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Explanations Using PDP The PDP plots for various characteristics of breast cell
nuclei are shown in Fig.10. The PDP plot of mean concavity shows that the effect
on diagnosis prediction decreases as mean concavity increases until 0.18. A slight
increase in the same plot is seen at 0.27, but after 0.29, the diagnosis prediction is
not affected by the increase in mean concavity. Similarly, in the PDP plot of mean
compactness, the effect of mean compactness on diagnosis prediction is increased
with increasing value of mean compactness initially, then afterwards a decrease was
observed with increase of mean compactness.
XAI is adequately effective in generating explanations for the black-box models;
however, there exist some challenges and gaps which are essential to address. The
following section discusses the pros and cons of the XAI methods and addresses the
challenges in XAI.
6 Discussion
The paper discusses various XAI methods that are being used in different applications of healthcare. LIME [25] is an approximation algorithm which provides explanations (local) for each instance. It can be applied with varied data formats including
Fig. 8 (a) Reasoning by LIME method for correct breast cancer prediction. (b) Reasoning by
LIME method for wrong breast cancer prediction

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texts [25], images (Case Study 1 in Sect. 5), and relational data [26]. However, it
cannot generate generalised explanations (global) for a set of instances. There are
XAI methods such as SHAP [26], PDP [17], AL [17], LD [17], and Saliency maps
[28] that can be used to generate global explanations. SHAP and Saliency maps can
be applied to varied data formats such as relational data [26] and images (Case
Study 1 in Sect. 5) whereas PDP, AL, and LD apply to numerical and categorical
values. Saliency maps are more suitable for high-dimensional data such as images.
PDP, AL, and LD are compatible with fewer attributes for the regression or classication problems. LIME, SHAP, Saliency maps, PDP, AL, and LD are modelindependent methods and can be applied to any ML/DL model. There are XAI
Fig. 9 Summary plot describing the impact of the feature on model output

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methods which are model dependent such as GNNExplainer [27] which is specic
to Graph Neural Networks, and Grad-CAM [23] which can explain CNN models.
The XAI methods show promising results in explaining ML/DL model- generated
predictions. However, some limitations exist, such as the illusion of explanatory
depth, lack of evaluation of generated recommendations, and subjective inferences
in the explanations generated by XAI methods. These limitations are discussed
briey in this section.
Lack of Evaluation Metric for XAI Numerous XAI methods are available to provide explanations for the machine-generated predictions. The explanations can be
local (explanation for an instance) or global (explanation for the whole dataset).
However, in both explanations, different XAI methods can give contradictory results
(regarding feature importance and feature values) [39]. It raises the issue of which
model provides the correct explanations and on what foundation we should believe
these explanations. There is no standard evaluation metric to estimate the correctness
of XAI-based explanations. The lack of evaluation metrics for the XAI- generated
explanations creates uncertainty about their accuracy.
The Illusion of Explanatory Depth The lack of evaluation metrics for XAI methods sometimes gives rise to another challenge called the illusion of explanatory
depth. Users accept the algorithmically generated explanations without validation
and verication due to the illusion of explanatory depth. It causes overcondence in
explanations and indifference to the present uncertainties. The illusion of explana-
Fig. 10 PDP plot for breast cancer predictions

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tory depth can cause harm on a large scale for non-technical users since the testing
of explanations generated by XAI algorithms relies on the verication of end users
only. In [40], the authors experimented with observing the effect of the illusion of
explanatory depth in non-technical XAI users. During the experiment, users were
asked to write interpretations of the explanations generated by the SHAP XAI
method. It was observed that the interpretations differ signicantly despite the
users’ condence in their explanations.
Subjective Interpretation XAI aims to make ML/DL models explainable by providing reasons for model-based predictions. These reasons/explanations should be
understandable to every user irrespective of their domain expertise. However, XAIgenerated explanations can be interpreted differently by individuals. This is mainly
due to two factors: an individual’s expertise area and biases. The expertise of an
individual dramatically affects their interpretation of the explanation. On the other
hand, even if the end user is an expert, their critical thinking can inuence their
interpretation of XAI explanations and may result in wrong decision-making [41].
Transparency and Trust The adoption of AI-based systems is limited due to a lack
of trust in their predicted decisions. Researchers believe increasing transparency in
AI-based decisions by including explanations can help enhance users’ trust in
AI-based systems. However, the relationship between transparency and trust is
complicated. Unquestionably, XAI methods increase transparency, but it does not
always increase trust in AI-based applications as expected [42]. A behavioural
experiment was conducted to observe the effect on human trust after including
insights/explanations in an ML-based ‘text classication decision support’ tool
[43]. Two types of insights, highlighting the decisive words in the input text and the
condence score of the decision support tool, were provided to the users. An adverse
effect on trust was seen, and it was observed predominantly with correct predictions. In conclusion, increased transparency may also raise mistrust, which is a signicant barrier to societal acceptance of AI.
Natural Language Explanations Natural language is the standard and most preferred method of communication among humans. End users of different elds, be
they doctors from the medicinal eld, educators from the education eld, or farmers
from agriculture, prefer recommendations in natural (text) language only [44].
However, visuals are the more prominent form of explanation in XAI because it is
simpler to visualise generated data than to represent the same in textual form.
Therefore, XAI researchers need to focus on creating explanations in the preferred
(textual) form or generate hybrid explanations containing visuals and text that
enhance explanations and remove the ambiguity in interpretations of explanations.
These problems with XAI demonstrate that there is signicant scope for improvement in XAI research.

