Environmental Earth Sciences (2024) 83:244

https://doi.org/10.1007/s12665-024-11534-0

ORIGINAL ARTICLE

Improving permeability prediction via Machine Learning

in a heterogeneous carbonate reservoir: application to Middle
Miocene Nullipore, Ras Fanar field, Gulf of Suez, Egypt
Mostafa S. Khalid1 · Ahmed S. Mansour2 · Saad El‑Din M. Desouky1 · Walaa S. M. Afify3 · Sayed F. Ahmed4 ·
Osama M. Elnaggar1

Received: 9 October 2023 / Accepted: 3 March 2024

© The Author(s) 2024

Abstract
Predicting and interpolating the permeability between wells to obtain the 3D distribution is a challenging mission in reser-
voir simulation. The high degree of heterogeneity and diagenesis in the Nullipore carbonate reservoir provide a significant
obstacle to accurate prediction. Moreover, intricate relationships between core and well logging data exist in the reservoir.
This study presents a novel approach based on Machine Learning (ML) to overcome such difficulties and build a robust
permeability predictive model. The main objective of this study is to develop an ML-based permeability prediction approach
to predict permeability logs and populate the predicted logs to obtain the 3D permeability distribution of the reservoir. The
methodology involves grouping the reservoir cored intervals into flow units (FUs), each of which has distinct petrophysical
characteristics. The probability density function is used to investigate the relationships between the well logs and FUs to
select high-weighted input features for reliable model prediction. Five ML algorithms, including Linear Regression (LR),
Polynomial Regression (PR), Support Vector Regression (SVR), Decision Trees (DeT), and Random Forests (RF), have been
implemented to integrate the core permeability with the influential well logs to predict permeability. The dataset is randomly
split into training and testing sets to evaluate the performance of the developed models. The models’ hyperparameters were
tuned to improve the model’s prediction performance. To predict permeability logs, two key wells containing the whole res-
ervoir FUs are used to train the most accurate ML model, and other wells to test the performance. Results indicate that the RF
model outperforms all other ML models and offers the most accurate results, where the adjusted coefficient of determination
(R2adj) between the predicted permeability and core permeability is 0.87 for the training set and 0.82 for the testing set, mean
absolute error and mean squared error (MSE) are 0.32 and 0.19, respectively, for both sets. It was observed that the RF model
exhibits high prediction performance when it is trained on wells containing the whole reservoir FUs. This approach aids in
detecting patterns between the well logs and permeability along the profile of wells and capturing the wide permeability
distribution of the reservoir. Ultimately, the predicted permeability logs were populated via the Gaussian Random Function
Simulation geostatistical method to build a 3D permeability distribution for the reservoir. The study outcomes will aid users
of ML to make informed choices on the appropriate ML algorithms to use in carbonate reservoir characterization for more
accurate permeability predictions and better decision-making with limited available data.

Keywords Permeability prediction · Nullipore carbonate reservoir · Heterogeneity · Flow units · Machine learning ·
Hyperparameters tuning
Abbreviations
* Mostafa S. Khalid AI Artificial intelligence
mostafashafik579@gmail.com ANN Artificial neural networks
1
Production Department, Egyptian Petroleum Research
D Density
Institute, Cairo, Egypt DeT Decision trees
2
Faculty of Science, Alexandria University, Alexandria, Egypt
DT Delay time recorded by sonic log
3
FZI Flow zone indicator
Faculty of Education, Alexandria University, Alexandria,
Egypt
GRFS Gaussian Random Function Simulation
4
HFUs Hydraulic flow units
Rashpetco, Cairo, Egypt

