Ecological Informatics
journal homepage: www.elsevier.com/locate/ecolinf
Department of Signal Processing and Communications, Universidad de Alcal, Alcal de Henares, Spain
CARMABI Research Station, Willemstad, Curaao
Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 700, 1098 XH, Amsterdam, The Netherlands
a r t i c l e
i n f o
Article history:
Received 11 November 2015
Received in revised form 26 January 2016
Accepted 27 January 2016
Available online 6 February 2016
Keywords:
Computational Intelligence techniques
Coral reefs
Applications
Algorithms
a b s t r a c t
Studies on coral reefs increasingly combine aspects of science and technology to understand the complex dynamics and processes that shape these benthic ecosystems. Recently, the use of advanced computational algorithms
has entered coral reef science as new powerful tools that help solve complex coral reef related questions, which
were unsolvable just a decade earlier. Some of these advanced algorithms consist of Computational Intelligence
(CI) approaches, a branch of Articial Intelligence that uses intelligent systems to address complex real-world
problems yielding more robust, tractable and simpler solutions than those obtained by conventional mathematical techniques. This paper describes the most commonly used CI techniques related to coral reefs and the main
improvements obtained with these methods over classical algorithms in this eld. Some recommendations are
given for the application of CI techniques to complex coral reef related problems, and vice-versa, for the application of novel coral reef dynamics concepts to improve the Coral Reef Optimization (CRO) algorithm, an optimization method inspired by coral reef dynamics.
2016 Elsevier B.V. All rights reserved.
Contents
1.
2.
3.
4.
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
A brief introduction to computational intelligence . . . . . . . . . . . . . . .
2.1.
Neural computation approaches . . . . . . . . . . . . . . . . . . .
2.1.1.
Multi-layer perceptron (MLP) . . . . . . . . . . . . . . . .
2.1.2.
Support vector machine . . . . . . . . . . . . . . . . . . .
2.2.
Evolutionary computation approaches . . . . . . . . . . . . . . . . .
2.2.1.
Genetic algorithms . . . . . . . . . . . . . . . . . . . . .
2.2.2.
Simulated annealing . . . . . . . . . . . . . . . . . . . . .
2.2.3.
Particle swarm optimization algorithm . . . . . . . . . . . .
2.2.4.
A coral reef-based algorithm for optimization problems . . . . .
2.3.
Fuzzy computation . . . . . . . . . . . . . . . . . . . . . . . . .
2.3.1.
Fuzzy logic . . . . . . . . . . . . . . . . . . . . . . . . .
Computational intelligence in coral reef applications . . . . . . . . . . . . . .
3.1.
Coral reef data. The need for CI techniques . . . . . . . . . . . . . . .
3.2.
Review based on the CI technique used . . . . . . . . . . . . . . . .
3.2.1.
Neural network applications in coral reef problems . . . . . . .
3.3.
SVM applications for coral reefs . . . . . . . . . . . . . . . . . . . .
3.4.
Evolutionary-type approaches in reef-related applications . . . . . . . .
3.5.
Fuzzy computation in coral reef applications . . . . . . . . . . . . . .
Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.1.
The application of CI techniques in mapping-related problems is coral reefs
4.1.1.
Monitoring . . . . . . . . . . . . . . . . . . . . . . . . .
4.1.2.
Modeling . . . . . . . . . . . . . . . . . . . . . . . . . .
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Corresponding author at: Department of Signal Processing and Communications, Universidad de Alcal, 28871 Alcal de Henares, Madrid, Spain. Tel.: +34 91 885 6698; fax: +34 91
885 6699.
E-mail address: sancho.salcedo@uah.es (S. Salcedo-Sanz).
http://dx.doi.org/10.1016/j.ecoinf.2016.01.008
1574-9541/ 2016 Elsevier B.V. All rights reserved.
108
4.2.
Answering the research questions
5.
Conclusions . . . . . . . . . . . . .
Appendix A.
Supplementary data . . . . .
References . . . . . . . . . . . . . . . .
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1. Introduction
Coral reefs are one of the ecologically, biologically and physically
most complex ecosystems on Earth (Ferrario et al., 2014; Kline et al.,
2015; Knowlton and Jackson, 2013; Lamy et al., 2015; Roberts, 2009).
