Drug Repurposing Prediction for Immune-Mediated Cutaneous Diseases using a Word-Embedding-Based Machine Learning Approach

Artificial Intelligence: A Snapshot of Its Application in Chronic Inflammatory and Autoimmune Skin Diseases

Immuno-correlated dermatological pathologies refer to skin disorders that are closely associated with immune system dysfunction or abnormal immune responses. Advancements in the field of artificial intelligence (AI) have shown promise in enhancing the diagnosis, management, and assessment of immuno-correlated dermatological pathologies. This intersection of dermatology and immunology plays a pivotal role in comprehending and addressing complex skin disorders with immune system involvement. The paper explores the knowledge known so far and the evolution and achievements of AI in diagnosis; discusses segmentation and the classification of medical images; and reviews existing challenges, in immunological-related skin diseases. From our review, the role of AI has emerged, especially in the analysis of images for both diagnostic and severity assessment purposes. Furthermore, the possibility of predicting patients' response to therapies is emerging, in order to create tailored therapies.

Application of artificial intelligence and machine learning in drug repurposing

The purpose of drug repurposing is to leverage previously approved drugs for a particular disease indication and apply them to another disease. It can be seen as a faster and more cost-effective approach to drug discovery and a powerful tool for achieving precision medicine. In addition, drug repurposing can be used to identify therapeutic candidates for rare diseases and phenotypic conditions with limited information on disease biology. Machine learning and artificial intelligence (AI) methodologies have enabled the construction of effective, data-driven repurposing pipelines by integrating and analyzing large-scale biomedical data. Recent technological advances, especially in heterogeneous network mining and natural language processing, have opened up exciting new opportunities and analytical strategies for drug repurposing. In this review, we first introduce the challenges in repurposing approaches and highlight some success stories, including those during the COVID-19 pandemic. Next, we review some existing computational frameworks in the literature, organized on the basis of the type of biomedical input data analyzed and the computational algorithms involved. In conclusion, we outline some exciting new directions that drug repurposing research may take, as pioneered by the generative AI revolution.

Artificial intelligence in psoriasis: Where we are and where we are going

Artificial intelligence (AI) is a field of computer science that involves the development of programs designed to replicate human cognitive processes and the analysis of complex data. In dermatology, which is predominantly a visual-based diagnostic field, AI has become increasingly important in improving professional processes, particularly in the diagnosis of psoriasis. In this review, we summarized current AI applications in psoriasis: (i) diagnosis, including identification, classification, lesion segmentation, lesion severity and area scoring; (ii) treatment, including prediction treatment efficiency and prediction candidate drugs; (iii) management, including e-health and preventive medicine. Key challenges and future aspects of AI in psoriasis were also discussed, in hope of providing potential directions for future studies.

Current state and prospects of artificial intelligence in allergy

The field of medicine is witnessing an exponential growth of interest in artificial intelligence (AI), which enables new research questions and the analysis of larger and new types of data. Nevertheless, applications that go beyond proof of concepts and deliver clinical value remain rare, especially in the field of allergy. This narrative review provides a fundamental understanding of the core concepts of AI and critically discusses its limitations and open challenges, such as data availability and bias, along with potential directions to surmount them. We provide a conceptual framework to structure AI applications within this field and discuss forefront case examples. Most of these applications of AI and machine learning in allergy concern supervised learning and unsupervised clustering, with a strong emphasis on diagnosis and subtyping. A perspective is shared on guidelines for good AI practice to guide readers in applying it effectively and safely, along with prospects of field advancement and initiatives to increase clinical impact. We anticipate that AI can further deepen our knowledge of disease mechanisms and contribute to precision medicine in allergy.

Therapeutic application of machine learning in psoriasis: A Prisma systematic review

Dermatology, being a predominantly visual-based diagnostic field, has found itself to be at the epitome of artificial intelligence (AI)-based advances. Machine learning (ML), a subset of AI, goes a step further by recognizing patterns from data and teaches machines to automatically learn tasks. Although artificial intelligence in dermatology is mostly developed in melanoma and skin cancer diagnosis, advances in AI and ML have gone far ahead and found its application in ulcer assessment, psoriasis, atopic dermatitis, onychomycosis, etc. This article is focused on the application of ML in the therapeutic aspect of psoriasis.

