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Author Sonia Baeza; R.Domingo; M.Salcedo; G.Moragas; J.Deportos; I.Garcia Olive; Carles Sanchez; Debora Gil; Antoni Rosell
Title Artificial Intelligence to Optimize Pulmonary Embolism Diagnosis During Covid-19 Pandemic by Perfusion SPECT/CT, a Pilot Study Type (up) Journal Article
Year 2021 Publication American Journal of Respiratory and Critical Care Medicine Abbreviated Journal
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Notes IAM; 600.145 Approved no
Call Number Admin @ si @ BDS2021 Serial 3591
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Author Mireia Sole; Joan Blanco; Debora Gil; Oliver Valero; Alvaro Pascual; B. Cardenas; G. Fonseka; E. Anton; Richard Frodsham; Francesca Vidal; Zaida Sarrate
Title Chromosomal positioning in spermatogenic cells is influenced by chromosomal factors associated with gene activity, bouquet formation, and meiotic sex-chromosome inactivation Type (up) Journal Article
Year 2021 Publication Chromosoma Abbreviated Journal
Volume 130 Issue Pages 163-175
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Abstract 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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Notes IAM; 600.145 Approved no
Call Number Admin @ si @ SBG2021 Serial 3592
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Author 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
Title A CT-based radiomics signature is associated with response to immune checkpoint inhibitors in advanced solid tumors Type (up) Journal Article
Year 2021 Publication Radiology Abbreviated Journal
Volume 299 Issue 1 Pages 109-119
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Abstract 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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Notes IAM; 600.145 Approved no
Call Number Admin @ si @ LGV2021 Serial 3593
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Author Trevor Canham; Javier Vazquez; Elise Mathieu; Marcelo Bertalmío
Title Matching visual induction effects on screens of different size Type (up) Journal Article
Year 2021 Publication Journal of Vision Abbreviated Journal JOV
Volume 21 Issue 6(10) Pages 1-22
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Abstract In the film industry, the same movie is expected to be watched on displays of vastly different sizes, from cinema screens to mobile phones. But visual induction, the perceptual phenomenon by which the appearance of a scene region is affected by its surroundings, will be different for the same image shown on two displays of different dimensions. This phenomenon presents a practical challenge for the preservation of the artistic intentions of filmmakers, because it can lead to shifts in image appearance between viewing destinations. In this work, we show that a neural field model based on the efficient representation principle is able to predict induction effects and how, by regularizing its associated energy functional, the model is still able to represent induction but is now invertible. From this finding, we propose a method to preprocess an image in a screen–size dependent way so that its perception, in terms of visual induction, may remain constant across displays of different size. The potential of the method is demonstrated through psychophysical experiments on synthetic images and qualitative examples on natural images.
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Notes CIC Approved no
Call Number Admin @ si @ CVM2021 Serial 3595
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Author Pau Riba; Andreas Fischer; Josep Llados; Alicia Fornes
Title Learning graph edit distance by graph neural networks Type (up) Journal Article
Year 2021 Publication Pattern Recognition Abbreviated Journal PR
Volume 120 Issue Pages 108132
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Abstract The emergence of geometric deep learning as a novel framework to deal with graph-based representations has faded away traditional approaches in favor of completely new methodologies. In this paper, we propose a new framework able to combine the advances on deep metric learning with traditional approximations of the graph edit distance. Hence, we propose an efficient graph distance based on the novel field of geometric deep learning. Our method employs a message passing neural network to capture the graph structure, and thus, leveraging this information for its use on a distance computation. The performance of the proposed graph distance is validated on two different scenarios. On the one hand, in a graph retrieval of handwritten words i.e. keyword spotting, showing its superior performance when compared with (approximate) graph edit distance benchmarks. On the other hand, demonstrating competitive results for graph similarity learning when compared with the current state-of-the-art on a recent benchmark dataset.
