ISG anagram: Intelligent Systems Group of Basque Country University

Dr. Jose Antonio Fernandes Salvador
(2011) PhD with honours in Probabilistic Methods for Data Mining and Artificial Intelligence (University of Basque Country)
(2003) MSc in Computer Systems Security with honours in Linux Security and Cryptography (University of Glamorgan)
(2002) Computer Engineer (Universidad de Deusto).
(2000) Technical Engineering in Computer Managements (Universidad de Deusto).
(1996) High School in Management and Finances with honours (Instituto Politécnico Jesus Obrero)

Phone number logo: +34 656731025 SPAIN: +34 656 73 10 25
email logo: ja.fernandes.sp AT gmail DOT com ja.fernandes.sp AT gmail DOT com
Currently, Senior scientist in Big Data for Marine Research and Innovation at AZTI-Tecnalia Marine Science and Food research fundation (AZTI; Pasaia, Spain). I am a data scientist from computing and artificial intelligence studies with the skills and experience needed to translate the data into valuable information for marine research, policy and industrial applications. These skills are curiosity, economic knowledge, knowing how to find information, have an understanding of statistics and machine learning, knows about history, and finally have multidisciplinary communicative skills.

Work experience

Thesis

Publications in refereed JCR-Journals

Supervisison experience

International conferences

Member and chair of international scientific groups, workshops and panels

  • (2017) Member of the Scientific Committee. I International Conference on Informatics, Computing and Applied Mathematics South Asia. July 18-20, Kuala Terengganu, Malaysia.
  • (2017) Invited speaker in ICES/PICES Symposium on Drivers of dynamics of small pelagic fish resources. October 7-9. Victoria. Canada.
  • (2017) Invited speaker in ESPA fisheries working group in London. 24 February.
  • (2016) Chair of ICES workshop on FISH DIstribution SHifts (WKFISHDISH). 22-25 November. Copenhagen. Denmark. Report
  • (2016) Participant of ICES/PICES Workshop on Economic Modelling of the Effects of Climate Change on Fish and Fisheries (WKeconSICCME). 3-4 June. Brest. France. Report
  • (2016) Conservation of natural resources in coastal ecosystems for the benefit of humankind and global balance. Universiti Sains Malaysia, Centre for Marine and Coastal Studies (CEMACS), in Muka Head National Park, Penang, Malaysia. 25-29 January.
  • (2016) MSCC/MASTS Bioeconomic Modelling in Policy & Management. Didcot, UK. 3-4 February.
  • (2015) Dynamic spatio-temporal hybrid life cycle analysis (LCA) at PML. 26 June.
  • (2015) Global change in coastal marine ecosystems: science, policy and sustainable development. Santos, Brazil, 17-20 March.
  • (2015) Addressing uncertainty in projecting climate change impacts in marine ecosystems. Santos, Brazil, 22 March.
  • (2014) MSCC/MASTS Ecosystem Modelling. UK 4-15 May.
  • (2009) Member of ICES benchmark workshop on short lived species (WKSHORT)

