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	Author	Ahmed M. A. Salih; Ilaria Boscolo Galazzo; Federica Cruciani; Lorenza Brusini; Petia Radeva
	Title	Investigating Explainable Artificial Intelligence for MRI-based Classification of Dementia: a New Stability Criterion for Explainable Methods			Type	Conference Article
	Year	2022	Publication	29th IEEE International Conference on Image Processing	Abbreviated Journal
	Volume		Issue		Pages
	Keywords	Image processing; Stability criteria; Machine learning; Robustness; Alzheimer's disease; Monitoring
	Abstract	Individuals diagnosed with Mild Cognitive Impairment (MCI) have shown an increased risk of developing Alzheimer’s Disease (AD). As such, early identification of dementia represents a key prognostic element, though hampered by complex disease patterns. Increasing efforts have focused on Machine Learning (ML) to build accurate classification models relying on a multitude of clinical/imaging variables. However, ML itself does not provide sensible explanations related to the model mechanism and feature contribution. Explainable Artificial Intelligence (XAI) represents the enabling technology in this framework, allowing to understand ML outcomes and derive human-understandable explanations. In this study, we aimed at exploring ML combined with MRI-based features and XAI to solve this classification problem and interpret the outcome. In particular, we propose a new method to assess the robustness of feature rankings provided by XAI methods, especially when multicollinearity exists. Our findings indicate that our method was able to disentangle the list of the informative features underlying dementia, with important implications for aiding personalized monitoring plans.
	Address	Bordeaux; France; October 2022
	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	ICIP
	Notes	MILAB			Approved	no
	Call Number	Admin @ si @ SBC2022			Serial	3789
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	Author	Javier Rodenas; Bhalaji Nagarajan; Marc Bolaños; Petia Radeva
	Title	Learning Multi-Subset of Classes for Fine-Grained Food Recognition			Type	Conference Article
	Year	2022	Publication	7th International Workshop on Multimedia Assisted Dietary Management	Abbreviated Journal
	Volume		Issue		Pages	17–26
	Keywords
	Abstract	Food image recognition is a complex computer vision task, because of the large number of fine-grained food classes. Fine-grained recognition tasks focus on learning subtle discriminative details to distinguish similar classes. In this paper, we introduce a new method to improve the classification of classes that are more difficult to discriminate based on Multi-Subsets learning. Using a pre-trained network, we organize classes in multiple subsets using a clustering technique. Later, we embed these subsets in a multi-head model structure. This structure has three distinguishable parts. First, we use several shared blocks to learn the generalized representation of the data. Second, we use multiple specialized blocks focusing on specific subsets that are difficult to distinguish. Lastly, we use a fully connected layer to weight the different subsets in an end-to-end manner by combining the neuron outputs. We validated our proposed method using two recent state-of-the-art vision transformers on three public food recognition datasets. Our method was successful in learning the confused classes better and we outperformed the state-of-the-art on the three datasets.
	Address	Lisboa; Portugal; October 2022
	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	MADiMa
	Notes	MILAB			Approved	no
	Call Number	Admin @ si @ RNB2022			Serial	3797
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	Author	Roberto Morales; Juan Quispe; Eduardo Aguilar
	Title	Exploring multi-food detection using deep learning-based algorithms			Type	Conference Article
	Year	2023	Publication	13th International Conference on Pattern Recognition Systems	Abbreviated Journal
	Volume		Issue		Pages	1-7
	Keywords
	Abstract	People are becoming increasingly concerned about their diet, whether for disease prevention, medical treatment or other purposes. In meals served in restaurants, schools or public canteens, it is not easy to identify the ingredients and/or the nutritional information they contain. Currently, technological solutions based on deep learning models have facilitated the recording and tracking of food consumed based on the recognition of the main dish present in an image. Considering that sometimes there may be multiple foods served on the same plate, food analysis should be treated as a multi-class object detection problem. EfficientDet and YOLOv5 are object detection algorithms that have demonstrated high mAP and real-time performance on general domain data. However, these models have not been evaluated and compared on public food datasets. Unlike general domain objects, foods have more challenging features inherent in their nature that increase the complexity of detection. In this work, we performed a performance evaluation of Efficient-Det and YOLOv5 on three public food datasets: UNIMIB2016, UECFood256 and ChileanFood64. From the results obtained, it can be seen that YOLOv5 provides a significant difference in terms of both mAP and response time compared to EfficientDet in all datasets. Furthermore, YOLOv5 outperforms the state-of-the-art on UECFood256, achieving an improvement of more than 4% in terms of mAP@.50 over the best reported.