Corals enlarge three dimensional habitat complexity (Schoening et al.,
2012) and play a key role in deep-sea epibenthic megafauna
(animals N 1 cm) (Dunlop et al., 2015), which capture carbon through
the redistribution of nutrients such as organic matter and oxygen
(Bett et al., 2001; Dunlop et al., 2015; Ruhl, 2007; Schoening et al.,
2012). Coral reefs are thus hot spots of marine biodiversity (Purser,
2015; Shantz et al., 2015; Tittensor et al., 2010), provide important
ecosystem services (Dulvy and Kindsvater, 2015; Purser et al., 2013a),
support the livelihood of millions of people (Ault et al., 2014; Burke
et al., 2011; Chen et al., 2015; Kittinger et al., 2015), and act as early
warning indicators of global climate change (Baker et al., 2008;
Freeman, 2015; Mooney et al., 2009; Woodroffe and Webster, 2014).
Climate change is probably the most dangerous threat to coral reefs
(Baker et al., 2004; Toth et al., 2015) because of the rise of thermal stress
events (which increase coral mortality (Eakin et al., 2010)) and the
increment of severe storms and ocean acidity (Anthony et al., 2008;
Hoegh-Guldberg et al., 2007) (which causes bleaching (Wooldridge
and Done, 2004) in tropical corals, damage reef structure and reduce
coral growth rates (Hoegh-Guldberg et al., 2007; Hooidonk et al.,
2014; Manzello et al., 2013)). In addition to climate change, anthropogenic local stressors such as overshing (which reduces and even
exhausts key species from the ecosystem (Januchowski-Hartley
et al., 2015; Mumby et al., 2006; Wilson et al., 2006)), mechanical
damage from shing (Clark and Rowden, 2009; Fossaa and Skjoldal,
2010; Orejas et al., 2009), offshore oil and gas industry (Allers et al.,
2013; Gates and Jones, 2012; Larsson and Purser, 2011; Larsson et al.,
2013; Pabortsava et al., 2011; Purser, 2015; Purser and Thomsen,
2012), sediments (Ban et al., 2014; Bartley et al., 2014; Kroon et al.,
2014; Larsson and Purser, 2011; Yamazaki et al., 2011), and marine
litter (Pham et al., 2014) are also degrading coral reef ecosystems.
These combined stressors, which have undermined the resilience
(Anthony et al., 2011; Hughes et al., 2003, 2007; McClanahan et al.,
2012; Putra et al., 2015) of coral reef-based ecosystems (Hughes et al.,
2010; Pratchett et al., 2014; Rowlands et al., 2015), operate at multiple
scales (Carilli et al., 2009; McClanahan et al., 2014), which range from
meters to thousands of kilometers (Hatcher, 1997). Monitoring the
evolution of coral reef ecosystems at a decadal scale is necessary to
understand and predict their dynamics and to design tools for coral
reef management (Scoplitis et al., 2009). Monitoring is carried out via
localized in situ observations, time-series of aerial photographs and
remotely sensed images.
Because of the combination of all these factors, the study of coral
reefs requires multi-disciplinary approaches that combine aspects of
eld observations (Andrew and Mapstone, 1987; Foster et al., 1991;
Leujak and Ormond, 2007; Pielou, 1974; Purser, 2015; Whorff and
Grifng, 1992), ecological theory (Fox and Bellwood, 2014), modeling
(Harborne et al., 2006; Webster et al., 2007) and simulation
(Langmead and Sheppard, 2004), and increasingly more often Computational Intelligence (CI) techniques (Bandyopadhyay et al., 2009; Beijbom
et al., 2012; Beneld et al., 2007; Chang et al., 2014; Collin and Planes,
2012; Elawady, 2015; Elith et al., 2006; Gao and Hailu, 2012, 2013;
Guinan et al., 2009; Halide and Ridd, 2002; Henriques et al., 2010;
Huang et al., 2011a; Johnson-Roberson et al., 2006, 2007; Juillet-Leclerc,
2006, 2007, 2009; Juillet-Leclerc and Thiria, 2007, 2008; Juillet-Leclerc
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et al., 2006, 2007; Knudby et al., 2010, 2013; Leslie et al., 2003; Marcos
et al. 2005; Meesters et al., 1998; Mehta et al., 2007; Nagamani et al.,
2012; Naveau et al., 2004; OConnor, 2000; Padmavathi et al., 2010;
Pican et al., 1998; Pittman et al., 2009; Purser et al., 2008, 2009;
Ruitenbeek et al., 1999; Schoening et al., 2012; Shihavuddin et al., 2013;
Tong et al., 2013; Wahidin et al., 2015; Wang et al., 2004; Watts et al.,
2011; Wooldridge and Done, 2004; Yamamoto and Sugiura, 2002;
Zhang, 2015). Historically, data-driven approaches have been most
commonly used in coral reef research, but the rise of big data
approaches (Kemp and Sadler, 2014) has rendered some traditional
forms of data-analyses insufcient (Andrew and Mapstone, 1987;
Leujak and Ormond, 2007; Pielou, 1974) and novel computational
techniques are increasingly used to address this problem.