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7 Conclusion
Explainable AI (XAI) recently gained attention when researchers started trying to
generate explanations and reasons behind the black-box models’ predicted outcomes. In this chapter, we have studied and explored various XAI methods and
existing taxonomies. A comprehensive all-inclusive taxonomy was proposed in the
chapter while considering various XAI categories and criteria. The effective use of
post-hoc methods of XAI, including Local Interpretable Model Agnostic Explanation
(LIME), Shapley Additive Explanations (SHAP), Partial Dependence Plot (PDP),
and Gradient Class Activation Map (Grad-CAM) in AI-based applications were discussed. The working principles of these methods were analysed in depth across
various domains, particularly in healthcare. This chapter examined different XAI
applications for disease detection, including Grad-CAM in arrhythmia detection,
PDP and accumulated proles in cancer prediction, LIME in early detection of fatal
blood disease, and SHAP in Parkinson’s disease. Analysis of XAI revealed that it is
portrayed in a favourable way as a tool for increasing transparency, but its limitations have not been made explicit. This chapter discussed signicant challenges in
XAI, such as the lack of standard evaluation metrics, subjective interpretations, the
illusion of explanatory depth, and the relation between transparency and trust in
XAI.The discussion included the analysis and results of trials conducted in the literature to study the impact of these challenges on decision-making.
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Explainable Articial Intelligence inDrug
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Discovery
AbinV.Geevarghese
Abstract Creation of drugs using computers has been impacted by computational
intelligence. This growth continues to be fuelled by, amongst other factors, the
widespread application of machine learning, and especially deep learning, throughout an array of academic regions, in addition to advances in computing software and
hardware. Medical chemistry is beneting as a consequence of the early scepticism
related to the use of AI in pharmaceutical discovery starting to dissipate. The use of
deep learning has promise for the development of drugs because it enables advanced
image comprehension, molecule function, and structure forecasting, including the
computerised generation of new chemical compounds having particular characteristics. Overview of the present situation with AI in chemoinformatics. De novo
molecular design, structure-based modelling, and chemical reaction prediction are
among the topics covered in this chapter. To satisfy the demand for an innovative
narrative of the computational language of molecular sciences, there’s an appetite
for “explainable” methods for deep learning. The most signicant and explainable
articial intelligence concepts are laid out in this chapter, which additionally expects
potential uses and an array of unsolved challenges. I also hope that this chapter
stimulates additional research on developing and implementation of methods of
articial intelligence in drug discovery.
Keywords QSAR · Drug discovery · Articial intelligence · De novo drug design
A. V. Geevarghese (*)
Department of Pharmacology, PSG College of Pharmacy, Coimbatore, Tamil Nadu, India
e-mail: abin@psgpharma.ac.in
Ltd. 2024
R. Aluvalu et al. (eds.), Explainable AI in Health Informatics, Computational
Intelligence Methods and Applications,
https://doi.org/10.1007/978-981-97-3705-5_6
113© The Author(s), under exclusive license to Springer Nature Singapore Pte