Vol.:(0123456789)
244 Page 2 of 20
LR Linear regression
MAE Mean absolute error
ML Machine learning
MSE Mean squared error
Pdf Probability density function
PR Polynomial regression
phiE Effective porosity
RF Random forests
RQI Reservoir quality index
SVR Support vector regression
Vminerals Volume of minerals
Symbols
Fs Pore shape factor
LK Logarithm of permeability
R Pearson coefficient of correlation
R2adj Adjusted coefficient of determination
mright/left Number of instances in the right/left subset of
Decision Tree
Svgr Specific area per unit grain volume
T Tortuosity
∆t Interval transit time, µs/ft
Φ Porosity, fraction
Φz Normalized porosity
Introduction
Permeability is a crucial petrophysical parameter for res-
ervoir simulation. It is essential for selecting the optimum
development scenarios. It can be measured via core sam-
pling or pressure testing methods. However, these meth-
ods are limited, costly, and time-consuming. Thus, several
researchers tried integrating permeability with well logs
to obtain a continuous permeability profile along the res-
ervoir. Kozeny (1927) and Carman (1937) created the per-
meability correlation with formation porosity. This model
assumes that pores are cylindrical. However, pore shape
can vary from one unit to another within the reservoir.
Moreover, the model ignores the lack of a basic relation-
ship between porosity and permeability; as zones with
equal porosity but different permeability exist in the same
reservoir. Besides, some carbonate reservoirs constitute
low porosity and high permeability due to fractures. Both
depositional factors—such as pore geometry, grain size,
tortuosity-, and diagenetic ones—as cementation, dissolu-
tion, and fracturing-affect permeability. Subsequently, a
more reliable approach was needed to take into account
the fundamentals of geology and flow physics in porous
media.
Environmental Earth Sciences (2024) 83:244
Wendt et al. (1986), Balan et al. (1995), and Xue et al.
(1997) reported that integrating permeability with logs other
than porosity and using multiple linear regression analysis
increases the correlation between measured and predicted
permeability. This approach assumes a linear relationship
between permeability and influential well logs. However,
this is not the case in many reservoirs, especially in hetero-
geneous ones, where non-linear and complex relationships
exist between well logs and permeability.
To overcome such challenges, Machine Learning (ML)
has been extensively introduced and tested as a regression
tool for the prediction of reservoir permeability from well
logs (Akande et al. 2017; Zhu et al. 2017; Elkatatny et al.
2018; Okon et al. 2021; Male et al. 2020; Lv et al. 2021;
Kamali et al. 2022; Abbas et al. 2023; Matinkia et al. 2023;
Mahdy et al. 2024).
In some reservoirs, categorizing the reservoir into
hydraulic flow units (HFUs), where each unit has geo-
logical and petrophysical characteristics different from the
other, improves the permeability prediction. Amaefule et al.
(1993) presented the Flow Zone Indicator (FZI) concept to
group the reservoir into HFUs, where each unit has a similar
FZI. Several researchers integrated the FZI with well logs
via multiple regression analysis, artificial neural networks
(ANN), and adaptive neuro-fuzzy inference system to esti-
mate the FZI from logs, thereafter computed permeability
from FZI (Aminian et al.; 2003; Kharrat et al. 2009; Khalid
et al. 2020; Alizadeh et al. 2022; Djebbas et al. 2023).
Although ML-based models have been extensively used
for permeability prediction, there are significant challenges
and shortcomings in the application of these models to het-
erogeneous reservoirs. Most ML studies did not present a
systematic approach to predict permeability in complex
carbonate reservoirs along the wells profile to be further
populated in 3D. In the present study, a systematic novel
approach based on Machine Learning is presented to pre-
dict the permeability logs in the Nullipore heterogeneous
carbonate reservoir in Ras Fanar field using core and well
logs data. In this approach, the reservoir is divided into dif-
ferent HFUs. Five Machine Learning algorithms, namely
Linear Regression (LR), Polynomial Regression (PR), Sup-
port Vector Regression (SVR), Decision Trees (DeT), and
Random Forests (RF), were applied to integrate the core per-
meability data with well logging ones and their performance
was evaluated. The most accurate algorithm was applied to
predict permeability logs along the profile of wells. Contrary
to the existing models in the literature, the new approach
presented in this study is applied to two key wells containing
all the reservoir HFUs to train the algorithm. Other wells are
used as blind test wells for model validation. This approach
Environmental Earth Sciences (2024) 83:244
enables the model to detect the patterns between the input
and output data for the whole permeability variation range,
hence capturing the permeability heterogeneity of the reser-
voir. The study aims to (a) identify the reservoir HFUs from
core data, (b) analyze the quality of the reservoir in terms of
storage and flow capacities, and (c) develop an ML-based
permeability prediction approach to predict permeability
logs along the wells profile and populate the predicted logs
to obtain 3D permeability distribution of the reservoir. Fur-
thermore, the study provides a reference for predicting per-
meability in complex carbonate reservoirs, which can be fol-
lowed in other areas that have similar geological conditions.
Location and geology of the study area
The most prolific hydrocarbon province in Egypt is the Gulf
of Suez rift basin. It has 80% of oil reserves and gives 75%
of oil production in Egypt. Ras Fanar field is an oil field
Fig. 1  Location map of Ras Fanar field
Page 3 of 20 244
located on the offshore western side of the central province
of the Gulf of Suez (G.O.S), Egypt (Fig. 1). The field lies
3.5 km east of Ras Gharib shoreline in the Belayim dip prov-
ince of northeast direction; between latitudes 28° 13ʹ and 28°
18ʹ to the north, and longitudes 33° 11ʹ and 33° 17ʹ to the
east. The Middle Miocene Nullipore reservoir is the main
oil-producing unit in the field. It is equivalent to the Ham-
mam Faraun Member of the Belayim Formation. Belayim
formation represents a part of the Middle Miocene syn-rift
succession in the Ras Fanar field (Moustafa 1976).
Three depositional sequences characterize the rift stratig-
raphy of G.O.S, as follows: Pre-rift sequence (Paleozoic to
Late Eocene), syn-rift (Early to Late Miocene), and post-rift
(Post-Miocene). The Ras Fanar field was produced from an
NW–SE structural trap bounded by a major fault system to
the SW and tilted to NE. The Ras Fanar area sedimentary
succession ranges in age from Paleozoic to recent, as shown
in Fig. 2. The syn-rift succession is represented by Belayim
244 Page 4 of 20 Environmental Earth Sciences (2024) 83:244

