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Jose A Fernandes

Jose A Fernandes
AZTI · Marine Research Division

Dr.

About

140
Publications
116,761
Reads
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2,461
Citations
Introduction
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, and finally have multidisciplinary communicative skills.
Additional affiliations
April 2017 - April 2017
AZTI
Position
  • Researcher
January 2013 - present
Plymouth Marine Laboratory (PML)
Position
  • Bio-economic Modeller
February 2012 - February 2012
Finnish Environment Institute (SYKE)
Position
  • Research consultant: MARMONI project, automatic classification of zooplankton
Education
January 2007 - May 2011
September 2002 - October 2003
University of South Wales
Field of study
  • Computer security
September 2000 - June 2002
Universidad de Deusto
Field of study
  • Computer Engenieering

Publications

Publications (140)
Article
The effect of different factors (spawning biomass, environmental conditions) on recruitment is a subject of great importance in the management of fisheries, recovery plans and scenarios exploration. In this study, recently proposed supervised classification techniques, tested by the machine-learning community, are applied to forecast the recruitmen...
Article
Full-text available
Improving our ability to predict recruitment is a key element in fisheries management. However, the interactions between population dynamics and different environmental factors are complex and often non-linear, making it difficult to produce robust predictions. ‘Machine-learning’ techniques (in particular, supervised classification methods) have be...
Article
This paper describes the development of the EU Water Framework Directive central water quality elements from 1970 to 2010 in the Gulf of Finland, a eutrophied sub-basin of the Baltic Sea. The likelihood of accomplishing the management objectives simultaneously is assessed using Bayesian networks. The objectives of good ecological status in winter-t...
Article
Full-text available
Zooplankton biomass and abundance estimation, based on surveys or time-series, is carried out routinely. Automated or semi-automated image analysis processes, combined with machine-learning techniques for the identification of plankton, have been proposed to assist in sample analysis. A difficulty in automated plankton recognition and classificatio...
Book
This study reviews current artificial intelligence (AI) systems legislation, the AI techniques definition proposed by the AI Act and main applications of AI methods in the fisheries sector with special focus on applications to enhance traceability of fishery products, fishing gear selectivity, good practices, and potential to help young people find...
Technical Report
Full-text available
The WGMLEARN group was formed to explore the use of machine learning in the marine sci-ences, and work towards increasing knowledge of and competence with relevant methods among marine scientists. The specific objectives were to review methods, applications, and im-plementations, to gather knowledge about them from a wide array of scientists, to ad...
Article
Full-text available
Projections of climate change impacts on marine ecosystems have revealed long-term declines in global marine animal biomass and unevenly distributed impacts on fisheries. Here we apply an enhanced suite of global marine ecosystem models from the Fisheries and Marine Ecosystem Model Intercomparison Project (Fish-MIP), forced by new-generation Earth...
Poster
Full-text available
Route optimization methods offer an opportunity to the fisheries industry to enhance their efficiency, sustainability, and safety. However, the use of route optimization Decision Support Systems (DSS), which have been widely used in the shipping industry, is limited in the case of fisheries. In the first part, this work describes the fishing routin...
Article
Fishery monitoring programs are essential for effective management of marine resources, as they provide scientists and managers with the necessary data for both the preparation of scientific advice and fisheries control and surveillance. The monitoring is generally done by human observers, both in port and onboard, with a high cost involved. Conseq...
Article
Different fishing strategies have been adopted in the last decades by tropical tuna purse seiners fleet, including fish aggregating device (FAD) and free-swimming school (FSC) fishing strategies, which has raised issues about the different carbon footprint of those fishing modes. Here we show the activity and energy patterns of a Spanish tuna purse...
Chapter
The original version of the book was inadvertently published with wrong affiliation of the editor “Tomas Mildorf” in frontmatter. The affiliation has been changed from “Plan4All Horní Bříza, Czech Republic” to “University of West Bohemia, Univerzitni 8, 301 00 Plzen, Czech Republic”.
Article
Full-text available
Marine spatial planning that addresses ocean climate-driven change (‘climate-smart MSP’) is a global aspiration to support economic growth, food security and ecosystem sustainability. Ocean climate change (‘CC’) modelling may become a key decision-support tool for MSP, but traditional modelling analysis and communication challenges prevent their br...
