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Spyridon Bakas; Mauricio Reyes; Andras Jakab; Stefan Bauer; Markus Rempfler; Alessandro Crimi; Russell Takeshi Shinohara; Christoph Berger; Sung Min Ha; Martin Rozycki; Marcel Prastawa; Esther Alberts; Jana Lipkova; John Freymann; Justin Kirby; Michel Bilello; Hassan Fathallah-Shaykh; Roland Wiest; Jan Kirschke; Benedikt Wiestler; Rivka Colen; Aikaterini Kotrotsou; Pamela Lamontagne; Daniel Marcus; Mikhail Milchenko; Arash Nazeri; Marc-Andre Weber; Abhishek Mahajan; Ujjwal Baid; Dongjin Kwon; Manu Agarwal; Mahbubul Alam; Alberto Albiol; Antonio Albiol; Varghese Alex; Tuan Anh Tran; Tal Arbel; Aaron Avery; Subhashis Banerjee; Thomas Batchelder; Kayhan Batmanghelich; Enzo Battistella; Martin Bendszus; Eze Benson; Jose Bernal; George Biros; Mariano Cabezas; Siddhartha Chandra; Yi-Ju Chang; Joseph Chazalon; Shengcong Chen; Wei Chen; Jefferson Chen; Kun Cheng; Meinel Christoph; Roger Chylla; Albert Clérigues; Anthony Costa; Xiaomeng Cui; Zhenzhen Dai; Lutao Dai; Eric Deutsch; Changxing Ding; Chao Dong; Wojciech Dudzik; Theo Estienne; Hyung Eun Shin; Richard Everson; Jonathan Fabrizio; Longwei Fang; Xue Feng; Lucas Fidon; Naomi Fridman; Huan Fu; David Fuentes; David G Gering; Yaozong Gao; Evan Gates; Amir Gholami; Mingming Gong; Sandra Gonzalez-Villa; J Gregory Pauloski; Yuanfang Guan; Sheng Guo; Sudeep Gupta; Meenakshi H Thakur; Klaus H Maier-Hein; Woo-Sup Han; Huiguang He; Aura Hernandez-Sabate; Evelyn Herrmann; Naveen Himthani; Winston Hsu; Cheyu Hsu; Xiaojun Hu; Xiaobin Hu; Yan Hu; Yifan Hu; Rui Hua |
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Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the BRATS challenge |
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Miscellaneous |
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2018 |
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Arxiv |
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BraTS; challenge; brain; tumor; segmentation; machine learning; glioma; glioblastoma; radiomics; survival; progression; RECIST |
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Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multiparametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e. 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in preoperative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that undergone gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset. |
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ADAS; 600.118;MILAB;IAM |
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Admin @ si @ BRJ2018 |
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3252 |
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Debora Gil; Katerine Diaz; Carles Sanchez; Aura Hernandez-Sabate |
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Early Screening of SARS-CoV-2 by Intelligent Analysis of X-Ray Images |
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2020 |
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Arxiv |
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Future SARS-CoV-2 virus outbreak COVID-XX might possibly occur during the next years. However the pathology in humans is so recent that many clinical aspects, like early detection of complications, side effects after recovery or early screening, are currently unknown. In spite of the number of cases of COVID-19, its rapid spread putting many sanitary systems in the edge of collapse has hindered proper collection and analysis of the data related to COVID-19 clinical aspects. We describe an interdisciplinary initiative that integrates clinical research, with image diagnostics and the use of new technologies such as artificial intelligence and radiomics with the aim of clarifying some of SARS-CoV-2 open questions. The whole initiative addresses 3 main points: 1) collection of standardize data including images, clinical data and analytics; 2) COVID-19 screening for its early diagnosis at primary care centers; 3) define radiomic signatures of COVID-19 evolution and associated pathologies for the early treatment of complications. In particular, in this paper we present a general overview of the project, the experimental design and first results of X-ray COVID-19 detection using a classic approach based on HoG and feature selection. Our experiments include a comparison to some recent methods for COVID-19 screening in X-Ray and an exploratory analysis of the feasibility of X-Ray COVID-19 screening. Results show that classic approaches can outperform deep-learning methods in this experimental setting, indicate the feasibility of early COVID-19 screening and that non-COVID infiltration is the group of patients most similar to COVID-19 in terms of radiological description of X-ray. Therefore, an efficient COVID-19 screening should be complemented with other clinical data to better discriminate these cases. |
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IAM; 600.139; 600.145; 601.337 |
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Admin @ si @ GDS2020 |
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3474 |
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Oriol Ramos Terrades; Albert Berenguel; Debora Gil |
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A flexible outlier detector based on a topology given by graph communities |
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2020 |
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Arxiv |
