Artificial intelligence and machine learning in precision and genomic medicine.

The advancement of precision medicine in medical care has led behind the conventional symptom-driven treatment process by allowing early risk prediction of disease through improved diagnostics and customization of more effective treatments. It is necessary to scrutinize overall patient data alongside broad factors to observe and differentiate between ill and relatively healthy people to take the most appropriate path toward precision medicine, resulting in an improved vision of biological indicators that can signal health changes. Precision and genomic medicine combined with artificial intelligence have the potential to improve patient healthcare. Patients with less common therapeutic responses or unique healthcare demands are using genomic medicine technologies. AI provides insights through advanced computation and inference, enabling the system to reason and learn while enhancing physician decision making. Many cell characteristics, including gene up-regulation, proteins binding to nucleic acids, and splicing, can be measured at high throughput and used as training objectives for predictive models. Researchers can create a new era of effective genomic medicine with the improved availability of a broad range of datasets and modern computer techniques such as machine learning. This review article has elucidated the contributions of ML algorithms in precision and genome medicine.

Introduction

Precision medicine is a rapidly growing branch of therapeutics developed on human genetic makeup, lifestyle, gene expression, and surrounding environment [1, 2]. Researchers can use it to tailor prevention and treatment through the identification of the characteristics which expose people to a particular disease and characterizing the primary biological pathways which cause the disorder. It is one of the most exciting and promising advancements in modern medicine. It transforms healthcare from a suitable for all medical practice to individualized and data-driven, allowing for more efficient expenditure and better patient results. It has contributed to curing cancer, cardiovascular disease, HIV, and many more inflammatory-related conditions.

In contrast, Genomic medicine is a relatively new medical specialty that focuses on using genetic information about an individual in treatment for diagnostic or therapeutic purposes and the associated health outcomes and policy implications. It already has potential changes in oncology, pharmacology, rare and undiscovered disorders, and infectious disease.

Since heart failure and cancer, medical error is the third most significant cause of mortality [3]. According to recent studies, about 180 000 to 251 000 individuals die each year in the USA because of medical reports [3]. This number has been increasing as our existing medical system becomes more complex and of lower quality, as seen by breakdowns in communication, errors in diagnosis, poor patient care, and rising costs. In recent years, personalized medicine has been a great innovation pillar for leading health-related research, and it has immense promise for patient care [4, 5]. Precision medicine can significantly improve conventional symptom-driven medicine by skillfully combining multi-omics profiles with epidemiological, demographic, clinical, and imaging data to enable various prior initiatives for developed diagnostics and more effective and cost-effective personalized treatment. It necessitates a forward-thinking Medicare environment that allows clinicians and researchers to construct a clear view of a patient by incorporating extra primary information from clinical data, including phenotypic details, lifestyle, and non-medical factors that can influence medical resolutions. It also focuses on the four “Ps” methods known as predictive, preventive, personalized, and participatory. By focusing on these four “Ps” treatment methods, precision medicine strives to help clinicians quickly grasp how individual clinical data differentiation can affect health and disease diagnosis and anticipate the best dosage of treatment for individuals [6].

While the intricacy of disorders at the interpersonal level has created it challenging to use healthcare data in therapeutic decision making, technological advancements have helped overcome some of the barriers [7]. It is essential to maximize the usage of EHRs by incorporating different datasets and identifying particular patterns of patients' disease progression to deliver high decision support and apply personalized and population health effects, which has a greater possibility to enhance positive clinical outcomes. While the value of clinical data mining cannot be overstated, the issues associated with extensive data management remain enormous [8].

Biotechnology has advanced tremendously throughout the years. Computers are becoming quicker and smaller in size, datasets are becoming more heterogeneous, and their volume is growing at a rapid rate. These developments enable artificial Intelligence (AI) to uncover numerous technical advancements necessary to address complicated issues in practically every aspect of medicine, science, and life.

Computer science technology consists of distinct areas; artificial intelligence is considered one of them that enables computers to carry out versatile tasks that typically necessitate human brains. AI possesses extensive analytical skills to solve problems, including prediction, dimensionality, data integration, reasoning about underlying phenomena, and changing large amounts of data into clinically actionable knowledge, all of which are gathered out of ideal datasets. The learning ability has increased through optimizing the identification task using problem-specific performance measurements. In particular, ML and DL centered methodologies have gained popularity and developed as critical components of biomedical data analysis, owing to the abundance of medical data and the rapid advancement of analytics tools [9-13]. AI is presently being utilized to automate data retrieved from sources, summaries EHRs, or handwritten physician notes, combine health records, and store data on a cloud scale [14-19]. Artificial neural networks (ANN), Machine Learning, and Deep Learning are referred artificial intelligence. Since artificial intelligence has incorporated high-performance computing, we can determine and anticipate disease risk based on patients' data [20]. The translation of such massive information into clinical data is done through machine learning/artificial intelligence platforms. These systems have demonstrated promising outcomes in forecasting disease risk with increased precision [21-24]. While Artificial Intelligence launches into the field of precision and genomic medicine, it can assist organizations in various ways and contribute to understanding the genesis and progression of chronic diseases. The administration of ML algorithms in precision medicine [25-27] to assess diverse patient data, such as clinical, genomics, metabolomics, imaging, claims, experimental, nutrition, and lifestyle, is one of the most current trends. This review article is concentrated on the contributions of machine learning in precision and genomic medicine. Moreover, it also emphasizes the employment of ML algorithms in distinct diseases, including cancer and cardiovascular disease.