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1 Introduction
Computer-aided drug development has made extensive use of machine learning
techniques [1–3]. The ability of articial neural networks with several hidden processing layers, or “deep learning” approaches, to use input data to automatically
discover characteristics that might express non-linear input-output correlations has
recently sparked renewed attention. These enhanced features of deep learning methodology improve existing articial intelligence techniques that rely on unique
molecular descriptors [4, 5]. The application of deep learning has seen a relatively
late rise in interest in the eld of medicinal drug discovery [6], which has already
sparked an unparalleled boom of innovative modelling techniques and applications [7–10].
The ever-evolving advancements in deep learning are currently assisting several
elds of the chemical sciences [11–13]. In the past few years, several “articial
intelligence” (AI) principles have been successfully used to computerised drug discovery [11, 12, 14]. The ability of advanced learning algorithms to simulate complex non-linear input-output relationships, perform pattern recognition, and extract
features from low-level data representations is primarily responsible for this growth.
Articial neural networks with several processing layers are what deep learning
algorithms are made of. Some deep learning models have been shown to outperform
well-known machine learning and quantitative structure-activity relationship
(QSAR) methods for drug development [15–17]. Deep learning has further expanded
the potential and utility of computer-assisted discovery, for example, in the elds of
protein structure prediction, macromolecular target identication, molecule design,
and chemical synthesis planning [18–21]. A model’s limited understanding frequently pays for the ability to capture complicated non-linear relationships between
the input data (such as chemical structure representations) and the corresponding
outputs (such as assay results). While efforts are currently made to clarify QSARs
using computational insights and molecular descriptor analysis [22–27], models of
deep neural networks are infamous for being inaccessible to the human mind right
away [28]. The abundance of “rules of thumb” linking biological effects with physicochemical qualities, particularly in medicinal chemistry, highlights the readiness
to sometimes trade precision in favour of models that better match human intuition
[29, 30]. With the recent resurgence of neural networks in chemistry and medicine,
automated analysis of medical and chemical information to extract and depict characteristics in a human-intelligible manner has been around since 1990s [31, 32].
There will be a greater demand for techniques that help in understanding and
interpreting the models that underneath given the speed at which AI is being applied
in drug development and related domains. Emphasis has been focused on explainable AI (XAI) techniques in an attempt to reduce the uninterpretability of some
machine learning models and to improve human reasoning and decision-making
[33, 34]. Establishing the fundamental decision-making process transparent
(“understandable”) avoiding making precise forecasts for the incorrect causes (the
so-called clever Hans effect) [35], preventing unfair biases or unlawful injustice,

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and bridging gaps among the machine learning group and other disciplines of science all have the goals of offering useful explanations with the mathematical frameworks. Competent XAI may help scientists in overcoming “cognitive valleys”
improving their comprehension and convictions on the process under investigation
[36, 37].
Although there is some disagreement on the precise meaning of XAI, the author
believes that a number of its characteristics are unquestionably favourable for drug
design programmes [38]. Although there is some disagreement over the exact denition of XAI, the author is of the opinion that a number of its features are undoubtedly advantageous for applications in drug development [39].
• Transparency—knowing how the system arrived at a particular conclusion.
• Justication—stating the merits of the model’s proposed solution.
• Informativeness—supplying fresh information to decision-makers.
• Calculating the degree of uncertainty in a prediction.
XAI-generated justications can usually be categorised into two distinct groups:
global (which highlights the importance of the input variables in the model) and
local (which focuses on individual predictions). Additionally, XAI might be modeldependent or model-agnostic, which inuences the possible application of each
approach. There is no one-size-ts-all XAI technique in this architecture [40].
Future domain-specic challenges to AI-assisted medication development
include the data structure that these approaches employ. In contrast to many other
areas where deep learning has been shown to succeed, such as the processing of
spoken languages and image identication, there is no naturally applicable, complete, “raw” molecular description. After all, molecules are models in and of themselves as far as science is concerned. Therefore, using an “inductive” method that
builds higher-order (like deep learning) models from lower-order ones (like molecular representations or descriptors based on observable statements) is philosophically
dubious [41]. The selection of the molecular “representation model” limits the
amount of chemical information that can be retained, including pharmacophores,
physicochemical properties, and functional groups, as well as the amount of information that can be explained and how well the resulting AI model performs.
Drug development is a difcult procedure. Inaccuracy, non-linearity, and seemingly random events set it apart from simple engineering. I must admit that I have a
poor understanding of molecular pathology, and we are unable to create mathematical models of pharmacological impact and accompanying reasons that are 100%
accurate. Here, XAI holds forth the prospect of fostering human ingenuity and aptitude for producing novel bioactive compounds with desired properties [42].
The foundation of generating novel medications is the investigation into whether
pharmacological activity (or rather, “function”) may be deduced from the molecular
structure and what components of the structure are signicant. The added difculties and poorly communicated problems presented by multi-objective designing
lead to molecular designs that all too frequently serve as compromise solutions. The
practical strategy is to reduce the amount of syntheses and testing required to identify and improve innovative hit and lead compounds, particularly when complex and
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