2021 |
Cid-Mejías, A; Alonso-Calvo, R; Gavilán, H; Crespo, J; Maojo, V A deep learning approach using synthetic images for segmenting and estimating 3D orientation of nanoparticles in EM images Artículo de revista En: Computer Methods and Programs in Biomedicine, vol. 202, 2021, ISSN: 0169-2607. Resumen | Enlaces | BibTeX | Etiquetas: @article{CIDMEJIAS2021105958, Background and objective: Nanoparticles present properties that can be applied to a wide range of fields such as biomedicine, electronics or optics. The type of properties depends on several characteristics, being some of them related with the particle structure. A proper characterization of nanoparticles is crucial since it could affect their applications. To characterize a particle shape and size, the nanotechnologists employ Electron Microscopy (EM) to obtain images of nanoparticles and perform measures over them. This task could be tedious, repetitive and slow, we present a Deep Learning method based on Convolutional Neural Networks (CNNs) to detect, segment, infer orientations and reconstruct microscope images of nanoparticles. Since machine learning algorithms depend on annotated data and there is a lack of annotated datasets of nanoparticles, our work makes use of artificial datasets of images resembling real nanoparticles photographs. Methods: Our work is divided into three tasks. Firstly, a method to create annotated datasets of artificial images resembling Scanning Electron Microscope (SEM). Secondly, two models of convolutional neural networks are trained using the artificial datasets previously generated, the first one is in charge of the detection and segmentation of the nanoparticles while the second one will infer the nanoparticle orientation. Finally, the 3D reconstruction module will recreate in a 3D scene the set of detected particles. Results: We have tested our method with five different shapes of basic nanoparticles: spheres, cubes, ellipsoids, hexagonal discs and octahedrons. An analysis of the reconstructions was conducted by manually comparing each of them with the real images. The results obtained have been promising, the particles are segmented and reconstructed accordingly to their shapes and orientations. Conclusions: We have developed a method for nanoparticle detection and segmentation in microscope images. Moreover, we can also infer an approximation of the 3D orientation of the particles and, in conjunction with the detections, create a 3D reconstruction of the photographs. The novelty of our approximation lies in the dataset used. Instead of using annotated images, we have created the datasets simulating the microscope images by using basic geometrical objects that imitate real nanoparticles. |
2019 |
Hernandez-Ibarburu, G; Perez-Rey, D; Alonso-Oset, E; Alonso-Calvo, R; [de K Schepper],; Meloni, L; Claerhout, B ICD-10-CM extension with ICD-9 diagnosis codes to support integrated access to clinical legacy data Artículo de revista En: International Journal of Medical Informatics, vol. 129, pp. 189 - 197, 2019, ISSN: 1386-5056. Resumen | Enlaces | BibTeX | Etiquetas: clinical terminologies, component, data integration, ICD-10, ICD-9, interoperability @article{HERNANDEZIBARBURU2019189, Introduction ICD is currently the most widely used terminology to code diagnosis and procedures. The transition from ICD-9-CM to ICD-10-CM became effective on October 1, 2015 in US and many other countries. Projects that use this codification for research purposes, requires advanced methods to exploit data with both versions of ICD. Although the General Equivalence Mappings (GEMs), provided by the Centers for Medicare and Medicaid Services, might help to overcome these challenges, their direct use as translation mappings is not possible, mostly due to the further specificity of ICD-10-CM concepts. Objective We propose a methodology to generate an extended version of ICD-10-CM with selected ICD-9-CM diagnosis codes. Methods The extension was generated using the GEMs relations between concepts of both terminologies and the hierarchical relations of ICD-10-CM. Results This extended ICD-10-CM, together with modifications to the mapping of ICD-9-CM concepts that were not inserted, allows the generation of an improved translation of legacy data, raising the number of 1-to-1 correspondences by +13.81%. Conclusion The extended ICD-10-CM enables the accurate integration of ICD-9-CM and ICD-10-CM diagnosis data into a single terminology. With such analysis of data possible without having to specify both ICD-9-CM and ICD-10-CM separately for each query. |