Preprint
The National Marine Planning Framework (NMPF) provides a long-term structure for the effective spatial management of marine activities reliant upon Ireland’s marine space and resources. This assessment was co-developed to support the ambition to enable climate-adaptive spatial management through the NMPF, supporting the sustainable use of the Irish...
Article
Full-text available
Climate change is warming the ocean and impacting lower trophic level (LTL) organisms. Marine ecosystem models can provide estimates of how these changes will propagate to larger animals and impact societal services such as fisheries, but at present these estimates vary widely. A better understanding of what drives this inter-model variation will i...
Article
Global ocean warming, wave extreme events, and accelerating sea-level rise are challenges that coastal communities must address to anticipate damages in coming decades. The objective of this study is to undertake a time-series analysis of climate change (CC) indicators within the Bay of Biscay, including the Basque coast. We used an integrated and...
Chapter
Full-text available
This chapter demonstrates the potential of tuna fishing fleets to reduce their fuel oil consumption. In the “Oceanic tuna fisheries, immediate operational choices” pilot, the data monitoring system on vessels periodically upload data to the server for shore analysis. The data analytics employs fuel oil consumption equations and propulsion engine fa...
Chapter
Full-text available
The digitalization of the fisheries sector has been limited. However, in this book, the potential for making the sector more competitive and resilient through higher digitalization has been demonstrated using pelagic fisheries as an example. COVID-19 has recently shown the resilience advantages of having a more digitalized industry that makes large...
Chapter
Full-text available
The use of big data methods and tools are expected to have a profound effect on the pelagic fisheries sustainability and value creation. The potential impact on fuel consumption, planning and fish stock assessments is demonstrated in six different pilot cases. These cases cover the Spanish tropical tuna fisheries in Indian Ocean and the Norwegian s...
Article
Route optimization methods offer an opportunity to the fisheries industry to enhance their efficiency, sustainability, and safety. However, the use of route optimization Decision Support Systems (DSS), which have been widely used in the shipping industry, is limited in the case of fisheries. In the first part, this work describes the fishing routin...
Article
Full-text available
Across the European Atlantic Arc (Scotland, Ireland, England, France, Spain, and Portugal) the shellfish aquaculture industry is dominated by the production of mussels, followed by oysters and clams. A range of spatially and temporally variable harmful algal bloom species (HABs) impact the industry through their production of biotoxins that accumul...
Article
Full-text available
Small- and intermediate-size pelagic fisheries are highly impacted by environmental variability and climate change. Their wide geographical distribution and high mobility makes them more likely to shift their distribution under climate change. Here, we explore the potential impact of different climate change scenarios on the four main commercial pe...
Technical Report
Full-text available
New global standards on sulphur content in marine fuels have led to an increasing number of ships installing exhaust gas cleaning systems (EGCS), also known as scrubbers, to reduce their emissions of sulphur oxides to the atmosphere. Ships equipped with a scrubber can continue to use heavy fuel oil, and the process results in discharges of large vo...
Article
Full-text available
Large‐scale and long‐term changes in fish abundance and distribution in response to climate change have been simulated using both statistical and process‐based models. However, national and regional fisheries management requires also shorter term projections on smaller spatial scales, and these need to be validated against fisheries data. A 26‐year...
Article
The study covers two important deltaic systems of the north-east coast of India, viz. the Bengal and Mahanadi delta that support about 1.25 million people. The changes in potential marine fish production and socio-economic conditions were modelled for these two deltas under long-term changes in environmental conditions (sea surface temperature and...
Article
Full-text available
Changes in fish distribution are being observed across the globe. In Europe's Common Fisheries Policy, the share of the catch of each fish stock is split among management areas using a fixed allocation key known as ‘Relative Stability’: in each management area, member states get the same proportion of the total catch each year. That proportion is l...
Book
Full-text available
The Automatic Identification System (AIS) provides detailed tracks of tens of thousands of industrial fishing vessels, and these detailed tracking data have the potential to provide estimates of fishing activity and effort in near real time. Realizing this potential, though, is not straightforward and depends on the vessel size, gear type, and the...