The current huge amount of coral reef data arises mainly from two
technologies whose capabilities are continuously being improved:
remote sensing and underwater vehicles. On the one, coral reef remote
sensing techniques (Goodman et al., 2013) both aerial imagery from
satellites or aircrafts (Shihavuddin et al., 2013; Xu and Zhao, 2014)
and bathymetric data via Airborne Light Detection and Ranging
(LiDAR) (Pittman et al., 2009), ship-based Multi-Beam Echo-Sounder
(MBES) and Sound Navigation and Ranging (SoNAR) (Costa et al.,
2009) are able to provide repeatable observations in large areas
(Lucas and Goodman, 2014; Maina et al., 2008; Rowlands, 2013;
Rowlands et al., 2012; Xu and Zhao, 2014) to quantify proxies of biodiversity (Shihavuddin et al., 2013; Turner et al., 2003), and has become a
relevant additional tool to in situ approaches (Mumby et al., 2004a;
Scoplitis et al., 2009, 2010; Shihavuddin et al., 2013; Wang et al.,
2007). On the other hand, underwater vehicles Remotely Operated
Vehicles (ROVs) (Neves et al., 2014; Purser, 2015), Deep Sea Crawler
(Purser et al., 2013b), autonomous underwater vehicles (AUVs), and
mobile robots (Thomsen et al., 2015) allow image acquisition at
depths and over spatial scales that are not possible with divers. Underwater vehicles provide large amounts of high spatial resolution imagery,
from which benthic organisms under study can be resolved
(Shihavuddin et al., 2013), (Turner et al., 2003). Both data acquisition technologies require increasingly the use of CI techniques, not
only because of the large amount of data and the difculty to classify
or detect biota from data (the classical manual analysis is both timeconsuming and labor-intensive) but also because of the need to
extract non-obvious relationships among the many factors that
interact with each other, and which arise from the inherent complexity of coral reefs mentioned in the rst paragraph.
CI is a branch of Articial Intelligence (AI), focused on the design of
robust and intelligent systems to tackle complex real-world problems
for which traditional approaches fail or are inefcient. For example, in
optimization problems, traditional techniques such as Newton-type
algorithms need continuous and derivable objective functions to be
applied, while CI techniques such as evolutionary computation (EC)
algorithms do not need this requisite. There are other problems such
as regression models (RMs) or classication approaches where CI techniques are known to obtain better results than traditional algorithms.
For example, in regression problems, traditional regression (LR) analysis
(Montgomery et al., 2012; Seber and Lee, 2012) or multi-linear regression
(MLR) models (Chatterjee and Hadi, 2015) are usually considered a baseline algorithm to be beaten by CI techniques. In classication problems,
the traditional nave k-nearest neighbors approach (Soriano et al., 2001)
is usually improved by CI techniques such as Support Vector Machines
(SVMs) or neural classiers. In this respect, note that CI is not a single
technique, but a set of techniques belonging to different subelds such
109
Fig. 1. Time evolution of published works. Blue bars represent research contributions using CI
techniques to solve coral reef related problems. For the sake of clarity, references have been
listed in Table 1 along with the CI method used. Red bars represent the yearly number of
works that apply coral reef concepts via the CRO algorithm to general-purpose
optimization problems.
110
111
Table 1
List of works using CI in coral reef related problems. See Table 2 for acronyms.
Ref.
