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Tectonic discrimination of olivine in basalt using

data mining techniques based on major elements:
a comparative study from multiple perspectives

Qiubing Ren, Mingchao Li & Shuai Han

To cite this article: Qiubing Ren, Mingchao Li & Shuai Han (2019) Tectonic discrimination of
olivine in basalt using data mining techniques based on major elements: a comparative study
from multiple perspectives, Big Earth Data, 3:1, 8-25, DOI: 10.1080/20964471.2019.1572452

To link to this article: https://doi.org/10.1080/20964471.2019.1572452

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Francis Group and Science Press on behalf
of the International Society for Digital Earth,
supported by the CASEarth Strategic Priority
Research Programme.

Published online: 19 Feb 2019.

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BIG EARTH DATA
2019, VOL. 3, NO. 1, 8–25
https://doi.org/10.1080/20964471.2019.1572452

RESEARCH ARTICLE

Tectonic discrimination of olivine in basalt using data mining

techniques based on major elements: a comparative study
from multiple perspectives
Qiubing Ren, Mingchao Li and Shuai Han
State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, China

ABSTRACT ARTICLE HISTORY

The olivine in basalt records much information about formation Received 8 November 2018
and evolution of basaltic magma, which may help to discriminate Accepted 14 January 2019
basalt tectonic settings. However, the viewpoint that olivine is KEYWORDS
connected with the tectonic setting where it formed is controver- Olivine in basalt; tectonic
sial. To verify the hypothesis, we intend to discriminate the basalt setting; geochemical
tectonic settings by geochemical characteristics of olivine. The discrimination; data mining;
data mining technique is selected as an effective tool for this comparative study
study, which is a new attempt in geochemical research. The geo-
chemical data of olivine used is extracted from open-access and
comprehensive petrological databases. The classification perfor-
mance of Logistic regression classifier, Naïve Bayes, Random
Forest and Multi-layer perception (MLP) algorithms is firstly com-
pared under some constraints. The results of the basic experiment
indicate that MLP has the highest classification accuracy of about
88% based on raw data, followed by Random Forest. But this does
not fully prove the hypothesis is credible. Then, the cross-
validation method and other measurement criteria are integrated
for scientific and in-depth comparative analysis. The advanced
experiments mainly include the comparison of different data pre-
processing methods, combinations of geochemical characteristics
and sample data volumes. It turns out that chemical composition
of olivine in basalt has the function of discriminating tectonic
settings.

1. Introduction
Olivine is one of the most common minerals on earth, which is the main mineral composition
of mantle rock, and one of the earliest minerals formed when magma crystallizes (Zhou, Chen,
& Chen, 1980). Olivine is also a major rock-forming mineral in basic and ultrabasic igneous
rocks, such as basalt, gabbro and peridotite. Olivine mainly composes of Mg or Fe and
contains other elements, such as Mn, Ni and Co, whose crystals are granular and dispersed
in rocks or granular aggregates (Enciso-Maldonado et al., 2015). As we all know, the basalt
and its minerals have always been the main means to explore the magmatic process, the
hot state of the mantle and the composition of the mantle elements (Di et al., 2017). As the
most important mineral composition of mantle rock and the earliest crystalline mineral of

CONTACT Mingchao Li lmc@tju.edu.cn

© 2019 The Author(s). Published by Taylor & Francis Group and Science Press on behalf of the International Society for Digital Earth,
supported by the CASEarth Strategic Priority Research Programme.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/
by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
 BIG EARTH DATA 9

magma, the basic elements of olivine in basalt can provide effective information about the
partial melting of mantle, early crystallization process of magma and mantle metasomatism
(Howarth & Harris, 2017).
The basalt is usually divided into different types based on the tectonic setting. The
mid-ocean ridge basalt (MORB), ocean island basalt (OIB) and island arc basalt (IAB) are
the three types of basalt most concerned by the academic community (Vermeesch,
2006). Then, how to discriminate the tectonic settings of basalt has become an impor-
tant issue in geochemistry. In general, we can discriminate the tectonic settings formed
by magmatic rocks, mainly including the basalt and granite, and master the chemical
properties of magma sources in terms of the chemical composition of magmatic rocks.
This is a common and feasible discrimination approach, which has been proved by many
facts (Bhatia & Crook, 1986; Li, Arndt, Tang, & Ripley, 2015; Sánchez-Muñoz et al., 2017).
The olivine in basalt records much information about the formation and evolution of
basaltic magma, which is helpful to discriminate the three tectonic settings. At present,
it is generally believed that the chemical composition of olivine is one piece of impor-
tant evidence to identify whether basalt is primitive magma, but the viewpoint that
olivine is closely related to the tectonic setting where it formed is controversial. The
paper aims to prove the rationalization of the latter.
In the 1970s, Pearce and Cann (1973) first proposed the basalt discrimination diagram
based on the chemical composition. The basalt discrimination diagram organically
combines the tectonic setting with the geochemical characteristics of basalt, thus open-
ing up a new way for the study of plate tectonics and continental orogenic belts. This
greatly enriched the research contents of basalt. The basalt discriminant diagrams have
been widely used in academic circles due to their solid theoretical foundations and
concise forms of expression (Pearce, 1996). The study of basalt tectonic setting has also
been pushed to the peak since then. Even now, the discrimination diagram is still the
main method for basalt tectonic setting discrimination. However, with the increasing use
of the discrimination diagram, its inherent defects gradually appear, such as the empiri-
cism and subjectivity, lack of rigorous theory, contradiction of discrimination and
limitation of application (Luo et al., 2018; Zhang, 1990). The drawbacks mentioned
above greatly affect the classification accuracy and work reliability of the discrimination
diagram. To our knowledge, it is difficult to discriminate the basalt tectonic settings
using the discrimination diagram based on the geochemical characteristics of olivine in
basalt. And also, there is almost no introduction about the use of olivine in the basalt
tectonic setting discrimination in the literatures. Therefore, we need to find another way
to discriminate the tectonic settings of basalt on the basis of the chemical composition
of olivine.
The data mining technique is a good choice. With the rapid development of new
technologies, such as big data and cloud computing, as well as the substantial improve-
ment of the computing capacity of computer hardware, the data mining technique has
increasingly aroused great concern among domestic and foreign scholars in recent years
(Zhou et al., 2018). In the areas of pattern recognition, function approximation and
simulation modeling, fruitful results have been achieved. But now in geochemistry, the
research on discriminating the tectonic settings of basalt using data mining is still in the
initial stage. Petrelli and Perugini (2016) used Support Vector Machines (SVM) to discrimi-
nate the tectonic settings of volcanic rocks and obtained high classification scores. Ueki,
10 Q. REN ET AL.