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Outlier, or anomaly, detection is essential for optimal performance of machine learning methods and statistical predictive models. It is not just a technical step in a data cleaning process but a key topic in many fields such as fraudulent document detection, in medical applications and assisted diagnosis systems or detecting security threats. In contrast to population-based methods, neighborhood based local approaches are simple flexible methods that have the potential to perform well in small sample size unbalanced problems. However, a main concern of local approaches is the impact that the computation of each sample neighborhood has on the method performance. Most approaches use a distance in the feature space to define a single neighborhood that requires careful selection of several parameters. This work presents a local approach based on a local measure of the heterogeneity of sample labels in the feature space considered as a topological manifold. Topology is computed using the communities of a weighted graph codifying mutual nearest neighbors in the feature space. This way, we provide with a set of multiple neighborhoods able to describe the structure of complex spaces without parameter fine tuning. The extensive experiments on real-world data sets show that our approach overall outperforms, both, local and global strategies in multi and single view settings. |
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IAM; DAG; 600.139; 600.145; 600.140; 600.121 |
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Admin @ si @ RBG2020 |
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3475 |
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Author |
Enric Marti; Jordi Vitria; Alberto Sanfeliu |
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Title |
Reconocimiento de Formas y Análisis de Imágenes |
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1998 |
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Asociación Española de Reconocimientos de Formas y Análisis de Imágenes |
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Los sistemas actuales de reconocimiento automático del lenguaje oral se basan en dos etapas básicas de procesado: la parametrización, que extrae la evolución temporal de los parámetros que caracterizan la voz, y el reconocimiento propiamente dicho, que identifica la cadena de palabras de la elocución recibida con ayuda de los modelos que representan el conocimiento adquirido en la etapa de aprendizaje. Tomando como línea divisoria la palabra, dichos modelos son de tipo acústicofonético o gramatical. Los primeros caracterizan las palabras incluidas en el vocabulario de la aplicación o tarea a la que está orientado el sistema de reconocimiento, usando a menudo para ello modelos de unidades de habla de extensión inferior a la palabra, es decir, de unidades subléxicas. Por otro lado, la gramática incluye el conocimiento acerca de las combinaciones permitidas de palabras para formar las frases o su probabilidad. Queda fuera del esquema la denominada comprensión del habla, que utiliza adicionalmente el conocimiento semántico y pragmático para captar el significado de la elocución de entrada al sistema a partir de la cadena (o cadenas alternativas) de palabras que suministra el reconocedor. |
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AERFAI |
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84–922529–4–4 |
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IAM;OR;MV |
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IAM @ iam @ MVS1998 |
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1620 |
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Oriol Ramos Terrades; Albert Berenguel; Debora Gil |
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Title |
A Flexible Outlier Detector Based on a Topology Given by Graph Communities |
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Journal Article |
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2022 |
Publication |
Big Data Research |
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BDR |
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29 |
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100332 |
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Classification algorithms; Detection algorithms; Description of feature space local structure; Graph communities; Machine learning algorithms; Outlier detectors |
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Outlier detection is essential for optimal performance of machine learning methods and statistical predictive models. Their detection is especially determinant in small sample size unbalanced problems, since in such settings outliers become highly influential and significantly bias models. This particular experimental settings are usual in medical applications, like diagnosis of rare pathologies, outcome of experimental personalized treatments or pandemic emergencies. In contrast to population-based methods, neighborhood based local approaches compute an outlier score from the neighbors of each sample, are simple flexible methods that have the potential to perform well in small sample size unbalanced problems. A main concern of local approaches is the impact that the computation of each sample neighborhood has on the method performance. Most approaches use a distance in the feature space to define a single neighborhood that requires careful selection of several parameters, like the number of neighbors.