CI method
Goal
Input
FL
SOM
FL
FL
FL
NN
SA
NN
BBN
FL
NN
NN
NN
SVM
SVM
NN
NN
NN
SVM
FL
NN
SOM
GARP
NN
SOM
NN
BRT
SVM
SVM
PNN
SVM
NN
SVM
NN
AHP-fuzzy
SVM
SVM
NN
MaxEnt
FL
RF
GA
SVM
NN
SVM
Suspended particulate
ROV underwater imagery
Sedimentation, nutrient inux
Suspended particulate
Temperatures
Coral variables
26 habitat data
SST, SSS, and coral data
Input
Spectral information
Underwater images
SST, SSS, coral data
SST, SSS, and coral data
Images
Underwater imagery
SST, SSS, and coral data
SST, SSS, and coral data
SST, SSS, and coral data
Images
Images
Input
ROV images
Bathymetric data
Reectance patterns
Video transect
SST, SSS, and coral data
LiDAR bathymetry
Spectral data from images and bathymetric data
Satellite images
Underwater images
25 marine environmental variables
Bathymetry data
Multispectral image
Bathymetry
Benthos percentage
Underwater images
Underwater images
Underwater images
Terrain variables
Recreational shing data
High spatial resolution satellite data
Remote sensing reectance
Hyperspectral data and aerial photography
Underwater images
Underwater images
112
Table 2
List of acronyms used in this paper.
Acronym
Meaning
AHP
AI
ANN
AUV
BBN
BRT
CI
CRO
CWC
DSS
EC
ELM
ENFA
ENSO
FC
FL
FS
GA
GAM
GARP
GM
H2SOM
k-NN
LiDAR
LR
MaxEnt
MBES
MLC
MLP
MPAs
MLR
NN
NTA
OBIA
PNN
POM
PSO
ROVs
RFs
RM
RSP
SA
SDM
SOM
SoNAR
SSS
SST
SVM
SVR
function. The CRO is based on the fact that reefs endure as long as
healthier corals better solutions to the problem at hand survive
even if less healthy corals perish.
Algorithm 1. Pseudo-code for the CRO algorithm
113
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116
then mutated and evaluated by the GARP. Whether or not a single rule
should be included into the model population was decided by
comparing the predictive accuracy of each iteration to that of the next.
The main conclusions of this work were that the three methods were
able to predict the most adequate habitats for both gorgonian species,
and that these species colonize topographic highs.
The use of GARP has also been investigated, along with 14 other
predictive models (including MLP and SVM, regression models and
others (Huang et al., 2011a)), to predict the distribution of sponge
assemblies on the Australian continental shelf. The research made use
of 25 marine environmental variables (Huang et al., 2011a) and
concluded that MLP, SVM, and GARP algorithms successfully predict
the spatial distribution of sponge abundance, outperforming the results
obtained with regression models.
A novel approach that hybridizes a shallow water semi-analytical
(SSA) model and a GA to identify 5 bottom categories from subsurface
remote sensing reectance measurements was described in (Chang
et al., 2014). The algorithm is designed and tested based on a synthetic
database. The promising results (a probability of correct classication of
80% of the benthic community involved) suggest the viability of this
novel method, but the GA-SSA approach is yet to be tested for real
coral reefs.
Simulated annealing has also been successfully applied to a coral
reef-related problem aiming to design and implement marine reserves
to efciently conserve biodiversity (Leslie et al., 2003). Efciently
means here that the reserve design has to fulll a balance between
protecting a given percentage of habitat types and minimizing the
area and perimeter of the marine reserve to be designed. This is
a constrained optimization problem, the so-called Reserve Selection
Problem (RSP). In the RSP, the objective function is formed by a cost
term (related to the area of each site considered in the reserve) plus a
term related to boundary length. In turn, the problem's constraints are
related to the percentage of each habitat type that requires to be
protected. In particular, a RSP with 26 habitats was tackled using data
from the 9500 km 2 of the Florida Keys National Marine Sanctuary
(Leslie et al., 2003). A comparison between SA and a greedy approach
showed that the CI algorithm obtained excellent results to address this
problem. Specically, the SA approach was able to generate marine
reserves conserving the target habitats percentage while minimizing
the perimeter: 720 km (SA), much lower than that obtained by the
greedy approach (3376 km). Furthermore, from a practical viewpoint,
another key result obtained by (Leslie et al., 2003) was that the SA led
to reserve forms with less perimeter and larger overall areas, which is
supposed to be preferable for sociopolitical reasons.