The role of machine learning in developing non-magnetic resonance imaging based biomarkers for multiple sclerosis: a systematic review

Background

Multiple sclerosis (MS) is a neurological condition whose symptoms, severity, and progression over time vary enormously among individuals. Ideally, each person living with MS should be provided with an accurate prognosis at the time of diagnosis, precision in initial and subsequent treatment decisions, and improved timeliness in detecting the need to reassess treatment regimens. To manage these three components, discovering an accurate, objective measure of overall disease severity is essential. Machine learning (ML) algorithms can contribute to finding such a clinically useful biomarker of MS through their ability to search and analyze datasets about potential biomarkers at scale. Our aim was to conduct a systematic review to determine how, and in what way, ML has been applied to the study of MS biomarkers on data from sources other than magnetic resonance imaging.

Methods

Systematic searches through eight databases were conducted for literature published in 2014–2020 on MS and specified ML algorithms.

Results

Of the 1, 052 returned papers, 66 met the inclusion criteria. All included papers addressed developing classifiers for MS identification or measuring its progression, typically, using hold-out evaluation on subsets of fewer than 200 participants with MS. These classifiers focused on biomarkers of MS, ranging from those derived from omics and phenotypical data (34.5% clinical, 33.3% biological, 23.0% physiological, and 9.2% drug response). Algorithmic choices were dependent on both the amount of data available for supervised ML (91.5%; 49.2% classification and 42.3% regression) and the requirement to be able to justify the resulting decision-making principles in healthcare settings. Therefore, algorithms based on decision trees and support vector machines were commonly used, and the maximum average performance of 89.9% AUC was found in random forests comparing with other ML algorithms.

Conclusions

ML is applicable to determining how candidate biomarkers perform in the assessment of disease severity. However, applying ML research to develop decision aids to help clinicians optimize treatment strategies and analyze treatment responses in individual patients calls for creating appropriate data resources and shared experimental protocols. They should target proceeding from segregated classification of signals or natural language to both holistic analyses across data modalities and clinically-meaningful differentiation of disease.

CHAC1 as a novel biomarker for distinguishing alopecia from other dermatological diseases and determining its severity

Alopecia Areata (AA) is characterised by an autoimmune response to hair follicles (HFs) and its exact pathobiology remains unclear. The current study aims to look into the molecular changes in the skin of AA patients as well as the potential underlying molecular mechanisms of AA in order to identify potential candidates for early detection and treatment of AA. We applied Weighted Gene Co-expression Network Analysis (WGCNA) to identify key modules, hub genes, and mRNA-miRNA regulatory networks associated with AA. Furthermore, Chi2 as a machine-learning algorithm was used to compute the gene importance in AA. Finally, drug-target construction revealed the potential of repositioning drugs for the treatment of AA. Our analysis using four AA data sets established a network strongly correlated to AA pathogenicity based on GZMA, OXCT2, HOXC13, KRT40, COMP, CHAC1, and KRT83 hub genes. Interestingly, machine learning introduced these genes as important in AA pathogenicity. Besides that, using another ten data sets, we showed that CHAC1 could clearly distinguish AA from similar clinical phenotypes, such as scarring alopecia due to psoriasis. Also, two FDA-approved drug candidates and 30 experimentally validated miRNAs were identified that affected the co-expression network. Using transcriptome analysis, suggested CHAC1 as a potential diagnostic predictor to diagnose AA.