Hino, and Kuwatani (2018) adopted SVM, Random Forest and Sparse Multinomial
Regression approaches for classification performance comparison. The results indicated
that data mining is a highly effective tool in geochemical research. Based on the two
successful cases, we intend to employ data mining to do some simulation experiments,
which all involves the tectonic setting discrimination of basalt based on the chemical
composition of olivine. Being an attempt in geochemical research, we proceed from the
perspective of comparative research, which may lay the groundwork for future research
(Han, Li, Ren, & Liu, 2018). This just determines that there are some fundamental compara-
tive tests, mainly including the comparison of different data mining algorithms, data
preprocessing methods, combinations of geochemical characteristics and sample data
volumes. Nevertheless, we have to admit that the experimental results acquired certainly
contain some drawbacks and are open to comments and further research.
This paper is organized as follows. In Section 2, an overall research framework of this
paper is introduced. Section 3 presents a brief description of different data mining
algorithms, followed by a synopsis of the cross-validation method and measurement
criteria. The data description, preliminary experiment and benchmark classification
effects are provided in Section 4. Section 5 illustrates and discusses the experimental
results and analysis for four comparative tests. The concluding remarks and future work
are finally mentioned in Section 6.

2. Overall framework
The overall research framework shown in Figure 1 is outlined below.

(1) The geochemical data of olivine are collected from the GEOROC and PetDB
databases, followed by data cleaning and management, thus laying a good data
foundation for this study. It is worth mentioning that the olives data used are
measured via common methods of major element analysis, e.g. electron probe
microanalysis, EPMA, or instrumental neutron activation analysis, INAA (Arevalo,
McDonough, & Luong, 2009).

Front-end Data collection and

processing filtering

Data mining Data preprocessing

algorithms techniques
Comparative
studies
Sample data Feature importance
volumes measurement

Research Conclusions and

findings suggestions

Figure 1. Overall framework diagram.

 BIG EARTH DATA 11

(2) Different data mining algorithms are used to discriminate tectonic settings of the
collated olivine in basalt in terms of geochemical characteristics. The classification
performance of different data mining algorithms is compared.
(3) The effect of data preprocessing on the discrimination results of tectonic settings
of olivine has not been considered in the previous step. Hence, the impacts of
different data preprocessing techniques on the classification performance of four
classifiers are compared.
(4) The importance score of each geochemical characteristic of olivine is analyzed
through Random Forest. The effects of different combinations of geochemical
characteristics on the single and overall classification accuracy of four classifiers
are considered. The relationship between the cumulative feature importance and
the classification accuracy is also studied.
(5) It is necessary to research on the effects of different sample data volumes on the
single and overall classification accuracy of four classifiers, when big data mining
is used to discriminate tectonic settings of olivine. This will provide a reference for
subsequent studies.
(6) Four comparative studies are conducted, including the classification performance of
four classifiers, the impacts of different data preprocessing techniques, combinations
of geochemical characteristics and sample data volumes. Some important conclu-
sions are drawn, and a few valuable suggestions for future research are proposed.

3. Methodology
3.1. Data mining algorithms
3.1.1. Logistic regression classifier (LRC)
Logistic regression is an approach to learning functions of the form f : X ! Y, or PðYjXÞ
in the case where Y is discrete-valued, and X ¼ ðX1 ; X2 ;    ;Xn Þ is any vector containing
discrete or continuous variables (Mitchell, 2005; Subasi & Ercelebi, 2005). In this section,
we will primarily consider the case where Y is a boolean variable, in order to simplify
notation. More generally, Y can take on any of the discrete values fy1 ; y2 ;    ; yk g
which is used in experiments.
Logistic regression assumes a parametric form for the distribution PðYjXÞ, then
directly estimates its parameters from the training data. The parametric model assumed
by Logistic regression in the case where Y is boolean as follows

1
PðY ¼ 1jXÞ ¼  P  (1)
1 þ exp w0 þ ni¼1 wi Xi

and
 P 
exp w0 þ ni¼1 wi Xi
PðY ¼ 0jXÞ ¼  P  (2)
1 þ exp w0 þ ni¼1 wi Xi

Notice that Equation (2) follows directly from Equation (1), because the sum of these two
probabilities must equal one.
12 Q. REN ET AL.

One highly expedient property of this form for PðYjXÞ is that it leads to a simple linear
expression for classification. To classify any given X, we generally want to assign the
value yk that maximizes PðY ¼ yk jXÞ. In other word, we assign the label Y ¼ 0 if the
PðY¼0jXÞ
following condition holds PðY¼1jXÞ > 1. Substituting from Equations (1) and (2), this
 Pn 
becomes exp w0 þ i¼1 wi Xi > 1.
Then taking the natural log of both sides, we have a linear classification rule that
P
assigns label Y ¼ 0 if X satisfies w0 þ ni¼1 wi Xi > 0, and assigns Y ¼ 1 otherwise.

