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Debora Gil; Oriol Ramos Terrades; Raquel Perez |
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Topological Radiomics (TOPiomics): Early Detection of Genetic Abnormalities in Cancer Treatment Evolution |
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2021 |
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Extended Abstracts GEOMVAP 2019, Trends in Mathematics 15 |
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15 |
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89–93 |
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Abnormalities in radiomic measures correlate to genomic alterations prone to alter the outcome of personalized anti-cancer treatments. TOPiomics is a new method for the early detection of variations in tumor imaging phenotype from a topological structure in multi-view radiomic spaces. |
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Springer Nature |
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IAM; DAG; 600.120; 600.145; 600.139 |
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Admin @ si @ GRP2021 |
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3594 |
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Marta Ligero; Alonso Garcia Ruiz; Cristina Viaplana; Guillermo Villacampa; Maria V Raciti; Jaid Landa; Ignacio Matos; Juan Martin Liberal; Maria Ochoa de Olza; Cinta Hierro; Joaquin Mateo; Macarena Gonzalez; Rafael Morales Barrera; Cristina Suarez; Jordi Rodon; Elena Elez; Irene Braña; Eva Muñoz-Couselo; Ana Oaknin; Roberta Fasani; Paolo Nuciforo; Debora Gil; Carlota Rubio Perez; Joan Seoane; Enriqueta Felip; Manuel Escobar; Josep Tabernero; Joan Carles; Rodrigo Dienstmann; Elena Garralda; Raquel Perez Lopez |
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A CT-based radiomics signature is associated with response to immune checkpoint inhibitors in advanced solid tumors |
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Journal Article |
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2021 |
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Radiology |
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299 |
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1 |
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109-119 |
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Background Reliable predictive imaging markers of response to immune checkpoint inhibitors are needed. Purpose To develop and validate a pretreatment CT-based radiomics signature to predict response to immune checkpoint inhibitors in advanced solid tumors. Materials and Methods In this retrospective study, a radiomics signature was developed in patients with advanced solid tumors (including breast, cervix, gastrointestinal) treated with anti-programmed cell death-1 or programmed cell death ligand-1 monotherapy from August 2012 to May 2018 (cohort 1). This was tested in patients with bladder and lung cancer (cohorts 2 and 3). Radiomics variables were extracted from all metastases delineated at pretreatment CT and selected by using an elastic-net model. A regression model combined radiomics and clinical variables with response as the end point. Biologic validation of the radiomics score with RNA profiling of cytotoxic cells (cohort 4) was assessed with Mann-Whitney analysis. Results The radiomics signature was developed in 85 patients (cohort 1: mean age, 58 years ± 13 [standard deviation]; 43 men) and tested on 46 patients (cohort 2: mean age, 70 years ± 12; 37 men) and 47 patients (cohort 3: mean age, 64 years ± 11; 40 men). Biologic validation was performed in a further cohort of 20 patients (cohort 4: mean age, 60 years ± 13; 14 men). The radiomics signature was associated with clinical response to immune checkpoint inhibitors (area under the curve [AUC], 0.70; 95% CI: 0.64, 0.77; P < .001). In cohorts 2 and 3, the AUC was 0.67 (95% CI: 0.58, 0.76) and 0.67 (95% CI: 0.56, 0.77; P < .001), respectively. A radiomics-clinical signature (including baseline albumin level and lymphocyte count) improved on radiomics-only performance (AUC, 0.74 [95% CI: 0.63, 0.84; P < .001]; Akaike information criterion, 107.00 and 109.90, respectively). Conclusion A pretreatment CT-based radiomics signature is associated with response to immune checkpoint inhibitors, likely reflecting the tumor immunophenotype. © RSNA, 2021 Online supplemental material is available for this article. See also the editorial by Summers in this issue. |
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IAM; 600.145 |
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Admin @ si @ LGV2021 |
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3593 |
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Mireia Sole; Joan Blanco; Debora Gil; Oliver Valero; Alvaro Pascual; B. Cardenas; G. Fonseka; E. Anton; Richard Frodsham; Francesca Vidal; Zaida Sarrate |
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Chromosomal positioning in spermatogenic cells is influenced by chromosomal factors associated with gene activity, bouquet formation, and meiotic sex-chromosome inactivation |
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2021 |
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Chromosoma |
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130 |
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163-175 |
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Chromosome territoriality is not random along the cell cycle and it is mainly governed by intrinsic chromosome factors and gene expression patterns. Conversely, very few studies have explored the factors that determine chromosome territoriality and its influencing factors during meiosis. In this study, we analysed chromosome positioning in murine spermatogenic cells using three-dimensionally fluorescence in situ hybridization-based methodology, which allows the analysis of the entire karyotype. The main objective of the study was to decipher chromosome positioning in a radial axis (all analysed germ-cell nuclei) and longitudinal axis (only spermatozoa) and to identify the chromosomal factors that regulate such an arrangement. Results demonstrated that the radial positioning of chromosomes during spermatogenesis was cell-type specific and influenced by chromosomal factors associated to gene activity. Chromosomes with specific features that enhance transcription (high GC content, high gene density and high numbers of predicted expressed genes) were preferentially observed in the inner part of the nucleus in virtually all cell types. Moreover, the position of the sex chromosomes was influenced by their transcriptional status, from the periphery of the nucleus when its activity was repressed (pachytene) to a more internal position when it is partially activated (spermatid). At pachytene, chromosome positioning was also influenced by chromosome size due to the bouquet formation. Longitudinal chromosome positioning in the sperm nucleus was not random either, suggesting the importance of ordered longitudinal positioning for the release and activation of the paternal genome after fertilisation. |