Machine learning in precision medicine

In AI, ML is a computer-based model used to acknowledge and understand patterns in an overall volume of information to build classification and prediction models based on the training data. Arthur Samuel, an IBM employee, firstly created the word “machine learning” in the 1950s. Machine learning has progressed significantly since then [28]. ML is divided into supervised and unsupervised learning, as well as reinforcement learning [29]. The reward for good performance and punishment for bad performance is used to train reinforcement learning models. Positive feedback effectively guides the ML model to make the same choice again in the future.

In contrast, negative feedback essentially guides the ML model to evade making the same decision again in the hereafter. In contrast to supervised or unsupervised ML techniques, reinforcement learning plays a minor part in precision medicine approaches because of the direct response. Machine learning is primarily classified into three types: classification, clustering, and regression. Supervised learning techniques include classification and regression, whereas clustering is an unsupervised learning technique. Classification uses labels and parameters to predict discrete, categorical response values, such as detecting malignancy through biopsy samples. Clustering is used to segment data, for example, to determine the currency of a disease in a given community as a result of pollution or chemical spills. Regression forecasts continuous-response numeric data to discover administration trends, such as the time interval between a patient's discharge and readmission to the hospital (positive/negative).

Machine Learning is transforming healthcare by guiding individual and population health through a variety of computational benefits. It contributes to observing sick patients, disease pattern analysis, diagnosis and making prescriptions of a drug, providing patient-centered care, reducing clinical errors, predictive scoring, therapeutic decision making, detecting sepsis, and high-risk emergencies in patients. A genetic flowchart of machine learning is illustrated in Fig. 1.

Fig. 1

A generic flowchart of machine-learning workflow

It also identifies phenotypes, decode clinical statements out of death certificates and post-mortem reports of patients, identifies cardiovascular diseases, cancer, and symptoms related to different diseases, predicting and inter-venting risk, and paneling and resourcing [30-40]. In precision medicine, there are ten algorithms which are generally used. They are SVM, genetic algorithm, hidden Markov, linear regression, DA, decision tree, logistic regression, Naïve Bayes, deep-learning model (HMM), random forest, and K-nearest neighbor (KNN) (Fig. 2) [41].

Fig. 2

An overview of topmost machine-learning algorithms

Machine learning in oncology

The development in multidimensional “omics” technology from NGS to mass spectrometry has provided much information. Artificial Intelligence can integrate data from distinct “omics,” including genomics, proteomics, metabolomics, and transcriptomics. It has permitted the description of practically all biological molecules spanning from DNA to metabolites, enabling the study of complex biological systems. Identifying disease biomarkers using omics data simplifies patient cohort categorization and gives preliminary diagnostic data to optimize management of patients and avoid negative consequences. Coudray et al. used CNN to reliably and intensively diagnose sub-division of lung cancer, such as squamous cell carcinoma (LUSC) and adenocarcinoma (LUAD), as well as normal lung tissue, using digital scans of samples from The Cancer Genome Atlas [113]. Huttunen et al. employed automated classification to classify microscopy images of ovarian tissue with multiphoton fluorescence [114]. They also reported that their anticipation was comparable with the pathologists. Brinker et al. used CNN to automate the classification of dermoscopic melanoma images and found that it outperformed both board-certified and junior dermatologists [115]. Another method for subdividing patients in terms of risk variables is to use circulating cell-free DNA for molecular profiling of cancer [116].

Scientists discovered protein biomarkers in limited sample sizes. They found that it was prone to overfitting and misinterpretation of proteomic data. The combination of proteomics and genomics datasets led to the invention of a new targeted drug in breast cancer (hormone receptor positive), such as an altered PI3K pathway [117]. Combining proteomics and transcriptomics datasets in glioblastoma guides discovering the gonadotropin-releasing hormone (GnRH) signaling pathway, which could not be understood with a single omics dataset [118].

Similarly, combining the copy number of DNA variations with breast cancer patients' gene expression helped researchers who learn the disease's mechanism and developed new treatment strategies [119]. Reliable integrated data analysis of transcriptomic and metabolomics has found four distinct urine biomarkers [120]. Alteration in the proteome and metabolism of the liver was discovered by integrating proteogenomic data analysis of matched tumors and surrounding liver samples. The researchers discovered biomarkers and smaller groups of patients with specific microenvironment dysregulation, cell proliferation, metabolic reprogramming, and possible treatments [121] (Table 1).