	Address	Guayaquil; Ecuador; July 2023
	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	ICPRS
	Notes	MILAB			Approved	no
	Call Number	Admin @ si @ MQA2023			Serial	3843
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	Author	Bhalaji Nagarajan; Marc Bolaños; Eduardo Aguilar; Petia Radeva
	Title	Deep ensemble-based hard sample mining for food recognition			Type	Journal Article
	Year	2023	Publication	Journal of Visual Communication and Image Representation	Abbreviated Journal	JVCIR
	Volume	95	Issue		Pages	103905
	Keywords
	Abstract	Deep neural networks represent a compelling technique to tackle complex real-world problems, but are over-parameterized and often suffer from over- or under-confident estimates. Deep ensembles have shown better parameter estimations and often provide reliable uncertainty estimates that contribute to the robustness of the results. In this work, we propose a new metric to identify samples that are hard to classify. Our metric is defined as coincidence score for deep ensembles which measures the agreement of its individual models. The main hypothesis we rely on is that deep learning algorithms learn the low-loss samples better compared to large-loss samples. In order to compensate for this, we use controlled over-sampling on the identified ”hard” samples using proper data augmentation schemes to enable the models to learn those samples better. We validate the proposed metric using two public food datasets on different backbone architectures and show the improvements compared to the conventional deep neural network training using different performance metrics.
	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	MILAB			Approved	no
	Call Number	Admin @ si @ NBA2023			Serial	3844
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	Author	Roger Max Calle Quispe; Maya Aghaei Gavari; Eduardo Aguilar Torres
	Title	Towards real-time accurate safety helmets detection through a deep learning-based method			Type	Journal
	Year	2023	Publication	Ingeniare. Revista chilena de ingenieria	Abbreviated Journal
	Volume	31	Issue	12	Pages
	Keywords
	Abstract	Occupational safety is a fundamental activity in industries and revolves around the management of the necessary controls that must be present to mitigate occupational risks. These controls include verifying the use of Personal Protection Equipment (PPE). Within PPE, safety helmets are vital to reducing severe or fatal consequences caused by head injuries. This problem has been addressed recently by various research based on deep learning to detect the usage of safety helmets by the present people in the industrial field. These works have achieved promising results for safety helmet detection using object detection methods from the YOLO family. In this work, we propose to analyze the performance of Scaled-YOLOv4, a novel model of the YOLO family that has yet to be previously studied for this problem. The performance of the Scaled-YOLOv4 is evaluated on two public databases, carefully selected among the previously proposed datasets for the occupational safety framework. We demonstrate the superiority of Scaled-YOLOv4 in terms of mAP and Fl-score concerning the previous works for both databases. Further, we summarize the currently available datasets for safety helmet detection purposes and discuss their suitability.
	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	MILAB			Approved	no
	Call Number	Admin @ si @ CAA2023			Serial	3846
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	Author	P. Canals; Simone Balocco; O. Diaz; J. Li; A. Garcia Tornel; M. Olive Gadea; M. Ribo
	Title	A fully automatic method for vascular tortuosity feature extraction in the supra-aortic region: unraveling possibilities in stroke treatment planning			Type	Journal Article
	Year	2023	Publication	Computerized Medical Imaging and Graphics	Abbreviated Journal	CMIG
	Volume	104	Issue	102170	Pages
	Keywords	Artificial intelligence; Deep learning; Stroke; Thrombectomy; Vascular feature extraction; Vascular tortuosity
	Abstract	Vascular tortuosity of supra-aortic vessels is widely considered one of the main reasons for failure and delays in endovascular treatment of large vessel occlusion in patients with acute ischemic stroke. Characterization of tortuosity is a challenging task due to the lack of objective, robust and effective analysis tools. We present a fully automatic method for arterial segmentation, vessel labelling and tortuosity feature extraction applied to the supra-aortic region. A sample of 566 computed tomography angiography scans from acute ischemic stroke patients (aged 74.8 ± 12.9, 51.0% females) were used for training, validation and testing of a segmentation module based on a U-Net architecture (162 cases) and a vessel labelling module powered by a graph U-Net (566 cases). Successively, 30 cases were processed for testing of a tortuosity feature extraction module. Measurements obtained through automatic processing were compared to manual annotations from two observers for a thorough validation of the method. The proposed feature extraction method presented similar performance to the inter-rater variability observed in the measurement of 33 geometrical and morphological features of the arterial anatomy in the supra-aortic region. This system will contribute to the development of more complex models to advance the treatment of stroke by adding immediate automation, objectivity, repeatability and robustness to the vascular tortuosity characterization of patients.