Chapter
Full-text available
European fleets in the northern half of FAO Area 37 have adopted AIS for almost 100 percent of vessels larger than 15 m, whereas African and Middle East countries have extremely low AIS use in southern and eastern areas where AIS reception is also poor. Most vessels broadcasting AIS in the area use high quality Class A AIS devices, and the AIS rece...
Chapter
Full-text available
The Arctic, due to its extensive ice cover and remoteness, sees comparatively low amounts of industrial fishing. The only areas with many months of ice-free water are off far western Russia and in the waters near the Hudson Bay; partially as a result, all AIS fishing is concentrated in these regions. According to the Global Fisheries Landing Databa...
Chapter
Full-text available
The United States of America and Canada, which are responsible for most of the fishing activity in the FAO Area 21, have good use of AIS for vessels larger than 24 m. In addition, AIS reception is very good all over the area for larger vessels broadcasting with high-quality Class A AIS devices. However, reception is quite poor for lower quality Cla...
Chapter
Full-text available
AIS use in this region is dominated by vessels from the United States of America (trawlers in their majority), largely because most other countries in the region have a very low use of AIS. Class A reception is poor in the Gulf of Mexico, missing much of the fishing activity in that zone, but better in the southern and eastern parts of the region....
Chapter
Full-text available
Most of the fishing activity detected by AIS included fleets from Morocco and distant water fleets from Europe and Asia. In contrast, little activity by west African nations was seen because few vessels in these fleets carry AIS. Trawling, the most important activity identified by AIS in the region, showed clear concentration patterns along the coa...
Chapter
Full-text available
AIS use is high by Argentina, Uruguay, the Falkland Islands and foreign fleets fishing in the southern half of the area. Farther north, in the Brazilian EEZ, AIS provides a poor assessment of activity due to low use of AIS. The AIS reception for class A is excellent across the area, while it is poor for class B. There is a high number of distant fl...
Chapter
Full-text available
Among coastal countries/territories, AIS use is low for Angola and Saint Helena, Ascension and Tristan da Cunha, but significant for South Africa and Namibia. For distant water fleets, with several operating in the region, AIS use is high. AIS Class A and B device reception is good except in northern areas for Class B devices. Trawler intensity and...
Chapter
Full-text available
In the northern portion of the Western Indian Ocean region, the ability to map fishing activity through AIS data is limited by poor AIS reception and low levels of AIS use in artisanal and semi-industrial fleets from coastal countries. Throughout the region, gillnet is one of the main fishing gears for the artisanal and semi-industrial fleets, but...
Chapter
Full-text available
Class A AIS device reception is good throughout the area, except in northern areas around the Bay of Bengal. However, Class B AIS device reception is good only in the southern half of the Indian Ocean, and very poor in the northern half including the Bay of Bengal. Fishing activity in the eastern Indian Ocean is poorly represented by AIS data, even...
Chapter
Full-text available
AIS use in FAO Area 61 is dominated by the Chinese fleet. Because of poor AIS reception in the western part of this region and the difficulties accessing regional fleet registries to verify GFW vessel classification, the usefulness of AIS data to identify the fishing level activity by gear type is very limited in this area. AIS identifies fishing a...
Chapter
Full-text available
This comparison highlights that Automatic Identification System (AIS)-based methods to estimate fishing effort such as the Global Fishing Watch (GFW) methodology can provide the general pattern of relative distribution of fishing effort intensity. These results were obtained in an area where coverage is quite good in general and with good vessels r...
Chapter
Full-text available
AIS use in the area was relatively low for Mexico and Central America due to the high proportion of domestic near-shore small scale fishing fleets, but high for the United States of America and the distant water fleets. AIS reception was excellent for Class A AIS devices across the entire area. Class B AIS device reception performed poorly in the s...
Chapter
Full-text available
AIS use is good in the high seas, especially for distant water fleets, but low in the coastal regions. Class A reception is good across the region, while Class B performs well except for vessels operating just outside the South American EEZs. Coastal AIS data, including the highly productive Peruvian fleet fishing anchoveta, is poorly represented i...
Chapter
Full-text available
Fishing in the Northeast Pacific is dominated by the fleets of the United States of America and Canada, both of which have a high adoption of AIS by larger vessels. AIS Class A reception is excellent, but Class B device reception is medium to poor in most of the area. Trawlers are the most important gear in FAO Area 67, where AIS data highlight wel...