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Notes DAG; 600.140; 600.121 Approved no
Call Number Admin @ si @ RFL2021 Serial 3611
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Author Lei Kang; Pau Riba; Marcal Rusinol; Alicia Fornes; Mauricio Villegas
Title Content and Style Aware Generation of Text-line Images for Handwriting Recognition Type (up) Journal Article
Year 2021 Publication IEEE Transactions on Pattern Analysis and Machine Intelligence Abbreviated Journal TPAMI
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Abstract Handwritten Text Recognition has achieved an impressive performance in public benchmarks. However, due to the high inter- and intra-class variability between handwriting styles, such recognizers need to be trained using huge volumes of manually labeled training data. To alleviate this labor-consuming problem, synthetic data produced with TrueType fonts has been often used in the training loop to gain volume and augment the handwriting style variability. However, there is a significant style bias between synthetic and real data which hinders the improvement of recognition performance. To deal with such limitations, we propose a generative method for handwritten text-line images, which is conditioned on both visual appearance and textual content. Our method is able to produce long text-line samples with diverse handwriting styles. Once properly trained, our method can also be adapted to new target data by only accessing unlabeled text-line images to mimic handwritten styles and produce images with any textual content. Extensive experiments have been done on making use of the generated samples to boost Handwritten Text Recognition performance. Both qualitative and quantitative results demonstrate that the proposed approach outperforms the current state of the art.
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Notes DAG; 600.140; 600.121 Approved no
Call Number Admin @ si @ KRR2021 Serial 3612
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Author S.K. Jemni; Mohamed Ali Souibgui; Yousri Kessentini; Alicia Fornes
Title Enhance to Read Better: A Multi-Task Adversarial Network for Handwritten Document Image Enhancement Type (up) Journal Article
Year 2022 Publication Pattern Recognition Abbreviated Journal PR
Volume 123 Issue Pages 108370
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Abstract Handwritten document images can be highly affected by degradation for different reasons: Paper ageing, daily-life scenarios (wrinkles, dust, etc.), bad scanning process and so on. These artifacts raise many readability issues for current Handwritten Text Recognition (HTR) algorithms and severely devalue their efficiency. In this paper, we propose an end to end architecture based on Generative Adversarial Networks (GANs) to recover the degraded documents into a and form. Unlike the most well-known document binarization methods, which try to improve the visual quality of the degraded document, the proposed architecture integrates a handwritten text recognizer that promotes the generated document image to be more readable. To the best of our knowledge, this is the first work to use the text information while binarizing handwritten documents. Extensive experiments conducted on degraded Arabic and Latin handwritten documents demonstrate the usefulness of integrating the recognizer within the GAN architecture, which improves both the visual quality and the readability of the degraded document images. Moreover, we outperform the state of the art in H-DIBCO challenges, after fine tuning our pre-trained model with synthetically degraded Latin handwritten images, on this task.
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Notes DAG; 600.124; 600.121; 602.230 Approved no
Call Number Admin @ si @ JSK2022 Serial 3613
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Author Lluis Gomez; Ali Furkan Biten; Ruben Tito; Andres Mafla; Marçal Rusiñol; Ernest Valveny; Dimosthenis Karatzas
Title Multimodal grid features and cell pointers for scene text visual question answering Type (up) Journal Article
Year 2021 Publication Pattern Recognition Letters Abbreviated Journal PRL
Volume 150 Issue Pages 242-249
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Abstract This paper presents a new model for the task of scene text visual question answering. In this task questions about a given image can only be answered by reading and understanding scene text. Current state of the art models for this task make use of a dual attention mechanism in which one attention module attends to visual features while the other attends to textual features. A possible issue with this is that it makes difficult for the model to reason jointly about both modalities. To fix this problem we propose a new model that is based on an single attention mechanism that attends to multi-modal features conditioned to the question. The output weights of this attention module over a grid of multi-modal spatial features are interpreted as the probability that a certain spatial location of the image contains the answer text to the given question. Our experiments demonstrate competitive performance in two standard datasets with a model that is faster than previous methods at inference time. Furthermore, we also provide a novel analysis of the ST-VQA dataset based on a human performance study. Supplementary material, code, and data is made available through this link.