The key ndings of this review of evolutionary-type approaches
in coral reef problems is that, in general, they work better than more
commonly used classical methods (greedy, regression approaches).
Evolutionary-type approaches have so far been useful to accurately
predict the distribution of species and to the identication of areas
that would be suitable to become designated as reserves.
3.5. Fuzzy computation in coral reef applications
Fuzzy Computation is profusely used to model different effect of
coral reefs. This ranges from the prediction of coral reef development
under nutrient and sediment stress (Meesters et al., 1998) and
modeling coral blenching (Halide and Ridd, 2002) to model economic
policies (Ruitenbeek et al., 1999) and management options (Gao and
Hailu, 2012, 2013) in coral reefs.
The degradation over time that coral reefs in Curaao (and their
corresponding diversity) could suffer, caused by eutrophication and
other anthropogenic stressors, has been also explored using a fuzzy
logic by (Meesters et al., 1998). The fuzzy logic approach made use of
seven input variables (dissolved inorganic nitrogen and phosphate,
suspended particulate matter, maximum colony size, substratum available for colonization, coral cover, and coral diversity) with possible
values (low, medium, and high) into three triangular fuzzy sets. The
boundaries between each fuzzy set along with the corresponding rules
were based on data and expert knowledge. The results showed that
fuzzy logic is useful to describe coral reef processes and the interactions
between variables and assist non experts in taking decisions for a better
management of coral reefs.
The prediction of occurrence of coral bleaching events on Magnetic Island (North Queensland, Australia) was also investigated
using a fuzzy logic framework (Halide and Ridd, 2002), based on
four input variables: 1) seawater temperatures, 2) temperatures
computed (for a specic year) subtracting temperatures of the former year from those of that year, 3) temperatures computed (for a
particular year) by subtracting the mean temperatures of the two
previous years, and 4) temperatures calculated by subtracting the
3 year average before.
Fuzzy logic models were used to evaluate the impact of various
stressors on coral reef health in Montego Bay (Jamaica), and to decide
the most adequate management interventions to be implemented
(Ruitenbeek et al., 1999). Specically, the goal was to identify and
decide among a variety of cost-efcient management approaches the
one that would be most likely to improve the health status of a coral
reef. The fuzzy model used comprised 14 ecological variables (effective
nutrient concentration, sediment deposition, % of algae on available
substrate, etc. (Ruitenbeek et al., 1999)), and classied reef quality
according to 5 possible fuzzy values (low, medium-low, medium,
medium high, and high). The study concluded that, when compared
to conventional economic approaches, the fuzzy logic approach leads
to more accurately models of the complex interactions between
natural and human-made factors, and assists in evaluating the effect
of different management scenarios on coral reef quality before they
had been implemented.
Although at a lesser extent, FL, within the context of Object-Based
Image Analysis (OBIA) (Leon and Woodroffe, 2009), has been used in
(Beneld et al., 2007; Wang et al., 2004) to map the distribution of
coral reefs.
The main conclusion, common to the application above, is that fuzzy
logic is useful, especially, to model different phenomena (development
under nutrient and sediment stress, coral blenching, etc.) and to help
make more informed policy decisions, and to design better management
strategies of coral reef ecosystems.
4. Discussion
As mentioned in Section 1, coral reefs are extremely complex
ecosystems (Bett et al., 2001; Dunlop et al., 2015; Ferrario et al.,
2014; Kline et al., 2015; Knowlton and Jackson, 2013; Lamy et al.,
2015; Purser, 2015; Roberts, 2009; Ruhl, 2007; Schoening et al.,
2012; Shantz et al., 2015; Tittensor et al., 2010) that play a key role
at both local and planetary scale (Baker et al., 2008; Freeman, 2015;
Mooney et al., 2009; Woodroffe and Webster, 2014). Study, recovery
(Gates and Jones, 2012; MacNeil et al., 2015; Morri et al., 2015) and
management (D'Angelo and Wiedenmann, 2014; Lim et al., 2009;
McClanahan et al., 2012; Weijerman et al., 2015) of coral reef ecosystems is a compulsory duty to both politicians and scientists. Aiming at
achieving these goals there are basically three types of generic groups
of tasks (Goodman et al., 2013; Phinn et al., 2006): mapping, monitoring
and modeling. In the following sub-sections we review the use of CI
techniques in these applications.