Other publications and technical reports

  • (2016) Modelling standards across the DECCMA project. Payo A., Hill C., Haque A., Mukhopadhyay A., Raju P. V., Addo A., Francheschini G., Kay S., Fernandes J. A., Macadam I., Whitehead P., 2016. DECCMA Working Paper, Deltas, Vulnerability and Climate Change: Migration and Adaptation, IDRC Project Number 107642.
  • (2015) DEVOTES deliverable 4.3: Report on the analysis of reference levels for indicators of biodiversity for selected pilot areas.Lynam C, Niquil N, Andonegi E, Queiros A, Tecchio S, Fernandes JA, Patrício J., Piroddi C., Thorpe R.
  • (2015) ESPA-DELTA Work Package 5: Final Report. Quantitative Bio-Physical Modelling. Wolf J, Barange M, Barbour E, Bricheno L, Caesar J, Clarke D, Darby S, Fernandes JA, Ghosh T, Haque A, Hazra S, Islam S, Kay S, Lazar A, Mondal S, Rahman M, Salehin M, Torres R, Whitehead P.
  • (2014) EURO-BASIN Deliverable 8.1: Report outlining the range of costs caused by changes in the Carbon budget of the North Atlantic,: based on predictive modelling of future North Atlantic ecosystem states. Barange M, Fernandes J.A., Beaumont N., Kay S., Butenschon M., Yool A.
  • (2014) VECTORS Deliverable 3.3.1: Impact of ecological changes on economic results of marine sectors. Buisman, F.C., R.A Groeneveld, H. Bartelings, J.A. Fernandes, K. Hamon, F. Maynou, P. Nunes, L. Piñol, L. Rodríguez, S. Sastre, F.E. Schasfoort, S. Simons, A. N. Walker, M. Austen, J. Bishop, R. van Duinen, T. Fileman, G. Merino, M. Loureiro, L. P. Pérez, J-J. Poos,A.M. Queirós, L. Santos, D. Smith, T. Vance, L. Voltaire, F. Viard, H.-P. Weikard
  • (2014) ESPA-DELTA project report: Bio-Physical Model Descriptions and Interactions (Bangladesh - Bay of Bengal). Wolf J, Barange M, Barbour E, Bricheno L, Caesar J, Clarke D, Darby S, Fernandes JA, Ghosh T, Haque A, Hazra S, Islam S, Kay S, Lazar A, Mondal S, Rahman M, Salehin M, Torres R, Whitehead P.
  • (2013) EURO-BASIN Deliverable 7.1: Hindcast estimation of potential and net economic benefits of N. Atlantic fisheries. Merino G, Barange M, Fernandes JA.
  • (2013) EURO-BASIN Deliverable 7.2: Scenarios for economic vs ecological optimisation in the future use of N. Atlantic fisheries. Merino G, Barange M, Fernandes JA.
  • (2013) EURO-BASIN Deliverable 7.3: Report on exploitation and management scenario workshop. Fernandes JA, Mullon C, Barange M, Gorka M.
  • (2013) Report on ESPA-DELTA Fisheries Meeting: biology, modelling and scenarios. Fernandes JA, Barange M, Hossain M, Ahmed M, Lazar A.
  • (2012) EURO-BASIN Deliverable 7.4: Projected future changes in maximum catch potential of key fish populations. Fernandes JA, Cheung WWL, Jennings S, Grant A, Steinmetz F., Yool A., Anderson TR.
  • (2012) EURO-BASIN Deliverable 7.5: A simulation model that account for trophic interaction in predicting distribution of exploited fish. Fernandes JA, Cheung WWL, Jennings S, Grant A, Butenschon M, de Mora L, Frölicher TL, Barange M.
  • (2012) Projecting distribution changes in marine fishes and invertebrates by integrating trophic interactions. Fernandes J.A., Cheung W.W.L., Jennings S., Grant A. 6th World Fisheries Congress 2012. 7-11 May. Edinburgh (Scotland).
  • (2011) Bay of Biscay: Analysis of climate impacts on anchovy and sardine via bottom up processes. Chapter 5 presented by Xabier Irigoien in Deliverable 1.1, Report on analyses of climate-driven processes on farage fish distribution an abundance within each Case Study region (Month 15). In: FACTS project (Forage Dish Interactions), collaborative Research Project on "Sustainable use of seas and oceans: importance of forage fish in the ecosystem". Chapter based on unpublished work by Fernandes J.A., Irigoien X., Lozano J.A., Inza I., Pérez A., Goikoetxea N.
  • (2011) Escenarios de reclutamiento para la anchoa en 2012 e implicaciones para la toma de decisiones de gestión. Ibaibarriaga L., Boyra E., Fernandes J.A., Uriarte A., Cotano U. Technical report for the Ministry of Agriculture, Fish and Food of Basque Country Government and for the Ministry of Environment of Spanish Government.
  • (2011) Manuscript on indicators for hard bottom substrata. Germán J., Fernandes J.A., Garmendia J.M., Muxika I., Borja A. Deliverable 4.3-4 of Water bodie in Europe: Integrative Systems to assess Ecological status and Recovery (WISER) project. Collaborative Project (large-scale integrating project), Theme 6: Environment (including Climate Change).
  • (2010) Use of juvenile abundance indices for the management of the Bay of Biscay. Ibaibarriaga L., Uriarte A., Sanchez S., Fernandes J.A., Irigoien X. Working document to WGANSA, 24-28 June 2010, Lisbon (Portugal).
  • (2010) The potential use of a Gadget model to predict stock responses to climate change in combination with Bayesian Networks: the case of the Bay of Biscay anchovy. Andonegi E., Fernandes J.A., Quincoces I., Irigoien X., Pérez A., Howell D., Stefánsson G. International Symposium “Climate Change Effects on Fish and Fisheries: Forecasting Impacts, Assessing Ecosystem Responses, and Evaluating Management Strategies.” Sendai (Japan), April 26-29.
  • (2010) UNCOVER: Fish stock recovery strategies - Report from the Bay of Biscay Andonegi E., Quincoces I., Murua H., Fernandes J.A., Uriarte A., Sanchez S., Cerviño S., Velasco F., Huret M., Lehuta S., Petitgas P.
  • (2009) Anchovy Recruitment Mixed Long Series prediction using supervised classification. Fernandes J.A., Irigoien X., Uriarte A., Ibaibarriaga L., Lozano J.A., Inza I. Working document to the ICES benchmark workshop on short lived species (WKSHORT) Bergen (Norway), 31 August-4 September.