Table 1

Algorithms of Machine Learning used in Cancer Diagnosis

Omics types	Data type	Analyzing tools	Cancer types
Non-Omics	Clinicopathological	Neural Networks, Decision Tree, Logistic Regression	Breast Cancer [122]
Non-Omics	Clinicopathological	ANN, SVM, semi-supervised learning	Breast Cancer [123]
Non-Omics	Clinicopathological	ELM, Neural Networks, Genetic Algorithm	Prostate Cancer [124]
Non-Omics	Clinicopathological	Two-stage fuzzy neural network	Prostate Cancer [125]
Non-Omics	Clinicopathological	Linear Regression, Support Vector Machines, Gradient Boosting Machines, Decision Tree,	Lung Cancer [126]
Non-Omics	Radiomics	DT, Adaboost, RUSBoost algorithm, Matthews correlation coefficient	Gliomas [127]
Non-Omics	MR Images and Clinicopathological	SVM, bagged SVM, KNN, Adaboost, RF, GBT	Bladder Cancer [128]
Single Omics	Genomics	SVM, log-rank test, Cox hazard regression model, genetic algorithm,	Ovarian Cancer [129]
Single Omics	Genomics	Pathway Based Deep Clustering Model, R89-restricted Boltzmann Machine, Deep Belief Network	GBM and Ovarian Cancer [130]
Single Omics	Metabolomics	SVM, Naive Bayes, RF, KNN, C4.5, PLS-DA, LASSO,	Colonic Cancer [131]
Single Omics	Metabolomics	SVM, RF, RPART, LDA, generalized boosted model	Breast Cancer [132]
Non-Omics and Single Omics	Clinicopathological and Genomics	Ensemble model SVM, ANN, KNN, ROC and calibration slope	Breast Cancer [133]
Non-Omics and Single Omics	Clinicopathological and Genomics	SVM, ROC	Prostate Cancer [134]
Non-Omics and Single Omics	Histopathology images and proteomics	RF, CNN	Kidney Cancer [134]
Multi-Omics	Genomics, Transcriptomics and proteomics	Random Forest Regressor, Wilcoxon signed ranked test, gene-specific model, Generic model, trans issue model and RF. l	Breast and Ovarian Cancer [135]

Machine learning in drug discovery of cancers

The precision oncology approach requires the detection of a panel of biomarkers linked to therapy responses. Using multi-omics data, ML-made computational models are being developed to anticipate drug response using response-predictive biomarkers [136]. Drug sensitivity prediction models relying on gene expression profiles are less reliable than multi-omics profiling-based models. While developing a drug response prediction model, the data type, complexity noise ratio, dimensionality, and heterogeneity are essential elements.

The superiority of gene expression profile datasets may make it challenging to understand prediction models, but this can be reduced using TANDEM, a two-stage method [137]. Bayesian efficient multiple kernel learning is a way to develop a response prediction model based on multi-omics data. The new drug sensitivity prediction challenge named NCI-DREAM7 is known as the best-performing model [138] in the National Cancer Institute.

Drug reactivity or accuracy is one of the primary clinical endpoints. It will be the most critical standard to anticipate preclinical data to increase drug trial success rates. In terms of observational data, a few organizations have published research articles in which biomarkers obtained from the machine-learning-driven response prediction model were crucial in the invention and advancement of new therapeutic drugs [139-141].

Li et al. used erlotinib to create drug reactivity patterns from cancer cell lines. It is an EGFR protein kinase inhibitor designated to treat patients with NSCLC by deleting the 19 number exon. Li and colleagues also used another drug to treat metastasized renal carcinoma named sorafenib [139, 142]. A clinical trial called Biomarker-integrated Approaches of Targeted Therapy for Lung Cancer Elimination [139, 143] employed models to stratify patients, with selected biomarkers explained with knowledge of each kinase inhibitor drug's mechanism of action. Scientists can go towards genuinely data-driven personalized oncology by mixing biomarker-driven adaptive clinical experiments like BATTLE with basket trials (tissue of origin agnostic).

An immune checkpoint inhibitor, PD1, named Pembrolizumab [144], was licensed in 2017 by the FDA for tumors with a particular genetic overview rather than the domain of pathogenesis [145]. It was the first-time treatment was approved for use across several indications based on a biomarker, highlighting the requirement for more research into data-driven biomarker discovery and drug repurposing in the future of genomic cancer care.

Several community efforts to aid review and standardize ML-based approaches have been made to overcome some of the challenges in clinical practice. The FDA, for example, has undertaken a validation program to compare machine-learning algorithms for anticipating clinical endpoints using RNA expression data [146]. Multiple myeloma, known as one of the common hematological malignancies [147], can be detected through ML algorithms. Many research groups were trusted with creating prediction approaches for different clinical endpoints in a MM dataset as part of the Microarray Quality Control II (MAQC II) effort. Using a univariant Cox regression model, the most effective strategy identified a gene profile linked with the person at high risk to survive [148]. The authors point out that arbitrary cutoffs in overall survival may be ineffective (two years was the cutoff for high risk, despite overall survival being a continuous variable suited to Cox modeling). Breast cancer gene expression data can be used to anticipate overall survival as a constant variable. Moreover, numerous researchers independently validated the multiple myeloma prognostic biomarker, which was discovered later [149-151].