Fig. 2  Lithostratigraphic column of Ras Fanar field. Modified after (El Naggar 1988)

formation at the base, South Gharib formation in the mid-
dle, and Zeit formation at the top (Souaya 1965; Hosny et al.
1986; Rateb 1988).
The Nullipore represents the main carbonate reservoir
unit in the Ras Fanar field. It contributes to about half of the
field production. Thiébaud and Robson (1979) introduced
the Nullipore reservoir as bioclastic Limestone exposed at
the G.O.S region, with frequent occurrence of reefs, corals,
and algae.
As a result of the rifting of the Suez Gulf, several
stratigraphic successions were developed on both sides
of the Gulf. Moreover, many grabens, half-grabens, and
horst blocks were created. Ras Fanar was a positive high-
land area during the Early Miocene and was subjected to
Environmental Earth Sciences (2024) 83:244 Page 5 of 20 244

severe erosion. In the adjacent lowland troughs, a thick
organic-rich shale sequence was deposited. The area was
submerged by a shallow sea during the Early Middle Mio-
cene. This allows the accumulation of thick algal-reefal
carbonate facies of the Nullipore reservoir. More arid con-
ditions exist by the end of the Middle Miocene, resulting
in vertical and lateral facies changes from carbonates to
alternative cycles of evaporates, siliciclastics, and car-
bonates of South Gharib and Zeit formations (Moustafa
1977; Thiébaud and Robson 1979; Chowdhary and Taha
1986; El Naggar 1988; Ouda and Masoud 1993; Khalil
and McClay 2001).
Materials and methodology
Four wells drilled in the Ras Fanar field have been assessed
in this study. The wells targeted the Middle Miocene Nul-
lipore reservoir. Routine core analysis (RCA) was performed
on 794 core plug samples from the four wells. RCA involves
porosity acquired by a helium porosimeter and horizontal
permeability measured by a permeameter. Conventional well
logs, comprising gamma-ray (GR), neutron (NPHI), density
(RHOB), and compressional slowness data in every 0.5 ft.
are available from the wells.

Select wells that have cored and logged

reservoir intervals with similar litho-facies

Select core porosity and permeability data

Group the reservoir into HFUs via the FZI approach

Select well logs that affect the permeability of each Import data to Python
HFU significantly via PDF

Group data into input features (influential

logs) and target (core permeability)

Random data split into training and testing

Train the ML algorithms with cross validation

and hyperparameters’ tuning

High R2adj, low MAE, and MSE

Test data validation

No
High R2adj, low MAE, and MSE
Yes

Train the model on data of wells containing the

reservoir HFUs

Check the trained model accuracy by predicting permeability

in the blind test wells

Predicting permeability logs for the logged intervals of the studied wells

Populate the permeability logs via geostatistics to create the 3D permeability distribution