Hernandez-Ibarburu, G; Perez-Rey, D; Alonso-Oset, E; Alonso-Calvo, R; Voets, D; Mueller, C; Claerhout, B; Custodix, N V ICD-10-PCS extension with ICD-9 procedure codes to support integrated access to clinical legacy data Artículo de revista En: International Journal of Medical Informatics, vol. 122, pp. 70 - 79, 2019, ISSN: 1386-5056. Resumen | Enlaces | BibTeX | Etiquetas: clinical terminologies, component, data integration, ICD-10, ICD-9, interoperability @article{HERNANDEZIBARBURU201970, Since the creation of The International Classification of Diseases (ICD), new versions have been released to keep updated with the current medical knowledge. Migrations of Electronic Health Records (EHR) from ICD-9 to ICD-10-PCS as clinical procedure codification system, has been a significant challenge and involved large resources. In addition, it created new barriers for integrated access to legacy medical procedure data (frequently ICD-9 coded) with current data (frequently ICD-10-PCS coded). This work proposes a solution based on extending ICD-10-PCS with a subgroup of ICD-9-CM concepts to facilitate such integrated access. The General Equivalence Mappings (GEMs) has been used as foundation to set the terminology relations of these inserted concepts in ICD-10-PCS hierarchy, but due to the existence of 1-to-many mappings, advanced rules are required to seamlessly integrate both terminologies. With the generation of rules based on GEMs relationships, 2014 ICD-9 concepts were included within the ICD-10-PCS hierarchy. For the rest of the concepts, a new method is also proposed to increase 1-to-1 mappings. As results, with the suggested approach, the percentage of ICD-9-CM procedure concepts that can be mapped accurately (avoiding mappings to a large number of concepts) rise from 11.56% to 69.01% of ICD-9-Proc, through the extended ICD-10-PCS hierarchy. |
Garcia-Giordano, L; Paraiso-Medina, S; Alonso-Calvo, R; Fern?ndez-Mart?nez, F J; Maojo, V genoĐraw: A Web Ŧool for Đeveloping Pedigree Điagrams Using the Standardized Ħuman Pedigree Nomenclature Integrated with Biomedical Vocabularies Artículo de revista En: vol. 2019, pp. 457–466, 2019. BibTeX | Etiquetas: @article{pmid32308839, |
Paraiso-Medina, S; Perez-Rey, D; Alonso-Calvo, R; Munteanu, CR; Pazos, Al; Kulikowski, CA; Maojo, V Translational Bioinformatics: Informatics, Medicine, and -Omics Capítulo de libro En: Narayan, Roger (Ed.): Encyclopedia of Biomedical Engineering, pp. 507 - 514, Elsevier, 2019, ISBN: 978-0-12-805144-3. Resumen | Enlaces | BibTeX | Etiquetas: Drugs discovery, Medical informatics, Personalized medicine, Precision medicine, Translational bioinformatics @inbook{PARAISOMEDINA2019507, This article reviews some recent achievements reported in the area of Translational Bioinformatics (TBI), which has evolved rapidly as result of the Human Genome Project and subsequent -omic projects. Our goal is to support the understanding and enhancement of informatics research and applications at the intersection between medicine and the -omics fields. We discuss current progress and directions in the road ahead for this field, which already involves a significant number of dedicated professionals in research projects and conferences. Through a literature review, a list of topics of informatics research in TBI has been created, including decision support systems, natural language processing, standards, information retrieval, data, text and opinion mining, electronic health records (EHRs), and data integration. We also describe examples of the most challenging categories for research, such as discovery in EHRs, pharmacogenomics, drug repurposing, and genomic testing for individuals. We conclude with an overview of some of the challenges and opportunities presented by this field for research and education, particularly from the perspective of precision medicine. |
Intriago-Pazmiño, M; Ibarra-Fiallo, J; Alonso-Calvo, R; Crespo, J Segmenting Retinal Vascular Net from Retinopathy of Prematurity Images Using Convolutional Neural Network Conferencia Proceedings of the Second International Conference on Data Science, E-Learning and Information Systems, DATA ’19 Association for Computing Machinery, Dubai, United Arab Emirates, 2019, ISBN: 9781450372848. Enlaces | BibTeX | Etiquetas: convolutional neural network, medical image processing, retinopathy of prematurity @conference{10.1145/3368691.3368711, |