3.1.2. Naïve bayes

Naïve Bayes algorithm is a simple probabilistic classifier based on applying Bayes
theorem with naive independence assumptions between the features, which only
requires a small number of training data to estimate the parameters necessary for
classification (Li, Miao, & Shi, 2014; Ren, Wang, Li, & Han, 2019). Now suppose that
a problem instance to be classified, represented by a vector X ¼ ðx1 ; x2 ;    ; xn Þ, it
assigns to this instance probabilities PðCk jx1 ; x2 ;    ; xn Þ for each of k possible cate-
gories. Using Bayes theorem, the conditional probability can be decomposed as
PðCk ÞPðXjCk Þ
PðCk jXÞ ¼ (3)
PðXÞ
PðCk ÞPðXjCk Þ is equivalent to the joint probability model PðCk jx1 ; x2 ;    ; xn Þbecause PðXÞ is
constant. Assume that each feature xi is conditionally independent of every other feature xj
for jÞi, given the category Ck. Thus, the conditional distribution over the class variable Ck is
1 Yn
PðCk jx1 ; x2 ;    ; xn Þ ¼ PðCk Þ i¼1 Pðxi jCk Þ (4)
Z
P
where the evidence Z ¼ PðXÞ ¼ k PðCk ÞPðXjCk Þ is a scaling factor dependent only on
x1 ; x2 ;    ; xn , namely, a constant if the values of the feature variables are known.
Naïve Bayes classifier combines the aforementioned probability model with a decision
rule that is known as the maximum a posteriori decision rule. The classifier is the
function that assigns a category label ^y ¼ Ck for k as follows
Yn
^y ¼ arg max PðCk Þ Pðxi jCk Þ (5)
i¼1
k2f1; 2; ; K g

All model parameters can be estimated by the correlation frequency of the training set.
The common method is maximum likelihood estimation. To estimate the parameters for
the distribution of a feature, we must assume a distribution or generate nonparametric
models for the features from the training set.

3.1.3. Random forest

Random Forest is a combined classification model based on classification and regression tree
(CART) decision trees, which is a supervised machine-learning algorithm and preeminent
classification technique (Breiman, 2001; Taalab, Cheng, & Zhang, 2018). The algorithm mainly
integrates two randomization ideas, including random subspace thought and bootstrap
aggregating (also called bagging) thought. The basic classification unit of the Random
Forest is the decision tree, which is essentially a classifier containing multiple decision trees,
 BIG EARTH DATA 13

and its output category is determined by the mode of the output of decision trees, as shown in
Figure 2.
Random Forest is an ensemble learning method composed of K decision
treesfhðX; Lk Þ; k ¼ 1; 2;    ; K g, and fLk ; k ¼ 1; 2;    ; K g is a random vector that is inde-
pendent and identically distributed, which is used to control the growth of each tree.
The algorithm first uses bootstrap sampling to extract k samples from a training set, then
establishes a decision tree for each sample, respectively, and finally obtains the
sequencefh1 ðX; L1 Þ; h2 ðX; L2 Þ;    ; hk ðX; Lk Þg. Under the given independent variable,
each decision tree acquires a classification result. The final classification result depends
on a simple majority vote for the result of each decision tree. The classification decision
can be expressed as
Xk
HðxÞ ¼ arg max i¼1
Iðhi ðx; Li Þ ¼ YÞ (6)
Y

where HðxÞ represents the combined classification model, hi is a single decision tree
classification model, IðÞ is an indicator function, and Y represents the output variable.

3.1.4. Multi-layer perception (MLP)

A MLP is a class of feedforward artificial neural network which consists of at least three
layers of nodes (an input and an output layer with one or more hidden layers) with
unidirectional connections, often trained by a supervised learning technique (Hannan,
Arebey, Begum, Mustafa, & Basri, 2013; Longstaff & Cross, 1987). Each node, except for
input nodes, is a neuron that uses a nonlinear activation function. MLP can distinguish
data that is not linearly separable, whose multiple layers and nonlinear activation
differentiate itself from a linear perceptron.
Learning occurs in the perceptron by changing connection weights after each piece
of data is processed, based on the amount of error in the output compared to the
expected result, which is constantly carried out through backpropagation. Suppose that
the error in output node j in the nth data point is ej ðnÞ ¼ dj ðnÞ  yj ðnÞ, where d is the
desired output and y is produced by the perceptron. The weights are adjusted based on
P
corrections that minimize the error function, given by εðnÞ ¼ 12 j ej 2 ðnÞ. Using gradient
descent, the change in each weight is

D1 Decision tree 1 Result 1

Vote for
D Randomize D2 Decision tree 2 Result 2
the best

DK Decision tree K Result K

Figure 2. Schematic diagram of Random Forest.

14 Q. REN ET AL.

@εðnÞ @εðnÞ
Δwji ðnÞ ¼ η yi ðnÞ;  ¼ ej ðnÞϕ0 ðvj ðnÞÞ (7)
@vj ðnÞ @vj ðnÞ
where yi is the output of the previous neuron, η is the learning rate, and ϕ0 is the
derivative of the activation function. Though the change in weights to a hidden node is
complicated, the relevant derivative is
@εðnÞ X @εðnÞ
 ¼ ϕ0 ðvj ðnÞÞ  wkj ðnÞ (8)
@vj ðnÞ k @vk ðnÞ
This relies on the change in weights of the kth nodes, and the algorithm represents
a backpropagation of the activation function.

3.2. Cross-validation method

Cross-validation is mainly used in both classification and regression modeling (Arlot & Celisse,
2010; Golub, Heath, & Wahba, 1979). To reduce the bias between the entire dataset and
training set (or test set), the K-fold cross-validation method is regarded as the scientific
evaluation method for classification modeling. The technique divides the raw dataset into
K subsets. One of the subsets is chosen as the test set, and the remaining K  1 data subsets
are regarded as the training set in each iteration, as shown in Figure 3. Then, the classification
accuracy of each classifier is expressed as the average value of the K models obtained from the
training number K. Therefore, the K-fold cross-validation method could effectively reduce the
randomness of dataset selection and scientifically evaluate the reliability of the classification
model.