Fig. 3  Flow chart of the proposed methodology to predict and distribute permeability logs
244 Page 6 of 20
The following steps were followed to achieve the aim of
the study: (1) reservoir litho-facies were determined at the
four wells, (2) wells that have cored and logged reservoir
intervals with similar litho-facies were selected, (3) Avail-
able cores from the selected wells were analyzed to identify
the hydraulic flow units (HFUs) in the reservoir, relying on
the concept of flow zone indicator (FZI), (4) Core-log depth
match was performed, (5) well logs, including gamma-ray,
resistivity, Neutron, bulk density, sonic, were analyzed at the
selected wells, (6) Five logs were initially selected as input
features to build the permeability model. The logs include
sonic, density, neutron, effective porosity, and volume of
minerals logs. The probability density function (PDF) was
used to investigate the relationships between the selected
logs and FUs, (7) the influential logs and the reservoir FUs
were integrated with permeability via five Machine Learning
algorithms to predict permeability from the logs.
The dataset was split into training and testing sets to eval-
uate the performance of each model via three evaluation
metrics: mean absolute error (MAE), mean squared error
(MSE), and adjusted coefficient of determination (R2adj).
Hyperparameters of the models were tuned to choose the
optimal values of parameters that improve the models' per-
formance and achieve high accuracy. The most accurate
model was selected to predict the permeability logs of the
studied wells. The data of two wells containing the whole
reservoir FUs were used to train the model. The model accu-
racy was checked by using other wells as blind test wells.
The developed model was used to predict the permeability in
logged un-cored intervals. The predicted permeability logs
were populated via geostatistics to create the 3D distribution
of reservoir permeability. Figure 3 indicates the workflow
used in this study for predicting permeability logs via ML.
Hydraulic flow units
Petroleum geologists and engineers have recognized the
need to define geological/engineering units to shape the
description of reservoir zones as storage containers and con-
duits for fluid flow. Depositional and diagenetic processes
result in the formation of different flow units in the reservoir.
A flow unit (FU) was defined by Bear (1988) as a repre-
sentative reservoir volume that has the same geological and
petrophysical characteristics. Hearn et al. (1984) defined the
FU as the reservoir portion that is continuous laterally and
vertically and has similar bedding characteristics, porosity,
and permeability.
To identify the trends between porosity and permeability,
Amaefule et al. (1993) presented the concept of Flow Zone
Indicator (FZI). The modified form of the Kozeny-Carman
equation for estimating permeability is given by:
Environmental Earth Sciences (2024) 83:244
1 Φ3
K = 1014.24
Fs T 2 Svgr
2 (1)
(1 − Φ)2
where K is the permeability, md, Fs is the pore shape factor,
T is the tortuosity of the path of flow, Svgr is the specific area
per unit grain volume, and Φ is the effective porosity, frac-
tion (Kozeny 1927; Carman 1937).
Since it is difficult to determine Fs , Svgr , and T, Amaefule
et al. (1993) defined the FZI parameter as the square root of
( F .T12 .S2 ) and developed an equation to calculate FZI from
s vgr
core data, as follows:
( )
FZI = RQI∕Φz (2)
√
RQI = 0.0314 ∗ K∕Φ (3)
Φz = Φ∕(1 − Φ) (4)
where RQI is the reservoir quality index, µm, and Φz is the
normalized porosity.
The calculated FZI is used to group the reservoir into
different FUs, through the following formula:
Log RQI = log FZI + log Φz (5)
The base of categorizing the reservoir into flow units is
identifying clusters that achieve unit slope straight lines on
the plot (log RQI vs. log Φz ), where each cluster has unique
geological and petrophysical characteristics (porosity and
permeability) (Tiab and Donaldson 2015).
Machine learning
In this study, we aim to integrate the core permeability of
each FU with the well logs via Machine Learning to predict
permeability logs along the wells profile.
Machine Learning (ML) evolved as a subfield of artifi-
cial intelligence (AI), including self-learning algorithms
that derive knowledge from data, instead of requiring
humans to manually derive rules and build models, to
improve the performance of predictive models, and make
data-driven decisions. ML is considered the cornerstone in
the new era of big data. It has been successfully applied in
the Geoscience field to predict different reservoir proper-
ties (Raschka and Mirjalili 2019; Al Khalifah et al. 2020;
Alizadeh et al. 2022).
This study focuses on a specific field of ML called pre-
dictive modeling of a continuous variable (permeability).
Predictive modeling focuses on developing models that cre-
ate accurate predictions at the expense of explaining why
Environmental Earth Sciences (2024) 83:244
the predictions are made. Five Machine Learning (ML)
algorithms were implemented via Python programming
language. The algorithms involve Linear Regression (LR),
Polynomial Regression (PR), Support Vector Regression
(SVR), Decision Trees (DeT), and Random Forests (RF).
Linear regression
Linear regression is a statistical method used to predict the
value of a response (dependent variable) from known values
of one or more independent variables (regressors). Transfor-
mation of data may be required to achieve a better fit between
variables. The general form of the equation is:
Y = bo + Σ bn. Xn (6)
where Y is the dependent variable, Xn is the independent
variable/s, bo is the intercept, and b’s are the regression
coefficients.
In this study, core permeability is the dependent variable,
while the FU and influential well logs are the independent
variables.
Polynomial regression
If the data of the model is more complex than a linear
straight line, the algorithm of Polynomial Regression (PR)
can be effective to fit the non-linearity. The algorithm
involves adding powers of each feature as new features and
thereafter trains a linear model on the new features. Moreo-
ver, PR can find relationships between features by adding
combinations of features up to the given degree. For exam-
ple, if the model has two input features a and b, Polynomial
features with degree 3 will not only add a2, a3, b2, and b3, but
also the combination ab, a2b, and ab2 (Géron 2022).
Support vector regression
One of the versatile Machine Learning algorithms that are
capable of performing linear or nonlinear classification and
regression issues is the Support Vector Machine (SVM).
SVM is particularly well suited for complex but small- to
medium-sized datasets for classification issues (Géron
2022).
In this article, we are concerned with Support Vector
Regression (SVR) to predict permeability. SVR differs from
Linear Regression (LR) in searching for a hyperplane that
best fits the data points in a continuous space, instead of fit-
ting a line to the data points. Besides, in contradiction with
LR which aims to minimize the sum of squared errors, the
objective function of SVR is to minimize the coefficients
of the variables and give the flexibility to define how much
Page 7 of 20 244
error is acceptable in the model. The error term is handled
in the constraints, where the absolute error is set less than
or equal to a specified margin, named the maximum error
(epsilon, ɛ). The epsilon must be tuned to gain the desired
accuracy of the model. The “C” hyperparameter controls
the balance between samples in the decision boundary and
margin violations (outliers).
To tackle non-linear problems, SVR maps the input fea-
tures into a higher dimension space through a kernel trick.
The kernel is a function that transforms the non-linear pat-
tern to a linear one in a higher dimension space. Polynomial,
sigmoid, and radial basis function (RBF) kernels can achieve
this task. One can select the kernel function type according
to the trends between the input features and the target vari-
able. In this study, linear, polynomial, and RBF kernels were
used sequentially, and the one that achieves the highest accu-
racy was selected to develop the SVR permeability model.
Since SVR relies on distances between data points, it is
beneficial to scale the input features to ensure that they fit
into the same range. In this study, the features are stand-
ardized by removing the mean and scaling to unit variance
(features range from − 1 to 1) (Géron 2022).
Decision trees
Decision trees (DeT) is a ML algorithm that can fit complex
datasets, and perform classification and regression tasks.
DeT are the basic components of Random Forests. DeT
aims to develop a model that predicts a target variable by
learning simple decision rules inferred from data features.
The algorithm splits the training set into two subsets using
a single feature (k) and a threshold (tk). The pair (k, tk) that
produces the least mean squared error (MSE) is considered
the best split. The prediction is the average target value of
the training instances associated with the leaf node. The cost
function that the algorithm tries to minimize is given by:
( ) m mright
J k, tk = left MSEleft + MSEright (7)
m m
where “mright/left” is the number of instances in the right/left
subset.
The tree starts at the root node (depth 0 at the top): this
node assumes certain condition. In other words, the node
asks whether a feature is smaller than a certain value. If the
data sample satisfies this condition, it will move down to the
root’s left child node (depth 1, left) and so on till it reaches
the leaf node (last node in the tree on the left side). On the
other hand, if the sample is greater than the value of the root
node, it will move to the root’s right child node (depth 1,
right), and so on till it reaches the leaf node (Géron 2022).
244 Page 8 of 20 Environmental Earth Sciences (2024) 83:244

