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Файл:Ординатура / Хирургия / Библиотека им академика М.И. Перельмана / Книга_5606_Библиотеки_им_академика_М_И_Перельмана.pdf
X
- •Foreword
- •Acknowledgments
- •Contents
- •1.1 Structure-Based Drug Discovery (SBDD)
- •1.2 Ligand-Based Drug Design (LBDD)
- •1.3 Echoes from the Past, Visions from the Future
- •References
- •1 Introduction
- •2.2 Second Step: Data Curation
- •2.4 Fourth Step: Updating and Maintenance
- •2 Databases and Curation
- •8 Perspectives
- •9 Conclusion
- •References
- •1 Introduction
- •2.1 Making and Matching Protein Models
- •2.2 Simulating Protein Movements
- •2.3 Analyzing Changes in Protein Shape
- •3 Pharmacogenomics in Drug Development
- •4 Case Studies of Genomics-Based Drug Design
- •References
- •1 Historical Background
- •1.1 Timeline
- •2 Methodology Overview
- •2.1 Neural Networks
- •2.1.1 Perceptron
- •2.1.2 Multilayer Neural Networks
- •2.1.3 Types of Neural Networks
- •Feedforward
- •Recurrent Neural Networks
- •LSTM
- •2.2 Deep Learning
- •3 Using Machine Learning
- •3.2 Data Collection
- •3.3 Data Preprocessing
- •3.4 Model Selection
- •3.5 Model Training
- •3.6 Validation
- •3.7 Tuning
- •3.8 Prediction
- •4 Limitations
- •4.1 Bias
- •4.3 Interpretability
- •4.4 Computational Cost
- •4.5 Data Dependency
- •4.6 Robustness
- •5 Applications in Drug Discovery
- •5.2 Lead Discovery
- •5.3 Preclinical and Clinical Development
- •6 Resources and Tools
- •7 Challenges and Perspectives
- •7.1 Future Trends
- •9 Conclusions
- •References
- •1 Historical Background
- •1.1 Applications in Drug Discovery
- •2 Validations and Controls
- •2.1 Internal Validation
- •2.2 External Validation
- •2.3 Relative Cluster Validation
- •3 Challenges and Perspectives
- •4 Conclusions
- •References
- •1 Historical Background
- •2 OECD Principles
- •2.1 A Defined Endpoint
- •2.2 An Unambiguous Algorithm
- •2.5 A Mechanistic Interpretation, if Possible
- •3 Software and Tools
- •4 Validations and Controls
- •4.1 Internal and External Validation
- •4.1.1 Regression Metrics
- •4.2 Applicability Domain
- •4.3 Randomization Tests
- •5 Interpretation
- •6 Practical Advice During QSAR Modeling
- •7 Application
- •8 Challenges and Perspectives
- •References
- •1 Molecular Docking
- •2 Advances in Scoring Functions and Search Algorithms
- •2.2 Critical Characteristics of Search Algorithms
- •2.3 Docking Programs and Scoring Functions
- •3 Calculations Performed During Docking Simulations
- •4 Essential Components for a Good Docking Program
- •5 Limitations of the Docking Technique
- •6 Validation of Docking Results
- •7 Inappropriate Use of Validation Methods in Docking
- •9 Use of Machine Learning in Molecular Docking
- •11 Challenges
- •12 Conclusions
- •References
- •3 System Preparation for MD Simulations
- •3.1 Solvation and Microensemble
- •3.2 Force Fields: General Concept and Relevant Choices
- •3.3 The Concept of Replicas and Timescale
- •4.1.2 Protein Root Mean Square Fluctuation (RMSF)
- •4.1.4 Protein Secondary Structure Analysis
- •4.1.5 Principal component Analysis (PCA)
- •4.1.6 Markov State Modelling
- •4.1.7 Distance Calculations
- •4.1.8 Angle and Plane Calculations
- •4.2.2 Distances and Ligand-Induced Geometry Rearrangements
- •4 Molecular Dynamics Analysis
- •4.1 Protein Perspective
- •4.1.1 Protein Root Mean Square Deviation (RMSD)
- •4.3 Ligand Perspective
- •4.3.1 Ligand Properties
- •4.3.2 Ligand Root Mean Square Deviation
- •4.3.3 Ligand Root Mean Square Fluctuation
- •4.3.4 Angles and Dihedrals
- •5.1 Protein Structure Prediction and Preparation
- •5.2 Molecular Docking
- •6 Concluding Remarks and Outlook
- •Glossary
- •References
- •1 Introduction
- •2.1 MDeNM
- •2.2 Collective Molecular Dynamics (coMD)
- •2.3 ClustENM and ClustENMD
- •3 Ensemble Docking
- •References
- •1 Introduction