This work presents a local approach based on a local measure of the heterogeneity of sample labels in the feature space considered as a topological manifold. Topology is computed using the communities of a weighted graph codifying mutual nearest neighbors in the feature space. This way, we provide with a set of multiple neighborhoods able to describe the structure of complex spaces without parameter fine tuning. The extensive experiments on real-world and synthetic data sets show that our approach outperforms, both, local and global strategies in multi and single view settings. |
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August 28, 2022 |
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DAG; IAM; 600.140; 600.121; 600.139; 600.145; 600.159 |
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Admin @ si @ RBG2022a |
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3718 |
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Mireia Sole; Joan Blanco; Debora Gil; G. Fonseka; Richard Frodsham; Francesca Vidal; Zaida Sarrate |
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Noves perspectives en l estudi de la territorialitat cromosomica de cel·lules germinals masculines: estudis tridimensionals |
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2017 |
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Biologia de la Reproduccio |
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JBR |
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15 |
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73-78 |
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In somatic cells, chromosomes occupy specific nuclear regions called chromosome territories which are involved in the
maintenance and regulation of the genome. Preliminary data in male germ cells also suggest the importance of chromosome
territoriality in cell functionality. Nevertheless, the specific characteristics of testicular tissue (presence of different
cell types with different morphological characteristics, in different stages of development and with different ploidy)
makes difficult to achieve conclusive results. In this study we have developed a methodology to approach the threedimensional
study of all chromosome territories in male germ cells from C57BL/6J mice (Mus musculus). The method
includes the following steps: i) Optimized cell fixation to obtain an optimal preservation of the three-dimensionality cell
morphology, ii) Chromosome identification by FISH (Chromoprobe Multiprobe® OctoChrome™ Murine System; Cytocell)
and confocal microscopy (TCS-SP5, Leica Microsystems), iii) Cell type identification by immunofluorescence
iv) Image analysis using Matlab scripts, v) Numerical data extraction related to chromosome features, chromosome
radial position and chromosome relative position. This methodology allows the unequivocally identification and the
analysis of the chromosome territories of all spermatogenic stages. Results will provide information about the features
that determine chromosomal position, preferred associations between chromosomes, and the relationship between chromosome
positioning and genome regulation. |
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978-84-697-3767-5 |
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IAM; 600.096; 600.145 |
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Admin @ si @ SBG2017c |
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2961 |
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David Roche; Debora Gil; Jesus Giraldo |
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Mechanistic analysis of the function of agonists and allosteric modulators: Reconciling two-state and operational models |
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2013 |
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British Journal of Pharmacology |
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BJP |
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169 |
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6 |
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1189-202 |
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Two-state and operational models of both agonism and allosterism are compared to identify and characterize common pharmacological parameters. To account for the receptor-dependent basal response, constitutive receptor activity is considered in the operational models. By arranging two-state models as the fraction of active receptors and operational models as the fractional response relative to the maximum effect of the system, a one-by-one correspondence between parameters is found. The comparative analysis allows a better understanding of complex allosteric interactions. In particular, the inclusion of constitutive receptor activity in the operational model of allosterism allows the characterization of modulators able to lower the basal response of the system; that is, allosteric modulators with negative intrinsic efficacy. Theoretical simulations and overall goodness of fit of the models to simulated data suggest that it is feasible to apply the models to experimental data and constitute one step forward in receptor theory formalism. |
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IAM; 600.044; 605.203 |
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IAM @ iam @ RGG2013b |
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2195 |
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Marta Diez-Ferrer; Debora Gil; Elena Carreño; Susana Padrones; Samantha Aso; Vanesa Vicens; Cubero Noelia; Rosa Lopez Lisbona; Carles Sanchez; Agnes Borras; Antoni Rosell |
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Positive Airway Pressure-Enhanced CT to Improve Virtual Bronchoscopic Navigation |
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Journal Article |
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2016 |
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Chest Journal |
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CHEST |
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150 |
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4 |
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1003A |
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IAM; 600.096; 600.075 |
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Admin @ si @ DGC2016 |
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3099 |
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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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Journal Article |
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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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Mireia Sole; Joan Blanco; Debora Gil; Oliver Valero; B. Cardenas; G. Fonseka; E. Anton; Alvaro Pascual; Richard Frodsham; Zaida Sarrate |
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Time to match; when do homologous chromosomes become closer? |
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Journal Article |
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2022 |
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Chromosoma |
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CHRO |
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In most eukaryotes, pairing of homologous chromosomes is an essential feature of meiosis that ensures homologous recombination and segregation. However, when the pairing process begins, it is still under investigation. Contrasting data exists in Mus musculus, since both leptotene DSB-dependent and preleptotene DSB-independent mechanisms have been described. To unravel this contention, we examined homologous pairing in pre-meiotic and meiotic Mus musculus cells using a threedimensional fuorescence in situ hybridization-based protocol, which enables the analysis of the entire karyotype using DNA painting probes. Our data establishes in an unambiguously manner that 73.83% of homologous chromosomes are already paired at premeiotic stages (spermatogonia-early preleptotene spermatocytes). The percentage of paired homologous chromosomes increases to 84.60% at mid-preleptotene-zygotene stage, reaching 100% at pachytene stage. Importantly, our results demonstrate a high percentage of homologous pairing observed before the onset of meiosis; this pairing does not occur randomly, as the percentage was higher than that observed in somatic cells (19.47%) and between nonhomologous chromosomes (41.1%). Finally, we have also observed that premeiotic homologous pairing is asynchronous and independent of the chromosome size, GC content, or presence of NOR regions. |
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August, 2022 |
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IAM; 601.139; 600.145; 600.096 |
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Admin @ si @ SBG2022 |
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3719 |
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