Chapter
Full-text available
AIS use and reception are extremely poor at the western end of this area, but relatively high and good on the eastern edge. As a result, AIS captures almost none of the important fishing activity in southeast Asia – particularly regarding the domestic fleets. Overall, all gear types are poorly represented except for pelagic longliners and purse sei...
Chapter
Full-text available
AIS use and reception in this area was relatively high. The exception was reception of Class B devices in the northwestern part of the area. Trawlers and drifting longliners were the most important gears in the area. The trawler industry operating in New Zealand waters appeared well represented in AIS data, but not the demersal activity off Tasmani...
Poster
Full-text available
Marine phytoplankton, as primary producers, contribute to the sustenance of bivalve aquaculture. However, some species can synthetize potent toxins, which are ingested by filter-feeding organisms and pose a threat to human health. Aquaculture has traditionally developed in coastal embayments and there, the responses of toxic phytoplankton species t...
Article
Full-text available
While the physical dimensions of climate change are now routinely assessed through multimodel intercomparisons, projected impacts on the global ocean ecosystem generally rely on individual models with a specific set of assumptions. To address these single-model limitations, we present standardized ensemble projections from six global marine ecosyst...
Chapter
Full-text available
Toxins from harmful algae and certain food pathogens (Escherichia coli and Norovirus) found in shellfish can cause significant health problems to the public and have a negative impact on the economy. For the most part, these outbreaks cannot be prevented but, with the right technology and know-how, they can be predicted. These Early Warning Systems...
Article
The Bay of Biscay is being affected by increasing level of marine litter, which is causing a wide variety of adverse environmental, social, public health, safety and economic impacts. The term “beach littering” has been coined to refer to the marine litter that is deposited on beaches. This litter may come from the sea and through land-based pathwa...
Article
In regression, a predictive model which is able to anticipate the output of a new case is learnt from a set of previous examples. The output or response value of these examples used for model training is known. When learning with aggregated outputs, the examples available for model training are individually unlabeled. Collectively, the aggregated o...
Article
Hilsa (Tenualosa ilisha) or river shad is an anadromous fish species widely distributed in the North Indian Ocean, mainly in the Bay of Bengal (BoB). Hilsa is the national fish of Bangladesh and it contributes 10% of the total fish production of the country, with a market value of $1.74 billion. Hilsa also holds a very important place in the econom...
Preprint
Full-text available
Climate change is shifting the abundance and distribution of marine species with consequences for ecosystem functioning, seafood supply, management and conservation. Several approaches for future projection exist but these have never been compared systematically to assess their variability. We conducted standardized ensemble projections including 6...
Chapter
Full-text available
Key messages • Pakistan, India, Bangladesh, Myanmar and Maldives are among the countries most affected by climate change and weather events. • There is strong socio-economic pressure from population growth, presence of dams and irrigation needs, heavy metal and waste pollution, habitat modification and destruction, illegal fishing, and insufficient...
Article
Full-text available
Deltas are home to a large and growing proportion of the world’s population, often living in conditions of extreme poverty. Deltaic ecosystems are ecologically significant as they support high biodiversity and a variety of fisheries, however these coastal environments are extremely vulnerable to climate change. The Ganges-Brahmaputra-Meghna (Bangla...
Conference Paper
Full-text available
The Bay of Biscay is being affected by increasing levels of marine litter, which are causing a wide variety of adverse environmental, social, public health, safety and economic impacts. The term "beach litter" is used by some authors to refer to the marine litter that is deposited on beaches. This litter can reach the coast due to the wind, the sea...
Chapter
Full-text available
A flexible meta-model, the Delta Dynamic Integrated Emulator Model (ΔDIEM), is developed to capture the socio-biophysical system of coastal Bangladesh as simply and efficiently as possible. Operating at the local scale, calculations occur efficiently using a variety of methods, including linear statistical emulators, which capture the behaviour of...
Chapter
Full-text available
Within the Bangladesh delta there is a significant dependence on aquatic ecosystem services both economically and for local well-being. The fisheries industry has seen steady growth with production tripling in the last two decades, largely driven by the expansion in inland aquaculture fisheries. Analysis shows that the impacts of climate change are...