Particularly, DeT does not require feature scaling or
centering at all. Moreover, the trees do not assume the
linearity of data. The tree adapts itself to the training
data. To avoid overfitting, hyperparameters of the tree
must be regularized, particularly its depth and the mini-
mum number of samples that can be split at each node
(Géron 2022).
Results and discussion
Core data
Nullipore reservoir penetrated by four wells in Ras Fanar
field is mainly dolomitic Limestone with considerable
amounts of Anhydrite and minor intercalations of Shale.

Random forests

A Random Forest (RF) is an ensemble of decision trees.

The concept of RF is to average multiple decision trees
that individually suffer from high variance to build a more
robust model that has a better generalization performance.
The algorithm can be summarized in four steps: choose “n”
samples from the training data randomly, grow a decision
tree from the selected samples via selecting some features
randomly and splitting the node using the feature that pro-
vides the best split, repeat steps 1 & 2 k-times, and finally,
aggregate the prediction of each tree and take the average
value (Raschka and Mirjalili 2019).

Fig. 4  A plot of core porosity vs. logarithm of core permeability of

the four wells
Cross‑validation

The accuracy and prediction performance of ML models

Table 1  Descriptive statistics Core parameters Phi LK
can be assessed using various techniques of cross-valida- of core porosity and logarithm
tion, such as random subsampling and K-fold cross-vali- of permeability of the studied No. of samples 794 794
dation. Random subsampling is carried out by splitting the wells
Mean 0.213 1.377
original dataset into two parts: training and testing sets. Median 0.222 1.613
The ML algorithm is trained on the first part, makes pre- Mode 0.27 − 1.7
dictions on the second part and evaluates the predictions Std. deviation 0.091 1.255
against the expected results. This prevents the problem Variance 0.008 1.575
of overfitting, assures the external prediction and gives Minimum 0.009 −2
more trust for the prediction given different datasets with Maximum 0.44 3.98
the same parameters. K-fold cross-validation is adopted
by partitioning the training dataset into k-folds (e.g. k = 5,
or k = 10). Each partition is called a fold. “k−1” folds are
used for training the algorithm and one is held back for
model validation. This procedure is repeated so that each
fold is given a chance to be used for testing. The dataset
size controls the number of folds. A small number of folds
leads to large bias and small variance with reduced com-
putation time. On the other hand, a large number of folds
leads to large variance and small bias with large com-
putation time. Using tenfold cross-validation is a com-
mon choice. The performance measure is then the average
of the values computed in the loop (Al-Mudhafar 2016;
Brownlee 2016).

Fig. 5  A plot of log normalized porosity vs. log RQI of the core data
Environmental Earth Sciences (2024) 83:244 Page 9 of 20 244

from the other. Hence, grouping the reservoir into different

FUs is essential. The approach of FZI was applied. Figure 5
shows a plot of log phiz vs. log RQI of the core data. The
figure indicates the existence of two FUs, where each unit
has a unit slope and mean FZI (0.51 and 2.42, respectively).
This reflects that each unit has fluid flow properties different
from the other.
A plot of porosity vs. log of permeability for each FU
is shown in Fig. 6. It is evident from the figure that the
porosity–permeability correlation is improved relative to
Fig. 4, where R2 is 0.74 for the first FU and 0.58 for the
second one.
The range of FZI, average value of FZI, porosity, and
Fig. 6  A plot of porosity vs. log of permeability for each FU permeability of each unit are summarized in Table 2. The
table indicates the notable difference in average perme-
ability between the two FUs, hence the difference in their
Table 2  Average values of FZI, porosity, and permeability of the FUs fluid flow capacity, where the average permeability of the
first FU is 0.19, whereas that of the second FU is 1.96.
FU 1 2
This means that the second FU with a higher FZI (2.42)
FZI range 0.07–0.99 0.99–18.23
has better reservoir quality and percolation capacity than
Avg. FZI 0.52 2.88
the first FU (FZI = 0.51).
Avg. porosity 0.2 0.23
Avg. permeability 0.19 1.96
Sensitivity analysis of well logs
A plot of core porosity vs. logarithm of permeability (LK) Five well logs were initially selected to create the perme-
of the cored intervals of the four wells is shown in Fig. 4. ability model, as follows: sonic log, bulk density (RHOB),
Descriptive statistics of core porosity and permeability are neutron porosity log (NPHI), effective porosity (phiE), and
summarized in Table 1. The figure indicates a very poor cor- volume of minerals log (Vminerals). It must be highlighted
relation (R2 = 0.4286) with high a degree of scatter and sam- that the effective porosity log was developed by combining
ples of the same porosity but different permeability. This is a the three porosity logs; neutron, density, and sonic. Besides,
result of the existence of more than one FU in the reservoir, the volume of minerals log was created from the density log.
where each unit has rock and fluid flow properties different