3.3. Measurement criteria

In order to comprehensively evaluate the classification effect of each classifier, a method
combining quantitative and qualitative evaluation is adopted (Pedregosa et al., 2011;
Townsend, 1971). On the one hand, the classification accuracy, containing the single and
overall classification accuracy, can describe classification results in the form of score. On

Iteration 1 Iteration 2 Iteration 3 Iteration K

Fold 1 Fold 1 Fold 1 Fold 1

Fold 2 Fold 2 Fold 2 Fold 2
Fold 3 Fold 3 Fold 3 Fold 3

Fold K Fold K Fold K Fold K

Training data Test data

Figure 3. K-fold cross-validation method.

 BIG EARTH DATA 15

the other hand, the confusion matrix, as a visual tool, can intuitively exhibit the
classification precision (Abdel-Zaher & Eldeib, 2016; Patil & Sherekar, 2013). Both con-
stitute a scientific and rounded evaluation system.

4. Data modeling experiment

4.1. Data collection and filtering
In total, 25,959 basalt samples, containing 2580 MORB, 18363 OIB and 5016 IAB, are
collected in this study. There are 12 basic elements for each sample, which are K2O, CaO,
SiO2, MgO, NiO, Na2O, FeOT, TiO2, Al2O3, MnO, Cr2O3 and P2O5. In these samples, MORB is
mainly distributed in the Atlantic and Pacific mid-ocean ridges, OIB is mostly distributed
in the Atlantic and Pacific regions, and IAB is principally distributed in the west and east
coast of the Pacific rim. Rigorous data filtering is necessary since the basalt samples are
from various batches and are acquired by different researchers using diverse instru-
ments. These samples that can be removed are: (1) samples that contain very few basic
elements, (2) samples that basic elements have outliers, and (3) samples that affect the
balance of the sample size of MORB, OIB and IAB and have more missing values (Wang
et al., 2017). Here, 12 basic elements do not need to be filtered in order to study the
relationship between geochemical characteristics and tectonic settings. Only 1582 basalt
samples containing olivine, the Fo value of which ranges from 36 to 88, remain after
data filtering, containing 539 MORB, 463 OIB and 580 IAB, as seen in Table 1. For the
convenience of statistics, all of the missing values that remain in the existing samples are
replaced with NA in study.

4.2. Experimental results

Totally, 80% of the existing basalt samples, containing 424 MORB, 374 OIB and 468 IAB,
are regarded as the training set and the rest (115 MORB, 89 OIB and 112 IAB) as the test
set. The output variables are MORB, OIB and IAB, with the input of 12 basic elements.
The critical parameters of each classification model are determined by grid search
method. Geochemical discrimination results of tectonic settings of olivine in basalt
using LRC, Naïve Bayes, Random Forest and MLP are shown in Table 2 and Figure 4.

Table 1. Data description of 1582 basalt samples used in this study.

MORB OIB IAB
Elements Minimum Maximum Mean Minimum Maximum Mean Minimum Maximum Mean
K2O 0.01 0.05 0.02 0.00 0.38 0.03 0.00 0.09 0.01
CaO 0.10 0.54 0.31 0.02 0.58 0.31 0.01 0.66 0.21
SiO2 29.93 41.85 40.12 34.71 42.43 39.71 27.32 42.93 39.01
MgO 36.43 51.30 46.64 23.64 51.71 45.47 25.24 52.66 42.65
NiO 0.01 0.44 0.20 0.01 0.43 0.22 0.00 0.55 0.16
Na2O 0.01 0.10 0.02 0.00 0.53 0.14 0.00 0.21 0.02
FeOT 7.72 23.90 12.59 7.58 42.33 14.28 7.11 37.35 17.18
TiO2 0.01 0.11 0.03 0.00 0.19 0.03 0.00 0.21 0.03
Al2O3 0.01 0.55 0.06 0.00 0.95 0.09 0.00 0.94 0.06
MnO 0.01 0.53 0.20 0.03 0.73 0.21 0.08 0.76 0.27
Cr2O3 0.01 0.21 0.06 0.00 0.23 0.05 0.00 0.29 0.04
P2O5 0.01 0.14 0.07 0.01 0.10 0.03 0.00 0.12 0.02
16 Q. REN ET AL.

Table 2. Discrimination results of tectonic settings of olivine based on four data mining algorithms.
LRC Naïve Bayes Random Forest MLP
Classes Test set Number Accuracy (%) Number Accuracy (%) Number Accuracy (%) Number Accuracy (%)
MORB 115 86 74.78 102 88.70 99 86.09 102 88.70
OIB 89 49 55.06 36 40.45 60 67.42 72 80.90
IAB 112 96 85.71 89 79.46 104 92.86 104 92.86
Overall 316 231 73.10 227 71.84 263 83.23 278 87.98
* Highlighted in bold denotes the best performance measure of the classifier for each tectonic setting.

100

MORB
MORB

80
80

Tr ue label
True label

60 60

OIB
OIB

40 40

IAB
IAB

20
20

0
MORB OIB IAB MORB OIB IAB
Predicted label Predicted label
(a) (b)

100 100
MORB
MORB

80 80
True label
Tr ue label

60 60
OIB
OIB

40 40
IAB
IAB

20 20

MORB OIB IAB MORB OIB IAB

Predicted label Predicted label
(c) (d)

Figure 4. Confusion matrixes of geochemical discrimination results of tectonic settings of olivine

based on four data mining algorithms: (a) LRC, (b) Naïve Bayes, (c) Random Forest and (d) MLP.

