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GOPHER, an HPC framework for large scale graph exploration and inference
dc.contributor.author | Josep Fabregó, Marc |
dc.contributor.author | Teruel García, Xavier |
dc.contributor.author | Giménez Ábalos, Víctor |
dc.contributor.author | Cirilo, Davide |
dc.contributor.author | Garcia Gasulla, Dario |
dc.contributor.author | Álvarez Napagao, Sergio |
dc.contributor.author | Garcia Gasulla, Marta |
dc.contributor.author | Ayguadé Parra, Eduard |
dc.contributor.author | Valencia, Alfonso |
dc.contributor.other | Universitat Politècnica de Catalunya. Departament de Ciències de la Computació |
dc.contributor.other | Universitat Politècnica de Catalunya. Departament d'Arquitectura de Computadors |
dc.contributor.other | Barcelona Supercomputing Center |
dc.date.accessioned | 2020-11-11T15:59:50Z |
dc.date.available | 2020-11-11T15:59:50Z |
dc.date.issued | 2020 |
dc.identifier.citation | Josep, M. [et al.]. GOPHER, an HPC framework for large scale graph exploration and inference. A: International Conference on High Performance Computing. "High Performance Computing: ISC High Performance 2020 International Workshops: Frankfurt, Germany, June 21–25, 2020: revised selected papers". Berlín: Springer, 2020, p. 211-222. ISBN 978-3-030-59851-8. DOI 10.1007/978-3-030-59851-8_13. |
dc.identifier.isbn | 978-3-030-59851-8 |
dc.identifier.uri | http://hdl.handle.net/2117/331891 |
dc.description.abstract | Biological ontologies, such as the Human Phenotype Ontology (HPO) and the Gene Ontology (GO), are extensively used in biomedical research to investigate the complex relationship that exists between the phenome and the genome. The interpretation of the encoded information requires methods that efficiently interoperate between multiple ontologies providing molecular details of disease-related features. To this aim, we present GenOtype PHenotype ExplOrer (GOPHER), a framework to infer associations between HPO and GO terms harnessing machine learning and large-scale parallelism and scalability in High-Performance Computing. The method enables to map genotypic features to phenotypic features thus providing a valid tool for bridging functional and pathological annotations. GOPHER can improve the interpretation of molecular processes involved in pathological conditions, displaying a vast range of applications in biomedicine. |
dc.description.sponsorship | This work has been developed with the support of the Severo Ochoa Program (SEV-2015-0493); the Spanish Ministry of Science and Innovation (TIN2015- 65316-P); and the Joint Study Agreement no. W156463 under the IBM/BSC Deep Learning Center agreement. |
dc.format.extent | 12 p. |
dc.language.iso | eng |
dc.publisher | Springer |
dc.subject | Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica |
dc.subject | Àrees temàtiques de la UPC::Informàtica::Intel·ligència artificial::Aprenentatge automàtic |
dc.subject.lcsh | Genomics |
dc.subject.lcsh | Ontologies (Information retrieval) |
dc.subject.lcsh | Machine learning |
dc.subject.other | Biological ontologies |
dc.subject.other | ML |
dc.subject.other | HPC |
dc.subject.other | Graph exploration |
dc.title | GOPHER, an HPC framework for large scale graph exploration and inference |
dc.type | Conference report |
dc.subject.lemac | Genòmica |
dc.subject.lemac | Ontologies (Informàtica) |
dc.subject.lemac | Aprenentatge automàtic |
dc.contributor.group | Universitat Politècnica de Catalunya. KEMLG - Grup d'Enginyeria del Coneixement i Aprenentatge Automàtic |
dc.contributor.group | Universitat Politècnica de Catalunya. CAP - Grup de Computació d'Altes Prestacions |
dc.identifier.doi | 10.1007/978-3-030-59851-8_13 |
dc.description.peerreviewed | Peer Reviewed |
dc.relation.publisherversion | https://link.springer.com/chapter/10.1007/978-3-030-59851-8_13 |
dc.rights.access | Open Access |
local.identifier.drac | 29680792 |
dc.description.version | Postprint (author's final draft) |
dc.relation.projectid | info:eu-repo/grantAgreement/MINECO//TIN2015-65316-P/ES/COMPUTACION DE ALTAS PRESTACIONES VII/ |
local.citation.author | Josep, M.; Teruel, X.; Giménez, V.; Cirilo, D.; Garcia-Gasulla, D.; Álvarez-Napagao, S.; García, M.; Ayguadé, E.; Valencia, A. |
local.citation.contributor | International Conference on High Performance Computing |
local.citation.pubplace | Berlín |
local.citation.publicationName | High Performance Computing: ISC High Performance 2020 International Workshops: Frankfurt, Germany, June 21–25, 2020: revised selected papers |
local.citation.startingPage | 211 |
local.citation.endingPage | 222 |