Table 3  Statistical parameters Well logs Mean Median Mode Std. deviation Variance Minimum Maximum
of well logs of the first FU
DT 79.869 77.8 68.3 18.241 332.742 39.5 139.4
D 2.436 2.408 2.408 0.177 0.031 2.065 2.921
N 0.331 0.348 0.367 0.089 0.008 0.037 0.477
phiE 0.241 0.245 0.295 0.085 0.007 0.021 0.415
Vminerals 0.746 0.707 0.686 0.158 0.025 0.478 0.996

Table 4  Statistical parameters Well logs Mean Median Mode Std. deviation Variance Minimum Maximum
of well logs of the second FU
DT 90.42 87.2 79.6 24.493 599.919 21.7 182.1
D 2.382 2.355 2.309 0.132 0.017 2.076 2.888
N 0.333 0.335 0.341 0.073 0.005 0.032 0.55
phiE 0.266 0.284 0.3 0.075 0.006 0.018 0.44
Vminerals 0.728 0.712 0.68 0.145 0.021 0.327 0.981
244 Page 10 of 20
Fig. 7  The probability density functions of the selected logs for the reservoir FUs a sonic log, b density log, c neutron porosity, d effective
porosity log, and e volume of minerals log
Shale volume is not considered because its volume is very
low in the reservoir, hence is discarded. On the other hand,
sonic, neutron, and bulk density logs are raw logs. The sta-
tistical parameters of the logs of the two FUs are shown in
Tables 3 and 4, respectively.
The probability density function (PDF) was used to inves-
tigate the relationships between the selected logs and reser-
voir FUs. PDF of each log is plotted and compared. If the
two curves are distinctly separated, the log is considered a
good regressor and can be used in the predictive model. On
Environmental Earth Sciences (2024) 83:244
the other hand, if the curves are overlapping and forming one
cluster with almost the same mean, the log is not considered
a good regressor, hence discarded from the model.
The density functions of the sonic log are shown in
Fig. 7a. The second curve (FU 2) has a wider range of inter-
val transit time than the first curve. This is a result of the
higher porosity and permeability of the second flow unit
than the first one. Therefore, the sonic log is a good regres-
sor and can be used in the model.
Environmental Earth Sciences (2024) 83:244 Page 11 of 20 244

Figure 7b shows the density functions of the density log. imported as a feature to get one model for the whole reser-
The two curves are clearly separated, with different means, voir, instead of getting a model for each flow unit. Figure 8
where the second curve has a lower density (due to higher shows a heat map of the well logs and LK for the two FUs
porosity and permeability) than the second curve. Conse- of the reservoir based on the Pearson correlation coefficient
quently, the density log is good a regressor and can be used (R). The figure indicates that phiE and DT logs have high
in the model. positive R with LK for the two flow units (R = 0.73, 0.74,
The density functions of the neutron log of the two flow 0.63, and 0.7, respectively) for the two flow units, while
units are shown in Fig. 7c. The two curves of the two flow D has a high negative correlation (R = − 0.62, and − 0.63,
units are very similar with the same mean and are not dis- respectively).
tinctly separated, hence no relation exists between neu- The dataset was randomly split into 80% training (583
tron porosity and permeability as the log gives different data samples) and 20% testing sets (145 data samples). The
responses to the same permeability. So, the neutron log is random generator seed was set to “60” to better compare
discarded from the model. the models.
The density functions of the effective porosity log are In the case of SVR, DeT, and RF models, a grid search
shown in Fig. 7d. The two curves are separated. The first (LaValle et al. 2004) was conducted to select the optimum
curve has a lower mean value of porosity than the second hyperparameters that provide better performance. The grid
curve. Subsequently, the effective porosity log is a good search function searches for various values of the model
regressor and can be used in the model. hyperparameter/s. The range of hyperparameters that have
The volume of minerals log involves the volumes of cal- been tuned and that achieved the highest accuracy are shown
cite, dolomite, and anhydrite (the main minerals in the res- in Table 5.
ervoir). The density functions of the minerals log are shown
in Fig. 7e. The two curves are similar and not distinctly sepa-
rated, hence the log is discarded from the model.
According to the PDF, only sonic, density, and effective Table 5  Ranges of hyperparameters that have been tuned, and best
porosity logs can determine the reservoir FUs and can be hyperparameters of SVR, DeT, and RF models
used for building the permeability model. Model Hyperparameter Hyperparameter Best
search range hyperpa-
rameters
Core‑logs data integration
SVR Epsilon 0.001–1 0.001
Core permeability and the influential logs data were C 1–200 100
imported into Python. The dataset was grouped into input DeT Maximum depth (2–10) 5
features and target variable. FU, Sonic, Density (D), and Minimum samples split (5–50) 25
effective porosity (phiE) logs are the input features, whereas RF Number of estimators (2–100) 50
core permeability (LK) is the target variable. FU was Maximum depth (2–10) 6

Fig. 8  Heat map of well logs

and permeability of the reser-
voir flow units a heat map of
FU 1, and b heat map of FU 2
244 Page 12 of 20 Environmental Earth Sciences (2024) 83:244

