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Author Clementine Decamps; Alexis Arnaud; Florent Petitprez; Mira Ayadi; Aurelia Baures; Lucile Armenoult; Sergio Escalera; Isabelle Guyon; Remy Nicolle; Richard Tomasini; Aurelien de Reynies; Jerome Cros; Yuna Blum; Magali Richard
Title DECONbench: a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification Type Journal Article
Year 2021 Publication BMC Bioinformatics Abbreviated Journal
Volume (up) 22 Issue Pages 473
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Abstract Quantification of tumor heterogeneity is essential to better understand cancer progression and to adapt therapeutic treatments to patient specificities. Bioinformatic tools to assess the different cell populations from single-omic datasets as bulk transcriptome or methylome samples have been recently developed, including reference-based and reference-free methods. Improved methods using multi-omic datasets are yet to be developed in the future and the community would need systematic tools to perform a comparative evaluation of these algorithms on controlled data.
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Notes HUPBA; no proj Approved no
Call Number Admin @ si @ DAP2021 Serial 3650
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Author Akhil Gurram; Ahmet Faruk Tuna; Fengyi Shen; Onay Urfalioglu; Antonio Lopez
Title Monocular Depth Estimation through Virtual-world Supervision and Real-world SfM Self-Supervision Type Journal Article
Year 2021 Publication IEEE Transactions on Intelligent Transportation Systems Abbreviated Journal TITS
Volume (up) 23 Issue 8 Pages 12738-12751
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Abstract Depth information is essential for on-board perception in autonomous driving and driver assistance. Monocular depth estimation (MDE) is very appealing since it allows for appearance and depth being on direct pixelwise correspondence without further calibration. Best MDE models are based on Convolutional Neural Networks (CNNs) trained in a supervised manner, i.e., assuming pixelwise ground truth (GT). Usually, this GT is acquired at training time through a calibrated multi-modal suite of sensors. However, also using only a monocular system at training time is cheaper and more scalable. This is possible by relying on structure-from-motion (SfM) principles to generate self-supervision. Nevertheless, problems of camouflaged objects, visibility changes, static-camera intervals, textureless areas, and scale ambiguity, diminish the usefulness of such self-supervision. In this paper, we perform monocular depth estimation by virtual-world supervision (MonoDEVS) and real-world SfM self-supervision. We compensate the SfM self-supervision limitations by leveraging virtual-world images with accurate semantic and depth supervision and addressing the virtual-to-real domain gap. Our MonoDEVSNet outperforms previous MDE CNNs trained on monocular and even stereo sequences.
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Notes ADAS; 600.118 Approved no
Call Number Admin @ si @ GTS2021 Serial 3598
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Author Diana Ramirez Cifuentes; Ana Freire; Ricardo Baeza Yates; Nadia Sanz Lamora; Aida Alvarez; Alexandre Gonzalez; Meritxell Lozano; Roger Llobet; Diego Velazquez; Josep M. Gonfaus; Jordi Gonzalez
Title Characterization of Anorexia Nervosa on Social Media: Textual, Visual, Relational, Behavioral, and Demographical Analysis Type Journal Article
Year 2021 Publication Journal of Medical Internet Research Abbreviated Journal JMIR
Volume (up) 23 Issue 7 Pages e25925
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Abstract Background: Eating disorders are psychological conditions characterized by unhealthy eating habits. Anorexia nervosa (AN) is defined as the belief of being overweight despite being dangerously underweight. The psychological signs involve emotional and behavioral issues. There is evidence that signs and symptoms can manifest on social media, wherein both harmful and beneficial content is shared daily.
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Notes ISE Approved no
Call Number Admin @ si @ RFB2021 Serial 3665
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Author Sanket Biswas; Pau Riba; Josep Llados; Umapada Pal
Title Beyond Document Object Detection: Instance-Level Segmentation of Complex Layouts Type Journal Article
Year 2021 Publication International Journal on Document Analysis and Recognition Abbreviated Journal IJDAR
Volume (up) 24 Issue Pages 269–281
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Abstract Information extraction is a fundamental task of many business intelligence services that entail massive document processing. Understanding a document page structure in terms of its layout provides contextual support which is helpful in the semantic interpretation of the document terms. In this paper, inspired by the progress of deep learning methodologies applied to the task of object recognition, we transfer these models to the specific case of document object detection, reformulating the traditional problem of document layout analysis. Moreover, we importantly contribute to prior arts by defining the task of instance segmentation on the document image domain. An instance segmentation paradigm is especially important in complex layouts whose contents should interact for the proper rendering of the page, i.e., the proper text wrapping around an image. Finally, we provide an extensive evaluation, both qualitative and quantitative, that demonstrates the superior performance of the proposed methodology over the current state of the art.