- •1.1 Advantages, Disadvantages, Innovations, and Challenges
- •1.2 Recent Advances in Accessible FEP Software Tools
- •1.3 Applications of FEP in Industry and Consortiums
- •2 Expanding the Potential of FEP Calculations
- •2.1 Validating Binding Poses
- •2.2 Dealing with Solvent
- •2.3 FEP and Allostery
- •2.4 FEP and Covalent Ligands
- •2.5 Applications of FEP in Scaffold Hopping
- •2.6 Positional Analogue Scanning
- •2.7 Combinations and Alternative Approaches
- •3 Machine Learning for FEP
- •3.4 Implications for ML in FEP Calculations
- •4 Final Considerations
- •5 First Steps to FEP Simulations
- •References
- •1 Background
- •2 Ultra-Large Screening Libraries and Chemical Spaces
- •3.1 Implications of Dataset Size
- •4 Ligands on the Ultra-Large Scale
- •4.1 Ultra-Large 2D Similarity Searches
- •7 Challenges and Future Perspectives
- •7.1 Hit Triage: An Old Problem on a New Dimension
- •8 Conclusions
- •Appendix
- •References
- •1 Introduction
- •2 Enzymatic Activity Evaluations
- •3 Cytotoxicity Evaluation and Cell Viability
- •4 Antiviral Assays in Experimental Validation
- •6 In Vivo Evaluation of Compounds
- •7 Conclusions
- •References
- •1 Introduction
- •3.1 Data Collection
- •3.2 Data Preprocessing
- •3.4 Model Choice
- •3.5 Model Training
- •3.6 Model Assessment
- •3.7 External Validation
- •3.8 Implementation and Availability
- •3.9 Continuous Update
- •5 Conclusions and Perspectives
- •References
- •1 Experimental Approaches to Obtain Protein Structure
- •1.1 X-Ray Crystallography
- •1.2 Nuclear Magnetic Resonance
- •1.3 Cryo-EM
- •1.4 Hybrid Methods
- •2 Modeling Approaches to Obtain Protein Structure
- •2.1 Homology Modeling
- •2.2 Ab Initio Modeling
- •2.3 New Approaches
- •3 Conformational Diversity of Proteins
- •3.1 Characterization of Protein Conformational States
- •3.2 Experimental Methods to Study Protein Dynamics and Conformations
- •3.4 Molecular Dynamics Simulation
- •3.5 Sampling Strategies
- •4 Remarks and Perspectives
- •References
- •1 Introduction
- •2 Structure-Based Drug Design of HIV Protease Inhibitors
- •2.1 HIV-1 Protease as a Therapeutic Target
- •2.2.1 Saquinavir
- •2.2.2 Indinavir
- •2.3.1 Lopinavir
- •2.3.2 Darunavir
- •6 Conclusions
- •References
- •4 Experimental Methods to Analyze NR Activity
- •4.2 Coregulator-Recruitment
- •5 Concluding Remarks and Outlook
- •References

70 D. S. de Sousa et al.
Supervised
Unsupervised
ClassificationRegression Clustering
Partial least
square -
PLS
Random forest –
Linear
regressio n
Sparse linear
regression
Lasso regression
RF
Artificial neural
networks – ANNs
(CNNs, DNNs,
RNNs)
Decision trees
Support vector
regression - SVR
Gradient
boosted trees
Nearest
neighbor
Support vector
machine - SVMs
Natural language
processing – NLP
(Kernel methods
and Bayesian
classifier)
Random forest
classifier
Naive Bayes - NBs
Decision trees
classifier
Linear
discriminant
analysis - LDA
Artificial neural
networks – ANNs
Gradient boosting
K-means
Hierarchical
clustering
Artificial neural
networks – ANNs
(Kohonen maps,
autoencoders)
Hidden Markov
model
Gaussian
mixture
Mean shift
Fig. 4.3 Examples of machine learning methods used in drug discovery followed by their
classification based on their use and nature
Among these methods, NNs, which will be discussed in more detail later, along
with Random Forest (RF) and Support Vector Machine (SVM), are the most widely
employed approaches in drug design. [15]
RF is an ensemble ML method that combines multiple decision trees to make
predictions. This algorithm extends the capabilities of decision trees while
addressing their limitations. Its distinctive feature resides in creating an ensemble
of decision trees during the training process, with each tree derived from a random
sample of the training data, a procedure commonly referred to as bootstrapping.