2018 |
Hernandez-Ibarburu, G; Perez-Rey, D; Alonso-Oset, E; Alonso-Calvo, R; Voets, D; Mueller, C; Claerhout, B ICD-10-PCS Extension with ICD-9 Procedure Codes to Support Integrated Access to Clinical Legacy Data Artículo de revista En: International Journal of Medical Informatics, 2018. Resumen | Enlaces | BibTeX | Etiquetas: clinical terminologies, component, data integration, ICD-10, ICD-9, interoperability @article{hernandez2018icd, Since the creation of The International Classification of Diseases (ICD), new versions have been released to keep updated with the current medical knowledge. Migrations of Electronic Health Records (EHR) from ICD-9 to ICD-10-PCS as clinical procedure codification system, has been a significant challenge and involved large resources. In addition, it created new barriers for integrated access to legacy medical procedure data (frequently ICD-9 coded) with current data (frequently ICD-10-PCS coded). This work proposes a solution based on extending ICD-10-PCS with a subgroup of ICD-9-CM concepts to facilitate such integrated access. The General Equivalence Mappings (GEMs) has been used as foundation to set the terminology relations of these inserted concepts in ICD-10-PCS hierarchy, but due to the existence of 1-to-many mappings, advanced rules are required to seamlessly integrate both terminologies. With the generation of rules based on GEMs relationships, 2,014 ICD-9 concepts were included within the ICD-10-PCS hierarchy. For the rest of the concepts, a new method is also proposed to increase 1-to-1 mappings. As results, with the suggested approach, the percentage of ICD-9-CM procedure concepts that can be mapped accurately (avoiding mappings to a large number of concepts) rise from 11.56% to 69.01% of ICD-9-Proc, through the extended ICD-10-PCS hierarchy. |
2017 |
Moreira, A; Alonso-Calvo, R; Muñoz, A; Crespo, J Enhancing Collaborative Case Diagnoses Through Unified Medical Language System-Based Disambiguation: A Case Study of the Zika Virus Artículo de revista En: Telemed J E Health, vol. 23, no. 7, pp. 608–614, 2017. @article{pmid28092493b, |
Priyatna, F; Alonso-Calvo, R; Paraiso-Medina, S; Corcho, O Querying clinical data in HL7 RIM based relational model with morph-RDB Artículo de revista En: J Biomed Semantics, vol. 8, no. 1, pp. 49, 2017. @article{pmid28982381, |
Perez-Rey, D; Alonso-Calvo, R; Paraiso-Medina, S; Munteanu, C R; Garcia-Remesal, M SNOMED2HL7: A tool to normalize and bind SNOMED CT concepts to the HL7 Reference Information Model Artículo de revista En: Comput Methods Programs Biomed, vol. 149, pp. 1–9, 2017. @article{pmid28802325b, |
Alonso-Calvo, R; Paraiso-Medina, S; Perez-Rey, D; Alonso-Oset, E; van Stiphout, R; Yu, S; Maojo, V A semantic interoperability approach to support integration of gene expression and clinical data in breast cancer Artículo de revista En: Computers in Biology and Medicine, vol. 87, pp. 179–186, 2017. @article{pmid28601027, |
2016 |
Bucur, A; van Leeuwen, J; Chen, N Z; Claerhout, B; de Schepper, K; Perez-Rey, D; Paraiso-Medina, S; Alonso-Calvo, R; Mehta, K; Krykwinski, C Cohort Selection and Management Application Leveraging Standards-based Semantic Interoperability and a Groovy DSL Artículo de revista En: AMIA Joint Summits on Translational Science Proceedings, vol. 2016, pp. 25–32, 2016. @article{pmid27570644, |
2015 |
Paraiso-Medina, S; Perez-Rey, D; Bucur, A; Claerhout, B; Alonso-Calvo, R Semantic Normalization and Query Abstraction Based on SNOMED-CT and HL7: Supporting Multicentric Clinical Trials Artículo de revista En: IEEE J Biomed Health Inform, vol. 19, no. 3, pp. 1061-1067, 2015. @article{pmid25248204, |
Alonso-Calvo, R; Perez-Rey, D; Paraiso-Medina, S; Claerhout, B; Hennebert, P; Bucur, A Enabling semantic interoperability in multi-centric clinical trials on breast cancer Artículo de revista En: Computed Methods and Programs in Biomedicine, vol. 118, no. 3, pp. 322-329, 2015. @article{Alonso-Calvo2015, |
2014 |
Bucur, A; Leeuwen, J Van; Chen, N Z; Claerhout, B; Schepper, K De; Perez-Rey, D; Alonso-Calvo, R; Pugliano, L; Saini, K Supporting patient screening to identify suitable clinical trials Artículo de revista En: Stud Health Technol Inform, vol. 205, pp. 823–827, 2014. @article{pmid25160302b, |
2013 |