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IAM; 600.145 |
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Admin @ si @ SBG2021 |
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3592 |
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Sonia Baeza; R.Domingo; M.Salcedo; G.Moragas; J.Deportos; I.Garcia Olive; Carles Sanchez; Debora Gil; Antoni Rosell |
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Artificial Intelligence to Optimize Pulmonary Embolism Diagnosis During Covid-19 Pandemic by Perfusion SPECT/CT, a Pilot Study |
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2021 |
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American Journal of Respiratory and Critical Care Medicine |
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IAM; 600.145 |
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Admin @ si @ BDS2021 |
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3591 |
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Guillermo Torres; Debora Gil |
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A multi-shape loss function with adaptive class balancing for the segmentation of lung structures |
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2020 |
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International Journal of Computer Assisted Radiology and Surgery |
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IJCAR |
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15 |
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1 |
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S154-55 |
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3590 |
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Xim Cerda-Company; Olivier Penacchio; Xavier Otazu |
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Chromatic Induction in Migraine |
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2021 |
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VISION |
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5 |
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3 |
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37 |
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migraine; vision; colour; colour perception; chromatic induction; psychophysics |
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The human visual system is not a colorimeter. The perceived colour of a region does not only depend on its colour spectrum, but also on the colour spectra and geometric arrangement of neighbouring regions, a phenomenon called chromatic induction. Chromatic induction is thought to be driven by lateral interactions: the activity of a central neuron is modified by stimuli outside its classical receptive field through excitatory–inhibitory mechanisms. As there is growing evidence of an excitation/inhibition imbalance in migraine, we compared chromatic induction in migraine and control groups. As hypothesised, we found a difference in the strength of induction between the two groups, with stronger induction effects in migraine. On the other hand, given the increased prevalence of visual phenomena in migraine with aura, we also hypothesised that the difference between migraine and control would be more important in migraine with aura than in migraine without aura. Our experiments did not support this hypothesis. Taken together, our results suggest a link between excitation/inhibition imbalance and increased induction effects. |
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NEUROBIT; no proj |
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Admin @ si @ CPO2021 |
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3589 |
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Albin Soutif; Marc Masana; Joost Van de Weijer; Bartlomiej Twardowski |
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On the importance of cross-task features for class-incremental learning |
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2021 |
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Theory and Foundation of continual learning workshop of ICML |
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In class-incremental learning, an agent with limited resources needs to learn a sequence of classification tasks, forming an ever growing classification problem, with the constraint of not being able to access data from previous tasks. The main difference with task-incremental learning, where a task-ID is available at inference time, is that the learner also needs to perform crosstask discrimination, i.e. distinguish between classes that have not been seen together. Approaches to tackle this problem are numerous and mostly make use of an external memory (buffer) of non-negligible size. In this paper, we ablate the learning of crosstask features and study its influence on the performance of basic replay strategies used for class-IL. We also define a new forgetting measure for class-incremental learning, and see that forgetting is not the principal cause of low performance. Our experimental results show that future algorithms for class-incremental learning should not only prevent forgetting, but also aim to improve the quality of the cross-task features. This is especially important when the number of classes per task is small. |
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Virtual; July 2021 |
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ICMLW |
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LAMP |
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Admin @ si @ SMW2021 |
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3588 |
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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 |
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Winning Solutions and Post-Challenge Analyses of the ChaLearn AutoDL Challenge 2019 |
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2021 |