Books and chapters

  • (2017) Projection for Marine Ecosystems, Fish and Fisheries in Bangladesh over the 21st Century. Manuel Barange, Jose A. Fernandes, Susan Kay, Munir Ahmed, Mostafa Hossain, Valentina Lauria. In Integrated Assessment for Policy Analysis: Rural Livelihoods in Coastal Bangladesh. Eds. Nicholls, Hutton, Hanson, Rahman, Salehin.
  • (2013) Supervised classification in marine science and fisheries management: Methods and applications. Fernandes J.A. (ISBN 978-3-659-37983-3). LAP LAMBERT Academic Publishing.
  • (2011) Biodiversidad, ecosistemas y recursos marinos. J.M. Gorostiaga, Xabier Irigoien, Ángel Borja, Jose A. Fernandes, Marina Chifflet, Manuel González, Marta Revilla, Juan Bald, Mireia Valle, Joxe M. Garmendia, Víctor. Valencia, Almudena Fontán, Guillem Chust. (ISBN 978-3-659-37983-3). Gobierno Vasco, Servicio Central de Publicaciones del Gobierno Vasco. pp 53-63.

Prizes and Awards

  • (2016) One of the 3 best papers of te GLOBEC network for the paper "Scaling up experimental ocean acidification and warming research: from individuals to the ecosystem." in Global Change Biology
  • (2016) Summer hotpaper in ScienceWatch of Thomson Reuters for the paper "Scaling up experimental ocean acidification and warming research: from individuals to the ecosystem." in Global Change Biology
  • (2016) Best 'Early Career Researcher' poster at DECCMA 4th Consortium Workshop. Southampton, UK.
  • (2013) Extraordinary Prize of Doctorate of University of Basque Country 2010-2011

Reviewer for

Additional formation

  • (2015) Principal investigator workshop. 30 September.
  • (2015) Managing in the Present. Broadleaf Development Services at Plymouth Marine Laboratory. 13-14 May.
  • (2015) Trade, environment and growth. Basque Center for Climate Change, University of Basque Country and University of Groningen. By Prof. Erik Dietzenbacher. 9-13 March.
  • (2014) Postgraduate research (PGR) supervisor training. University of Exeter.
  • (2012) SAW training: Delivering science to children through science, art and writing. SAW Trust.
  • (2009) Fisheries acoustic training course. Simrad.
  • (2009) Creation of predictive theory through meta-analysis and secondary-analysis. Downing J.A. & Prairie Y.
  • (2008) Data exploration, regression, GLM & GAM course. Highland Statistics Ltd.
  • (2008) Time series analysis. Third CEU Summerschool on Advanced Data Analysis and Modelling. Sorzano O.
  • (2008) Supervised pattern recognition (Classification). Third CEU Summerschool on Advanced Data Analysis and Modelling. Larrañaga P.