It can be found that the classification accuracy of MORB, OIB and IAB based on MLP is
88.70%, 80.90% and 92.86%, respectively, and the overall classification accuracy is
87.98%. Compared with the other three classifiers, MLP has the best classification effect.
The second is Random Forest that has the same IAB classification accuracy as MLP, while
the MORB and OIB classification accuracy are lower. The classification performance of
LRC and Naïve Bayes is roughly similar. On the whole, though, LRC is better and simpler.
However, the results of the constrained experiment have some limitations and the more
advanced is necessary.
 BIG EARTH DATA 17

5. In-depth comparative analysis

5.1. Impact of data preprocessing
5.1.1. Preprocessing techniques
In the whole knowledge discovery process, data preprocessing plays a crucial role before
data mining itself. One of the first steps concerns the normalization of the data. This step
is very important when dealing with parameters of different units and scales. For
example, some data mining techniques use the Euclidean distance. Therefore, all para-
meters should have the same scale for a fair comparison between them. The min-max
normalization and zero-mean standardization are usually well known for rescaling data.
Min-max normalization (Jain & Bhandare, 2011) rescales the values into a range of
[0,1]. This might be useful to some extent where all parameters need to have the same
positive scale. One possible formula is given below

X  Xmin
Xnormalization ¼ (9)
Xmax  Xmin

where X represents each sample data, Xmax is the maximum value of sample data, and
Xmin is the minimum value of sample data.
Zero-mean standardization (Bo, Wang, & Jiao, 2006) transforms data to have zero
mean and unit variance. In most cases, standardization is recommended, for example
using the equation below

X μ
Xstandardization ¼ (10)
σ

where X represents each sample data, μ is the mean of sample data, and σ is the
standard deviation of sample data.
Missing value handling (Frane, 1976) is another important step in data preprocessing.
Missing data can distort the classification results and affect the classifier performance.
The direct deletion of data containing missing values can result in data waste, thus
affecting the generalization ability of the classifier. The imputation method (Donders,
van der Heijden, Stijnen, & Moons, 2006) based on statistics replaces the missing value
with a certain value, such as mean and mode, so that the data are relatively complete.
Since the missing value in the data used is numeric, the missing attribute value can be
replaced with the mean of all other values in this attribute.
However, all of these techniques mentioned above have their drawbacks (García,
Ramírez-Gallego, Luengo, Benítez, & Herrera, 2016). If you have outliers in your dataset,
normalizing your data will certainly scale the normal data to a very small interval. And
generally, most of datasets have outliers. When using standardization, your new data are
not bounded (unlike normalization). The mean imputation method is easy to implement
and does not affect the mean of sample data, but it could reduce the variance of the
data, which is not what we want. Therefore, it is necessary to do some research about
the impacts of three data preprocessing methods on the classification performance of
different classifiers.
18 Q. REN ET AL.

5.1.2. Comparison and analysis

The standardization, normalization and mean imputation methods are applied to the raw
geochemical data, respectively, to obtain the standardized, normalized and sound data
(equivalent to no missing values). When four classifiers are adopted to discriminate tectonic
settings of geochemical data from different preprocessing techniques, the corresponding
classification accuracy can be obtained by changing the fold K of the cross-validation
method. The classification accuracy can reflect the impacts of different data preprocessing
techniques on the classification performance of classifiers. The high precision indicates that
the integrated performance of the preprocessing method and the data mining algorithm is
better, otherwise the matching effect of the two is not good. In addition, the changes of the
overall classification accuracy corresponding to different folds K can show the robustness of
the data mining algorithm.
Figure 5 shows the impacts of different preprocessing techniques on the discrimination
results of tectonic settings of olivine based on four data mining algorithms, where raw data
are considered for a comprehensive comparison. The experimental results are not comple-
tely consistent with that in Section 4.2. Different data preprocessing methods have little
influence on the classification effect of LRC in Figure 5(a). Figure 5(b) indicates that the mean
imputation method raises the classification performance of Naïve Bayes to some extent,

77.0 75
Overall classification accuracy (%)
Overall classification accuracy (%)

Raw data
74 Standardized data
76.5 Normalized data
Data without missing values
73
76.0
72
Raw data
75.5 Standardized data
Normalized data 71
Data without missing values

75.0 70
4 6 8 10 12 14 16 4 6 8 10 12 14 16
K (a) K (b)
100 95
Overall classification accuracy (%)

Overall classification accuracy (%)

Raw data
Standardized data
95 Normalized data
90 Data without missing values

Raw data
90 Standardized data
Normalized data
Data without missing values 85
85

80 80
4 6 8 10 12 14 16 4 6 8 10 12 14 16
K (c) K (d)

Figure 5. Impacts of different data preprocessing techniques on the discrimination results of tectonic
settings of olivine based on four data mining algorithms: (a) LRC, (b) Naïve Bayes, (c) Random Forest,
and (d) MLP.
 BIG EARTH DATA 19

while the other two preprocessing methods do not work. It can also be found in Figure 5(c)
that the mean imputation method greatly improves the classification accuracy of Random
Forest, and the increase is much larger than that of Naïve Bayes, approximately 10%. The
standardization and normalization methods are equally ineffective. As shown in Figure 5(d),
the mean imputation technique unexpectedly reduces the classification accuracy of MLP,
while other techniques remain unchanged. Therefore, the classification accuracy of the
combination model of the mean imputation technique and the Random Forest algorithm is
the highest, which is about 6% higher than that of the single MLP. Moreover, the maximum
difference in classification accuracy of each data mining algorithm is very small within the
range of 5 to 15 folds. It turns out that the four classification models are all robust.

5.2. Feature importance measurement

5.2.1. Principle description
There are 12 basic elements as classification features in the geochemical data of olivine.
It is a crucial issue that how to select features that have the most influence on the
tectonic setting discrimination results, thus reducing features in modeling. There are
many ways to do this, and Random Forest is one of them. The idea is to use the Gini
index to measure the contribution of each feature to each tree in a random forest, and
then take the mean to obtain the importance score of each feature (Granitto, Furlanello,
Biasioli, & Gasperi, 2006; Menze et al., 2009).
Suppose that there are c features X1 ; X2 ;    ; Xc in total, and the Gini index (GI)
score for feature Xj is FIMj ðGiniÞ , that is the abbreviation for feature importance
PjK j
measures. The formula of Gini index is GIm ¼ 1  k¼1 p2mk , where K denotes the
number of categories, and pmk represents the proportion of category k in node m.
The importance of feature Xj in node m, that is, the change of Gini index before and
after node m branching is FIMjm ðGiniÞ ¼ GIm  GIl  GIr , where GIl and GIr represent the
Gini index of two new nodes after branching, respectively. The nodes that feature Xj
appears in decision tree i are in set M, then the importance of Xj in the ith tree is
P
FIMij ðGiniÞ ¼ m2M FIMjm ðGiniÞ . There are n trees in a random forest, so the importance
P
of Xj is FIMj ðGiniÞ ¼ ni¼1 FIMij ðGiniÞ . All of the importance scores obtained are finally
normalized, i.e. FIMj ðGiniÞ ¼ Pc j .
FIM
FIMi
i¼1