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Notes DAG; 600.121; 600.140; 110.312 Approved no
Call Number Admin @ si @ BRL2021b Serial 3574
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Author Minesh Mathew; Lluis Gomez; Dimosthenis Karatzas; C.V. Jawahar
Title Asking questions on handwritten document collections Type Journal Article
Year 2021 Publication International Journal on Document Analysis and Recognition Abbreviated Journal IJDAR
Volume (up) 24 Issue Pages 235-249
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Abstract This work addresses the problem of Question Answering (QA) on handwritten document collections. Unlike typical QA and Visual Question Answering (VQA) formulations where the answer is a short text, we aim to locate a document snippet where the answer lies. The proposed approach works without recognizing the text in the documents. We argue that the recognition-free approach is suitable for handwritten documents and historical collections where robust text recognition is often difficult. At the same time, for human users, document image snippets containing answers act as a valid alternative to textual answers. The proposed approach uses an off-the-shelf deep embedding network which can project both textual words and word images into a common sub-space. This embedding bridges the textual and visual domains and helps us retrieve document snippets that potentially answer a question. We evaluate results of the proposed approach on two new datasets: (i) HW-SQuAD: a synthetic, handwritten document image counterpart of SQuAD1.0 dataset and (ii) BenthamQA: a smaller set of QA pairs defined on documents from the popular Bentham manuscripts collection. We also present a thorough analysis of the proposed recognition-free approach compared to a recognition-based approach which uses text recognized from the images using an OCR. Datasets presented in this work are available to download at docvqa.org.
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Notes DAG; 600.121 Approved no
Call Number Admin @ si @ MGK2021 Serial 3621
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Author Shiqi Yang; Kai Wang; Luis Herranz; Joost Van de Weijer
Title On Implicit Attribute Localization for Generalized Zero-Shot Learning Type Journal Article
Year 2021 Publication IEEE Signal Processing Letters Abbreviated Journal
Volume (up) 28 Issue Pages 872 - 876
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Abstract Zero-shot learning (ZSL) aims to discriminate images from unseen classes by exploiting relations to seen classes via their attribute-based descriptions. Since attributes are often related to specific parts of objects, many recent works focus on discovering discriminative regions. However, these methods usually require additional complex part detection modules or attention mechanisms. In this paper, 1) we show that common ZSL backbones (without explicit attention nor part detection) can implicitly localize attributes, yet this property is not exploited. 2) Exploiting it, we then propose SELAR, a simple method that further encourages attribute localization, surprisingly achieving very competitive generalized ZSL (GZSL) performance when compared with more complex state-of-the-art methods. Our findings provide useful insight for designing future GZSL methods, and SELAR provides an easy to implement yet strong baseline.
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Notes LAMP; 600.120 Approved no
Call Number YWH2021 Serial 3563
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Author Sudeep Katakol; Basem Elbarashy; Luis Herranz; Joost Van de Weijer; Antonio Lopez
Title Distributed Learning and Inference with Compressed Images Type Journal Article
Year 2021 Publication IEEE Transactions on Image Processing Abbreviated Journal TIP
Volume (up) 30 Issue Pages 3069 - 3083
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Abstract Modern computer vision requires processing large amounts of data, both while training the model and/or during inference, once the model is deployed. Scenarios where images are captured and processed in physically separated locations are increasingly common (e.g. autonomous vehicles, cloud computing). In addition, many devices suffer from limited resources to store or transmit data (e.g. storage space, channel capacity). In these scenarios, lossy image compression plays a crucial role to effectively increase the number of images collected under such constraints. However, lossy compression entails some undesired degradation of the data that may harm the performance of the downstream analysis task at hand, since important semantic information may be lost in the process. Moreover, we may only have compressed images at training time but are able to use original images at inference time, or vice versa, and in such a case, the downstream model suffers from covariate shift. In this paper, we analyze this phenomenon, with a special focus on vision-based perception for autonomous driving as a paradigmatic scenario. We see that loss of semantic information and covariate shift do indeed exist, resulting in a drop in performance that depends on the compression rate. In order to address the problem, we propose dataset restoration, based on image restoration with generative adversarial networks (GANs). Our method is agnostic to both the particular image compression method and the downstream task; and has the advantage of not adding additional cost to the deployed models, which is particularly important in resource-limited devices. The presented experiments focus on semantic segmentation as a challenging use case, cover a broad range of compression rates and diverse datasets, and show how our method is able to significantly alleviate the negative effects of compression on the downstream visual task.