The DREAM7 challenge by the National Cancer Institute [152] was a community-driven strategy to provide standardized datasets for ML model benchmarking. This scenario guided models using data from thirty-five breast cancer cell lines treated with thirty-one anti-cancer medications, including mutation data (from SNP array), protein array data, RNA expression profiles, exome sequencing, and DNA methylation. After that the models had to estimate the outcome of a blinded dataset of eighteen cell lines given the same 31 medications. The sparse linear regression, regression trees, kernel technique, nonlinear regression, partial least squares regression, principal component regression, and ensemble approaches [152] were all regression-based models that performed well. The dataset is still being utilized to test several algorithms, including random forest ensemble frameworks [153], group factor analyses [154], and others [155].

Application of machine learning in cardiology through imaging, risk prediction, ECG, and genomics

Artificial Intelligence can diagnosis cardiovascular diseases in patients. By using a neural network classifier, congestive heart failure can be detected on chest radiographs. The research by Seah et al. [156] has shown an exciting outcome as it used a generative adversarial network to obtain direct visualization of the characteristics used to make the prediction. It enables creating a visual output, which was used to highlight relevant aberrant features in chest X-rays.

Machine Learning can be also be applied in echocardiography. It has been designed to automatically calculate the aortic valve area in aortic stenosis or aid in the differentiation of different prognostic phenotypes.[157]. In athletes, Narula et al. [158] used ML to distinguish hypertrophic cardiomyopathy from normal heart hypertrophy. Their classifier had an overall sensitivity of 87 percent and specificity of 82 percent in a cohort of 139 males who underwent 2D-echocardiography. According to Madani and colleagues, deep learning could aid in the classification of echocardiography views. Using a training and validation set of over 200,000 images and a test set of 20,000, they trained a convolutional neural network to recognize 15 standard echocardiographic views. With an overall accuracy level of 91.7%, it exceeded board-certified echocardiographers [159].

On magnetic resonance imaging, deep learning has also been used to detect and characterize delayed myocardial enhancement. This feature can help distinguish between ischemia and non-ischemic cardiomyopathy and reveal myocardial dysfunction. Researchers investigated a group of 200 patients and found that their accuracy ranged from 78.9% to 82.1 percent [160].

Although these findings are insufficient for daily clinical practice, they offer exciting applications that may be further improved if multi-institutional and larger datasets were available.

Automated computation of scores and assessment of heart function is another intriguing use.

González, et al. [161] used a convolutional neural network to generate the Agatston score from a database of 5,973 unenhanced chest CT scans without segmenting coronary artery calcifications beforehand. Compared to traditional methods, they were able to compute the score faster and more precisely (Pearson correlation coefficient: 0.923). Deep learning has also shown promise in the assessment of left ventricular function automatically. On a dataset of 596 MRI examinations acquired in various universities and on scanners from multiple vendors, Tao et al. [162] trained a convolutional neural network to produce a tool that surpassed manual segmentation. Furthermore, the efficiency of the approach improved as the number of cases included grew more diverse.

Machine learning can also be used to automate heart segmentation. The left ventricle's epicardium and endocardium must be separated to examine the circulatory system's function [163-166]. By utilizing a dataset of forty-five cardiac cine MRIs with ischemia and non-ischemic heart failure, left ventricular hypertrophy, and regular patients [167] employed machine learning to automate heart segmentation. Its precision was comparable to that of traditional approaches.

ML has a significant challenge in assisting cardiologists in generating accurate predictions and evaluating cardiovascular risk in various contexts, resulting in tailored therapy. A machine-learning classifier was employed by Przewlocka-Kosmala et al. [166] to discover prognostic characteristics in patients with heart failure and preserved ejection fraction. Deep learning could also be applied to the development of technologies that can anticipate specific cardiovascular events.

Kwon et al. [168] created a deep-learning method to detect in-hospital cardiac arrest and mortality without resuscitation attempts. They analyzed data from 52,131 individuals admitted to two hospitals over the course of 91 months.

It exceeded proven approaches such as AUC: 0.850; area under the Precision-Recall Curve: 0.044 in sensitivity and false alarm rates. A machine-learning-based model with high accuracy and sensitivity of 80% has demonstrated promising results in predicting in-hospital duration of stay among cardiac patients [169]. Mortazavi et al. [170] performed research where they reported that machine learning might aid to predict thirty-day all-cause hospital readmission in heart failure patients. Although it outperformed traditional statistical analysis, the difference was insufficient to justify its application in daily clinical practice, owing to the fact that various other factors should be considered during the algorithm's construction. Another potential administration of ML is the risk assessment of ventricular arrhythmia in hypertrophic cardiomyopathy, albeit its accuracy is presently insufficient for medical use [171].

Characterizing cardiovascular risk in asymptomatic people is the main challenge. This necessitates a thorough examination of various variables to detect patterns that may be undetectable by traditional statistical analysis. ML has much potential in this subject, according to various research. Alaa et al. [172] developed an automated machine-learning technique based on a dataset of over 400,000 people and over 450 variables. When compared to the Framingham score, it increases cardiovascular risk prediction. It also revealed novel cardiovascular risk factors and interactions between other personal characteristics.

