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

Potential of Artificial Intelligence to Accelerate Drug Development for Rare Diseases

The growth in breadth and depth of artificial intelligence (AI) applications has been fast, running hand in hand with the increasing amount of digital data available. Here, we comment on the application of AI in the field of drug development, with a strong focus on the specific achievements and challenges posed by rare diseases. Data paucity and high costs make drug development for rare diseases especially hard. AI can enable otherwise inaccessible approaches based on the large-scale integration of heterogeneous datasets and knowledge bases, guided by expert biological understanding. Obstacles still exist for the routine use of AI in the usually conservative pharmaceutical domain, which can easily become disillusioned. It is crucial to acknowledge that AI is a powerful, supportive tool that can assist but not replace human expertise in the various phases and aspects of drug discovery and development.

Supervised Machine Learning Methods for Seasonal Influenza Diagnosis

Influenza has been a stationary disease in Mexico since 2009, and this causes a high cost for the national public health system, including its detection using RT-qPCR tests, treatments, and absenteeism in the workplace. Despite influenza's relevance, the main clinical features to detect the disease defined by international institutions like the World Health Organization (WHO) and the United States Centers for Disease Control and Prevention (CDC) do not follow the same pattern in all populations. The aim of this work is to find a machine learning method to facilitate decision making in the clinical differentiation between positive and negative influenza patients, based on their symptoms and demographic features. The research sample consisted of 15480 records, including clinical and demographic data of patients with a positive/negative RT-qPCR influenza tests, from 2010 to 2020 in the public healthcare institutions of Mexico City. The performance of the methods for classifying influenza cases were evaluated with indices like accuracy, specificity, sensitivity, precision, the f1-measure and the area under the curve (AUC). Results indicate that random forest and bagging classifiers were the best supervised methods; they showed promise in supporting clinical diagnosis, especially in places where performing molecular tests might be challenging or not feasible.

Modern Methods of Diagnostics and Treatment of Neurodegenerative Diseases and Depression

This paper discusses the promising areas of research into machine learning applications for the prevention and correction of neurodegenerative and depressive disorders. These two groups of disorders are among the leading causes of decline in the quality of life in the world when estimated using disability-adjusted years. Despite decades of research, the development of new approaches for the assessment (especially pre-clinical) and correction of neurodegenerative diseases and depressive disorders remains among the priority areas of research in neurophysiology, psychology, genetics, and interdisciplinary medicine. Contemporary machine learning technologies and medical data infrastructure create new research opportunities. However, reaching a consensus on the application of new machine learning methods and their integration with the existing standards of care and assessment is still a challenge to overcome before the innovations could be widely introduced to clinics. The research on the development of clinical predictions and classification algorithms contributes towards creating a unified approach to the use of growing clinical data. This unified approach should integrate the requirements of medical professionals, researchers, and governmental regulators. In the current paper, the current state of research into neurodegenerative and depressive disorders is presented.

Deep learning can predict survival directly from histology in clear cell renal cell carcinoma

For clear cell renal cell carcinoma (ccRCC) risk-dependent diagnostic and therapeutic algorithms are routinely implemented in clinical practice. Artificial intelligence-based image analysis has the potential to improve outcome prediction and thereby risk stratification. Thus, we investigated whether a convolutional neural network (CNN) can extract relevant image features from a representative hematoxylin and eosin-stained slide to predict 5-year overall survival (5y-OS) in ccRCC. The CNN was trained to predict 5y-OS in a binary manner using slides from TCGA and validated using an independent in-house cohort. Multivariable logistic regression was used to combine of the CNNs prediction and clinicopathological parameters. A mean balanced accuracy of 72.0% (standard deviation [SD] = 7.9%), sensitivity of 72.4% (SD = 10.6%), specificity of 71.7% (SD = 11.9%) and area under receiver operating characteristics curve (AUROC) of 0.75 (SD = 0.07) was achieved on the TCGA training set (n = 254 patients / WSIs) using 10-fold cross-validation. On the external validation cohort (n = 99 patients / WSIs), mean accuracy, sensitivity, specificity and AUROC were 65.5% (95%-confidence interval [CI]: 62.9–68.1%), 86.2% (95%-CI: 81.8–90.5%), 44.9% (95%-CI: 40.2–49.6%), and 0.70 (95%-CI: 0.69–0.71). A multivariable model including age, tumor stage and metastasis yielded an AUROC of 0.75 on the TCGA cohort. The inclusion of the CNN-based classification (Odds ratio = 4.86, 95%-CI: 2.70–8.75, p < 0.01) raised the AUROC to 0.81. On the validation cohort, both models showed an AUROC of 0.88. In univariable Cox regression, the CNN showed a hazard ratio of 3.69 (95%-CI: 2.60–5.23, p < 0.01) on TCGA and 2.13 (95%-CI: 0.92–4.94, p = 0.08) on external validation. The results demonstrate that the CNN’s image-based prediction of survival is promising and thus this widely applicable technique should be further investigated with the aim of improving existing risk stratification in ccRCC.

