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Cristina Sanchez Montes; F. Javier Sanchez; Jorge Bernal; Henry Cordova; Maria Lopez Ceron; Miriam Cuatrecasas; Cristina Rodriguez de Miguel; Ana Garcia Rodriguez; Rodrigo Garces Duran; Maria Pellise; Josep Llach; Gloria Fernandez Esparrach |
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Computer-aided Prediction of Polyp Histology on White-Light Colonoscopy using Surface Pattern Analysis |
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2019 |
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Endoscopy |
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51 |
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3 |
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261-265 |
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Background and study aims: To evaluate a new computational histology prediction system based on colorectal polyp textural surface patterns using high definition white light images.
Patients and methods: Textural elements (textons) were characterized according to their contrast with respect to the surface, shape and number of bifurcations, assuming that dysplastic polyps are associated with highly contrasted, large tubular patterns with some degree of bifurcation. Computer-aided diagnosis (CAD) was compared with pathological diagnosis and the diagnosis by the endoscopists using Kudo and NICE classification.
Results: Images of 225 polyps were evaluated (142 dysplastic and 83 non-dysplastic). CAD system correctly classified 205 (91.1%) polyps, 131/142 (92.3%) dysplastic and 74/83 (89.2%) non-dysplastic. For the subgroup of 100 diminutive (<5 mm) polyps, CAD correctly classified 87 (87%) polyps, 43/50 (86%) dysplastic and 44/50 (88%) non-dysplastic. There were not statistically significant differences in polyp histology prediction based on CAD system and on endoscopist assessment.
Conclusion: A computer vision system based on the characterization of the polyp surface in the white light accurately predicts colorectal polyp histology. |
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MV; 600.096; 600.119; 600.075 |
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Admin @ si @ SSB2019 |
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3164 |
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Ana Garcia Rodriguez; Yael Tudela; Henry Cordova; S. Carballal; I. Ordas; L. Moreira; E. Vaquero; O. Ortiz; L. Rivero; F. Javier Sanchez; Miriam Cuatrecasas; Maria Pellise; Jorge Bernal; Gloria Fernandez Esparrach |
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In vivo computer-aided diagnosis of colorectal polyps using white light endoscopy |
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2022 |
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Endoscopy International Open |
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10 |
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9 |
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E1201-E1207 |
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Background and study aims Artificial intelligence is currently able to accurately predict the histology of colorectal polyps. However, systems developed to date use complex optical technologies and have not been tested in vivo. The objective of this study was to evaluate the efficacy of a new deep learning-based optical diagnosis system, ATENEA, in a real clinical setting using only high-definition white light endoscopy (WLE) and to compare its performance with endoscopists. Methods ATENEA was prospectively tested in real life on consecutive polyps detected in colorectal cancer screening colonoscopies at Hospital Clínic. No images were discarded, and only WLE was used. The in vivo ATENEA's prediction (adenoma vs non-adenoma) was compared with the prediction of four staff endoscopists without specific training in optical diagnosis for the study purposes. Endoscopists were blind to the ATENEA output. Histology was the gold standard. Results Ninety polyps (median size: 5 mm, range: 2-25) from 31 patients were included of which 69 (76.7 %) were adenomas. ATENEA correctly predicted the histology in 63 of 69 (91.3 %, 95 % CI: 82 %-97 %) adenomas and 12 of 21 (57.1 %, 95 % CI: 34 %-78 %) non-adenomas while endoscopists made correct predictions in 52 of 69 (75.4 %, 95 % CI: 60 %-85 %) and 20 of 21 (95.2 %, 95 % CI: 76 %-100 %), respectively. The global accuracy was 83.3 % (95 % CI: 74%-90 %) and 80 % (95 % CI: 70 %-88 %) for ATENEA and endoscopists, respectively. Conclusion ATENEA can accurately be used for in vivo characterization of colorectal polyps, enabling the endoscopist to make direct decisions. ATENEA showed a global accuracy similar to that of endoscopists despite an unsatisfactory performance for non-adenomatous lesions. |
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2022 Sep 14 |
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PMID |
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Admin @ si @ GTC2022b |
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3752 |
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Giuseppe Pezzano; Vicent Ribas Ripoll; Petia Radeva |
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CoLe-CNN: Context-learning convolutional neural network with adaptive loss function for lung nodule segmentation |
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2021 |
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Computer Methods and Programs in Biomedicine |