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Notes DAG; 600.084; 600.121 Approved no
Call Number Admin @ si @ GBT2021 Serial 3620
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Author Minesh Mathew; Lluis Gomez; Dimosthenis Karatzas; C.V. Jawahar
Title Asking questions on handwritten document collections Type (up) Journal Article
Year 2021 Publication International Journal on Document Analysis and Recognition Abbreviated Journal IJDAR
Volume 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 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 (up) Journal Article
Year 2021 Publication International Journal of Imaging Systems and Technology Abbreviated Journal IMA
Volume 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 Alina Matei; Andreea Glavan; Petia Radeva; Estefania Talavera
Title Towards Eating Habits Discovery in Egocentric Photo-Streams Type (up) Journal Article
Year 2021 Publication IEEE Access Abbreviated Journal ACCESS
Volume 9 Issue Pages 17495-17506
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Abstract Eating habits are learned throughout the early stages of our lives. However, it is not easy to be aware of how our food-related routine affects our healthy living. In this work, we address the unsupervised discovery of nutritional habits from egocentric photo-streams. We build a food-related behavioral pattern discovery model, which discloses nutritional routines from the activities performed throughout the days. To do so, we rely on Dynamic-Time-Warping for the evaluation of similarity among the collected days. Within this framework, we present a simple, but robust and fast novel classification pipeline that outperforms the state-of-the-art on food-related image classification with a weighted accuracy and F-score of 70% and 63%, respectively. Later, we identify days composed of nutritional activities that do not describe the habits of the person as anomalies in the daily life of the user with the Isolation Forest method. Furthermore, we show an application for the identification of food-related scenes when the camera wearer eats in isolation. Results have shown the good performance of the proposed model and its relevance to visualize the nutritional habits of individuals.
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Notes MILAB; no proj Approved no
Call Number Admin @ si @ MGR2021 Serial 3637
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Author Dorota Kaminska; Kadir Aktas; Davit Rizhinashvili; Danila Kuklyanov; Abdallah Hussein Sham; Sergio Escalera; Kamal Nasrollahi; Thomas B. Moeslund; Gholamreza Anbarjafari
Title Two-stage Recognition and Beyond for Compound Facial Emotion Recognition Type (up) Journal Article
Year 2021 Publication Electronics Abbreviated Journal ELEC
Volume 10 Issue 22 Pages 2847
Keywords compound emotion recognition; facial expression recognition; dominant and complementary emotion recognition; deep learning
Abstract Facial emotion recognition is an inherently complex problem due to individual diversity in facial features and racial and cultural differences. Moreover, facial expressions typically reflect the mixture of people’s emotional statuses, which can be expressed using compound emotions. Compound facial emotion recognition makes the problem even more difficult because the discrimination between dominant and complementary emotions is usually weak. We have created a database that includes 31,250 facial images with different emotions of 115 subjects whose gender distribution is almost uniform to address compound emotion recognition. In addition, we have organized a competition based on the proposed dataset, held at FG workshop 2020. This paper analyzes the winner’s approach—a two-stage recognition method (1st stage, coarse recognition; 2nd stage, fine recognition), which enhances the classification of symmetrical emotion labels.
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Notes HUPBA; no proj Approved no
Call Number Admin @ si @ KAR2021 Serial 3642
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Author Hugo Bertiche; Meysam Madadi; Sergio Escalera
Title PBNS: Physically Based Neural Simulation for Unsupervised Garment Pose Space Deformation Type (up) Journal Article
Year 2021 Publication ACM Transactions on Graphics Abbreviated Journal
Volume 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 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 (up) Journal Article
Year 2021 Publication BMC Bioinformatics Abbreviated Journal
Volume 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 Javier Marin; Sergio Escalera
Title SSSGAN: Satellite Style and Structure Generative Adversarial Networks Type (up) Journal Article
Year 2021 Publication Remote Sensing Abbreviated Journal
Volume 13 Issue 19 Pages 3984
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Abstract This work presents Satellite Style and Structure Generative Adversarial Network (SSGAN), a generative model of high resolution satellite imagery to support image segmentation. Based on spatially adaptive denormalization modules (SPADE) that modulate the activations with respect to segmentation map structure, in addition to global descriptor vectors that capture the semantic information in a vector with respect to Open Street Maps (OSM) classes, this model is able to produce
consistent aerial imagery. By decoupling the generation of aerial images into a structure map and a carefully defined style vector, we were able to improve the realism and geodiversity of the synthesis with respect to the state-of-the-art baseline. Therefore, the proposed model allows us to control the generation not only with respect to the desired structure, but also with respect to a geographic area.
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Notes HUPBA; no proj Approved no
Call Number Admin @ si @ MaE2021 Serial 3651
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