Furthermore, when splitting nodes in the tree, only a random subset of features is
considered, which reduces correlation and enhances the model’s robustness. To
make predictions, Random Forest employs a majority vote mechanism in classification tasks, selecting the most frequently predicted class by individual trees, and it
averages tree predictions in regression tasks. A key advantage of Random Forest is
its ability to mitigate over fitting. This is achieved by allowing individual trees to be
highly customized to the training data, while the combination of predictions from
multiple trees results in a more general and accurate model. Additionally, Random
Forest provides a measure of feature importance for each attribute used in training,
which facilitates feature selection and aids in understanding which variables have the
greatest impact on predictions [ 15, 40].
SVM is a class of ML algorithms widely employed for classification and regression tasks. These models are rooted in convex optimization theory, aiming to find the
decision hyperplane that best separates classes within a feature space. The primary
goal of SVM is to maximize the margin between data points from different classes,

4 Machine Learning and Neural Network Methods Applied to Drug Discovery 71
which contributes to the robust generalization of the model to unseen data. In cases
where data are not linearly separable, SVM can resort to kernel functions, which map
data to a higher-dimensional space, enabling efficient separation of nonlinear classes. This ability to handle complex, nonlinearly separable data makes SVM a
powerful tool in various ML and pattern recognition applications [15, 41, 42].
Both RF and SVM are relevant methods in drug design and related applications.
They offer different approaches to modeling and solving complex problems, and
their selection often depends on the specific characteristics of the data and the nature
of the problem at hand. RF’s ensemble nature enhances robustness, while SVM’s
emphasis on finding optimal decision boundaries makes it suitable for classification
tasks, even with complex data sets [15, 42].
2.1 Neural Networks
The human brain is a marvel of complexity and power, exhibiting an astonishing
capacity to process vast amounts of information in a short period. At its core, the
brain operates through intricate networks of neurons, which are responsible for the
transmission and processing of information. This remarkable mechanism has
inspired numerous researchers to emulate its functionality, particularly the experiential learning process. This endeavor has given rise to what we know as neural
networks, also called artificial neural networks (ANNs) [38].
ANNs have been meticulously designed to address a wide range of tasks spanning from the simplest to the most complex, all within a rema rkably short period.
This ability to solve a broad spectrum of issues promptly stems from the foundational design of ANNs, which closely mirror the biological functioning of the human
brain. This structure comprises a multitude of interconnected artificial neurons,
which operate together to process information and make decisions. Within the
architecture of an ANN, each component performs similarly to the organization of
the human brain [38]. To illustrate these components, we will begin by presenting
different forms of ANNs, which vary in compl exity and operating principles.
2.1.1 Perceptron
As previously pointed out, a perceptron is the simplest model of a neural network,
with its main characteristic being that it has only a single layer, hence the name
Single-Layer Artificial Neural Network. To understand how it operates, we can
break down its core components and processes. Inputs (x) represent the numerical
values provided to the perceptron (independent variables), while weights (w) are
adjustable parameters that determine the relative importance of these inputs, which
are fine-tuned during training. A bias (b) is a constant value added to the weighted
sum of inputs, allowing control of the output. The operation of the perceptron can be
summarized by the equation for the weighted sum (Z ), which is calculated as the sum

72 D. S. de Sousa et al.
of the products of inputs and their corresponding weights, plus the bias, as
represented in Eq. 4.1:
b
þx1w1þ ...þ xnwn: ð4:1Þ
0
Z =
n
xiwi= x0w
i = 0
A node (neuron), which in the case of a perceptron is singular, serves as a
processing unit that receives Z, as input and applies an acti vation function ( f )
which in this model is essential a step function. The primary purpose of this
activation function is to generate the output, the dependent variable (Y ), as
established in Eq. 4.2 [43, 44].
Y = fZðÞ=
1ifZ > 0,
0ifZ ≤ 0:
ð4:2Þ
The perceptron’s outputs represent the final results, commonly used for tasks like
binary classification. However, its main limitation is that, since it only consists of a
single neuron, it is primarily suitable for addressing linearly separable problems.