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CMPB |
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198 |
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105792 |
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Background and objective:An accurate segmentation of lung nodules in computed tomography images is a crucial step for the physical characterization of the tumour. Being often completely manually accomplished, nodule segmentation turns to be a tedious and time-consuming procedure and this represents a high obstacle in clinical practice. In this paper, we propose a novel Convolutional Neural Network for nodule segmentation that combines a light and efficient architecture with innovative loss function and segmentation strategy. Methods:In contrast to most of the standard end-to-end architectures for nodule segmentation, our network learns the context of the nodules by producing two masks representing all the background and secondary-important elements in the Computed Tomography scan. The nodule is detected by subtracting the context from the original scan image. Additionally, we introduce an asymmetric loss function that automatically compensates for potential errors in the nodule annotations. We trained and tested our Neural Network on the public LIDC-IDRI database, compared it with the state of the art and run a pseudo-Turing test between four radiologists and the network. Results:The results proved that the behaviour of the algorithm is very near to the human performance and its segmentation masks are almost indistinguishable from the ones made by the radiologists. Our method clearly outperforms the state of the art on CT nodule segmentation in terms of F1 score and IoU of and respectively. Conclusions: The main structure of the network ensures all the properties of the UNet architecture, while the Multi Convolutional Layers give a more accurate pattern recognition. The newly adopted solutions also increase the details on the border of the nodule, even under the noisiest conditions. This method can be applied now for single CT slice nodule segmentation and it represents a starting point for the future development of a fully automatic 3D segmentation software. |
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MILAB; no proj |
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Admin @ si @ PRR2021 |
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3530 |
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Sumit K. Banchhor; Tadashi Araki; Narendra D. Londhe; Nobutaka Ikeda; Petia Radeva; Ayman El-Baz; Luca Saba; Andrew Nicolaides; Shoaib Shafique; John R. Laird; Jasjit S. Suri |
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Five multiresolution-based calcium volume measurement techniques from coronary IVUS videos: A comparative approach |
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2016 |
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Computer Methods and Programs in Biomedicine |
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CMPB |
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134 |
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237-258 |
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BACKGROUND AND OBJECTIVE:
Fast intravascular ultrasound (IVUS) video processing is required for calcium volume computation during the planning phase of percutaneous coronary interventional (PCI) procedures. Nonlinear multiresolution techniques are generally applied to improve the processing time by down-sampling the video frames.
METHODS:
This paper presents four different segmentation methods for calcium volume measurement, namely Threshold-based, Fuzzy c-Means (FCM), K-means, and Hidden Markov Random Field (HMRF) embedded with five different kinds of multiresolution techniques (bilinear, bicubic, wavelet, Lanczos, and Gaussian pyramid). This leads to 20 different kinds of combinations. IVUS image data sets consisting of 38,760 IVUS frames taken from 19 patients were collected using 40 MHz IVUS catheter (Atlantis® SR Pro, Boston Scientific®, pullback speed of 0.5 mm/sec.). The performance of these 20 systems is compared with and without multiresolution using the following metrics: (a) computational time; (b) calcium volume; (c) image quality degradation ratio; and (d) quality assessment ratio.
RESULTS:
Among the four segmentation methods embedded with five kinds of multiresolution techniques, FCM segmentation combined with wavelet-based multiresolution gave the best performance. FCM and wavelet experienced the highest percentage mean improvement in computational time of 77.15% and 74.07%, respectively. Wavelet interpolation experiences the highest mean precision-of-merit (PoM) of 94.06 ± 3.64% and 81.34 ± 16.29% as compared to other multiresolution techniques for volume level and frame level respectively. Wavelet multiresolution technique also experiences the highest Jaccard Index and Dice Similarity of 0.7 and 0.8, respectively. Multiresolution is a nonlinear operation which introduces bias and thus degrades the image. The proposed system also provides a bias correction approach to enrich the system, giving a better mean calcium volume similarity for all the multiresolution-based segmentation methods. After including the bias correction, bicubic interpolation gives the largest increase in mean calcium volume similarity of 4.13% compared to the rest of the multiresolution techniques. The system is automated and can be adapted in clinical settings.