Big data analyses and individual health profiling in the arena of rheumatic and musculoskeletal diseases (RMDs)

Health care processes are under constant development and will need to embrace advances in technology and health science aiming to provide optimal care. Considering the perspective of increasing treatment options for people with rheumatic and musculoskeletal diseases, but in many cases not reaching all treatment targets that matter to patients, care systems bare potential to improve on a holistic level. This review provides an overview of systems and technologies under evaluation over the past years that show potential to impact diagnosis and treatment of rheumatic diseases in about 10 years from now. We summarize initiatives and studies from the field of electronic health records, biobanking, remote monitoring, and artificial intelligence. The combination and implementation of these opportunities in daily clinical care will be key for a new era in care of our patients. This aims to inform rheumatologists and healthcare providers concerned with chronic inflammatory musculoskeletal conditions about current important and promising developments in science that might substantially impact the management processes of rheumatic diseases in the 2030s.

DDREL: From drug-drug relationships to drug repurposing

Analyzing the relationships among various drugs is an essential issue in the field of computational biology. Different kinds of informative knowledge, such as drug repurposing, can be extracted from drug-drug relationships. Scientific literature represents a rich source for the retrieval of knowledge about the relationships between biological concepts, mainly drug-drug, disease-disease, and drug-disease relationships. In this paper, we propose DDREL as a general-purpose method that applies deep learning on scientific literature to automatically extract the graph of syntactic and semantic relationships among drugs. DDREL remarkably outperforms the existing human drug network method and a random network respected to average similarities of drugs’ anatomical therapeutic chemical (ATC) codes. DDREL is able to shed light on the existing deficiency of the ATC codes in various drug groups. From the DDREL graph, the history of drug discovery became visible. In addition, drugs that had repurposing score 1 (diflunisal, pargyline, fenofibrate, guanfacine, chlorzoxazone, doxazosin, oxymetholone, azathioprine, drotaverine, demecarium, omifensine, yohimbine) were already used in additional indication. The proposed DDREL method justifies the predictive power of textual data in PubMed abstracts. DDREL shows that such data can be used to 1- Predict repurposing drugs with high accuracy, and 2- Reveal existing deficiencies of the ATC codes in various drug groups.

A Study of the Recent Trends of Immunology: Key Challenges, Domains, Applications, Datasets, and Future Directions

The human immune system is very complex. Understanding it traditionally required specialized knowledge and expertise along with years of study. However, in recent times, the introduction of technologies such as AIoMT (Artificial Intelligence of Medical Things), genetic intelligence algorithms, smart immunological methodologies, etc., has made this process easier. These technologies can observe relations and patterns that humans do and recognize patterns that are unobservable by humans. Furthermore, these technologies have also enabled us to understand better the different types of cells in the immune system, their structures, their importance, and their impact on our immunity, particularly in the case of debilitating diseases such as cancer. The undertaken study explores the AI methodologies currently in the field of immunology. The initial part of this study explains the integration of AI in healthcare and how it has changed the face of the medical industry. It also details the current applications of AI in the different healthcare domains and the key challenges faced when trying to integrate AI with healthcare, along with the recent developments and contributions in this field by other researchers. The core part of this study is focused on exploring the most common classifications of health diseases, immunology, and its key subdomains. The later part of the study presents a statistical analysis of the contributions in AI in the different domains of immunology and an in-depth review of the machine learning and deep learning methodologies and algorithms that can and have been applied in the field of immunology. We have also analyzed a list of machine learning and deep learning datasets about the different subdomains of immunology. Finally, in the end, the presented study discusses the future research directions in the field of AI in immunology and provides some possible solutions for the same.

An introduction to machine learning and analysis of its use in rheumatic diseases

Machine learning (ML) is a computerized analytical technique that is being increasingly employed in biomedicine. ML often provides an advantage over explicitly programmed strategies in the analysis of multidimensional information by recognizing relationships in the data that were not previously appreciated. As such, the use of ML in rheumatology is increasing, and numerous studies have employed ML to classify patients with rheumatic autoimmune inflammatory diseases (RAIDs) from medical records and imaging, biometric or gene expression data. However, these studies are limited by sample size, the accuracy of sample labelling, and absence of datasets for external validation. In addition, there is potential for ML models to overfit or underfit the data and, thereby, these models might produce results that cannot be replicated in an unrelated dataset. In this Review, we introduce the basic principles of ML and discuss its current strengths and weaknesses in the classification of patients with RAIDs. Moreover, we highlight the successful analysis of the same type of input data (for example, medical records) with different algorithms, illustrating the potential plasticity of this analytical approach. Altogether, a better understanding of ML and the future application of advanced analytical techniques based on this approach, coupled with the increasing availability of biomedical data, may facilitate the development of meaningful precision medicine for patients with RAIDs.