Nevertheless, understanding the operation of the perceptron is essential as it lays the
foundation for comprehending more intricate neural network models with multiple
layers and interconnected neurons. These advanced models have the capacity to
express probabilities or continuous values, making them applicable to a wider range
of complex tasks [43, 44]. Figure 4.4 illustrates a perceptron’s structure, aiding in the
visualization of its basic components.
2.1.2 Multilayer Neural Networks
A Multilayer Neural Network or multilayer perceptron (MLP) as the name suggests
represents an advanced form of neural network that incorporates the presence of
more than one layer of interconnected neurons, resulting in a more intricate architecture when compared to the traditional perceptron. The fundamental structure of an
MLP closely resembles that of a perceptron, comprising an input layer that receives
input data, one or more hidden layers that process and transform these data, and an
output layer that furnishes the final network output following processing. These
layers play distinct roles and perform specific functions within the network [45, 46].
The input layer is the initial layer of the network and is designed to accept input
data, which may encompass features, characteristics, or information fed into the
network for processing. This layer does not engage in any calculations but simply
conveys the data to the intermediary layers [45, 46].
The hidden layers are the heart of the MLP and are tasked with processing input
data through mathematical operations such as weight multiplication, bias addition,
and applying activation functions. These layers are termed “hidden” because their

4 Machine Learning and Neural Network Methods Applied to Drug Discovery 73
x
1
Neuron
Output
Input Layer
Fig. 4.4 Representative diagram of the architecture of a perceptron
operations are not directly observable in the network training process but are
essential in feature extraction and data representation [45 , 46].
The output layer constitutes the final layer of the network and generates the
ultimate output, which may take the form of a prediction, classification, or any
other desired outcome based on the specific problem at hand. The structure and the
number of neurons in this layer depend on the nature of the task for which the
network is being designed [45, 46]. Figure 4.5 illustrates an example of the generic
structure of an MLP, providing a visual aid for understanding its fundamental
components.
In the case of these models, the increase in the number of layers and neurons
allows for the execution of more complex and nonlinear tasks, as the model’s
capacity for representation and learning becomes more sophisticated. This is due
to the enhanced ability to express and adapt to intricate patterns in the data. As part of
this process, new activation functions can be applied, with the most common ones
being the ReLU and sigmoid functions [47, 48].
The ReLU (Rectified Linear Unit) activation function is widely used due to its
simplicity and effectiveness in overcoming gradient vanishing problems. It

74 D. S. de Sousa et al.
Fig. 4.5 Architecture of a
multilayer neural network:
7 input neurons (blue),
15 neurons in the first
hidden layer (gray),
8 neurons in the second
hidden layer (gray), and
2 neurons in the output layer
(green)
Input Layer
Output
Layer
Hidden
Layers
transforms negative values into zero while leaving positive values unchanged, as
expressed in Eq. 4.3 [47, 48].
fZðÞ=
Z if Z ≥ 0,
0ifZ < 0:
ð4:3Þ
On the other hand, the sigmoid function is a classic activation function that is
often used in output layers of neural networks, especially in binary classification
problems. It maps input values to the range from 0 to 1, which is useful for
estimating probabilities [47, 48]. The expression that represents this function is
shown in Eq. 4.4.
fZðÞ=
1
1 þ e
-z
ð4:4Þ
Moreover, there are other activation functions, such as the hyperbolic tangent
(tanH) and the parametric rectified linear unit (PReLU), which also are important in
different contexts and can be chosen based on the characteristics of the problem
being addressed [47 , 48]. Table 4.1 summarizes the other activation functions.
2.1.3 Types of Neural Networks
Neural networks not only vary in the number of neurons and layers but can also take
on various formats that directly influence their operating principle s, opening a wider
range of applications and distinct purposes. This gives rise to a variety of neural

4 Machine Learning and Neural Network Methods Applied to Drug Discovery 75
Table 4.1 Mathematical formulations of other examples
of activation functions
Name Equation
Identity f(Z ) = Z
TanH
ArcTan f(Z ) = tan
PReLU
ELU
SoftPlus f(Z ) = ln (1 + e
fZðÞ=
fZðÞ=
fZðÞ=
2
-2Z
1þe
-1
(Z)
Zif Z≥0,
αZif Z< 0:
α eZ- 1ðÞif Z < 0
- 1
Zif Z≥ 0,
Z
)
network architectures [38, 45]. Figure 4.6 illustrates the most well-known types of
neural networks.
It is possible to observe in Fig. 4.6 that neural network methods vary fundamentally in shape, neuron composition, operating direction, and activation functions.