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IEEE Transactions on Pattern Analysis and Machine Intelligence |
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TPAMI |
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43 |
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9 |
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3108 - 3125 |
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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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HUPBA; no proj |
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Admin @ si @ LPX2021 |
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3587 |
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Bartlomiej Twardowski; Pawel Zawistowski; Szymon Zaborowski |
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Metric Learning for Session-Based Recommendations |
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2021 |
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43rd edition of the annual BCS-IRSG European Conference on Information Retrieval |
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12656 |
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650-665 |
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Session-based recommendations; Deep metric learning; Learning to rank |
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Session-based recommenders, used for making predictions out of users’ uninterrupted sequences of actions, are attractive for many applications. Here, for this task we propose using metric learning, where a common embedding space for sessions and items is created, and distance measures dissimilarity between the provided sequence of users’ events and the next action. We discuss and compare metric learning approaches to commonly used learning-to-rank methods, where some synergies exist. We propose a simple architecture for problem analysis and demonstrate that neither extensively big nor deep architectures are necessary in order to outperform existing methods. The experimental results against strong baselines on four datasets are provided with an ablation study. |
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Virtual; March 2021 |
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ECIR |
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LAMP; 600.120 |
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Admin @ si @ TZZ2021 |
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3586 |
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Hannes Mueller; Andre Groeger; Jonathan Hersh; Andrea Matranga; Joan Serrat |
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Monitoring war destruction from space using machine learning |
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2021 |
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Proceedings of the National Academy of Sciences of the United States of America |
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PNAS |
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118 |
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23 |
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e2025400118 |
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Existing data on building destruction in conflict zones rely on eyewitness reports or manual detection, which makes it generally scarce, incomplete, and potentially biased. This lack of reliable data imposes severe limitations for media reporting, humanitarian relief efforts, human-rights monitoring, reconstruction initiatives, and academic studies of violent conflict. This article introduces an automated method of measuring destruction in high-resolution satellite images using deep-learning techniques combined with label augmentation and spatial and temporal smoothing, which exploit the underlying spatial and temporal structure of destruction. As a proof of concept, we apply this method to the Syrian civil war and reconstruct the evolution of damage in major cities across the country. Our approach allows generating destruction data with unprecedented scope, resolution, and frequency—and makes use of the ever-higher frequency at which satellite imagery becomes available. |
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ADAS; 600.118 |
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Admin @ si @ MGH2021 |
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3584 |
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Armin Mehri; Parichehr Behjati Ardakani; Angel Sappa |
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LiNet: A Lightweight Network for Image Super Resolution |
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2021 |
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25th International Conference on Pattern Recognition |
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This paper proposes a new lightweight network, LiNet, that enhancing technical efficiency in lightweight super resolution and operating approximately like very large and costly networks in terms of number of network parameters and operations. The proposed architecture allows the network to learn more abstract properties by avoiding low-level information via multiple links. LiNet introduces a Compact Dense Module, which contains set of inner and outer blocks, to efficiently extract meaningful information, to better leverage multi-level representations before upsampling stage, and to allow an efficient information and gradient flow within the network. Experiments on benchmark datasets show that the proposed LiNet achieves favorable performance against lightweight state-of-the-art methods. |
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Virtual; January 2021 |
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MSIAU; 600.130; 600.122 |
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Admin @ si @ MAS2021a |
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3583 |
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Armin Mehri; Parichehr Behjati Ardakani; Angel Sappa |
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MPRNet: Multi-Path Residual Network for Lightweight Image Super Resolution |
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2021 |
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IEEE Winter Conference on Applications of Computer Vision |
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2703-2712 |