Artificial Intelligence-Enabled Electrocardiography Predicts Left Ventricular Dysfunction and Future Cardiovascular Outcomes: A Retrospective Analysis

BACKGROUND: The ejection fraction (EF) provides critical information about heart failure (HF) and its management. Electrocardiography (ECG) is a noninvasive screening tool for cardiac electrophysiological activities that has been used to detect patients with low EF based on a deep learning model (DLM) trained via large amounts of data. However, no studies have widely investigated its clinical impacts. OBJECTIVE: This study developed a DLM to estimate EF via ECG (ECG-EF). We further investigated the relationship between ECG-EF and echo-based EF (ECHO-EF) and explored their contributions to future cardiovascular adverse events. METHODS: There were 57,206 ECGs with corresponding echocardiograms used to train our DLM. We compared a series of training strategies and selected the best DLM. The architecture of the DLM was based on ECG12Net, developed previously. Next, 10,762 ECGs were used for validation, and another 20,629 ECGs were employed to conduct the accuracy test. The changes between ECG-EF and ECHO-EF were evaluated. The primary follow-up adverse events included future ECHO-EF changes and major adverse cardiovascular events (MACEs). RESULTS: The sex-/age-matching strategy-trained DLM achieved the best area under the curve (AUC) of 0.9472 with a sensitivity of 86.9% and specificity of 89.6% in the follow-up cohort, with a correlation of 0.603 and a mean absolute error of 7.436. In patients with accurate prediction (initial difference < 10%), the change traces of ECG-EF and ECHO-EF were more consistent (R-square = 0.351) than in all patients (R-square = 0.115). Patients with lower ECG-EF (≤35%) exhibited a greater risk of cardiovascular (CV) complications, delayed ECHO-EF recovery, and earlier ECHO-EF deterioration than patients with normal ECG-EF (>50%). Importantly, ECG-EF demonstrated an independent impact on MACEs and all CV adverse outcomes, with better prediction of CV outcomes than ECHO-EF. CONCLUSIONS: The ECG-EF could be used to initially screen asymptomatic left ventricular dysfunction (LVD) and it could also independently contribute to the predictions of future CV adverse events. Although further large-scale studies are warranted, DLM-based ECG-EF could serve as a promising diagnostic supportive and management-guided tool for CV disease prediction and the care of patients with LVD.

Machine learning & deep learning in data-driven decision making of drug discovery and challenges in high-quality data acquisition in the pharmaceutical industry

Predicting novel small molecule bioactivities for the target deconvolution, hit-to-lead optimization in drug discovery research, requires molecular representation. Previous reports have demonstrated that machine learning (ML) and deep learning (DL) have substantial implications in virtual screening, peptide synthesis, drug ADMET screening and biomarker discovery. These strategies can increase the positive outcomes in the drug discovery process without false-positive rates and can be achieved in a cost-effective way with a minimum duration of time by high-quality data acquisition. This review substantially discusses the recent updates in AI tools as cheminformatics application in medicinal chemistry for the data-driven decision making of drug discovery and challenges in high-quality data acquisition in the pharmaceutical industry while improving small-molecule bioactivities and properties.