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Notes LAMP; ADAS; 600.120; 600.118 Approved no
Call Number Admin @ si @ KEH2021 Serial 3543
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Author Manisha Das; Deep Gupta; Petia Radeva; Ashwini M. Bakde
Title Multi-scale decomposition-based CT-MR neurological image fusion using optimized bio-inspired spiking neural model with meta-heuristic optimization Type Journal Article
Year 2021 Publication International Journal of Imaging Systems and Technology Abbreviated Journal IMA
Volume (up) 31 Issue 4 Pages 2170-2188
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Abstract Multi-modal medical image fusion plays an important role in clinical diagnosis and works as an assistance model for clinicians. In this paper, a computed tomography-magnetic resonance (CT-MR) image fusion model is proposed using an optimized bio-inspired spiking feedforward neural network in different decomposition domains. First, source images are decomposed into base (low-frequency) and detail (high-frequency) layer components. Low-frequency subbands are fused using texture energy measures to capture the local energy, contrast, and small edges in the fused image. High-frequency coefficients are fused using firing maps obtained by pixel-activated neural model with the optimized parameters using three different optimization techniques such as differential evolution, cuckoo search, and gray wolf optimization, individually. In the optimization model, a fitness function is computed based on the edge index of resultant fused images, which helps to extract and preserve sharp edges available in the source CT and MR images. To validate the fusion performance, a detailed comparative analysis is presented among the proposed and state-of-the-art methods in terms of quantitative and qualitative measures along with computational complexity. Experimental results show that the proposed method produces a significantly better visual quality of fused images meanwhile outperforms the existing methods.
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Notes MILAB; no menciona Approved no
Call Number Admin @ si @ DGR2021a Serial 3630
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Author Daniel Hernandez; Antonio Espinosa; David Vazquez; Antonio Lopez; Juan C. Moure
Title 3D Perception With Slanted Stixels on GPU Type Journal Article
Year 2021 Publication IEEE Transactions on Parallel and Distributed Systems Abbreviated Journal TPDS
Volume (up) 32 Issue 10 Pages 2434-2447
Keywords Daniel Hernandez-Juarez; Antonio Espinosa; David Vazquez; Antonio M. Lopez; Juan C. Moure
Abstract This article presents a GPU-accelerated software design of the recently proposed model of Slanted Stixels, which represents the geometric and semantic information of a scene in a compact and accurate way. We reformulate the measurement depth model to reduce the computational complexity of the algorithm, relying on the confidence of the depth estimation and the identification of invalid values to handle outliers. The proposed massively parallel scheme and data layout for the irregular computation pattern that corresponds to a Dynamic Programming paradigm is described and carefully analyzed in performance terms. Performance is shown to scale gracefully on current generation embedded GPUs. We assess the proposed methods in terms of semantic and geometric accuracy as well as run-time performance on three publicly available benchmark datasets. Our approach achieves real-time performance with high accuracy for 2048 × 1024 image sizes and 4 × 4 Stixel resolution on the low-power embedded GPU of an NVIDIA Tegra Xavier.
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Notes ADAS; 600.124; 600.118 Approved no
Call Number Admin @ si @ HEV2021 Serial 3561
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Author Hugo Bertiche; Meysam Madadi; Sergio Escalera
Title PBNS: Physically Based Neural Simulation for Unsupervised Garment Pose Space Deformation Type Journal Article
Year 2021 Publication ACM Transactions on Graphics Abbreviated Journal
Volume (up) 40 Issue 6 Pages 1-14
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Abstract We present a methodology to automatically obtain Pose Space Deformation (PSD) basis for rigged garments through deep learning. Classical approaches rely on Physically Based Simulations (PBS) to animate clothes. These are general solutions that, given a sufficiently fine-grained discretization of space and time, can achieve highly realistic results. However, they are computationally expensive and any scene modification prompts the need of re-simulation. Linear Blend Skinning (LBS) with PSD offers a lightweight alternative to PBS, though, it needs huge volumes of data to learn proper PSD. We propose using deep learning, formulated as an implicit PBS, to unsupervisedly learn realistic cloth Pose Space Deformations in a constrained scenario: dressed humans. Furthermore, we show it is possible to train these models in an amount of time comparable to a PBS of a few sequences. To the best of our knowledge, we are the first to propose a neural simulator for cloth.