	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	MILAB			Approved	no
	Call Number	Admin @ si @ CBD2023			Serial	4005
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	Author	Mohammad Momeny; Ali Asghar Neshat; Ahmad Jahanbakhshi; Majid Mahmoudi; Yiannis Ampatzidis; Petia Radeva
	Title	Grading and fraud detection of saffron via learning-to-augment incorporated Inception-v4 CNN			Type	Journal Article
	Year	2023	Publication	Food Control	Abbreviated Journal	FC
	Volume	147	Issue		Pages	109554
	Keywords
	Abstract	Saffron is a well-known product in the food industry. It is one of the spices that are sometimes adulterated with the sole motive of gaining more economic profit. Today, machine vision systems are widely used in controlling the quality of food and agricultural products as a new, non-destructive, and inexpensive approach. In this study, a machine vision system based on deep learning was used to detect fraud and saffron quality. A dataset of 1869 images was created and categorized in 6 classes including: dried saffron stigma using a dryer; dried saffron stigma using pressing method; pure stem of saffron; sunflower; saffron stem mixed with food coloring; and corn silk mixed with food coloring. A Learning-to-Augment incorporated Inception-v4 Convolutional Neural Network (LAII-v4 CNN) was developed for grading and fraud detection of saffron in images captured by smartphones. The best policies of data augmentation were selected with the proposed LAII-v4 CNN using images corrupted by Gaussian, speckle, and impulse noise to address overfitting the model. The proposed LAII-v4 CNN compared with regular CNN-based methods and traditional classifiers. Ensemble of Bagged Decision Trees, Ensemble of Boosted Decision Trees, k-Nearest Neighbor, Random Under-sampling Boosted Trees, and Support Vector Machine were used for classification of the features extracted by Histograms of Oriented Gradients and Local Binary Patterns, and selected by the Principal Component Analysis. The results showed that the proposed LAII-v4 CNN with an accuracy of 99.5% has achieved the best performance by employing batch normalization, Dropout, and leaky ReLU.
	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	MILAB			Approved	no
	Call Number	Admin @ si @ MNJ2023			Serial	3882
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	Author	Albert Tatjer; Bhalaji Nagarajan; Ricardo Marques; Petia Radeva
	Title	CCLM: Class-Conditional Label Noise Modelling			Type	Conference Article
	Year	2023	Publication	11th Iberian Conference on Pattern Recognition and Image Analysis	Abbreviated Journal
	Volume	14062	Issue		Pages	3-14
	Keywords
	Abstract	The performance of deep neural networks highly depends on the quality and volume of the training data. However, cost-effective labelling processes such as crowdsourcing and web crawling often lead to data with noisy (i.e., wrong) labels. Making models robust to this label noise is thus of prime importance. A common approach is using loss distributions to model the label noise. However, the robustness of these methods highly depends on the accuracy of the division of training set into clean and noisy samples. In this work, we dive in this research direction highlighting the existing problem of treating this distribution globally and propose a class-conditional approach to split the clean and noisy samples. We apply our approach to the popular DivideMix algorithm and show how the local treatment fares better with respect to the global treatment of loss distribution. We validate our hypothesis on two popular benchmark datasets and show substantial improvements over the baseline experiments. We further analyze the effectiveness of the proposal using two different metrics – Noise Division Accuracy and Classiness.
