models disregarding architecture connectivity. |
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IAM; 600.096; 601.323; 600.139; 600.145 |
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Admin @ si @ GAB2019a |
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3133 |
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Marta Diez-Ferrer; Arturo Morales; Rosa Lopez Lisbona; Noelia Cubero; Cristian Tebe; Susana Padrones; Samantha Aso; Jordi Dorca; Debora Gil; Antoni Rosell |
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Ultrathin Bronchoscopy with and without Virtual Bronchoscopic Navigation: Influence of Segmentation on Diagnostic Yield |
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Journal Article |
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2019 |
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Respiration |
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RES |
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97 |
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3 |
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252-258 |
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Lung cancer; Peripheral lung lesion; Diagnosis; Bronchoscopy; Ultrathin bronchoscopy; Virtual bronchoscopic navigation |
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Background: Bronchoscopy is a safe technique for diagnosing peripheral pulmonary lesions (PPLs), and virtual bronchoscopic navigation (VBN) helps guide the bronchoscope to PPLs. Objectives: We aimed to compare the diagnostic yield of VBN-guided and unguided ultrathin bronchoscopy (UTB) and explore clinical and technical factors associated with better results. We developed a diagnostic algorithm for deciding whether to use VBN to reach PPLs or choose an alternative diagnostic approach. Methods: We compared diagnostic yield between VBN-UTB (prospective cases) and unguided UTB (historical controls) and analyzed the VBN-UTB subgroup to identify clinical and technical variables that could predict the success of VBN-UTB. Results: Fifty-five cases and 110 controls were included. The overall diagnostic yield did not differ between the VBN-guided and unguided arms (47 and 40%, respectively; p = 0.354). Although the yield was slightly higher for PPLs ≤20 mm in the VBN-UTB arm, the difference was not significant (p = 0.069). No other clinical characteristics were associated with a higher yield in a subgroup analysis, but an 85% diagnostic yield was observed when segmentation was optimal and the PPL was endobronchial (vs. 30% when segmentation was suboptimal and 20% when segmentation was optimal but the PPL was extrabronchial). Conclusions: VBN-guided UTB is not superior to unguided UTB. A greater impact of VBN-guided over unguided UTB is highly dependent on both segmentation quality and an endobronchial location of the PPL. Segmentation quality should be considered before starting a procedure, when an alternative technique that may improve yield can be chosen, saving time and resources. |
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IAM; 600.145; 600.139 |
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Admin @ si @ DML2019 |
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3134 |
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Marta Diez-Ferrer; Debora Gil; Cristian Tebe; Carles Sanchez |
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Title |
Positive Airway Pressure to Enhance Computed Tomography Imaging for Airway Segmentation for Virtual Bronchoscopic Navigation |
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Journal Article |
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Year |
2018 |
Publication |
Respiration |
Abbreviated Journal |
RES |
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96 |
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6 |
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525-534 |
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Multidetector computed tomography; Bronchoscopy; Continuous positive airway pressure; Image enhancement; Virtual bronchoscopic navigation |
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Abstract
RATIONALE:
Virtual bronchoscopic navigation (VBN) guidance to peripheral pulmonary lesions is often limited by insufficient segmentation of the peripheral airways.
OBJECTIVES:
To test the effect of applying positive airway pressure (PAP) during CT acquisition to improve segmentation, particularly at end-expiration.
METHODS:
CT acquisitions in inspiration and expiration with 4 PAP protocols were recorded prospectively and compared to baseline inspiratory acquisitions in 20 patients. The 4 protocols explored differences between devices (flow vs. turbine), exposures (within seconds vs. 15-min) and pressure levels (10 vs. 14 cmH2O). Segmentation quality was evaluated with the number of airways and number of endpoints reached. A generalized mixed-effects model explored the estimated effect of each protocol.
MEASUREMENTS AND MAIN RESULTS:
Patient characteristics and lung function did not significantly differ between protocols. Compared to baseline inspiratory acquisitions, expiratory acquisitions after 15 min of 14 cmH2O PAP segmented 1.63-fold more airways (95% CI 1.07-2.48; p = 0.018) and reached 1.34-fold more endpoints (95% CI 1.08-1.66; p = 0.004). Inspiratory acquisitions performed immediately under 10 cmH2O PAP reached 1.20-fold (95% CI 1.09-1.33; p < 0.001) more endpoints; after 15 min the increase was 1.14-fold (95% CI 1.05-1.24; p < 0.001).