Aso, S; Perez-Rey, D; Alonso-Calvo, R; Rico-Diez, A; Bucur, A; Claerhout, B; Maojo, V 14th World Congress on Medical and Health (medinfo2013), 2013. @conference{Aso2013, |
Moratilla, J M; Alonso-Calvo, R; Molina-Vaquero, G; Paraiso-Medina, S; Perez-Rey, D; Maojo, V 14th World Congress on Medical and Health (medinfo2013), 2013. @conference{Moratilla2013, |
Paraiso-Medina, S; Perez-Rey, D; Alonso-Calvo, R; Claerhout, B; de Schepper, K; Hennebert, P; van Leeuwen, J; Bucur, A Semantic Interoperability Solution for Multicentric Breast Cancer Trials at the INTEGRATE EU Project. Conferencia Healthinf 2013, VI International Conference on Health Informatics, 2013. @conference{Paraiso-Medina2013, |
2012 |
Bucur, A; van Leeuwen, J; Perez-Rey, D; Alonso-Calvo, R; Claerhout, B; de Schepper, K Identifying the Semantics of Eligibility Criteria of Clinical Trials based on relevant Medical Ontologies Conferencia IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE2012), 2012. @conference{Bucur2012, |
Jimenez-Castellanos, A; de la Calle, G; Alonso-Calvo, R; Hussein, R; Maojo, V Accessing advanced computational resources in Africa through Cloud Computing Conferencia 25th IEEE International Symposium on Computer-Based Medical System (CBMS 2012)., 2012. @conference{Jimenez-Castellanos2012b, |
Alonso-Calvo, R; Crespo, J; Muñoz-Mármol, M; Monserrate, I; Jimenez-Castellanos, A A Cloud Computing Service for Managing Biomedical Image Collections Conferencia 25th IEEE International Symposium on Computer-Based Medical System (CBMS 2012), 2012. @conference{Alonso-Calvo2012, |
2010 |
Alonso-Calvo, R; Crespo, J; Garcia-Remesal, M; Anguita, A; Maojo, V On distributing load in cloud computing: A real application for very-large image datasets Artículo de revista En: Proceedings of International Conference on Computational Science, 2010. @article{Alonso-Calvo2010, |
2007 |
Alonso-Calvo, R; Maojo, V; Billhardt, H; Martin-Sánchez, F; Garcia-Remesal, M; Perez-Rey, D An agent- and ontology-based system for integrating public gene, protein, and disease databases Artículo de revista En: Journal of Biomedical Informatics, vol. 40, no. 1, pp. 17-29, 2007. @article{Alonso-Calvo2007, |
2006 |
Perez-Rey, D; Maojo, V; Garcia-Remesal, M; Alonso-Calvo, R; Billhardt, H; Martin-Sanchez, F; Sousa, A ONTOFUSION: ontology-based integration of genomic and clinical databases Artículo de revista En: Comput. Biol. Med., vol. 36, no. 7-8, pp. 712–730, 2006. @article{pmid16144697b, |
Maojo, V; Garcia-Remesal, M; Billhardt, H; Alonso-Calvo, R; Perez-Rey, D; Martin-Sanchez, F Designing new methodologies for integrating biomedical information in clinical trials Artículo de revista En: Methods Inf Med, vol. 45, no. 2, pp. 180–185, 2006. @article{pmid16538285b, |
0000 |
Intriago-Pazmino, M; Ibarra-Fiallo, J; Crespo, J; Alonso-Calvo, R Enhancing vessel visibility in fundus images to aid the diagnosis of retinopathy of prematurity Artículo de revista En: Health Informatics Journal, vol. 26, no. 4, pp. 2722-2736, 0000. Resumen | Enlaces | BibTeX | Etiquetas: @article{nokey, Retinopathy of prematurity is a disease that can affect premature or in similar conditions babies. For diagnosing of retinopathy of prematurity, the infant is examined as soon as possible. Due to the nature of the examination, the images obtained are poor in quality. This article presents an automated method for processing fundus images to improve the visibility of the vascular network. The method includes several processing tasks whose parameters are predicted using an artificial neural network. A set of 88 clinical images were used in this work. The performance of our proposal is efficient, and the average processing time was 42 ms. The method was assessed using both the contrast improvement index and expert opinions. The contrast improvement index average was 2; this means the processed image successfully improved its contrast. Three pediatric ophthalmologists validated the proposed method and agreed that the visual enhancement can help observe clearly the retinal vessels. |
2021 |
A deep learning approach using synthetic images for segmenting and estimating 3D orientation of nanoparticles in EM images Artículo de revista En: Computer Methods and Programs in Biomedicine, vol. 202, 2021, ISSN: 0169-2607. |
2019 |
ICD-10-CM extension with ICD-9 diagnosis codes to support integrated access to clinical legacy data Artículo de revista En: International Journal of Medical Informatics, vol. 129, pp. 189 - 197, 2019, ISSN: 1386-5056. |