5.2.2. Results and discussion

According to the method described in Section 5.2.1, the importance score of each basic
element of the olivine in basalt samples is summarized, as shown in Figure 6. As you can see
in the figure, the sum of the feature importance ( > 5%) of the seven basic elements,
including K2O, CaO, SiO2, MgO, NiO, Na2O and FeOT, has exceeded 0.80. This indicates
that these seven basic elements play a role of over 80% in the process of tectonic setting
discrimination, which should be given more attention in the following studies. However,
there are doubts about the order of the feature importance of 12 basic elements. On the one
hand, Section 5.1 has proven that the mean imputation method does affect the perfor-
mance of a classifier. Figure 5 illustrates this intuitively. On the other hand, Table 1 and
Figure 6 show that the number of missing values for an element might influence its
20 Q. REN ET AL.

P2O5
Cr2O3
MnO
Al2O3

Basic elements
TiO2
FeOT
Na2O
NiO
MgO
SiO2
CaO
K2O
0 5 10 15 20
Feature importance (%)

Figure 6. Feature importance evaluation results of 12 basic elements using Random Forest.

importance score. For example, P2O5 is the least important element, with a miss rate of up to
93%. Although Na2O is the sixth important element now, it may be more important as the
number of missing values decreases. The only exception is that though there are many
missing values for K2O, it is still the most important. In view of these points, relatively large
amounts of complete data need to be collected to achieve more reliable evaluation results
of the feature importance. Therefore, the order of the feature importance of basic elements
shown in Figure 6 is only for the geochemical data used in this study.
In order to quantitatively measure the contribution of each basic element to the model
classification performance, all of the elements are sorted by feature importance from large to
small, and the simulation experiment is carried out by adding them one by one. There are 12
experimental conditions in all, as illustrated in Table 3. The sum of the feature importance of
corresponding basic elements under each condition is listed in the table, for the convenience
of studying the relationship between the cumulative feature importance and the single and
overall classification accuracy. And also, the 10-fold cross-validation method and the combi-
nation model of the mean imputation technique and the Random Forest algorithm are
adopted in this experiment.
The experimental results are summarized in Figure 7. When the input variable is only K2O,
the classification accuracy of MORB is 0, while the classification accuracy of OIB and IAB are
both as high as 90%. The overall classification accuracy is just 60% due to the poor classifica-
tion effect of MORB. The number of missing values for 12 basic elements in different tectonic
settings is listed in Table 4. Both MORB and IAB have higher miss rate, and it is obvious that the
missing value has greater effects on MORB. On the other hand, when the number of elements
is between two and five, the single and overall classification accuracy increase with the rise of
the number of elements. The classification effect remains stable when the number of
elements is greater than five. The number of missing values has little effect on the classifica-
tion accuracy in these two cases because there exists no mutation. As a whole, the change
trends of both the cumulative feature importance and the classification accuracy are not
entirely consistent. The accumulative feature importance is increasing all the time, while the
classification accuracy improves at the beginning and then keeps steady.
 BIG EARTH DATA 21

Table 3. Combination results of basic elements on the basis of feature importance measurement.
Combination of basic elements (note that feature importance goes from large Sum of feature importance
Number to small) (%)
1 K2O 20.69
2 K2O, CaO 40.78
3 K2O, CaO, SiO2 50.93
4 K2O, CaO, SiO2, MgO 59.64
5 K2O, CaO, SiO2, MgO, NiO 68.00
6 K2O, CaO, SiO2, MgO, NiO, Na2O 76.19
T
7 K2O, CaO, SiO2, MgO, NiO, Na2O, FeO 82.74
8 K2O, CaO, SiO2, MgO, NiO, Na2O, FeOT, TiO2 87.60
9 K2O, CaO, SiO2, MgO, NiO, Na2O, FeOT, TiO2, Al2O3 92.04
10 K2O, CaO, SiO2, MgO, NiO, Na2O, FeOT, TiO2, Al2O3, MnO 95.82
T
11 K2O, CaO, SiO2, MgO, NiO, Na2O, FeO , TiO2, Al2O3, MnO, Cr2O3 99.31
12 K2O, CaO, SiO2, MgO, NiO, Na2O, FeOT, TiO2, Al2O3, MnO, Cr2O3, P2O5 100.00

100

80
Accuracy (%)

60

40
Overall classification
MORB classification
20 OIB classification
IAB classification
Cumulative importance
0
0 2 4 6 8 10 12
Number of basic elements

Figure 7. Impacts of different combinations of basic elements (note that feature importance goes from
large to small) on the discrimination results of tectonic settings of olivine based on Random Forest.

Table 4. Number of missing values for 12 basic elements in different tectonic settings.
Number of missing values
Basic elements MORB (539) OIB (463) IAB (580) Total (1582)
K2O 441 0 480 921
CaO 0 1 0 1
SiO2 0 0 0 0
MgO 0 0 0 0
NiO 266 88 0 354
Na2O 380 182 423 985
FeOT 0 0 0 0
TiO2 362 144 2 508
Al2O3 0 88 0 88
MnO 0 5 0 5
Cr2O3 0 0 0 0
P2O5 503 433 535 1471
*(·) denotes the total number of basalt samples for each tectonic setting.
22 Q. REN ET AL.