Another fascinating area of Machine-Learning application in cardiology is the automatic identification of aberrant results of ECG, which might be immensely beneficial as the number of wearable devices grows. DL algorithm was utilized by Isin et al., where they applied an online dataset of over 4000 long-term ECG Holter recordings to detect arrhythmia on ECG. It had a 98.5 percent correct recognition rate and a 92 percent accuracy rate.

ECG could also be used to identify patients with asymptomatic left ventricular systolic failure using convolutional neural networks. [164]. Galloway et al. [165] ML to screen for hyperkalemia in severe renal disease patients using ECG from three Mayo Clinic facilities in Florida, Minnesota, and Arizona. They evaluated a database of 449,380 patients from several hospitals and found a high sensitivity (AUC range: 0.853–0.883).

One of the genomics' key goals is to define gene function by establishing links between genotype and phenotype. This is critical for developing predictive models and precision medicine, but the complexity of DNA remains a limitation. Deep learning could be used to perform large-scale genome-wide association studies that are both accurate and quick. [173, 174]

By using a large-scale genome-wide association investigation of single-nucleotide polymorphisms, Oguz et al. [175] constructed a neural network to predict progressive coronary artery calcium.

They looked at clinical as well as genetic data. They also tested their model on various network topologies and found it to be highly accurate (AUC > 0.8).

A higher number of long non-coding RNA have been linked to the development of atherosclerosis. Therefore, genetics is thought to play a crucial role. Many of the techniques used to conduct these analyses are ML based [176]. Burghardt et al. [177] analyzed SNPs linked to inheritable cardiac disorders using a neural network. The most frequently implicated proteins were ventricular myosin and cardiac myosin-binding protein C. As a result, this method can be used to discover genes linked to heart disease phenotypes that are more severe or premature.

Application of ML in other human diseases

Machine-Learning algorithms are practical when the terms come to recognize intricate patterns throughout vast and successful data. This technique is generally applied in clinical applications, especially on individuals who depend on advanced genomics and proteomics. Several human diseases can be detected and diagnosed through ML algorithms. By implementing a sound healthcare system, it can generate higher decisions on patients’ treatment. Despite cancers and cardiovascular diseases, ML algorithms can be used in several pieces of research to diagnose different human diseases (Table 2).

Table 2

Machine-Learning algorithms application on human diseases

Human diseases	ML Algorithms	Features	Reference
Covid-19	ES, LR, LASSO, SVM	The goal was to demonstrate how ML approaches may be utilized to estimate the number of future individuals impacted by COVID-19, commonly recognized as a potential threat to humanity	[178]
Brain Stroke	SVM	The hematoma growth is due to the prediction that ICH will naturally arise from a comparable resource when SVM is used	[179]
Brain Tumor	KNN, SVM, RF, LDA	The goal of the best machine-learning and classification algorithms was to learn from training automatically and make a wise judgment with high accuracy	[180]
Liver Disease	J48, SVM& NB	Compare algorithm strategies with a greater accuracy rate for identifying liver disease to anticipate the same conclusive conclusion	[181]
Alzheimer	CNN	The project's goal was to improve accuracy to levels comparable to the highest development, address the issue of overfitting, and look at validated brain technologies with visible AD diagnostic markers	[182]
Alzheimer	SVM	This study aimed to look at several aspects of Alzheimer's disease diagnosis to see whether it can be used as a biomarker to differentiate between AD and other subjects	[183]
Parkinson’s Disease	SVM	The study discovered the most effective and comprehensive technique to suggest for improving Parkinson's disease identification accuracy	[184]
Thyroid Disease	SVM	The study's objective was to select the prime approach to classify thyroid disease, which is one of the most challenging classification tasks	[185]
Diabetes	SVM	Determine the most effective methods for detecting breast cancer early	[186]

Genomic medicine and machine learning

Genomic medicine has expanded fast as an interdisciplinary medical specialty incorporating the utilization of genomic information since the Human Genome Project has completed. The basic concept of genomic medicine contains the definition of DNA, RNA, genome, exome, exon, codon, biomarker, germline, intron, micro-array, and somatic.

Genes, the minor units of heredity, are thought to number between 20,000 and 25,000 in humans [187]. Humans are inherited with two copies of the gene, one from each parent. Human Genome consists of coding genes (both protein and non-protein). Genes can include as little as a hundred or as many as two million DNA bases [187]. As a result, the genome reflects the number of genes and the complexity of gene networks [188]. “The human genome is fiercely innovative, dynamic, sections of it are unexpectedly beautiful, encrusted with history, inscrutable, vulnerable, resilient, adaptable, repetitious, and unique,” writes Mukherjee [188].

Several noteworthy advancements have been developed in genomic medicine: precision Medicine, CRISPR, Omics, Genetic testing, and Gene therapy.