	Address	Alicante; Spain; June 2023
	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	IbPRIA
	Notes	MILAB			Approved	no
	Call Number	Admin @ si @ TNM2023			Serial	3925
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	Author	David Dueñas; Mostafa Kamal; Petia Radeva
	Title	Efficient Deep Learning Ensemble for Skin Lesion Classification			Type	Conference Article
	Year	2023	Publication	Proceedings of the 18th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications	Abbreviated Journal
	Volume		Issue		Pages	303-314
	Keywords
	Abstract	Vision Transformers (ViTs) are deep learning techniques that have been gaining in popularity in recent years. In this work, we study the performance of ViTs and Convolutional Neural Networks (CNNs) on skin lesions classification tasks, specifically melanoma diagnosis. We show that regardless of the performance of both architectures, an ensemble of them can improve their generalization. We also present an adaptation to the Gram-OOD* method (detecting Out-of-distribution (OOD) using Gram matrices) for skin lesion images. Moreover, the integration of super-convergence was critical to success in building models with strict computing and training time constraints. We evaluated our ensemble of ViTs and CNNs, demonstrating that generalization is enhanced by placing first in the 2019 and third in the 2020 ISIC Challenge Live Leaderboards (available at https://challenge.isic-archive.com/leaderboards/live/).
	Address	Lisboa; Portugal; February 2023
	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	VISIGRAPP
	Notes	MILAB			Approved	no
	Call Number	Admin @ si @ DKR2023			Serial	3928
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	Author	Mariella Dimiccoli
	Title	Figure-ground segregation: A fully nonlocal approach			Type	Journal Article
	Year	2016	Publication	Vision Research	Abbreviated Journal	VR
	Volume	126	Issue		Pages	308-317
	Keywords	Figure-ground segregation; Nonlocal approach; Directional linear voting; Nonlinear diffusion
	Abstract	We present a computational model that computes and integrates in a nonlocal fashion several configural cues for automatic figure-ground segregation. Our working hypothesis is that the figural status of each pixel is a nonlocal function of several geometric shape properties and it can be estimated without explicitly relying on object boundaries. The methodology is grounded on two elements: multi-directional linear voting and nonlinear diffusion. A first estimation of the figural status of each pixel is obtained as a result of a voting process, in which several differently oriented line-shaped neighborhoods vote to express their belief about the figural status of the pixel. A nonlinear diffusion process is then applied to enforce the coherence of figural status estimates among perceptually homogeneous regions. Computer simulations fit human perception and match the experimental evidence that several cues cooperate in defining figure-ground segregation. The results of this work suggest that figure-ground segregation involves feedback from cells with larger receptive fields in higher visual cortical areas.
	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	MILAB;			Approved	no
	Call Number	Admin @ si @ Dim2016b			Serial	2623
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	Author	Tadashi Araki; Sumit K. Banchhor; Narendra D. Londhe; Nobutaka Ikeda; Petia Radeva; Devarshi Shukla; Luca Saba; Antonella Balestrieri; Andrew Nicolaides; Shoaib Shafique; John R. Laird; Jasjit S. Suri
	Title	Reliable and Accurate Calcium Volume Measurement in Coronary Artery Using Intravascular Ultrasound Videos			Type	Journal Article
	Year	2016	Publication	Journal of Medical Systems	Abbreviated Journal	JMS
	Volume	40	Issue	3	Pages	51:1-51:20
	Keywords	Interventional cardiology; Atherosclerosis; Coronary arteries; IVUS; calcium volume; Soft computing; Performance Reliability; Accuracy
	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.
	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	MILAB;			Approved	no
	Call Number	Admin @ si @ ABL2016			Serial	2729
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	Author	Mariella Dimiccoli; Jean-Pascal Jacob; Lionel Moisan
	Title	Particle detection and tracking in fluorescence time-lapse imaging: a contrario approach			Type	Journal Article
	Year	2016	Publication	Journal of Machine Vision and Applications	Abbreviated Journal	MVAP
	Volume	27	Issue		Pages	511-527
	Keywords	particle detection; particle tracking; a-contrario approach; time-lapse fluorescence imaging
	Abstract	In this work, we propose a probabilistic approach for the detection and the tracking of particles on biological images. In presence of very noised and poor quality data, particles and trajectories can be characterized by an a-contrario model, that estimates the probability of observing the structures of interest in random data. This approach, first introduced in the modeling of human visual perception and then successfully applied in many image processing tasks, leads to algorithms that do not require a previous learning stage, nor a tedious parameter tuning and are very robust to noise. Comparative evaluations against a well established baseline show that the proposed approach outperforms the state of the art.