CONCLUSIONS:
CT acquisitions with PAP segment more airways and reach more endpoints than baseline inspiratory acquisitions. The improvement is particularly evident at end-expiration after 15 min of 14 cmH2O PAP. Further studies must confirm that the improvement increases diagnostic yield when using VBN to evaluate peripheral pulmonary lesions. |
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IAM; 600.145 |
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Admin @ si @ DGT2018 |
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3135 |
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Katerine Diaz; Jesus Martinez del Rincon; Marçal Rusiñol; Aura Hernandez-Sabate |
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Feature Extraction by Using Dual-Generalized Discriminative Common Vectors |
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Journal Article |
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2019 |
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Journal of Mathematical Imaging and Vision |
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JMIV |
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61 |
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3 |
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331-351 |
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Online feature extraction; Generalized discriminative common vectors; Dual learning; Incremental learning; Decremental learning |
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In this paper, a dual online subspace-based learning method called dual-generalized discriminative common vectors (Dual-GDCV) is presented. The method extends incremental GDCV by exploiting simultaneously both the concepts of incremental and decremental learning for supervised feature extraction and classification. Our methodology is able to update the feature representation space without recalculating the full projection or accessing the previously processed training data. It allows both adding information and removing unnecessary data from a knowledge base in an efficient way, while retaining the previously acquired knowledge. The proposed method has been theoretically proved and empirically validated in six standard face recognition and classification datasets, under two scenarios: (1) removing and adding samples of existent classes, and (2) removing and adding new classes to a classification problem. Results show a considerable computational gain without compromising the accuracy of the model in comparison with both batch methodologies and other state-of-art adaptive methods. |
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DAG; ADAS; 600.084; 600.118; 600.121; 600.129;IAM |
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Admin @ si @ DRR2019 |
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3172 |
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Santi Puch; Irina Sanchez; Aura Hernandez-Sabate; Gemma Piella; Vesna Prckovska |
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Global Planar Convolutions for Improved Context Aggregation in Brain Tumor Segmentation |
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2018 |
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International MICCAI Brainlesion Workshop |
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11384 |
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393-405 |
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Brain tumors; 3D fully-convolutional CNN; Magnetic resonance imaging; Global planar convolution |
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In this work, we introduce the Global Planar Convolution module as a building-block for fully-convolutional networks that aggregates global information and, therefore, enhances the context perception capabilities of segmentation networks in the context of brain tumor segmentation. We implement two baseline architectures (3D UNet and a residual version of 3D UNet, ResUNet) and present a novel architecture based on these two architectures, ContextNet, that includes the proposed Global Planar Convolution module. We show that the addition of such module eliminates the need of building networks with several representation levels, which tend to be over-parametrized and to showcase slow rates of convergence. Furthermore, we provide a visual demonstration of the behavior of GPC modules via visualization of intermediate representations. We finally participate in the 2018 edition of the BraTS challenge with our best performing models, that are based on ContextNet, and report the evaluation scores on the validation and the test sets of the challenge. |
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MICCAIW |
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ADAS; 600.118;IAM |
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Admin @ si @ PSH2018 |
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3251 |
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Spyridon Bakas; Mauricio Reyes; Andras Jakab; Stefan Bauer; Markus Rempfler; Alessandro Crimi; Russell Takeshi Shinohara; Christoph Berger; Sung Min Ha; Martin Rozycki; Marcel Prastawa; Esther Alberts; Jana Lipkova; John Freymann; Justin Kirby; Michel Bilello; Hassan Fathallah-Shaykh; Roland Wiest; Jan Kirschke; Benedikt Wiestler; Rivka Colen; Aikaterini Kotrotsou; Pamela Lamontagne; Daniel Marcus; Mikhail Milchenko; Arash Nazeri; Marc-Andre Weber; Abhishek Mahajan; Ujjwal Baid; Dongjin Kwon; Manu Agarwal; Mahbubul Alam; Alberto Albiol; Antonio Albiol; Varghese Alex; Tuan Anh Tran; Tal Arbel; Aaron Avery; Subhashis Banerjee; Thomas Batchelder; Kayhan Batmanghelich; Enzo Battistella; Martin Bendszus; Eze Benson; Jose Bernal; George Biros; Mariano Cabezas; Siddhartha Chandra; Yi-Ju Chang; Joseph Chazalon; Shengcong Chen; Wei Chen; Jefferson Chen; Kun Cheng; Meinel Christoph; Roger Chylla; Albert Clérigues; Anthony Costa; Xiaomeng Cui; Zhenzhen Dai; Lutao Dai; Eric Deutsch; Changxing Ding; Chao Dong; Wojciech Dudzik; Theo Estienne; Hyung Eun Shin; Richard Everson; Jonathan Fabrizio; Longwei Fang; Xue Feng; Lucas Fidon; Naomi Fridman; Huan Fu; David Fuentes; David G Gering; Yaozong Gao; Evan Gates; Amir Gholami; Mingming Gong; Sandra Gonzalez-Villa; J Gregory Pauloski; Yuanfang Guan; Sheng Guo; Sudeep Gupta; Meenakshi H Thakur; Klaus H Maier-Hein; Woo-Sup Han; Huiguang He; Aura Hernandez-Sabate; Evelyn Herrmann; Naveen Himthani; Winston Hsu; Cheyu Hsu; Xiaojun Hu; Xiaobin Hu; Yan Hu; Yifan Hu; Rui Hua |
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Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the BRATS challenge |
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2018 |
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Arxiv |
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BraTS; challenge; brain; tumor; segmentation; machine learning; glioma; glioblastoma; radiomics; survival; progression; RECIST |
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Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multiparametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e. 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in preoperative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that undergone gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset. |
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ADAS; 600.118;MILAB;IAM |
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Admin @ si @ BRJ2018 |
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3252 |
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