Precision medicine and genomics are inextricably linked. Precision Medicine (an acronym for personalized medicine) is a patient-centered novel way of treatment that incorporates genetics, behavior, and environment intending to employ a patient- or population-specific treatment intervention rather than a suitable approach for all individuals. Precision medicine is estimated to make eighty-seven billion dollars in the market by 2023. To minimize the potential of complications, an individual in need of a blood transfusion would be paired to a donor with the same blood group rather than an aimlessly chosen donor. The main challenges to wider precision medicine adoption are high costs and technological restrictions.

Numerous researchers are employing machine-learning techniques to help them deal with the enormous amounts of clinical data that must be collected and evaluated and save money. Machine-learning applications are changing genetic research, doctors prescribe patient care, and genomics research, making this area more accessible to people who want to understand more about how their genes may affect their health. DNA sequencing to phenotyping and variation identification to downstream interpretation, ML and DL have influenced nearly every genomics study. Machine-learning methods have been implemented in bioinformatics operations like genome annotation and variation effect prediction for a long time.

Advancements in computation, deep learning, and the expansion of biological datasets allow established areas of utility to be improved.

Such improvements, combined with an elevated level in open-access research and instruments, propel AI use across a wide range of genomics analyses. Machine-learning techniques are being integrated into proprietary software providers' genomics analysis tools and services, in addition to open-source resources. In genomics, the great bulk of AI effort is still in the research stage.

Deep learning, in particular, is generating a lot of hype and enthusiasm, with much research being done to use these methods to explore the fundamental biological mechanisms that underpin disease [189].

A. genome sequencing

Any sequencing process can create mistakes and errors; the types of faults differ, counting on the process and platform used. ML can aid in the improvement of sequencing accuracy. Some sequencing techniques depend on complementary DNA ‘probes' to capture DNA target areas, which can differ by a factor of 10,000 in binding efficiency. Researchers have created an ML model to anticipate DNA-binding rates from sequence data to aid in constructing effective probes. Another source of mistake is base calling from raw DNA-sequencing data. Some DL methods have been created to identify Oxford Nanopore long-read sequencers [190-192].

Improved base-calling methods are one strategy to increase third-generation sequencing accuracy beneath certain short-read sequencing technologies. DL may provide computational tools for tackling long-read sequencing data accuracy and, by extension, clinical usability.

WGS (Whole Genome Sequencing) has become a hot topic in medical diagnostics. The traditional Sanger sequencing method took over ten years to complete the entire human genome to be sequenced. In contrast, the Next Generation Sequencing has become a talking point encompassing the modern DNA-sequencing process, which permits scientists to sequence the entire genome in one day. Companies like Deep Genomics use machine learning to assist scientists in interpreting genetic alternation. The ML models are created based on the arrangements discovered in big genome datasets that are then converted into computer models to assist scientists in understanding how genetic diversity influences critical cellular processes. DNA repair, metabolism, and cell development are known as cellular activities. Disruption of these pathways' regular function has the potential to induce disorders like carcinogenesis.

In 2014, the Toronto-based company was founded, which has obtained seed funding of $3.7 million from three firms named Bloomberg Beta, Eleven Two Capital, and True Ventures. Deep Genomics' funders suggested the company stay in Toronto and flourish rather than migrating to Silicon Valley.

B. Phenotyping

Phenotyping is the procedure to evaluate and describe a patient's characteristics in a clinical setting.

Phenotype data might be utilized in several phases of the diagnostic process, from guiding the selection of a test to interpreting genetic results.

Machine-learning approaches are being developed to extract phenotypic information from EHR [193], refine phenotype classification [194], and make phenotype data analysis easier.

Deep-learning algorithms for visual interpretation for uncommon disease and cancer phenotyping, in particular, have shown considerable promise.

C. Variant identification and interpretation

The bioinformatics analysis of alternation identification in the gene, also known as a variant calling, is concerned with finding the location where a patient's genome differs from a reference sequence.

It is essential to identify variants in order to discover disease-causing variants appropriately correctly. A variety of DL models are currently under development to enhance variant call accuracy.

Many companies are working on deep-learning-based variant callers to solve accuracy difficulties with platforms like single-molecule long-read sequencing technologies and variations, such as somatic cancer mutations.

Somatic genetic variations are genetic alterations that occur in specific cell subsets over time and are not inherited or handed down through the generations. These variations are mostly harmless. Some can cause everyday alterations in the nearby tissue, making them interested in cancer research and patient therapy. With the complicated character of tumor biology, tumor-normal cross-contamination, sequencing artifacts, and the low frequency of these variants, accurately detecting somatic variants is inherently tricky. Many ML processes [195] have been used to improve their specificity to find actual somatic variations. Currently, DL methods are also being developed [196, 197].

Through gathering knowledge from training data, DNA can better distinguish actual variant calls from artifacts caused by sequencing mistakes, coverage biases, or cross-contamination [198].

Copy number variations are a difficult-to-identify subset of variants in which ML processes are implemented [199]. CNVs are a sort of alteration in which sections of DNA are deleted or duplicated.

A machine-learning strategy was guided to detect absolute CNVs with greater precision than individual CNV callers [200]. This strategy can be achieved by learning genomic characteristics from a limited subset of verified CNVs and using data (CNV calls) from many existing CNV detection algorithms.