	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	MILAB;			Approved	no
	Call Number	Admin @ si @ DJM2016			Serial	2735
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	Author	Maedeh Aghaei; Mariella Dimiccoli; Petia Radeva
	Title	Multi-face tracking by extended bag-of-tracklets in egocentric photo-streams			Type	Journal Article
	Year	2016	Publication	Computer Vision and Image Understanding	Abbreviated Journal	CVIU
	Volume	149	Issue		Pages	146-156
	Keywords
	Abstract	Wearable cameras offer a hands-free way to record egocentric images of daily experiences, where social events are of special interest. The first step towards detection of social events is to track the appearance of multiple persons involved in them. In this paper, we propose a novel method to find correspondences of multiple faces in low temporal resolution egocentric videos acquired through a wearable camera. This kind of photo-stream imposes additional challenges to the multi-tracking problem with respect to conventional videos. Due to the free motion of the camera and to its low temporal resolution, abrupt changes in the field of view, in illumination condition and in the target location are highly frequent. To overcome such difficulties, we propose a multi-face tracking method that generates a set of tracklets through finding correspondences along the whole sequence for each detected face and takes advantage of the tracklets redundancy to deal with unreliable ones. Similar tracklets are grouped into the so called extended bag-of-tracklets (eBoT), which is aimed to correspond to a specific person. Finally, a prototype tracklet is extracted for each eBoT, where the occurred occlusions are estimated by relying on a new measure of confidence. We validated our approach over an extensive dataset of egocentric photo-streams and compared it to state of the art methods, demonstrating its effectiveness and robustness.
	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	MILAB;			Approved	no
	Call Number	Admin @ si @ ADR2016b			Serial	2742
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	Author	Mariella Dimiccoli
	Title	Fundamentals of cone regression			Type	Journal
	Year	2016	Publication	Journal of Statistics Surveys	Abbreviated Journal
	Volume	10	Issue		Pages	53-99
	Keywords	cone regression; linear complementarity problems; proximal operators.
	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.
	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	1935-7516	ISBN		Medium
	Area		Expedition		Conference
	Notes	MILAB;			Approved	no
	Call Number	Admin @ si @Dim2016a			Serial	2783
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	Author	Jean-Pascal Jacob; Mariella Dimiccoli; L. Moisan
	Title	Active skeleton for bacteria modelling			Type	Journal Article
	Year	2017	Publication	Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualization	Abbreviated Journal	CMBBE
	Volume	5	Issue	4	Pages	274-286
	Keywords
	Abstract	The investigation of spatio-temporal dynamics of bacterial cells and their molecular components requires automated image analysis tools to track cell shape properties and molecular component locations inside the cells. In the study of bacteria aging, the molecular components of interest are protein aggregates accumulated near bacteria boundaries. This particular location makes very ambiguous the correspondence between aggregates and cells, since computing accurately bacteria boundaries in phase-contrast time-lapse imaging is a challenging task. This paper proposes an active skeleton formulation for bacteria modelling which provides several advantages: an easy computation of shape properties (perimeter, length, thickness and orientation), an improved boundary accuracy in noisy images and a natural bacteria-centred coordinate system that permits the intrinsic location of molecular components inside the cell. Starting from an initial skeleton estimate, the medial axis of the bacterium is obtained by minimising an energy function which incorporates bacteria shape constraints. Experimental results on biological images and comparative evaluation of the performances validate the proposed approach for modelling cigar-shaped bacteria like Escherichia coli. The Image-J plugin of the proposed method can be found online at http://fluobactracker.inrialpes.fr.
	Address
	Corporate Author				Thesis
	Publisher	Taylor & Francis Group	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	MILAB;			Approved	no
	Call Number	Admin @ si @JDM2017			Serial	2784
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