4.1. The application of CI techniques in mapping-related problems is coral
reefs
Mapping coral reef involves, in broad sense (Goodman et al., 2013),
many research activities such as mapping itself (Beijbom et al., 2012;
Wahidin et al., 2015; Zhang, 2015), habitat mapping (Andrfout
et al., 2003; Call et al., 2003; Capolsini et al., 2003; Maeder et al., 2002;
Mishra et al., 2006; Mumby and Edwards, 2002; Stumpf et al., 2003),
coral reef topography (Yamano, 2007), resource stocktaking
(Andrefouet et al., 2004), (Andrfout et al., 2009; Hochberg and
Atkinson, 2008), coral reef productivity (Andrfout and Payri, 2001;
Brock et al., 2006; Hochberg and Atkinson, 2008; Moses et al., 2009),
habitat diversity (Harborne et al., 2006; Mumby, 2001), biodiversity
(Dalleau et al., 2010; Mellin et al., 2009; Mumby et al., 2008), or MPA
planning and evaluation(Beger et al., 2006; Mora et al., 2006;
Rioja-Nieto and Sheppard, 2008). Many works focused on coral reef
mapping from remote sensing data have tackled the problem of coral
classication by using conventional algorithms, such as the k-means
or maximum likelihood classication (MLC) algorithms (Andrfout
et al., 2003; Warren et al., 2015), (Lim et al., 2009), as implemented in
software packages (Goodman et al., 2013) like ENVI (Exelis, 2012) or
ERDAS IMAGINE (Bertels et al., 2008; Capolsini et al., 2003; ERDAS.
ERDAS IMAGINE, 2015), (Harborne et al., 2006). However, as shown
in Table 1, CI techniques are now playing an increasingly important
role and, as will be shown, exhibit, in general terms, better performance.
The ranking is as follows: First, SVMs have been found to be the most CI
technique used for mapping (Beijbom et al., 2012; Wahidin et al., 2015;
Zhang, 2015), classication (Henriques et al., 2010; Johnson-Roberson
et al., 2006; Mehta et al., 2007; Padmavathi et al., 2010; Shihavuddin
et al., 2013; Zhang, 2015), segmentation and classication (JohnsonRoberson et al., 2007), detection (Collin and Planes, 2012), and semiautomated image analysis (Schoening et al., 2012). The second most
used CI techniques in mapping are NNs for mapping (Watts et al.,
2011), classication (Elawady, 2015; Marcos et al., 2005; Nagamani
et al., 2012; Padmavathi et al., 2010), classication and mapping
(Bandyopadhyay et al., 2009), and detection (Purser et al., 2009). FL,
in the context of Object-Based Image Analysis (OBIA) (Leon and
Woodroffe, 2009), has been used in (Beneld et al., 2007; Wang et al.,
2004) to map the distribution of coral reefs. Finally, RF (Knudby et al.,
2013) and GA (Chang et al., 2014) are the less widely used in mapping
and identication of bottom types.
4.1.1. Monitoring
Monitoring coral reefs include various activities such as exploring
habitat change (Dustan et al., 2001; LeDrew et al., 2004; Palandro
et al., 2003, 2008; Schuyler et al., 2006; Sharma et al., 2008), coral
decline (Abram et al., 2003; Hu et al., 2003; Shinn et al., 2000), or
coral reef productivity (Moses et al., 2008). The use of CI techniques is
lower in monitoring than in mapping and is limited to SVM (Zhang,
2015) and NN (Yamamoto and Sugiura, 2002) (coral growth).
4.1.2. Modeling
Modeling in coral reefs involves many different research tasks,
ranging from modeling population dynamics (Riegl and Purkis,
2005; Scoplitis et al., 2007) and sediment transport (Ouillon et al.,
2004; Yokoki et al., 2006), to prediction of coral reef development
under nutrient and sediment stress (Meesters et al., 1998), or even
optimization of cost-effectiveness models for coral reef management
(Gao and Hailu, 2012; Ruitenbeek et al., 1999). The most widely used
technique in coral reef modeling is the NN approach. NNs have been
used to model coral growth (Yamamoto and Sugiura, 2002), coral
skeleton growth (Juillet-Leclerc and Thiria, 2007, 2008), SST and
SSS reconstructions from coral skeleton (Juillet-Leclerc, 2009), and
cold-water coral habitats (Purser et al., 2008) (based on SOM), or
to predict large-scale coral bleaching (Wooldridge and Done, 2004)
(BBN). FL is the second most used technique in coral reef modeling.