Fig. 9  Comparison of performance of kernel tricks of SVR of training and testing sets

Fig. 10  A plot of the logarithm of predicted permeability and measured core permeability of the five ML models for the training sets
Environmental Earth Sciences (2024) 83:244 Page 13 of 20 244

Evaluation of prediction accuracy of ML models Adjusted R2 is a statistical metric used to evaluate the good-
ness of fit of a regression model. It takes into account only the
One or more evaluation metrics must be used to evaluate the significant predictors that explain the variability in the data and
performance of any ML model. In this study, three evalua- improve the model performance. It is be expressed by:
tion metrics were used to monitor the permeability prediction
SSE∕(n − p)
accuracy: Mean absolute error, mean squared error (MSE), R2adj = 1 − (10)
and adjusted coefficient of determination (R2adj). MAE is the SST∕(n − 1)
arithmetic average of the absolute errors between true values where SSE is the error sum of squares, n is the number of
and predicted ones, where: samples, p is the number of predictors, and SST is the total
1 ∑| sum of squares.
MAE = ̈|
|Y − Υ| (8)
n
where Y is the logarithm of core permeability (LK), ϔ is the Performance of ML models
predicted logarithm of permeability, and n is the number of
samples. In this section, the performance of the permeability predic-
MSE is the average squared difference between true and tion of LR, PR, SVR (with kernel trick that provides the
predicted values, where: best performance), DeT, and RF models are evaluated and
1 ∑( )2 compared to core permeability for both training and testing
MSE = Y − Ϋ (9) sets. Performance of the linear, polynomial, and radial basis
n