Teaching

  • (2016) Introduction to Probabilistic Graphical Models (PGMs) for environmental modelling and social sciences. Plymouth Marine Laboratory, Plymouth (UK).
  • (2016) Guest lecturer lecture for the contemporary issues in marine science module of the applied marine science MSc course. Plymouth University, Plymouth (UK).
  • (2012) ZooImage software and plankton classification. (IMRH), Casablanca (Morocco).
  • (2012) ZooImage software and plankton classification. Finnish Environment Institute (SYKE), Helsinki (Finland).
  • (2011) Guest lecturer in the subject "Machine learning", Computer Engineering Degree. University of Basque Country, San Sebastian (Spain).
  • (2011) EURO-BASIN Training Workshop on Introduction to statistical modelling tools, for habitat models development: Model Validation, performance measures, models comparison and Weka (open source software for data mining). AZTI-Tecnalia, Pasaia (Spain). [pdf]
  • (2007-2010) ZooImage software and plankton classification. AZTI-Tecnalia, Pasaia (Spain).
  • (2008-2009) Flowcam for phytoplankton digitalization and classification. AZTI-Tecnalia, Pasaia (Spain). CMIMA (CSIC), Barcelona (Spain).

Talks & Tutorials

  • (2016) Fisheries-aquaculture interaction and aquatic sector relevance to national economies. CERES meeting, Majorca, Spain. 5 April.
  • (2016) Projection modelling of changes in distribution and productivity of commercial fish. CERES meeting, Majorca, Spain. 5 April.
  • (2016) Bio-economic modelling. Jose A. Fernandes. At the workshop Conservation of natural resources in coastal ecosystems for the benefit of humankind and global balance. Universiti Sains Malaysia, Centre for Marine and Coastal Studies (CEMACS), in Muka Head National Park, Penang, Malaysia. 25-29 January.
  • (2015) Scaling up impacts from physiology to ecosystems: a specific example. Queirós A.M., Fernandes, J.A., Faulwetter S., Nunes J., Rastrick S.P.S., Mieszkowska N., Artioli Y., Yool A., Calosi P., Arvanitidis C., Findlay H.S., Barange M., Cheung W.W.L., Widdicombe S. Ocean acidification: what’s it all about? The Royal Society, 6-9 Carlton House Terrace, London SW1Y 5AG, United Kingdom, 4-5 June.
  • (2015) Ocean acidification effects on commercially-important species – and wider impacts. Flynn, K., Fernandes, J.A., Hattam C., Beaumont N., Papathanasopoulou E., Quieros A., Widdicombe S., Barange M., Turley, C., Williamson, P., Lewis, C., Heath, M., Wilson, R., Speirs, D., Pope E.C., Cripps, G.L., Ocean acidification: what’s it all about? The Royal Society, 6-9 Carlton House Terrace, London SW1Y 5AG, United Kingdom, 4-5 June.
  • (2015) From natural sciences to socio-economics using models: a bio-economic perspective within an Ecosystem Service (ES) approach. Jose A. Fernandes. At the workshop Global change in coastal marine ecosystems: science, policy and sustainable development. Santos, Brazil, 17-20 March.
  • (2014) End-to-end assessment of ocean warming and acidification on fisheries and other ecosystem services: from experiments and models to economic and social impacts and perceptions. BioAcid meeting at GEOMAR. Kiel. Germany. September.
  • (2012) From samples automatic classification to incorporating thropic interactions into projecting distribution of fishes under climatic change. University of British Columbia. Vancouver. Canada. May.
  • (2012) Data mining in fisheries reseach: from zooplankton automated classification to fish recruitment forecasting. Brunel University. London. UK. February.
  • (2011) Data mining in fisheries reseach: from zooplankton automated classification to fish recruitment forecasting. University of East Anglia. Norwich. UK. September.
  • (2011) Supervised classification in fisheries reseach: from zooplankton automated classification to recruitment forecasting. CEFAS. Lowestoft. UK. September.
  • (2011) Supervised classification applications in natural resources modelling. Greenland Institute of Natural Resources. Nuuk. Greenland. February.
  • (2011) Supervised classification applications in fisheries management. Helsinki Institute for Information Technology. Helsinki. Finland. February.
  • (2010) New approaches for fish recruitment forecasting: supervised classification, naive Bayes for regression and multi-dimensional classification. Institute of Information Theory and Automation, Academy of Sciences of the Czech Republic. Prague. July.
  • (2010) IBAM: Evaluation of feasibility of reaching water framework directives objectives (WFD and HELCOM) in the Gulf of Finland. Finnish Environment Institute (SYKE). Helsinki. June.
  • (2010) New approaches for fish recruitment forecasting: supervised classification, naive Bayes for regression and multi-dimensional classification. University of Helsinki. Helsinki. April.
  • (2010) New approaches for fish recruitment forecasting. AZTI-Tecnalia. March.
  • (2010) Supervised pre-processing approaches in multiple class-variables classification for fish recruitment forecasting. Universidad Politécnica de Madrid. March. [pdf]
  • (2009) JUVENA 2009: Campaña, proyecciones y consecuencias. Irigoien X., Andrés M., Fernandes J.A. AZTI-Tecnalia. November.
  • (2009) Recruitment prediction, classification, secondary analysis and meta-analysis. AZTI-Tecnalia. June. [pdf]
  • (2009) Robust approaches to machine learning techniques for recruitment prediction in fisheries. UNCOVER (Barcelona). March. [pdf]
  • (2009) Robust fish recruitment prediction using supervised classification methods. ECOANCHOA, AZTI-Tecnalia. March. [pdf]
  • (2008) Problemas de clasificación supervisada en ciencias marinas: de la clasificación de imágenes de plancton a la predicción de reclutamiento. Fernandes J.A., Irigoien X., Lozano J.A, Inza I.. Suficiencia investigadora. 8 November, 2008. UPV-EHU, Donostia - San Sebastian (Spain).
  • (2008) Recruitment prediction, from BNs to DBNs and MDBNs. Basque Country University. October.
  • (2008) Recruitment prediction using supervised classification methods. AZTI-Tecnalia. September. [pdf]
  • (2008) Habitat modelling with Bayesian Networks. Basque Country University. April.
  • (2007) Procesamiento y clasificación automática. AZTI-Tecnalia. November. [pdf]
  • (2007) Data Mining, problemas de clasificación con Weka. Universidad de Deusto. E-ghost. July. [pdf]
Akcnoledgements to E-ghost group and Borja Sotomayor for training in latex use.