CONCLUSIONS:
We demonstrated the time improvement in calcium volume computation without compromising the quality of IVUS image. Among the 20 different combinations of multiresolution with calcium volume segmentation methods, the FCM embedded with wavelet-based multiresolution gave the best performance. |
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Admin @ si @ BAL2016 |
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2830 |
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Gloria Fernandez Esparrach; Jorge Bernal; Maria Lopez Ceron; Henry Cordova; Cristina Sanchez Montes; Cristina Rodriguez de Miguel; F. Javier Sanchez |
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Exploring the clinical potential of an automatic colonic polyp detection method based on the creation of energy maps |
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2016 |
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Endoscopy |
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48 |
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9 |
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837-842 |
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Background and aims: Polyp miss-rate is a drawback of colonoscopy that increases significantly in small polyps. We explored the efficacy of an automatic computer vision method for polyp detection.
Methods: Our method relies on a model that defines polyp boundaries as valleys of image intensity. Valley information is integrated into energy maps which represent the likelihood of polyp presence.
Results: In 24 videos containing polyps from routine colonoscopies, all polyps were detected in at least one frame. Mean values of the maximum of energy map were higher in frames with polyps than without (p<0.001). Performance improved in high quality frames (AUC= 0.79, 95%CI: 0.70-0.87 vs 0.75, 95%CI: 0.66-0.83). Using 3.75 as maximum threshold value, sensitivity and specificity for detection of polyps were 70.4% (95%CI: 60.3-80.8) and 72.4% (95%CI: 61.6-84.6), respectively.
Conclusion: Energy maps showed a good performance for colonic polyp detection. This indicates a potential applicability in clinical practice. |
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Admin @ si @FBL2016 |
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2778 |
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O.F.Ahmad; Y.Mori; M.Misawa; S.Kudo; J.T.Anderson; Jorge Bernal |
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Establishing key research questions for the implementation of artificial intelligence in colonoscopy: a modified Delphi method |
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2021 |
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Endoscopy |
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53 |
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9 |
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893-901 |
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BACKGROUND : Artificial intelligence (AI) research in colonoscopy is progressing rapidly but widespread clinical implementation is not yet a reality. We aimed to identify the top implementation research priorities. METHODS : An established modified Delphi approach for research priority setting was used. Fifteen international experts, including endoscopists and translational computer scientists/engineers, from nine countries participated in an online survey over 9 months. Questions related to AI implementation in colonoscopy were generated as a long-list in the first round, and then scored in two subsequent rounds to identify the top 10 research questions. RESULTS : The top 10 ranked questions were categorized into five themes. Theme 1: clinical trial design/end points (4 questions), related to optimum trial designs for polyp detection and characterization, determining the optimal end points for evaluation of AI, and demonstrating impact on interval cancer rates. Theme 2: technological developments (3 questions), including improving detection of more challenging and advanced lesions, reduction of false-positive rates, and minimizing latency. Theme 3: clinical adoption/integration (1 question), concerning the effective combination of detection and characterization into one workflow. Theme 4: data access/annotation (1 question), concerning more efficient or automated data annotation methods to reduce the burden on human experts. Theme 5: regulatory approval (1 question), related to making regulatory approval processes more efficient. CONCLUSIONS : This is the first reported international research priority setting exercise for AI in colonoscopy. The study findings should be used as a framework to guide future research with key stakeholders to accelerate the clinical implementation of AI in endoscopy. |
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Admin @ si @ AMM2021 |
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3670 |
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Laura Igual; Joan Carles Soliva; Antonio Hernandez; Sergio Escalera; Xavier Jimenez ; Oscar Vilarroya; Petia Radeva |
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A fully-automatic caudate nucleus segmentation of brain MRI: Application in volumetric analysis of pediatric attention-deficit/hyperactivity disorder |
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2011 |
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BioMedical Engineering Online |
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BEO |
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Brain caudate nucleus; segmentation; MRI; atlas-based strategy; Graph Cut framework |
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Background
Accurate automatic segmentation of the caudate nucleus in magnetic resonance images (MRI) of the brain is of great interest in the analysis of developmental disorders. Segmentation methods based on a single atlas or on multiple atlases have been shown to suitably localize caudate structure. However, the atlas prior information may not represent the structure of interest correctly. It may therefore be useful to introduce a more flexible technique for accurate segmentations.