Enriched Optimization Algorithm for Effective Skin Disease Prediction Using Soft Computing Techniques

In recent years, a usual worldwide problem is a skin disease—the diagnostics of infection and skin disease prediction based on the data mining techniques. The precise and cost-effective treatments obtain a technologybased data mining system that can consider making the right decision. Depends on data, there are 34 UCI datasets have in the skin disease prediction. All of the datasets are not much important when predicting the skin disease problem. In this study, the essential datasets to be analyzed because they only give the best accuracy in skin disease prediction. For an outstanding selection of allocation, to propose a novel feature selection approaches, Enriched Fruitfly Optimization Algorithm (EFOA), and Ensemble Classifiers that are helps for an early stage of skin disease prediction. A hybrid technique through the three essential hybrid feature selection approaches such as Chi-Square method, Information Gain method, and Principal Component Analysis (PCA) methods that are combined for better feature selection results. Based on the skin disease dataset, the resultant feature selection approach generated the reduced data subset. Then, the Enriched Fruitfly Optimization Algorithm (EFOA) offers the optimization of reduced data subset. Here, the accuracy estimation is the vital factor to optimize the effective and best prediction of skin disease affected regions. Afterward, the classification performs to classify the EFOA based optimized result by using the six different classification methods. Where, the classification helps to analyze the optimized results, which offers the better classification procedure. To predict the base learner’s performance, to utilize the Naive Bayesian, K-Nearest Neighbour, Decision Tree, Support Vector Machine, Random Forest, and Multilayer Perceptron (MLP) to classify the optimized result. Then, the ensemble techniques used to analyze the classifier’s results through the 3 different methods like Bagging, Boosting, Stacking, added on the base learners to improve the proposed work. Based on the performance, the base learners’ performance is larger than the input dataset. The base learner’s parameters are essential to calculate the accuracy of skin disease prediction performance. The performance of the proposed method will take and compare to each base learner, and the performance shows the accurate skin disease prediction improvement with other existing methods.

Modern computational intelligence based drug repurposing for diabetes epidemic

BACKGROUND AND AIM

Objectives are to explore recent advances in discovery of new antidiabetic agents using repurposing strategies and to discuss modern technologies used for drug repurposing highlighting diabetic specific web portal.

METHODS

Recent literature were studied and analyzed from various sources such as Scopus, PubMed, and IEEE Xplore databases.

RESULTS

Drugs like Niclosamideethanolamine, Methazolamide, Diacerein, Berberine, Clobetasol, etc. with possibility of repurposing to curb diabetes can be potential late-stage clinical candidates, providing access to information on pharmacology, formulation, and probable toxicity if any.

CONCLUSIONS

With collaboration of artificial intelligence (AI) with pharmacology, the efficiency of drug repurposing can improve significantly.

Advancement in predicting interactions between drugs used to treat psoriasis and its comorbidities by integrating molecular and clinical resources

OBJECTIVE

Drug-drug interactions (DDIs) can result in adverse and potentially life-threatening health consequences; however, it is challenging to predict potential DDIs in advance. We introduce a new computational approach to comprehensively assess the drug pairs which may be involved in specific DDI types by combining information from large-scale gene expression (984 transcriptomic datasets), molecular structure (2159 drugs), and medical claims (150 million patients).

MATERIALS AND METHODS

Features were integrated using ensemble machine learning techniques, and we evaluated the DDIs predicted with a large hospital-based medical records dataset. Our pipeline integrates information from >30 different resources, including >10 000 drugs and >1.7 million drug-gene pairs. We applied our technique to predict interactions between 37 611 drug pairs used to treat psoriasis and its comorbidities.