While deep-based approaches in the domain are becoming a trend, these are data-hungry models. Moreover, authors often propose complex formulations to better learn wrinkles from PBS data. Supervised learning leads to physically inconsistent predictions that require collision solving to be used. Also, dependency on PBS data limits the scalability of these solutions, while their formulation hinders its applicability and compatibility. By proposing an unsupervised methodology to learn PSD for LBS models (3D animation standard), we overcome both of these drawbacks. Results obtained show cloth-consistency in the animated garments and meaningful pose-dependant folds and wrinkles. Our solution is extremely efficient, handles multiple layers of cloth, allows unsupervised outfit resizing and can be easily applied to any custom 3D avatar.
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Call Number Admin @ si @ BME2021c Serial 3643
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Author Victor M. Campello; Polyxeni Gkontra; Cristian Izquierdo; Carlos Martin-Isla; Alireza Sojoudi; Peter M. Full; Klaus Maier-Hein; Yao Zhang; Zhiqiang He; Jun Ma; Mario Parreno; Alberto Albiol; Fanwei Kong; Shawn C. Shadden; Jorge Corral Acero; Vaanathi Sundaresan; Mina Saber; Mustafa Elattar; Hongwei Li; Bjoern Menze; Firas Khader; Christoph Haarburger; Cian M. Scannell; Mitko Veta; Adam Carscadden; Kumaradevan Punithakumar; Xiao Liu; Sotirios A. Tsaftaris; Xiaoqiong Huang; Xin Yang; Lei Li; Xiahai Zhuang; David Vilades; Martin L. Descalzo; Andrea Guala; Lucia La Mura; Matthias G. Friedrich; Ria Garg; Julie Lebel; Filipe Henriques; Mahir Karakas; Ersin Cavus; Steffen E. Petersen; Sergio Escalera; Santiago Segui; Jose F. Rodriguez Palomares; Karim Lekadir
Title Multi-Centre, Multi-Vendor and Multi-Disease Cardiac Segmentation: The M&Ms Challenge Type Journal Article
Year 2021 Publication IEEE Transactions on Medical Imaging Abbreviated Journal TMI
Volume (up) 40 Issue 12 Pages 3543-3554
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Abstract The emergence of deep learning has considerably advanced the state-of-the-art in cardiac magnetic resonance (CMR) segmentation. Many techniques have been proposed over the last few years, bringing the accuracy of automated segmentation close to human performance. However, these models have been all too often trained and validated using cardiac imaging samples from single clinical centres or homogeneous imaging protocols. This has prevented the development and validation of models that are generalizable across different clinical centres, imaging conditions or scanner vendors. To promote further research and scientific benchmarking in the field of generalizable deep learning for cardiac segmentation, this paper presents the results of the Multi-Centre, Multi-Vendor and Multi-Disease Cardiac Segmentation (M&Ms) Challenge, which was recently organized as part of the MICCAI 2020 Conference. A total of 14 teams submitted different solutions to the problem, combining various baseline models, data augmentation strategies, and domain adaptation techniques. The obtained results indicate the importance of intensity-driven data augmentation, as well as the need for further research to improve generalizability towards unseen scanner vendors or new imaging protocols. Furthermore, we present a new resource of 375 heterogeneous CMR datasets acquired by using four different scanner vendors in six hospitals and three different countries (Spain, Canada and Germany), which we provide as open-access for the community to enable future research in the field.