This ranges from the prediction of coral reef development under
nutrient and sediment stress (Meesters et al., 1998) and modeling
coral blenching (Halide and Ridd, 2002) to model economic policies
(Ruitenbeek et al., 1999) and management options (Gao and Hailu,
2012, 2013) in coral reefs. Other CI techniques used to a lesser extent
are: GARP, which has been used to predict species' distributions
(Elith et al., 2006) or distribution of cold-water coral habitat
117
(Guinan et al., 2009); SVM, which has been used to model richness
and diversity of reef sh species (Knudby et al., 2010); SA, that has
been found useful to design marine reserve networks (Leslie et al.,
2003). Boosted regression trees, which were used to predict the
diversity and abundance of sh and corals (Pittman et al., 2009)
and nally MaxEnt, that has recently used for modeling the habitat
suitability for deep-water gorgonian corals (Tong et al., 2013).
4.2. Answering the research questions
(1) What is the fastest and most accurate method to detect corals from
images? The SVM method has been found to be the better method
to detect corals in images, specially, in underwater images. The
SVM approach in Mehta et al. (2007) succeeds in classifying low
quality underwater images. A key benet is that the classifying
algorithm does not require the estimation of any intermediary
feature vector or histogram: the SVM made use of raw image as
input vectors, and achieved a successful classication probability
of 95%. This is a very important benet of SVMs since they enable
the use of raw image data as feature vectors, which is particularly
transcendent for random natural textures where geometrical
features are difcult to get (Henriques et al., 2010; In Kim et al.,
2002 Li et al., 2003), as in reef images, which exhibit rich patterns
of textures, shapes and colors. The SOM approach (Purser et al.,
2009) have also successfully detected (PCC ,SOM = 91.4%) coldwater corals (CWCs) based on video transect data taken in deepwater at Tisler Reef (Norway).
(2) What are the most suitable method to map coral reef ecosystems?
Although mapping has been carried out in the literature by almost
all the CI techniques, SVMs seem to be the most suitable method to
map coral reef ecosystems. They have been used the most in
mapping (Beijbom et al., 2012; Wahidin et al., 2015; Zhang,
2015), classication (Henriques et al., 2010; Johnson-Roberson
et al., 2006; Mehta et al., 2007; Padmavathi et al., 2010;
Shihavuddin et al., 2013; Zhang, 2015), segmentation and classication (Johnson-Roberson et al., 2007), detection (Collin and
Planes, 2012), and semi-automated image analysis (Schoening
et al., 2012). NNs have also proven a good performance for
mapping in a good number of papers: mapping (Watts et al.,
2011), classication (Elawady, 2015; Marcos et al., 2005;
Nagamani et al., 2012; Padmavathi et al., 2010), classication and
mapping (Bandyopadhyay et al., 2009), detection (Purser et al.,
2009).
(3) What are the best methods for designing marine reserves? What
are the best methods to help decision making in this regard? FL
has been found to be the most feasible method to model economic policies (Ruitenbeek et al., 1999) and management options (Gao and Hailu, 2012, 2013) in coral reefs. The SA
approach (Leslie et al., 2003) was able to generate marine reserves conserving the target habitats percentage while minimizing the perimeter, and led to reserve forms with less
perimeter and larger overall areas, which is supposed to be
preferable for sociopolitical reasons.
(4) What concepts of coral reefs can be applied to solve generalpurpose optimization problems? The inclusion of real coral
reef processes into computation approaches thus provides
useful novel models, that can be combined with other CI approaches in the future to improve the solution of both science
and engineering problems. For example, it is possible to dene
new CRO models considering different coral species in the
reef. This is useful for dening new co-evolution approaches
in just one CRO population, to exploit competitive cooperation schemes. Another real characteristic of corals that can
be included in the CRO is the fact that corals grew at different
rates depending on the substrate they are xed to (Vermeij,
118
the substrate they are xed to (Vermeij, 2005). This can be exploited
for evolving several models of problem encoding in a competitive way.
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