5.3. Differences in sample data

Sample data volume is not only related to the accuracy of tectonic setting discrimi-
nation but also connected with the deployment of computing resource. It is impera-
tive to research on the effects of sample data volumes on the classification accuracy.
To this end, the following simulation experiment is conducted. The sample data
volume of MORB, OIB and IAB is reduced by 50 at a time, respectively, that is, the
total number is reduced by 150 every time. A total of eight experimental conditions
are formed. The 5-fold cross-validation method and the combination model of the
mean imputation technique and the Random Forest algorithm are adopted in each
case. All the experimental conditions and results are shown in Table 5. Furthermore,
Figure 8 depicts the relationship between the total data volume and the single and
overall classification accuracy. As can be clearly seen from the picture, the single and
overall classification accuracy roughly decrease first and then improve with the
increase of the total data volume. The classification accuracy of OIB is more influ-
enced by data volume than that of others. It is also found that each classification
accuracy tends to be stable when the data volume is over 1400. In summary, the
appropriate data volume is selected for tectonic setting discrimination, which can

Table 5. Single and overall classification accuracy for different sample data volumes.
Sample data volume Classification accuracy (%)
Total MORB OIB IAB Overall MORB OIB IAB
532 189 113 230 95.30 95.77 92.92 96.09
682 239 163 280 94.13 96.23 87.73 96.07
832 289 213 330 92.91 93.08 86.85 96.67
982 339 263 380 92.57 92.92 89.73 94.21
1132 389 313 430 92.58 93.32 90.73 93.26
1282 439 363 480 92.59 94.08 89.81 93.33
1432 489 413 530 93.16 93.66 92.98 92.83
1582 539 463 580 93.74 94.06 92.66 94.31

100

95
Accuracy (%)

90

85 Overall classification
MORB classification
OIB classification
IAB classification
80
400 800 1200 1600
Total data volume

Figure 8. Impacts of different sample data volumes on the discrimination results of tectonic settings
of olivine based on Random Forest.
 BIG EARTH DATA 23

reduce the computing power and time consumption without affecting the discrimi-
nation accuracy.

6. Conclusions and future works

The data mining technique is introduced to discriminate tectonic settings of the olivine
in basalt in this paper. From this case, the effects of different data preprocessing
methods, combinations of geochemical characteristics and sample data volumes on
the model classification performance are also studied. The results show that the data
mining algorithm has comparable advantages in tectonic setting discrimination, mainly
including the following:

(1) It has been preliminarily proved that the composition of olivine in basalt has the
function of discriminating tectonic settings. However, the initial finding obtained by
the data-driven method needs further examination, because some scholars still do
not believe that olivine is closely related to the tectonic setting where it formed.
(2) The combination model of the mean imputation technique and the Random Forest
algorithm is recommended for discriminating tectonic settings of olivine in basalt.
Nevertheless, a single MLP is worth considering if the number of missing values is small.
(3) The seven basic elements, including K2O, CaO, SiO2, MgO, NiO, Na2O and FeOT,
play a role of over 80% in the course of tectonic setting discrimination of olivine
in basalt. It is worth mentioning that the first five basic elements are enough to
achieve good classification effects.
(4) The classification accuracy of OIB is more influenced by the data volume. The
single and overall classification accuracy can reach the large and stable value
when the data volume is over 1400. The more appropriate data volume calls for
more research.

It is convenient and accurate to discriminate tectonic settings by data mining

algorithms, which is worth spreading in geochemistry. However, it remains to be
studied that how to explain potential patterns obtained from data mining scientifi-
cally and reasonably.

Disclosure statement
No potential conflict of interest was reported by the authors.

Data availability statement

The data referred to in this paper is not publicly available at the current time.

Funding
This research was supported by the Tianjin Science Foundation for Distinguished Young Scientists
of China [Grant No. 17JCJQJC44000] and the National Natural Science Foundation for Excellent
Young Scientists of China [Grant No. 51622904].
24 Q. REN ET AL.

ORCID
Mingchao Li http://orcid.org/0000-0002-3010-0892

References
Abdel-Zaher, A. M., & Eldeib, A. M. (2016). Breast cancer classification using deep belief networks.
Expert Systems with Applications, 46, 139–144.
Arevalo, R., McDonough, W. F., & Luong, M. (2009). The K/U ratio of the silicate Earth: Insights into
mantle composition, structure and thermal evolution. Earth and Planetary Science Letters, 278(3),
361–369.
Arlot, S., & Celisse, A. (2010). A survey of cross-validation procedures for model selection. Statistics
Surveys, 4, 40–79.
Bhatia, M. R., & Crook, K. A. (1986). Trace element characteristics of graywackes and tectonic
setting discrimination of sedimentary basins. Contributions to Mineralogy and Petrology, 92(2),
181–193.
Bo, L., Wang, L., & Jiao, L. (2006). Feature scaling for kernel fisher discriminant analysis using
leave-one-out cross validation. Neural Computation, 18(4), 961–978.
Breiman, L. (2001). Random forests. Machine Learning, 45(1), 5–32.
Di, P., Wang, J., Zhang, Q., Yang, J., Chen, W., Pan, Z., . . . Jiao, S. (2017). The evaluation of basalt
tectonic discrimination diagrams: Constraints on the research of global basalt data. Bulletin of
Mineralogy, Petrology and Geochemistry, 36(6), 891–896.
Donders, A. R. T., Van Der Heijden, G. J., Stijnen, T., & Moons, K. G. (2006). A gentle introduction to
imputation of missing values. Journal of Clinical Epidemiology, 59(10), 1087–1091.
Enciso-Maldonado, L., Dyer, M. S., Jones, M. D., Li, M., Payne, J. L., Pitcher, M. J., . . . Rosseinsky, M. J.
(2015). Computational identification and experimental realization of lithium vacancy introduc-
tion into the olivine LiMgPO4. Chemistry of Materials, 27(6), 2074–2091.
Frane, J. W. (1976). Some simple procedures for handling missing data in multivariate analysis.
Psychometrika, 41(3), 409–415.
García, S., Ramírez-Gallego, S., Luengo, J., Benítez, J. M., & Herrera, F. (2016). Big data preproces-
sing: Methods and prospects. Big Data Analytics, 1(1), 9.
Golub, G. H., Heath, M., & Wahba, G. (1979). Generalized cross-validation as a method for choosing
a good ridge parameter. Technometrics, 21(2), 215–223.
Granitto, P. M., Furlanello, C., Biasioli, F., & Gasperi, F. (2006). Recursive feature elimination with
random forest for PTR-MS analysis of agroindustrial products. Chemometrics and Intelligent
Laboratory Systems, 83(2), 83–90.
Han, S., Li, M., Ren, Q., & Liu, C. (2018). Intelligent determination and data mining for tectonic
settings of basalts based on big data methods. Acta Petrologica Sinica, 34(11), 3207–3216.
Hannan, M. A., Arebey, M., Begum, R. A., Mustafa, A., & Basri, H. (2013). An automated solid waste
bin level detection system using Gabor wavelet filters and multi-layer perception. Resources,
Conservation and Recycling, 72, 33–42.
Howarth, G. H., & Harris, C. (2017). Discriminating between pyroxenite and peridotite sources for
continental flood basalts (CFB) in southern Africa using olivine chemistry. Earth and Planetary
Science Letters, 475, 143–151.
Jain, Y. K., & Bhandare, S. K. (2011). Min max normalization based data perturbation method for
privacy protection. International Journal of Computer and Communication Technology, 2(8),
45–50.
Li, C., Arndt, N. T., Tang, Q., & Ripley, E. M. (2015). Trace element indiscrimination diagrams. Lithos,
232, 76–83.
Li, M., Miao, L., & Shi, J. (2014). Analyzing heating equipment’s operations based on measured data.
Energy and Buildings, 82, 47–56.
Longstaff, I. D., & Cross, J. F. (1987). A pattern recognition approach to understanding the
multi-layer perception. Pattern Recognition Letters, 5(5), 315–319.
 BIG EARTH DATA 25