RESULTS

Our approach achieves >0.9 area under the receiver operator curve (AUROC) for differentiating 11 861 known DDIs from 25 750 non-DDI drug pairs. Significantly, we demonstrate that the novel DDIs we predict can be confirmed through independent data sources and supported using clinical medical records.

CONCLUSIONS

By applying machine learning and taking advantage of molecular, genomic, and health record data, we are able to accurately predict potential new DDIs that can have an impact on public health.

A computational workflow for the detection of candidate diagnostic biomarkers of Kawasaki disease using time-series gene expression data

Unlike autoimmune diseases, there is no known constitutive and disease-defining biomarker for systemic autoinflammatory diseases (SAIDs). Kawasaki disease (KD) is one of the "undiagnosed" types of SAIDs whose pathogenic mechanism and gene mutation still remain unknown. To address this issue, we have developed a sequential computational workflow which clusters KD patients with similar gene expression profiles across the three different KD phases (Acute, Subacute and Convalescent) and utilizes the resulting clustermap to detect prominent genes that can be used as diagnostic biomarkers for KD. Self-Organizing Maps (SOMs) were employed to cluster patients with similar gene expressions across the three phases through inter-phase and intra-phase clustering. Then, false discovery rate (FDR)-based feature selection was applied to detect genes that significantly deviate across the per-phase clusters. Our results revealed five genes as candidate biomarkers for KD diagnosis, namely, the HLA-DQB1, HLA-DRA, ZBTB48, TNFRSF13C, and CASD1. To our knowledge, these five genes are reported for the first time in the literature. The impact of the discovered genes for KD diagnosis against the known ones was demonstrated by training boosting ensembles (AdaBoost and XGBoost) for KD classification on common platform and cross-platform datasets. The classifiers which were trained on the proposed genes from the common platform data yielded an average increase by 4.40% in accuracy, 5.52% in sensitivity, and 3.57% in specificity than the known genes in the Acute and Subacute phases, followed by a notable increase by 2.30% in accuracy, 2.20% in sensitivity, and 4.70% in specificity in the cross-platform analysis.

Exploration of databases and methods supporting drug repurposing: a comprehensive survey

Drug development involves a deep understanding of the mechanisms of action and possible side effects of each drug, and sometimes results in the identification of new and unexpected uses for drugs, termed as drug repurposing. Both in case of serendipitous observations and systematic mechanistic explorations, confirmation of new indications for a drug requires hypothesis building around relevant drug-related data, such as molecular targets involved, and patient and cellular responses. These datasets are available in public repositories, but apart from sifting through the sheer amount of data imposing computational bottleneck, a major challenge is the difficulty in selecting which databases to use from an increasingly large number of available databases. The database selection is made harder by the lack of an overview of the types of data offered in each database. In order to alleviate these problems and to guide the end user through the drug repurposing efforts, we provide here a survey of 102 of the most promising and drug-relevant databases reported to date. We summarize the target coverage and types of data available in each database and provide several examples of how multi-database exploration can facilitate drug repurposing.

Machine Learning Applications in the Evaluation and Management of Psoriasis: A Systematic Review

Background

Machine learning (ML), a subset of artificial intelligence (AI) that aims to teach machines to automatically learn tasks by inferring patterns from data, holds significant promise to aid psoriasis care. Applications include evaluation of skin images for screening and diagnosis as well as clinical management including treatment and complication prediction.

Objective

To summarize literature on ML applications to psoriasis evaluation and management and to discuss challenges and opportunities for future advances.

Methods

We searched MEDLINE, Google Scholar, ACM Digital Library, and IEEE Xplore for peer-reviewed publications published in English through December 1, 2019. Our search queries identified publications with any of the 10 computing-related keywords and "psoriasis" in the title and/or abstract.

Results

Thirty-three studies were identified. Articles were organized by topic and synthesized as evaluation- or management-focused articles covering 5 content categories: (A) Evaluation using skin images: (1) identification and differential diagnosis of psoriasis lesions, (2) lesion segmentation, and (3) lesion severity and area scoring; (B) clinical management: (1) prediction of complications and (2) treatment.