For medical genetics and research, improvements in reliably identifying this class of variations are critical. CNVs [201] make up about 4.8–9.5 percent of the genome. Some of these have little influence on health, and others are linked to various hereditary and spontaneous genetic illnesses.

Splice sites, transcription start sites, promoters, and enhancers are examples of features that are identified and classified using machine-learning methods [202]. Because these genetic traits are linked to crucial functional, structural, and regulatory pathways, identifying them accurately is critical for clinical genome analysis.

Through tools like Polyphen, Mutation Taster, and CADD, algorithms use probabilities learned from labeled genomic data to form the degree of protein disruption caused by a given variant [203-205].

Other tools, such as Examiner and eXtasy, score and rank disease-causing variants using phenotype and genotype data. Differentiation is a challenge for clinical genomics laboratories.

Different predictions can be made using in silico tools. Discordant results could be due to variation in the datasets that underpin the devices, user-defined variables, or varying algorithm performance characteristics. Researchers have performed a study to distinguish between the performance of various tools and identify algorithm combinations that improve concordance. These prediction programs are frequently updated. While the training datasets improve and machine-learning technology advances, more will be released.

Drug discovery through AI/ML

Many pharmaceutical corporations have invested resources in this area because of the possibility to integrate machine-learning models through all the phases of drug discovery [206]. The chances of this report disallow for a detailed analysis of this action. ML is being used on these datasets in genomics for a variety of reasons, including defining disease subtypes, finding biomarkers of diseases, drug discovery [206] and repurposing [207], and medication response prediction [208].

Many large pharmaceutical businesses are working on AI-related research and development programs or collaborations. AstraZeneca and Benevolent, for example, are using AI to speed up the discovery of new potential drug targets by combining genomes, chemistry, and clinical data. GlaxoSmithKline (GSK) has invested in the biotechnology company 23andMe, acquiring entry to the company's datasets in order to use machine learning to discover pharmacological targets. The drugmaker has also developed collaborations with AI drug discovery businesses.

An additional area of therapeutics research aided by machine learning is genome editing, which involves removing, adding, or altering parts of DNA. The advent of targeted treatment has made growth in precision medicine [209].

Genome-editing techniques are increasingly employed for therapeutic purposes, such as replacing or altering a faulty gene in patients. The study better understands the significance of genes and DNA sequences.

CRISPR is the most flexible, cost-effective, and straightforward technology for genome editing currently available. It is trained with ML and DL algorithms to improve its efficiency and accuracy (Fig. 3).

Fig. 3

A hypothetical illustration of CRISPR gene editing through a machine-learning computational model

ML algorithmic approaches have been devised to forecast the activity of the editing system [210, 211], the precise differences caused by edits [210], and off-target consequences such as unintentional DNA alternation that might hamper the technology [211]. Advancement in silico prediction will be critical for developing experimental disease models and speeding up and notifying the development of safer and more precise medicines.

For these reasons, pharmaceutical corporations are prioritizing CRISPR technologies. GSK has announced a multi-million-dollar agreement with the University of California to build a CRISPR laboratory, with GSK's artificial intelligence section supporting data analysis.

Conclusion

Precision medicine is advancing, though there are still many challenges. The challenges include additional new equipment, public health systems, databases, and approaches to effectively augment networking and interoperability of clinical, laboratory, advanced technologies, problems in healthcare, and omics data. This area of medicine needs more effective data handling, which includes previously extracted consensus and actionable data. Extracting medical data from clinical systems, identifying unique and unknown functional variants, metabolite penetrance using listed features, scrutinizing relationships between metabolite levels and genomic variations, or analyzing biochemical pathways in metabolites with multimolecular patterns, all of these majority of current efforts are manual and time consuming. Promoting a healthy lifestyle and discovering creative techniques to identify, prevent, and treat diseases that commonly affect people are two public health goals. The advancement of precision medicine and the arrival of artificial intelligence in health care are heading toward an individualistic rather than a population-based approach to disease control [147]. Precision medicine, artificial intelligence, and the detailed information of disease conditions present a considerable chance to reduce costs for a one-size-fits-all and piecemeal approach to public health thinking and programming.

The quantity and breadth of applications for AI in genomics, on the other hand, are fast growing.

While AI has not yet produced a watershed moment in clinical genomics analysis, it makes significant contributions to the quality and accuracy of predictions made throughout the genomes analysis pipeline. Given the rising scope and pace of action, these changes could collectively result in significant improvement. The advantages provided by AI models for analyzing ample, complicated biomedical information have massive potential for speeding up genetic medicine breakthroughs. The future biotechnology will bring promising development through ML in the field of medicine [212].

The primary difficulty will be bridging the research-to-clinic divide as machine learning, and deep learning accelerates the pace of discoveries. Despite its enormous potential, numerous obstacles must be overcome if AI lives up to the lofty expectations of revolutionizing genomic medicine.