ICD-10-PCS extension with ICD-9 procedure codes to support integrated access to clinical legacy data Artículo de revista En: International Journal of Medical Informatics, vol. 122, pp. 70 - 79, 2019, ISSN: 1386-5056. |
genoĐraw: A Web Ŧool for Đeveloping Pedigree Điagrams Using the Standardized Ħuman Pedigree Nomenclature Integrated with Biomedical Vocabularies Artículo de revista En: vol. 2019, pp. 457–466, 2019. |
Translational Bioinformatics: Informatics, Medicine, and -Omics Capítulo de libro En: Narayan, Roger (Ed.): Encyclopedia of Biomedical Engineering, pp. 507 - 514, Elsevier, 2019, ISBN: 978-0-12-805144-3. |
Segmenting Retinal Vascular Net from Retinopathy of Prematurity Images Using Convolutional Neural Network Conferencia Proceedings of the Second International Conference on Data Science, E-Learning and Information Systems, DATA ’19 Association for Computing Machinery, Dubai, United Arab Emirates, 2019, ISBN: 9781450372848. |
2018 |
ICD-10-PCS Extension with ICD-9 Procedure Codes to Support Integrated Access to Clinical Legacy Data Artículo de revista En: International Journal of Medical Informatics, 2018. |
2017 |
Enhancing Collaborative Case Diagnoses Through Unified Medical Language System-Based Disambiguation: A Case Study of the Zika Virus Artículo de revista En: Telemed J E Health, vol. 23, no. 7, pp. 608–614, 2017. |
Querying clinical data in HL7 RIM based relational model with morph-RDB Artículo de revista En: J Biomed Semantics, vol. 8, no. 1, pp. 49, 2017. |
SNOMED2HL7: A tool to normalize and bind SNOMED CT concepts to the HL7 Reference Information Model Artículo de revista En: Comput Methods Programs Biomed, vol. 149, pp. 1–9, 2017. |
A semantic interoperability approach to support integration of gene expression and clinical data in breast cancer Artículo de revista En: Computers in Biology and Medicine, vol. 87, pp. 179–186, 2017. |
2016 |
Cohort Selection and Management Application Leveraging Standards-based Semantic Interoperability and a Groovy DSL Artículo de revista En: AMIA Joint Summits on Translational Science Proceedings, vol. 2016, pp. 25–32, 2016. |
2015 |
Semantic Normalization and Query Abstraction Based on SNOMED-CT and HL7: Supporting Multicentric Clinical Trials Artículo de revista En: IEEE J Biomed Health Inform, vol. 19, no. 3, pp. 1061-1067, 2015. |
Enabling semantic interoperability in multi-centric clinical trials on breast cancer Artículo de revista En: Computed Methods and Programs in Biomedicine, vol. 118, no. 3, pp. 322-329, 2015. |
2014 |
Supporting patient screening to identify suitable clinical trials Artículo de revista En: Stud Health Technol Inform, vol. 205, pp. 823–827, 2014. |
2013 |
14th World Congress on Medical and Health (medinfo2013), 2013. |
14th World Congress on Medical and Health (medinfo2013), 2013. |
Semantic Interoperability Solution for Multicentric Breast Cancer Trials at the INTEGRATE EU Project. Conferencia Healthinf 2013, VI International Conference on Health Informatics, 2013. |
2012 |
Identifying the Semantics of Eligibility Criteria of Clinical Trials based on relevant Medical Ontologies Conferencia IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE2012), 2012. |
Accessing advanced computational resources in Africa through Cloud Computing Conferencia 25th IEEE International Symposium on Computer-Based Medical System (CBMS 2012)., 2012. |
A Cloud Computing Service for Managing Biomedical Image Collections Conferencia 25th IEEE International Symposium on Computer-Based Medical System (CBMS 2012), 2012. |
2010 |
On distributing load in cloud computing: A real application for very-large image datasets Artículo de revista En: Proceedings of International Conference on Computational Science, 2010. |
2007 |
An agent- and ontology-based system for integrating public gene, protein, and disease databases Artículo de revista En: Journal of Biomedical Informatics, vol. 40, no. 1, pp. 17-29, 2007. |
2006 |
ONTOFUSION: ontology-based integration of genomic and clinical databases Artículo de revista En: Comput. Biol. Med., vol. 36, no. 7-8, pp. 712–730, 2006. |
Designing new methodologies for integrating biomedical information in clinical trials Artículo de revista En: Methods Inf Med, vol. 45, no. 2, pp. 180–185, 2006. |
0000 |
Enhancing vessel visibility in fundus images to aid the diagnosis of retinopathy of prematurity Artículo de revista En: Health Informatics Journal, vol. 26, no. 4, pp. 2722-2736, 0000. |