Thesis collaborations

  • (2009-2011) Influence of the northeastern Atlantic oceano-meteorological variability on the northern hake (Merluccius merluccius), based on the last three-decadal period data (1978-2006). Goikoetxea N. PhD thesis. AZTI-Tecnalia.
  • (2008-2011) Trophic Ecology of small pelagic species in the Bay of Biscay. Bachiller E. PhD thesis. AZTI-Tecnalia.
  • (2008-2009) Assessment of the discrimination potential of bathymetric LIDAR and multispectral imagery for intertidal and subtidal habitats. Grande M. European Master of Science in Marine Environment and Resources. AZTI-Tecnalia.
  • (2007-2008) Feeding behaviour and diet of anchovy juveniles (Engraulis encrasilous L.) in the Bay of Biscay. Bachiller E. European Master of Science in Marine Environment and Resources. AZTI-Tecnalia.
  • (2007) Description and modelling of plankton biomasa distribution in the Bay of Biscay by means of image analisis-based methods. Zarauz L. PhD thesis. AZTI-Tecnalia.

Basque, Spanish and European projects

Surveys designed and supervised

  • (2013-2014) Fish market data collection (sizes, species, price and abundance) in Bangladesh.
  • (2014) Shipping industry data in relation to the cost of non-indigenous specie mitigation measures (ballast water systems and anti bio-fouling).

Oceanographic surveys

  • (2009) Perfil at Mediterranean Sea. Flowcam. June.
  • (2008) Perfil at Cantabrian Sea. Flowcam. July.
  • (2008) Bioman at Cantabrian Sea. Pairovet and Flowcam. May.
  • (2007) Bioman at Cantabrian Sea. Cufes and Flowcam. May.