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Notes HUPBA; no proj Approved no
Call Number Admin @ si @ CGI2021 Serial 3653
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Author Zhengying Liu; Adrien Pavao; Zhen Xu; Sergio Escalera; Fabio Ferreira; Isabelle Guyon; Sirui Hong; Frank Hutter; Rongrong Ji; Julio C. S. Jacques Junior; Ge Li; Marius Lindauer; Zhipeng Luo; Meysam Madadi; Thomas Nierhoff; Kangning Niu; Chunguang Pan; Danny Stoll; Sebastien Treguer; Jin Wang; Peng Wang; Chenglin Wu; Youcheng Xiong; Arber Zela; Yang Zhang
Title Winning Solutions and Post-Challenge Analyses of the ChaLearn AutoDL Challenge 2019 Type Journal Article
Year 2021 Publication IEEE Transactions on Pattern Analysis and Machine Intelligence Abbreviated Journal TPAMI
Volume (up) 43 Issue 9 Pages 3108 - 3125
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Abstract This paper reports the results and post-challenge analyses of ChaLearn's AutoDL challenge series, which helped sorting out a profusion of AutoML solutions for Deep Learning (DL) that had been introduced in a variety of settings, but lacked fair comparisons. All input data modalities (time series, images, videos, text, tabular) were formatted as tensors and all tasks were multi-label classification problems. Code submissions were executed on hidden tasks, with limited time and computational resources, pushing solutions that get results quickly. In this setting, DL methods dominated, though popular Neural Architecture Search (NAS) was impractical. Solutions relied on fine-tuned pre-trained networks, with architectures matching data modality. Post-challenge tests did not reveal improvements beyond the imposed time limit. While no component is particularly original or novel, a high level modular organization emerged featuring a “meta-learner”, “data ingestor”, “model selector”, “model/learner”, and “evaluator”. This modularity enabled ablation studies, which revealed the importance of (off-platform) meta-learning, ensembling, and efficient data management. Experiments on heterogeneous module combinations further confirm the (local) optimality of the winning solutions. Our challenge legacy includes an ever-lasting benchmark (http://autodl.chalearn.org), the open-sourced code of the winners, and a free “AutoDL self-service.”
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Call Number Admin @ si @ LPX2021 Serial 3587
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Author O.F.Ahmad; Y.Mori; M.Misawa; S.Kudo; J.T.Anderson; Jorge Bernal
Title Establishing key research questions for the implementation of artificial intelligence in colonoscopy: a modified Delphi method Type Journal Article
Year 2021 Publication Endoscopy Abbreviated Journal END
Volume (up) 53 Issue 9 Pages 893-901
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Abstract 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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Notes ISE Approved no
Call Number Admin @ si @ AMM2021 Serial 3670
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Author AN Ruchai; VI Kober; KA Dorofeev; VN Karnaukhov; Mikhail Mozerov
Title Classification of breast abnormalities using a deep convolutional neural network and transfer learning Type Journal Article
Year 2021 Publication Journal of Communications Technology and Electronics Abbreviated Journal
Volume (up) 66 Issue 6 Pages 778–783
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Abstract A new algorithm for classification of breast pathologies in digital mammography using a convolutional neural network and transfer learning is proposed. The following pretrained neural networks were chosen: MobileNetV2, InceptionResNetV2, Xception, and ResNetV2. All mammographic images were pre-processed to improve classification reliability. Transfer training was carried out using additional data augmentation and fine-tuning. The performance of the proposed algorithm for classification of breast pathologies in terms of accuracy on real data is discussed and compared with that of state-of-the-art algorithms on the available MIAS database.
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Notes LAMP; Approved no
Call Number Admin @ si @ RKD2022 Serial 3680
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Author Manisha Das; Deep Gupta; Petia Radeva; Ashwini M. Bakde
Title Optimized CT-MR neurological image fusion framework using biologically inspired spiking neural model in hybrid ℓ1 - ℓ0 layer decomposition domain Type Journal Article
Year 2021 Publication Biomedical Signal Processing and Control Abbreviated Journal BSPC
Volume (up) 68 Issue Pages 102535
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Abstract Medical image fusion plays an important role in the clinical diagnosis of several critical neurological diseases by merging complementary information available in multimodal images. In this paper, a novel CT-MR neurological image fusion framework is proposed using an optimized biologically inspired feedforward neural model in two-scale hybrid ℓ1 − ℓ0 decomposition domain using gray wolf optimization to preserve the structural as well as texture information present in source CT and MR images. Initially, the source images are subjected to two-scale ℓ1 − ℓ0 decomposition with optimized parameters, giving a scale-1 detail layer, a scale-2 detail layer and a scale-2 base layer. Two detail layers at scale-1 and 2 are fused using an optimized biologically inspired neural model and weighted average scheme based on local energy and modified spatial frequency to maximize the preservation of edges and local textures, respectively, while the scale-2 base layer gets fused using choose max rule to preserve the background information. To optimize the hyper-parameters of hybrid ℓ1 − ℓ0 decomposition and biologically inspired neural model, a fitness function is evaluated based on spatial frequency and edge index of the resultant fused image obtained by adding all the fused components. The fusion performance is analyzed by conducting extensive experiments on different CT-MR neurological images. Experimental results indicate that the proposed method provides better-fused images and outperforms the other state-of-the-art fusion methods in both visual and quantitative assessments.
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Notes MILAB; no proj Approved no
Call Number Admin @ si @ DGR2021b Serial 3636
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