Method
We present Cau-dateCut: a new fully-automatic method of segmenting the caudate nucleus in MRI. CaudateCut combines an atlas-based segmentation strategy with the Graph Cut energy-minimization framework. We adapt the Graph Cut model to make it suitable for segmenting small, low-contrast structures, such as the caudate nucleus, by defining new energy function data and boundary potentials. In particular, we exploit information concerning the intensity and geometry, and we add supervised energies based on contextual brain structures. Furthermore, we reinforce boundary detection using a new multi-scale edgeness measure.
Results
We apply the novel CaudateCut method to the segmentation of the caudate nucleus to a new set of 39 pediatric attention-deficit/hyperactivity disorder (ADHD) patients and 40 control children, as well as to a public database of 18 subjects. We evaluate the quality of the segmentation using several volumetric and voxel by voxel measures. Our results show improved performance in terms of segmentation compared to state-of-the-art approaches, obtaining a mean overlap of 80.75%. Moreover, we present a quantitative volumetric analysis of caudate abnormalities in pediatric ADHD, the results of which show strong correlation with expert manual analysis.
Conclusion
CaudateCut generates segmentation results that are comparable to gold-standard segmentations and which are reliable in the analysis of differentiating neuroanatomical abnormalities between healthy controls and pediatric ADHD. |
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Dan Norton; Fernando Vilariño; Onur Ferhat |
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Memory Field – Creative Engagement in Digital Collections |
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2015 |
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Internet Librarian International Conference |
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“Memory Fields” is a trans-disciplinary project aiming at the (re)valorisation of digital collections.Its main deliverable is an interface for a dual screen installation, used to access and mix the public library digital collections. The collections being used in this case are a collection of digitised posters from the Spanish Civil War, belonging to the Arxiu General de Catalunya, and a collection of field recordings made by Dan Norton. The system generates visualisations, and the images and sounds are mixed together using narrative primitives of video dj. Users contribute to the digital collections by adding personal memories and observations. The comments and recollections appear as flowers growing in a “memory field” and memories remain public in a Twitter feed (@Memoryfields). |
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London; UK; October 2015 |
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Ivet Rafegas; Maria Vanrell |
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Color spaces emerging from deep convolutional networks |
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2016 |
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24th Color and Imaging Conference |
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Award for the best interactive session
Defining color spaces that provide a good encoding of spatio-chromatic properties of color surfaces is an open problem in color science [8, 22]. Related to this, in computer vision the fusion of color with local image features has been studied and evaluated [16]. In human vision research, the cells which are selective to specific color hues along the visual pathway are also a focus of attention [7, 14]. In line with these research aims, in this paper we study how color is encoded in a deep Convolutional Neural Network (CNN) that has been trained on more than one million natural images for object recognition. These convolutional nets achieve impressive performance in computer vision, and rival the representations in human brain. In this paper we explore how color is represented in a CNN architecture that can give some intuition about efficient spatio-chromatic representations. In convolutional layers the activation of a neuron is related to a spatial filter, that combines spatio-chromatic representations. We use an inverted version of it to explore the properties. Using a series of unsupervised methods we classify different type of neurons depending on the color axes they define and we propose an index of color-selectivity of a neuron. We estimate the main color axes that emerge from this trained net and we prove that colorselectivity of neurons decreases from early to deeper layers. |
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San Diego; USA; November 2016 |
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Admin @ si @ RaV2016a |
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2894 |
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Zhijie Fang; David Vazquez; Antonio Lopez |
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On-Board Detection of Pedestrian Intentions |
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2017 |
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Sensors |
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pedestrian intention; ADAS; self-driving |
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Avoiding vehicle-to-pedestrian crashes is a critical requirement for nowadays advanced driver assistant systems (ADAS) and future self-driving vehicles. Accordingly, detecting pedestrians from raw sensor data has a history of more than 15 years of research, with vision playing a central role.
During the last years, deep learning has boosted the accuracy of image-based pedestrian detectors.