Luo, J., Wang, X., Song, B., Yang, Z., Zhang, Q., Zhao, Y., & Liu, S. (2018). Discussion on the method
for quantitative classification of magmatic rocks: Taking it’s application in West Qinling of Gansu
Province for example. Acta Petrologica Sinica, 34(2), 326–332.
Menze, B. H., Kelm, B. M., Masuch, R., Himmelreich, U., Bachert, P., Petrich, W., & Hamprecht, F. A.
(2009). A comparison of random forest and its Gini importance with standard chemometric
methods for the feature selection and classification of spectral data. BMC Bioinformatics, 10(1), 213.
Mitchell, T. M. (2005). Generative and discriminative classifiers: Naive Bayes and logistic regression.
Machine Learning. New York: McGraw Hill.
Patil, T. R., & Sherekar, S. S. (2013). Performance analysis of Naive Bayes and J48 classification
algorithm for data classification. International Journal of Computer Science and Applications, 6(2),
256–261.
Pearce, J. A. (1996). A user’s guide to basalt discrimination diagrams. Trace element geochemistry
of volcanic rocks: Applications for massive sulphide exploration. Geological Association of
Canada, Short Course Notes, 12, 79–113.
Pearce, J. A., & Cann, J. R. (1973). Tectonic setting of basic volcanic rocks determined using trace
element analyses. Earth and Planetary Science Letters, 19(2), 290–300.
Pedregosa, F., Varoquaux, G., Gramfort, A., Michel, V., Thirion, B., Grisel, O., . . . Duchesnay, É. (2011).
Scikit-learn: Machine learning in Python. Journal of Machine Learning Research, 12(10),
2825–2830.
Petrelli, M., & Perugini, D. (2016). Solving petrological problems through machine learning: The
study case of tectonic discrimination using geochemical and isotopic data. Contributions to
Mineralogy and Petrology, 171(10), 81.
Ren, Q., Wang, G., Li, M., & Han, S. (2019). Prediction of rock compressive strength using machine
learning algorithms based on spectrum analysis of geological hammer. Geotechnical and
Geological Engineering, 37(1), 475–489.
Sánchez-Muñoz, L., Müller, A., Andrés, S. L., Martin, R. F., Modreski, P. J., & de Moura, O. J. (2017).
The P-Fe diagram for K-feldspars: A preliminary approach in the discrimination of pegmatites.
Lithos, 272, 116–127.
Subasi, A., & Ercelebi, E. (2005). Classification of EEG signals using neural network and logistic
regression. Computer Methods and Programs in Biomedicine, 78(2), 87–99.
Taalab, K., Cheng, T., & Zhang, Y. (2018). Mapping landslide susceptibility and types using Random
Forest. Big Earth Data, 2(2), 159–178.
Townsend, J. T. (1971). Theoretical analysis of an alphabetic confusion matrix. Perception &
Psychophysics, 9(1), 40–50.
Ueki, K., Hino, H., & Kuwatani, T. (2018). Geochemical discrimination and characteristics of mag-
matic tectonic settings: A machine-learning-based approach. Geochemistry, Geophysics,
Geosystems, 19(4), 1327–1347.
Vermeesch, P. (2006). Tectonic discrimination of basalts with classification trees. Geochimica et
Cosmochimica Acta, 70(7), 1839–1848.
Wang, J., Chen, W., Zhang, Q., Jiao, S., Yang, J., Pan, Z., & Wang, S. (2017). Preliminary research on
data mining of N-MORB and E-MORB: Discussion on method of the basalt discrimination
diagrams and the character of MORB’s mantle source. Acta Petrologica Sinica, 33(3), 993–1005.
Zhang, Q. (1990). The correct use of the basalt discrimination diagram. Acta Petrologica Sinica, 2,
87–94.
Zhou, X., Chen, Z., & Chen, T. (1980). Composition and evolution of olivine and pyroxene in alkali
basaltic rocks from Jiangsu Province. Geochimica, 33(3), 253–262.
Zhou, Y., Chen, S., Zhang, Q., Xiao, F., Wang, S., Liu, Y., & Jiao, S. (2018). Advances and prospects of
big data and mathematical geoscience. Acta Petrologica Sinica, 34(2), 255–263.