The purpose of this chapter is not to explain how all these methods work, so we will
highlight some more widely used methods in the field of drug discovery. For this, we
will divide them into two categories: Feedforward and Rec urrent Neural Network.
Feedforward
The feedforward models are a fundamental category in the field of ANNs due to their
simple and effective approach. Essentially, they follow the principle of a unidirectional flow of information, from input to output, without the formation of cycles or
loops. This characteristic makes feedforward methods especially suitable for handling tasks that do not involve temporal or sequential dependencies, such as classification tasks. The perceptron itself, one of the pioneering concepts in the field of
neural networks, is a classic example of this approach [38, 46, 49].
The operation of a feedforward method is relatively simple but effective. Initially,
a set of input information is provided to the model. This information is then
processed by a series of layers of neurons. Each neuron in a layer performs a
weighted linear combination of the input values and applies a nonlin ear activation
function. This activation function is essential because it introduces nonlinearity into
the network, allowing it to capture complex relationships in the data. This is
important for the ability of neural networks to model real-world problems, which
often involve nonlinear relationships [ 38, 46, 49].
The feedforward approac h encompasses a variety of algorithms and architectures
that are widely used in different application domains. Some notable examples
include Radial Basis Function (RBF) networks and Convolutional Neural Networks
(CNN) [38, 45, 50].
RBF
The structure of an RBF is typically the same as that of a Multilayer Perceptron, but
it utilizes radial functions as activation functions [49], as described in Eq. 4.5.

76 D. S. de Sousa et al.
Perceptron
CNN
LSTM
Autoencoder
GRU
Hopfield Network
Deep FeedforwardFeedforward
RNN
Sparse autoencoder
Kohonen Network
Input node
Backfed Input node
Recurrent node
Fig. 4.6 Architecture representation of some types of neural networks
Hidden node
Memory node with gates
Output node
n
f xðÞ=
wiφ x - c
i = 1
Kernel
ðÞ ð4:5Þ
kk
Convolution /pool
Memory node
Match Input output node
i
In this context, where the input is modeled as a vector x from the set of real
numbers of N dimensions, n is the number of neurons in the hidden layer, c
center vector for neuron i, and w
is the weight of neuron i in the linear output neuron.
i
is the
i

4 Machine Learning and Neural Network Methods Applied to Drug Discovery 77
Functions that depend only on the distance from a center vector are radially
symmetric about that vector, hence the name radial basis. In the basic form, all
inputs are connected to each hidden neuron. The norm is typically taken to be the
Euclidean distance, and the radial basis function is commonly taken to be
Gaussian [50].
The main characteristic of RBF networks is their ability to approximate complex
functions with an approach based on the nonlinear representation of data. This is
particularly useful in probl ems where the relationship between input and output data
cannot be easily modeled by linear functions. Additionally, RBF networks have the
ability to adapt automatically to training data, adjusting the weights and centers of
the neurons in the hidden layer [45, 50].
CNN
A Convolutional Neural Network stands as a widely employed neural network
architecture in tasks linked to image and video processing. This technology proves
indispensable in fields such as computer vision, pattern recognition, and ML applied
to visual data [51–53].
Drawing inspiration from the workings of the human visual cortex, CNNs operate
through convolutional layers, responsible for applying convolution operations to
input images. This convolution entails the use of filters to extract features such as
edges, textures, and relevant patterns in the image. Following the convolutional
layers, pooling layers come into play, tasked with reducing the spatial dimension of
feature maps, and preserving crucial infor mation while decreasing the network’s
parameter count. Proceeding with the process, fully connected layers are employed
to make decisions based on the previously extracted features. These layer s resemble
those found in traditional neural networks, where outputs are computed using
adjustable weights [51–53].
Activation functions, such as ReLU, are applied at each layer to introduce nonlinearities into the network, enabling the learning of more complex representations.
Additionally, normalization layers, like Batch Normalization, can be incorporated to
enhance the network’s training [51–53].
Recurrent Neural Networks
Recurrent Neural Networks (RNNs) constitute a type of neural network architecture
designed to handle sequential or temporal data. Unlike conventional feedforward
networks, RNNs feature feedback connections, allowing the output of a layer to be
fed back into the input of the same layer. This capability enables the network to
maintain an internal memory [49 , 54–56].
The key concept in RNNs is their ability to process sequences of data. Each unit
in an RNN layer retains an internal state updated based on the current input and the
previous state, enabling the network to capture contextual information over time.