However, detection is just the first step towards answering the core question, namely is the vehicle going to crash with a pedestrian provided preventive actions are not taken? Therefore, knowing as soon as possible if a detected pedestrian has the intention of crossing the road ahead of the vehicle is
essential for performing safe and comfortable maneuvers that prevent a crash. However, compared to pedestrian detection, there is relatively little literature on detecting pedestrian intentions. This paper aims to contribute along this line by presenting a new vision-based approach which analyzes the
pose of a pedestrian along several frames to determine if he or she is going to enter the road or not. We present experiments showing 750 ms of anticipation for pedestrians crossing the road, which at a typical urban driving speed of 50 km/h can provide 15 additional meters (compared to a pure pedestrian detector) for vehicle automatic reactions or to warn the driver. Moreover, in contrast with state-of-the-art methods, our approach is monocular, neither requiring stereo nor optical flow information. |
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Notes |
ADAS; 600.085; 600.076; 601.223; 600.116; 600.118 |
Approved |
no |
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Call Number |
Admin @ si @ FVL2017 |
Serial |
2983 |
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Author |
Miguel Oliveira; Victor Santos; Angel Sappa; P. Dias; A. Moreira |
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Title |
Incremental texture mapping for autonomous driving |
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Journal Article |
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Year |
2016 |
Publication |
Robotics and Autonomous Systems |
Abbreviated Journal |
RAS |
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Volume |
84 |
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Pages |
113-128 |
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Keywords |
Scene reconstruction; Autonomous driving; Texture mapping |
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Abstract |
Autonomous vehicles have a large number of on-board sensors, not only for providing coverage all around the vehicle, but also to ensure multi-modality in the observation of the scene. Because of this, it is not trivial to come up with a single, unique representation that feeds from the data given by all these sensors. We propose an algorithm which is capable of mapping texture collected from vision based sensors onto a geometric description of the scenario constructed from data provided by 3D sensors. The algorithm uses a constrained Delaunay triangulation to produce a mesh which is updated using a specially devised sequence of operations. These enforce a partial configuration of the mesh that avoids bad quality textures and ensures that there are no gaps in the texture. Results show that this algorithm is capable of producing fine quality textures. |
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ADAS; 600.086 |
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no |
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Call Number |
Admin @ si @ OSS2016b |
Serial |
2912 |
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Author |
Felipe Codevilla |
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Title |
On Building End-to-End Driving Models Through Imitation Learning |
Type |
Book Whole |
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Year |
2019 |
Publication |
PhD Thesis, Universitat Autonoma de Barcelona-CVC |
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Autonomous vehicles are now considered as an assured asset in the future. Literally, all the relevant car-markers are now in a race to produce fully autonomous vehicles. These car-makers usually make use of modular pipelines for designing autonomous vehicles. This strategy decomposes the problem in a variety of tasks such as object detection and recognition, semantic and instance segmentation, depth estimation, SLAM and place recognition, as well as planning and control. Each module requires a separate set of expert algorithms, which are costly specially in the amount of human labor and necessity of data labelling. An alternative, that recently has driven considerable interest, is the end-to-end driving. In the end-to-end driving paradigm, perception and control are learned simultaneously using a deep network. These sensorimotor models are typically obtained by imitation learning fromhuman demonstrations. The main advantage is that this approach can directly learn from large fleets of human-driven vehicles without requiring a fixed ontology and extensive amounts of labeling. However, scaling end-to-end driving methods to behaviors more complex than simple lane keeping or lead vehicle following remains an open problem. On this thesis, in order to achieve more complex behaviours, we
address some issues when creating end-to-end driving system through imitation
learning. The first of themis a necessity of an environment for algorithm evaluation and collection of driving demonstrations. On this matter, we participated on the creation of the CARLA simulator, an open source platformbuilt from ground up for autonomous driving validation and prototyping. Since the end-to-end approach is purely reactive, there is also the necessity to provide an interface with a global planning system. With this, we propose the conditional imitation learning that conditions the actions produced into some high level command. Evaluation is also a concern and is commonly performed by comparing the end-to-end network output to some pre-collected driving dataset. We show that this is surprisingly weakly correlated to the actual driving and propose strategies on how to better acquire data and a better comparison strategy. Finally, we confirmwell-known generalization issues
(due to dataset bias and overfitting), new ones (due to dynamic objects and the
lack of a causal model), and training instability; problems requiring further research before end-to-end driving through imitation can scale to real-world driving. |
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May 2019 |
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Ph.D. thesis |
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Publisher |
Ediciones Graficas Rey |
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Editor |
Antonio Lopez |