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Lightweight super resolution networks have extremely importance for real-world applications. In recent years several SR deep learning approaches with outstanding achievement have been introduced by sacrificing memory and computational cost. To overcome this problem, a novel lightweight super resolution network is proposed, which improves the SOTA performance in lightweight SR and performs roughly similar to computationally expensive networks. Multi-Path Residual Network designs with a set of Residual concatenation Blocks stacked with Adaptive Residual Blocks: ($i$) to adaptively extract informative features and learn more expressive spatial context information; ($ii$) to better leverage multi-level representations before up-sampling stage; and ($iii$) to allow an efficient information and gradient flow within the network. The proposed architecture also contains a new attention mechanism, Two-Fold Attention Module, to maximize the representation ability of the model. Extensive experiments show the superiority of our model against other SOTA SR approaches. |
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Virtual; January 2021 |
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WACV |
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MSIAU; 600.130; 600.122 |
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Admin @ si @ MAS2021b |
Serial |
3582 |
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Author |
Rafael E. Rivadeneira; Angel Sappa; Boris X. Vintimilla; Sabari Nathan; Priya Kansal; Armin Mehri; Parichehr Behjati Ardakani; A.Dalal; A.Akula; D.Sharma; S.Pandey; B.Kumar; J.Yao; R.Wu; KFeng; N.Li; Y.Zhao; H.Patel; V. Chudasama; K.Pjajapati; A.Sarvaiya; K.Upla; K.Raja; R.Ramachandra; C.Bush; F.Almasri; T.Vandamme; O.Debeir; N.Gutierrez; Q.Nguyen; W.Beksi |
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Title |
Thermal Image Super-Resolution Challenge – PBVS 2021 |
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Conference Article |
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2021 |
Publication |
Conference on Computer Vision and Pattern Recognition Workshops |
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4359-4367 |
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This paper presents results from the second Thermal Image Super-Resolution (TISR) challenge organized in the framework of the Perception Beyond the Visible Spectrum (PBVS) 2021 workshop. For this second edition, the same thermal image dataset considered during the first challenge has been used; only mid-resolution (MR) and high-resolution (HR) sets have been considered. The dataset consists of 951 training images and 50 testing images for each resolution. A set of 20 images for each resolution is kept aside for evaluation. The two evaluation methodologies proposed for the first challenge are also considered in this opportunity. The first evaluation task consists of measuring the PSNR and SSIM between the obtained SR image and the corresponding ground truth (i.e., the HR thermal image downsampled by four). The second evaluation also consists of measuring the PSNR and SSIM, but in this case, considers the x2 SR obtained from the given MR thermal image; this evaluation is performed between the SR image with respect to the semi-registered HR image, which has been acquired with another camera. The results outperformed those from the first challenge, thus showing an improvement in both evaluation metrics. |
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Virtual; June 2021 |
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CVPRW |
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MSIAU; 600.130; 600.122 |
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Admin @ si @ RSV2021 |
Serial |
3581 |
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Author |
Patricia Suarez; Angel Sappa; Boris X. Vintimilla; Riad I. Hammoud |
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Title |
Cycle Generative Adversarial Network: Towards A Low-Cost Vegetation Index Estimation |
Type |
Conference Article |
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Year |
2021 |
Publication |
28th IEEE International Conference on Image Processing |
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19-22 |
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This paper presents a novel unsupervised approach to estimate the Normalized Difference Vegetation Index (NDVI). The NDVI is obtained as the ratio between information from the visible and near infrared spectral bands; in the current work, the NDVI is estimated just from an image of the visible spectrum through a Cyclic Generative Adversarial Network (CyclicGAN). This unsupervised architecture learns to estimate the NDVI index by means of an image translation between the red channel of a given RGB image and the NDVI unpaired index’s image. The translation is obtained by means of a ResNET architecture and a multiple loss function. Experimental results obtained with this unsupervised scheme show the validity of the implemented model. Additionally, comparisons with the state of the art approaches are provided showing improvements with the proposed approach. |
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Anchorage-Alaska; USA; September 2021 |
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ICIP |
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MSIAU; 600.130; 600.122; 601.349 |
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no |
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Call Number |
Admin @ si @ SSV2021b |
Serial |
3579 |
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Author |
Patricia Suarez; Angel Sappa; Boris X. Vintimilla |
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Title |
Deep learning-based vegetation index estimation |
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Book Chapter |
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Year |
2021 |
Publication |
Generative Adversarial Networks for Image-to-Image Translation |
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205-234 |
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Chapter 9 |
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Elsevier |
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A.Solanki; A.Nayyar; M.Naved |
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MSIAU; 600.122 |
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Admin @ si @ SSV2021a |
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3578 |
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