78 D. S. de Sousa et al.
However, traditional RNNs face certain limitations, such as the vanishing or
exploding gradient problem, which hinders the training of long sequences. To
overcome these issues, more advanced variants have emerged, such as Long
Short-Term Memory (LSTM) and Gated Recurrent Unit (GRU). These architectures
introduce memory control mechanisms that aid in preserving and forgetting information more effectively [54–57].
LSTM
Long Short-Term Memory (LSTM) Networks emerge as a solution to the challenges
faced by conventional RNNs when dealing with sequential data. While RNNs are
widely employed for such tasks, they often struggle to capture long-term relationships. LSTMs offer a more effective approach, enabling the network to memorize
and access relevant information across extensive sequences, proving particularly
valuable in contexts where understanding temporal relationships is central [49, 57,
58].
The basic structure of an LSTM includes memory units called cells, each
equipped with three gates: the input gate, the forget gate, and the output gate.
These gates function as control mechanisms that regulate the amount of information
that enters, is forgotten, or is transmitted [57, 58].
The LSTM operates at each time step, making decisions based on the characteristics of sequential data and the previous memory. This allows the network to learn
complex temporal dependencies over time [57, 58].
The fundamental advantage of LSTMs lies in their ability to selec tively retain and
discard information. This flexibility makes LSTMs effective in modeling patterns in
sequential data, applicable in various areas such as pattern recognition, machine
translation, and time series prediction [57, 58].
GRU
Similar to LSTMs, Gated Recurrent Units, or GRUs, were developed to overcome
the limitations of traditional RNNs. GRUs simplify the structure of LSTMs by
combining the concept of memory units and gates into a single unit. They retain
the ability to capture long-term information but with a more streamlined architecture
[49, 57, 59].
In a GRU, we also find two main gates: the update gate and the reset gate. The
update gate determines how much of the previous memory should be retained, while
the reset gate decides how much of the previous information should be forgotten.
The simplicity of GRUs compared to LSTM s can result in more efficient computation and faster training in certain situations [57, 59].
2.2 Deep Learning
Deep learning, within the broader context of ML, is an approach that surpasses the
limitations of conventional neural networks by incorporating three or more layers.

4 Machine Learning and Neural Network Methods Applied to Drug Discovery 79
While traditional ML can be likened to a neural network with a single layer, deep
learning expands upon this architecture, mimicking to some extent the complexity of
the human brain [5, 18, 26, 33, 34].
By adding hidden layers, regardless of the method employed, the neural network
gains the ability to learn and generalize from vast amounts of data. While a single
neural layer can make basic predictions, additional layers enhance and refine the
model’s accuracy. This expansion not only increases the system’s complexity but
also intensifies its aptitude for learning [5, 18, 26, 33, 34].
As the neural network deepens, its capacity to extract abstract and hierarchical
features from data significantly improves. This feature enables the model to identify
complex patterns, contributing to a deeper and more refined understanding of the
data. The richness of data used during train ing not only fortifi es the model but also
empowers it to handle a broader range of situations, making it more versatile and
adaptable [5, 18, 26, 33, 34].
Comparatively, while traditional ML may be effective for specific tasks with
smaller data sets, deep learning excels in scenarios where the complexity and
diversity of the data demand a more sophisticated approach [5, 18, 26, 33, 34].
3 Using Machine Learning
ML and NNs, as discussed earlier, exhibit a variety of approaches in terms of
operation, structure, and purposes, offering a wide range of application possibilities.
To employ ML in a specific application, it is essential to thoroughly understand the
structure of the involved stages. In summary, these stages involve defining the
problem, data collection, data preprocessing, model selection, model training, validation, model tuning, and prediction (Fig. 4.7). Each of these steps is of fundamental importance in the development and successful application of solutions based on
this approach.
3.1 Problem Definition
In the ML journey, the initial phase of defining the problem, despite its apparent
simplicity, assumes elemental importance, serving as an essential foundation for the
project’s success. At this stage, it is imperative to cultivate a deep understanding not
only of the available data but also of the inherent peculiarities within the domain
where the model will be applied and the challenges to be faced.
Establishing a specific goal for the project is fundamental. Answering fundamental questions such as “What are we seeking to predict or classify?” is necessary,
delineating the precise task that the model must perform. Additionally, it is necessary
to identify the type of problem at hand, whether it is classification, regression,
clustering, or anomaly detection.
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