Visiting Scientist

  • (2012) University of British Columbia, Fisheries Centre, Vancouver, Canada. William Cheung. Thee months.
  • (2010) University of Helsinki, Finland. Sakari Kuikka and Laura Uusitalo. Financed by Spanish Ministry of Education. Fellowships for European PhDs. Thee months.
  • (2009) Ifremer, France. Alina Tunin Ley and Daniele Maurer. Financed by AZTI-Tecnalia. One week.
  • (2008) Mons-Hainaut University, Belgium. Philippe Grosjean and Kevin Denis. Financed by AZTI-Tecnalia. Two weeks.
  • (2007) Mons-Hainaut University, Belgium. Philippe Grosjean and Kevin Denis. Financed by AZTI-Tecnalia. One week.

Organized events and outreach activities

  • (2016) Marine food web activities for children at the British science week at Plymouth City Museum & Art gallery. 16 March. MERP project. 50 children from Mayflower Academy (Plymouth). 16 March.
  • (2012) Fish and climate at Scarning Primary School (Norwich). As part of SAW trust program: science, art and writing.
  • (2011-2012) Every two weeks "Fish coffee club at UEA", a serie of informal meetings/talks to gather multidisciplinar proffesors, postdocs and PhD students that work on issues related to Fisheries.

ZooImage training and counseling

ZooImage (http://www.sciviews.org/zooimage/) is a tool for automated classification of plankton images. It can be used for scanned samples and for FlowCam images, or for any other divice images if they have a uniform background. This tool has been used in some of my research projects and I have been providing training to people of several countries:
  • (2012) Morocco (Casablanca): National Institute of Fisheries Research (INRH).
  • (2011) Finland (Helsinki): Finnish Environment Institute (SYKE).
  • (2011) Chile: Karen Manríquez, Nicolás Bralic (COPAS Center-Universidad de Concepción).
  • (2010) France: Delphine Bonnet and Juliette Balavoine (CNRS-Université Montpellier II).
  • (2010) Taiwan: Elise Marquis (National Taiwan University).
  • (2009) Spain: Sonia Romero Romero (Universidad de Cádiz).
  • (2009) Spain: Cristina Garcia Muñoz (CSIC).
  • (2008-2009) Spain: María Lidia Nieves (Universidad de las Palmas).
  • (2008-2009) Spain: Pablo León (Universidad de Málaga).
  • (2008-2009) Spain: Enric Saiz (CMIMA), CSIC.
  • (2008) France: Serge A. Poulet (INRS).
  • (2008) Greece: Nikolaos Nikolioudakis (University of Crete).
  • (2008) South Africa: Fabienne Cazassus (MA-RE Institute, UCT).
  • (2007) Portugal: María Manuel Angelico (IPIMAR).
Our manuals and course materials can be downloaded:

Flowcam training and counseling:

  • (2009) Spain: Course in CMIMA (CSIC). Barcelona. June.
  • (2009) Spain: Courses in AZTI-Tecnalia. San Sebastian. May, June and July.
  • (2008) Spain: Courses in AZTI-Tecnalia. San Sebastian. May and July.

Television, newspapers and social media: Divulgative Science

Weka

  • Supervised version of Cmean missing values imputation filter based on the non-supervised version provided in weka. Download.

Favourite cites

  • "Luck is what happens when preparation meets opportunity." Seneca Roman dramatist, philosopher and politician (5 BC - 65 AD).

Other interests

  • Dancing: Salsa (combining Cuban style with other styles) and Argentine Tango. Teacher of salsa at "Keseakava" salsa bar (Bilbao, Spain), in the dance schools "Pasos de Baile" (Bilbao, Spain), "Estudio Rosa Mari" (Bilbao, Spain) and Chilli con Salsa (Norwich, UK).
  • Theater: Colaborations with La hAceria (El bosque encantado). Amateur groups: Cuerpo Escena (Temple and Cuadros Insolitos) and Uyu-Yui (Crimenes Ejemplares).
  • Martial arts: Penkat Silat (Indonesian and Malasian). Scottish and Auchi Jiu-Jitsu. Wing-chung. Budocan Karate. Viet vo dao. Aikido. Capoeira Gerais.
  • Volunteering: FoodCycle and the GreenHouse (Norwich)

Old pre-researcher curriculums

Scholar citations
ResearchGate
Academia.edu
Mendeley
Researcher ID: B-8985-2009
Linkedin
AnalyticBridge
ORCID