ML algorithms	Contributions
1. SVM	SVM classify and analyze symptoms to develop better diagnostic accuracy. The other contributions of SVM in precision medicine include identifying biomarkers of neurological and psychological diseases and analyzing SNPs to validate multiple myeloma and breast cancer. Clinical, pathological, and epidemiological data are analyzed by SVM to resist breast and cervical cancer. It analyzes clinical, molecular, and genomic data to validate oral cancer and diagnose mental disease [42–44]
2. Deep Learning	It is a commonly used algorithm in medicine. Generally, Deep Learning is utilized to analyzed images from different healthcare sectors, but it was highly employed in oncology. The algorithm was implemented to analyze lung cancer, CT scan, and MRI of the abdominal and pelvic area, colonoscopy, mammography, brain scan for brain tumors, radiation oncology, skin cancer, biopsy sample visualize, ultrasound of biopsy sample of prostate tumor, radiographs of malignant lung nodules, glioma through histopathological scanning, and biomarker data and sequencing (DNA and RNA). Moreover, it was also applied in the diagnostic process of many diseases, for instance, diabetic retinopathy, nodular BCC, histopathological anticipation in women with cytological deformations, dermal nevus and seborrheic keratosis, cardiac abnormalities, and cardiac muscle failure by analyzing MRI of ventricles of the heart [45–49]
3. Logistic Regression	This algorithm can evaluate the potential risk of several complex diseases such as breast cancer and tuberculosis. It also contributes to assessing patient survival rates and identifying cardiovascular disease. By analyzing prognostic factors, it can identify pulmonary thromboembolism (PTE) and non-lymphoma Hodgkin's diagnosis. [50–56]
4. Discriminant analysis	Application of discriminant analysis algorithm in medicine includes classification of patients for operation process, patients' symptom-relief satisfaction data, diagnosis of primary immunodeficiencies, BOLD MRI response classification to naturalistic movie stimuli, depression elements in cancer patients, and identifying protein-coding regions of cancer patients [57–63]
5. Decision Tree	This machine-learning algorithm is well applied for real-time healthcare monitoring, detecting and sensor aberrant data, data-extracting model for pollution prediction, and therapeutic decision support system. Some real-time application of decision tree algorithm includes challenges in order alternate therapies in oncology patients, identifying predictors of health outcomes, supporting clinical decisions, diagnosing hypertension through finding factors, locating genes associated with pressure ulcers (PUs) among elderly patients, therapeutic decision making in psychological patients, stratifying patient’s data in order to interpret decision making for precision medicine, finding the potential patients of telehealth services, diabetic foot amputation risk, and lastly it analyzes contents to help patients in medical decision [64–71]
6. Random Forest	This algorithm has been widely employed in several parts of the healthcare system. The reported contributions of this algorithm include prediction of metabolic pathways of individuals, predicting results of a patient’s encounter with psychiatrist, mortality prediction of ICU patients, classification and diagnosis of Alzheimer’s disease monitoring medical wireless sensors, detecting knee osteoarthritis, healthcare cost prediction, diagnosing mental illness, identifying non-medical factors related to health, predicting the risk of emergency admission, forecasting disease risks from clinical error data, finding factor accompanied with diabetic peripheral neuropathy diagnosis, identification of patients who are ready to get discharged from ICU, detecting depression Alzheimer patients, and diagnosing sleep disorders and non-assumptive diverse treatment effects [72–82]
7. Liner Regression	The reported contributions of this algorithm have been implemented in healthcare for several computational analyses and predictions, from monitoring treatment prescribing patterns, predicting hand surgery, decreasing the excess expenses of the healthcare system, analyzing imbalanced clinical cost data, detection of prognostically relevant risk factors, averaging decision making in healthcare, understanding the prevalence pattern of HIV, and ensuring its appropriateness [83–89]
8. Naïve Bayes	This algorithm is being used in distinct areas of medicine such as predicting risks by identifying Mucopolysaccharidosis type II, utilizing censored and time-to-event data, classifying EHR, shaping clinical diagnosis for decision support, extracting genome-wide data to identify Alzheimer's disease, modeling a decision related to cardiovascular disease, measuring quality healthcare services, constructing a predictive model for cancer in brain, asthma, prostate, and breast. [90–99]
9. KNN	KNN has been employed in various scientific domains, although it has just a few uses in the healthcare system. It was implemented in preserving the confidential information of clinical prediction in the e-Health cloud, pattern classification for breast cancer diagnosis, pancreatic cancer prediction using published literature, modeling diagnostic performance, detection of gastric cancer, pattern classification for health monitoring applications, medical dataset classification, and EHR data are some examples of real-time examples [100–105]
10. HMM	HMM algorithm was implemented in different areas of medicines, and its real-time contribution includes extraction of drug's side effects from online healthcare forums; decreasing the healthcare expenses; examine data on personal health check-up; observing circadian in telemetric activity data; clustering and modeling patient journey in medical; scrutinizing healthcare service utilization after injuries through transport system, analyzing infant cry signals and anticipating individuals entering countries with a large number of asynchronies [106–112]
11. Genetic Algorithm	It has vigorously contributed to the field of medicine. The reported contributions were observed in oncology, radiology, endocrinology, pediatrics, cardiology, pulmonology, surgery, infectious disease, neurology, orthopedics, gynecology, and many more