Fig. 11  A plot of the logarithm of predicted permeability and measured core permeability of the five ML models for the testing sets
244 Page 14 of 20
Fig. 12  Validation metrics of
permeability prediction of the
five ML models for the training
and testing sets
function kernel tricks of SVR for both training and testing
sets is shown in Fig. 9. It is observed that RBF kernel trick
outperforms the linear and polynomial tricks, where R2adj is
0.77, MAE is 0.34, and MSE is 0.29 for both training and
testing sets, while in case of linear trick, R2 is 0.66, MAE is
0.44, and MSE is 0.37 for both sets. Results of the polyno-
mial trick show R2 = 0.67, MAE = 0.44, and MSE = 0.42 for
both sets. Consequently, the RBF trick is used to build the
SVR permeability model.
Figures 10 and 11 show the logarithm of predicted perme-
ability vs. the measured core permeability of the training and
testing sets of the five ML models, respectively. Figure 12
indicates the evaluation metrics (R2adj, MAE, and MSE) of
the training and testing sets of the five models.
It is observed that poor correlation and high error
appear in the case of the LR model where R2adj is 0.69,
MAE is 0.44, and MSE is 0.36 for both the training
and testing sets. The data samples are away from the
45-degree line (the farther the data is away from the
Environmental Earth Sciences (2024) 83:244
45-degree line, the lower the prediction accuracy, and
vice versa). This can be attributed to the complex non-
linear relation between the well logs and the permeability
that the LR cannot capture since it assumes a linear rela-
tion between variables. Better correlation and lower error
than the LR are obvious in the case of the SVR model,
where R 2adj is 0.77, MAE is 0.34, and MSE is 0.29 for
both the training and testing sets. This is attributed to the
ability of SVR to track the non-linearity between vari-
ables via the radial basis function kernel trick. The per-
formance of the PR model is slightly better, where R2adj is
0.81 for the training set and 0.79 for the testing set, MAE
is 0.38, and MSE is 0.29 for both sets. PR tries to track
the non-linearity by increasing the polynomial degree of
the input features (degree 5) in this case offers better per-
formance than other polynomial degrees), hence correla-
tion increases. The performance of the DeT model is very
close to that of PR, where R2adj is 0.81 for the training set,
0.78 for the testing set, MAE is 0.39, and MSE is 0.28
Environmental Earth Sciences (2024) 83:244
Fig. 13  Comparison of the loga-
rithm of predicted permeability
and core permeability of the
train wells a train well 1, and b
train well 2
for both sets. RF model provides the highest correlation
and the least error among other ML models, where R2adj
reaches 0.87 for the training set and 0.82 for the testing
set, MAE is 0.32 for both sets, and MSE is 0.19 for both
sets. The RF cross plot indicates that the data samples are
closer to the 45-degree line than other models. RF pro-
vides high tree diversity via searching for the best feature
among a random subset of features (not the whole subset,
as DeT does), hence increasing the chance of determin-
ing the complex relationships between the features (well
logs) and target variable (permeability), hence providing
the best accuracy among all other models.
Page 15 of 20 244
Predicting permeability in the studied wells
Since the RF algorithm provides the most accurate predic-
tion results, it is used to predict the permeability logs in the
studied wells. A new approach is presented for prediction,
where two wells involving the two FUs were considered as
key wells to train and develop the RF model, and the other
two wells as blind test wells to evaluate the model perfor-
mance. The comparison between the logarithm of predicted
permeability and core permeability for the train wells, and
the test wells is shown in Figs. 13a, b, 14a, b, respectively.
Overall, the two figures indicate a good match between the
244 Page 16 of 20
Fig. 14  Comparison of the loga-
rithm of predicted permeability
and core permeability of the test
wells a test well 1, and b test
well 2
predicted permeability and core permeability for the four
wells. The approach of selecting wells constituting the
reservoir FUs to train the RF model enables the model to
select input and output data for the whole reservoir FUs.
This enables the model to detect the patterns between the
input and output data for the whole permeability variation
range, hence capturing the permeability heterogeneity of the
reservoir.
It must be highlighted that some high permeability values
are underestimated by the model since the model ignored the
higher values while fitting the pattern in the data, and such
performance occurs at the expense of the model’s ability to
fit the test (unseen) data. If the model fits the whole data-
set that has a wide range of values, the overfitting problem
Environmental Earth Sciences (2024) 83:244
will occur. Cross-validation was adopted and the pertinent
hyperparameters were tuned for their optimized values to
prevent this problem. This helps to apprehend the perme-
ability heterogeneity and develop the best performing pre-
dictive model.
The developed RF model was used to predict the perme-
ability logs for the logged uncored intervals of the reservoir
for the four wells. The permeability logs of the four wells
are shown in Fig. 15.
The wells data was imported in petrel software. The
predicted permeability logs were upscaled and populated
in the geological model by setting the appropriate vari-
ogram model and applying the Gaussian Random Func-
tion Simulation geostatistical method (GRFS). GRFS is
Environmental Earth Sciences (2024) 83:244
Fig. 15  The permeability logs of the whole logged reservoir intervals for the studied wells
a stochastic method that can produce local variation and
reproduce input histograms. It honors well data, distribu-
tions of inputs, variogram, and trends. Figure 16 indicates
the histogram of the K-log and upscaled log. It is evident
from the figure that the upscaled data honors the input data,
where 2.4% of data is > 1 md, 22% is between 3 and 9 md,
39% is between 30 and 90 md, 31.7% is between 300 and
900 md and 4.9% is > 2000 md. The parameters of the
developed permeability model are summarized in Table 6.
Figure 17 shows the 3D permeability distribution of the
reservoir.
Page 17 of 20 244
Summary and conclusions
This study provides a systematic approach for predicting
and distributing permeability logs from conventional well
logs via Machine Learning in the Middle Miocene Nul-
lipore carbonate reservoir. Nullipore reservoir is highly
heterogeneous with wide permeability distribution. Cat-
egorizing the cored intervals into flow units improves the
reservoir characterization and permeability prediction. In
this study, five ML algorithms were applied to integrate
the core permeability of each flow unit with the influential
244 Page 18 of 20
Fig. 16  Histogram of the K-log
and upscaled log
well logs, and their performance was evaluated. The mod-
els involve Linear Regression (LR), Polynomial Regres-
sion (PR), Support Vector Regression (SVR), Decision
Trees (DeT), and Random Forests (RF). Cross-validation
of the dataset and hyperparameters’ tuning of the mod-
els reveals that RF is the most powerful ML model in
tackling the complex non-linear relationships between
the influential well logs and permeability, based on three
evaluation metrics (R2adj, MAE, and MSE). Splitting the
data into train and test sets allows for producing exterior
prediction given the test dataset rather than prediction on
Table 6  Parameters of the permeability model
Method Property Variogaram
Gaussian random function simulation Permeability Spherical
Environmental Earth Sciences (2024) 83:244
the same data (interior prediction). A new approach is
presented to predict the permeability logs in each well.
The approach involves training the RF model on the core
and logging data of two wells containing all the reservoir
flow units and using the other wells as blind test wells.
This aids in capturing the heterogeneity of reservoir per-
meability. Gaussian Random Function Simulation geosta-
tistical method was used to populate the predicted per-
meability logs to obtain 3D distribution for the reservoir
permeability.
Major direction range Minor direction range Vertical range
725 725 82.2
Environmental Earth Sciences (2024) 83:244
Fig. 17  3D distribution of permeability of Nullipore reservoir
Author contributions Mostafa Khalid: conceptualization, method-
ology, writing, software, programming language. Ahmed Mansour:
supervision, visualization, writing—review and editing, validation.
Saad El-Din Desouky: review and editing. Walaa Afify: supervision,
visualization, review, and editing. Sayed Ahmed: visualization, review,
and editing. Osama Elnaggar: review and editing.
Funding Open access funding provided by The Science, Technology &
Innovation Funding Authority (STDF) in cooperation with The Egyp-
tian Knowledge Bank (EKB).
Data availability The data is confidential.
Declarations
Conflict of interests The authors confirm that they have no competing
financial interests or personal relationships that could have appeared to
influence the work reported in this paper.
Open Access This article is licensed under a Creative Commons Attri-
bution 4.0 International License, which permits use, sharing, adapta-
tion, distribution and reproduction in any medium or format, as long
as you give appropriate credit to the original author(s) and the source,
provide a link to the Creative Commons licence, and indicate if changes
were made. The images or other third party material in this article are
included in the article's Creative Commons licence, unless indicated
otherwise in a credit line to the material. If material is not included in
Page 19 of 20 244
the article's Creative Commons licence and your intended use is not
permitted by statutory regulation or exceeds the permitted use, you will
need to obtain permission directly from the copyright holder. To view a
copy of this licence, visit http://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/.
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