Conclusion

Machine learning has significant potential to aid psoriasis evaluation and management. Current topics popular in ML research on psoriasis are the evaluation of medical images, prediction of complications, and treatment discovery. For patients to derive the greatest benefit from ML advancements, it is helpful for dermatologists to have an understanding of ML and how it can effectively aid their assessments and decision-making.

IFN-γ enhances cell-mediated cytotoxicity against keratinocytes via JAK2/STAT1 in lichen planus

Lichen planus (LP) is a chronic debilitating inflammatory disease of unknown etiology affecting the skin, nails, and mucosa with no current FDA-approved treatments. It is histologically characterized by dense infiltration of T cells and epidermal keratinocyte apoptosis. Using global transcriptomic profiling of patient skin samples, we demonstrate that LP is characterized by a type II interferon (IFN) inflammatory response. The type II IFN, IFN-γ, is demonstrated to prime keratinocytes and increase their susceptibility to CD8⁺ T cell-mediated cytotoxic responses through MHC class I induction in a coculture model. We show that this process is dependent on Janus kinase 2 (JAK2) and signal transducer and activator of transcription 1 (STAT1), but not JAK1 or STAT2 signaling. Last, using drug prediction algorithms, we identify JAK inhibitors as promising therapeutic agents in LP and demonstrate that the JAK1/2 inhibitor baricitinib fully protects keratinocytes against cell-mediated cytotoxic responses in vitro. In summary, this work elucidates the role and mechanisms of IFN-γ in LP pathogenesis and provides evidence for the therapeutic use of JAK inhibitors to limit cell-mediated cytotoxicity in patients with LP.

Machine Learning Applied to Diagnosis of Human Diseases: A Systematic Review

Human healthcare is one of the most important topics for society. It tries to find the correct effective and robust disease detection as soon as possible to patients receipt the appropriate cares. Because this detection is often a difficult task, it becomes necessary medicine field searches support from other fields such as statistics and computer science. These disciplines are facing the challenge of exploring new techniques, going beyond the traditional ones. The large number of techniques that are emerging makes it necessary to provide a comprehensive overview that avoids very particular aspects. To this end, we propose a systematic review dealing with the Machine Learning applied to the diagnosis of human diseases. This review focuses on modern techniques related to the development of Machine Learning applied to diagnosis of human diseases in the medical field, in order to discover interesting patterns, making non-trivial predictions and useful in decision-making. In this way, this work can help researchers to discover and, if necessary, determine the applicability of the machine learning techniques in their particular specialties. We provide some examples of the algorithms used in medicine, analysing some trends that are focused on the goal searched, the algorithm used, and the area of applications. We detail the advantages and disadvantages of each technique to help choose the most appropriate in each real-life situation, as several authors have reported. The authors searched Scopus, Journal Citation Reports (JCR), Google Scholar, and MedLine databases from the last decades (from 1980s approximately) up to the present, with English language restrictions, for studies according to the objectives mentioned above. Based on a protocol for data extraction defined and evaluated by all authors using PRISMA methodology, 141 papers were included in this advanced review.

Machine Learning in Dermatology: Current Applications, Opportunities, and Limitations

Machine learning (ML) has the potential to improve the dermatologist's practice from diagnosis to personalized treatment. Recent advancements in access to large datasets (e.g., electronic medical records, image databases, omics), faster computing, and cheaper data storage have encouraged the development of ML algorithms with human-like intelligence in dermatology. This article is an overview of the basics of ML, current applications of ML, and potential limitations and considerations for further development of ML. We have identified five current areas of applications for ML in dermatology: (1) disease classification using clinical images; (2) disease classification using dermatopathology images; (3) assessment of skin diseases using mobile applications and personal monitoring devices; (4) facilitating large-scale epidemiology research; and (5) precision medicine. The purpose of this review is to provide a guide for dermatologists to help demystify the fundamentals of ML and its wide range of applications in order to better evaluate its potential opportunities and challenges.