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ADAS; 600.118 |
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no |
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Call Number |
Admin @ si @ Cod2019 |
Serial |
3387 |
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Author |
Javad Zolfaghari Bengar; Abel Gonzalez-Garcia; Gabriel Villalonga; Bogdan Raducanu; Hamed H. Aghdam; Mikhail Mozerov; Antonio Lopez; Joost Van de Weijer |
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Title |
Temporal Coherence for Active Learning in Videos |
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Conference Article |
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Year |
2019 |
Publication |
IEEE International Conference on Computer Vision Workshops |
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914-923 |
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Autonomous driving systems require huge amounts of data to train. Manual annotation of this data is time-consuming and prohibitively expensive since it involves human resources. Therefore, active learning emerged as an alternative to ease this effort and to make data annotation more manageable. In this paper, we introduce a novel active learning approach for object detection in videos by exploiting temporal coherence. Our active learning criterion is based on the estimated number of errors in terms of false positives and false negatives. The detections obtained by the object detector are used to define the nodes of a graph and tracked forward and backward to temporally link the nodes. Minimizing an energy function defined on this graphical model provides estimates of both false positives and false negatives. Additionally, we introduce a synthetic video dataset, called SYNTHIA-AL, specially designed to evaluate active learning for video object detection in road scenes. Finally, we show that our approach outperforms active learning baselines tested on two datasets. |
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Seul; Corea; October 2019 |
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ICCVW |
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Notes |
LAMP; ADAS; 600.124; 602.200; 600.118; 600.120; 600.141 |
Approved |
no |
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Call Number |
Admin @ si @ ZGV2019 |
Serial |
3294 |
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Author |
Felipe Codevilla; Antonio Lopez; Vladlen Koltun; Alexey Dosovitskiy |
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Title |
On Offline Evaluation of Vision-based Driving Models |
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Conference Article |
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2018 |
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15th European Conference on Computer Vision |
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11219 |
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246-262 |
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Autonomous driving; deep learning |
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Autonomous driving models should ideally be evaluated by deploying
them on a fleet of physical vehicles in the real world. Unfortunately, this approach is not practical for the vast majority of researchers. An attractive alternative is to evaluate models offline, on a pre-collected validation dataset with ground truth annotation. In this paper, we investigate the relation between various online and offline metrics for evaluation of autonomous driving models. We find that offline prediction error is not necessarily correlated with driving quality, and two models with identical prediction error can differ dramatically in their driving performance. We show that the correlation of offline evaluation with driving quality can be significantly improved by selecting an appropriate validation dataset and
suitable offline metrics. |
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Munich; September 2018 |
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ECCV |
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Notes |
ADAS; 600.124; 600.118 |
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no |
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Call Number |
Admin @ si @ CLK2018 |
Serial |
3162 |
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Author |
German Ros; Sebastian Ramos; Manuel Granados; Amir Bakhtiary; David Vazquez; Antonio Lopez |
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Title |
Vision-based Offline-Online Perception Paradigm for Autonomous Driving |
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Conference Article |
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2015 |
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IEEE Winter Conference on Applications of Computer Vision |
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231 - 238 |
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Autonomous Driving; Scene Understanding; SLAM; Semantic Segmentation |
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Autonomous driving is a key factor for future mobility. Properly perceiving the environment of the vehicles is essential for a safe driving, which requires computing accurate geometric and semantic information in real-time. In this paper, we challenge state-of-the-art computer vision algorithms for building a perception system for autonomous driving. An inherent drawback in the computation of visual semantics is the trade-off between accuracy and computational cost. We propose to circumvent this problem by following an offline-online strategy. During the offline stage dense 3D semantic maps are created. In the online stage the current driving area is recognized in the maps via a re-localization process, which allows to retrieve the pre-computed accurate semantics and 3D geometry in realtime. Then, detecting the dynamic obstacles we obtain a rich understanding of the current scene. We evaluate quantitatively our proposal in the KITTI dataset and discuss the related open challenges for the computer vision community. |
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Hawaii; January 2015 |
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WACV |
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ADAS; 600.076 |
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Call Number |
ADAS @ adas @ RRG2015 |
Serial |
2499 |
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