An end-to-end heterogeneous graph attention network for Mycobacterium tuberculosis drug-resistance prediction

Graph Attention Network-Based Prediction of Drug-Gene Interactions of Signal Transducer and Activator of Transcription (STAT) Receptor in Periodontal Regeneration

Introduction The signal transducer and activator of transcription-1 (STAT-1) are tightly controlled signaling pathways, with induced genes acting as positive and negative regulators. Persistent activation of the signal transducer and activator of transcription (STATs), particularly signal transducer and activator of transcription-3 (STAT-3) and signal transducer and activator of transcription-5 (STAT-5), is common in human tumors and cell lines. STAT molecules act as transcription factors, regulated by ligands like interferon-α (IFN-α), interferon-γ (IFN-γ), epidermal growth factor (EGF), platelet-derived growth factor (PDGF), interleukin-6 (IL-6) and interleukin-27 (IL-27). STAT-1 mutations can cause infections like periodontitis, a chronic inflammatory disease affecting gum tissue and bone. STAT-1 drug-gene interactions are being studied for therapeutic applications. Our study aims to predict drug-gene interactions of STAT-1 receptors in periodontal inflammation using graph attention networks (GATs). Methodology The study used a dataset of 215 drug-gene interactions to train and test a GAT model. The data was cleaned and normalized before being subjected to GATs using the Python library. Cytoscape and cytoHubba were used to visualize and analyze biological networks, including drug-gene interactome networks. The GAT model consisted of two graph attention layers, with the first layer producing eight features and the second layer aggregating outputs for binary classification. The model was trained using the Adam optimizer and CrossEntropyLoss function. Results The drug-gene interactome network, analyzed using Cytoscape, had 657 nodes, 1591 edges, and 4.755 neighbors. The predictive GAT model had low accuracy due to data availability and complexity. Conclusion The GAT model for drug-gene interactions in periodontal inflammation had low accuracy due to data limitations, complexity, and inability to capture all relevant features.

AI-Driven Thoracic X-ray Diagnostics: Transformative Transfer Learning for Clinical Validation in Pulmonary Radiography

Our research evaluates advanced artificial (AI) methodologies to enhance diagnostic accuracy in pulmonary radiography. Utilizing DenseNet121 and ResNet50, we analyzed 108,948 chest X-ray images from 32,717 patients and DenseNet121 achieved an area under the curve (AUC) of 94% in identifying the conditions of pneumothorax and oedema. The model's performance surpassed that of expert radiologists, though further improvements are necessary for diagnosing complex conditions such as emphysema, effusion, and hernia. Clinical validation integrating Latent Dirichlet Allocation (LDA) and Named Entity Recognition (NER) demonstrated the potential of natural language processing (NLP) in clinical workflows. The NER system achieved a precision of 92% and a recall of 88%. Sentiment analysis using DistilBERT provided a nuanced understanding of clinical notes, which is essential for refining diagnostic decisions. XGBoost and SHapley Additive exPlanations (SHAP) enhanced feature extraction and model interpretability. Local Interpretable Model-agnostic Explanations (LIME) and occlusion sensitivity analysis further enriched transparency, enabling healthcare providers to trust AI predictions. These AI techniques reduced processing times by 60% and annotation errors by 75%, setting a new benchmark for efficiency in thoracic diagnostics. The research explored the transformative potential of AI in medical imaging, advancing traditional diagnostics and accelerating medical evaluations in clinical settings.

Tackling the Antimicrobial Resistance "Pandemic" with Machine Learning Tools: A Summary of Available Evidence

Antimicrobial resistance is recognised as one of the top threats healthcare is bound to face in the future. There have been various attempts to preserve the efficacy of existing antimicrobials, develop new and efficient antimicrobials, manage infections with multi-drug resistant strains, and improve patient outcomes, resulting in a growing mass of routinely available data, including electronic health records and microbiological information that can be employed to develop individualised antimicrobial stewardship. Machine learning methods have been developed to predict antimicrobial resistance from whole-genome sequencing data, forecast medication susceptibility, recognise epidemic patterns for surveillance purposes, or propose new antibacterial treatments and accelerate scientific discovery. Unfortunately, there is an evident gap between the number of machine learning applications in science and the effective implementation of these systems. This narrative review highlights some of the outstanding opportunities that machine learning offers when applied in research related to antimicrobial resistance. In the future, machine learning tools may prove to be superbugs' kryptonite. This review aims to provide an overview of available publications to aid researchers that are looking to expand their work with new approaches and to acquaint them with the current application of machine learning techniques in this field.

Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes

The advent of rapid whole-genome sequencing has created new opportunities for computational prediction of antimicrobial resistance (AMR) phenotypes from genomic data. Both rule-based and machine learning (ML) approaches have been explored for this task, but systematic benchmarking is still needed. Here, we evaluated four state-of-the-art ML methods (Kover, PhenotypeSeeker, Seq2Geno2Pheno and Aytan-Aktug), an ML baseline and the rule-based ResFinder by training and testing each of them across 78 species-antibiotic datasets, using a rigorous benchmarking workflow that integrates three evaluation approaches, each paired with three distinct sample splitting methods. Our analysis revealed considerable variation in the performance across techniques and datasets. Whereas ML methods generally excelled for closely related strains, ResFinder excelled for handling divergent genomes. Overall, Kover most frequently ranked top among the ML approaches, followed by PhenotypeSeeker and Seq2Geno2Pheno. AMR phenotypes for antibiotic classes such as macrolides and sulfonamides were predicted with the highest accuracies. The quality of predictions varied substantially across species-antibiotic combinations, particularly for beta-lactams; across species, resistance phenotyping of the beta-lactams compound, aztreonam, amoxicillin/clavulanic acid, cefoxitin, ceftazidime and piperacillin/tazobactam, alongside tetracyclines demonstrated more variable performance than the other benchmarked antibiotics. By organism, Campylobacter jejuni and Enterococcus faecium phenotypes were more robustly predicted than those of Escherichia coli, Staphylococcus aureus, Salmonella enterica, Neisseria gonorrhoeae, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Streptococcus pneumoniae and Mycobacterium tuberculosis. In addition, our study provides software recommendations for each species-antibiotic combination. It furthermore highlights the need for optimization for robust clinical applications, particularly for strains that diverge substantially from those used for training.

Deep learning for precise diagnosis and subtype triage of drug-resistant tuberculosis on chest computed tomography

Deep learning, transforming input data into target prediction through intricate network structures, has inspired novel exploration in automated diagnosis based on medical images. The distinct morphological characteristics of chest abnormalities between drug-resistant tuberculosis (DR-TB) and drug-sensitive tuberculosis (DS-TB) on chest computed tomography (CT) are of potential value in differential diagnosis, which is challenging in the clinic. Hence, based on 1176 chest CT volumes from the equal number of patients with tuberculosis (TB), we presented a Deep learning-based system for TB drug resistance identification and subtype classification (DeepTB), which could automatically diagnose DR-TB and classify crucial subtypes, including rifampicin-resistant tuberculosis, multidrug-resistant tuberculosis, and extensively drug-resistant tuberculosis. Moreover, chest lesions were manually annotated to endow the model with robust power to assist radiologists in image interpretation and the Circos revealed the relationship between chest abnormalities and specific types of DR-TB. Finally, DeepTB achieved an area under the curve (AUC) up to 0.930 for thoracic abnormality detection and 0.943 for DR-TB diagnosis. Notably, the system demonstrated instructive value in DR-TB subtype classification with AUCs ranging from 0.880 to 0.928. Meanwhile, class activation maps were generated to express a human-understandable visual concept. Together, showing a prominent performance, DeepTB would be impactful in clinical decision-making for DR-TB.

TB-DROP: deep learning-based drug resistance prediction of Mycobacterium tuberculosis utilizing whole genome mutations

The most widely practiced strategy for constructing the deep learning (DL) prediction model for drug resistance of Mycobacterium tuberculosis (MTB) involves the adoption of ready-made and state-of-the-art architectures usually proposed for non-biological problems. However, the ultimate goal is to construct a customized model for predicting the drug resistance of MTB and eventually for the biological phenotypes based on genotypes. Here, we constructed a DL training framework to standardize and modularize each step during the training process using the latest tensorflow 2 API. A systematic and comprehensive evaluation of each module in the three currently representative models, including Convolutional Neural Network, Denoising Autoencoder, and Wide & Deep, which were adopted by CNNGWP, DeepAMR, and WDNN, respectively, was performed in this framework regarding module contributions in order to assemble a novel model with proper dedicated modules. Based on the whole-genome level mutations, a de novo learning method was developed to overcome the intrinsic limitations of previous models that rely on known drug resistance-associated loci. A customized DL model with the multilayer perceptron architecture was constructed and achieved a competitive performance (the mean sensitivity and specificity were 0.90 and 0.87, respectively) compared to previous ones. The new model developed was applied in an end-to-end user-friendly graphical tool named TB-DROP (TuBerculosis Drug Resistance Optimal Prediction: https://github.com/nottwy/TB-DROP ), in which users only provide sequencing data and TB-DROP will complete analysis within several minutes for one sample. Our study contributes to both a new strategy of model construction and clinical application of deep learning-based drug-resistance prediction methods.

Application of Graphs in a One Health Framework

The One Health framework, which advocates the crucial interconnection between environmental, animal, and human health and well-being, is becoming of increasing importance and acceptance in health sciences over the last years. The hottest public health topics of the latest years, like zoonotic diseases (e.g., the recent pandemic) or the increasing antibiotic resistance, characterized by many as "pandemic of the future," make the more holistic and combinatorial approach of One Health a necessity to combat such complex problems. Multiple graphs and graph theory have found applications in health sciences for many years, and they can now extend to usage across all levels of a One Health approach to health, ranging from genome, one disease level, to epidemiology and ecosystem graphs. For that last ecosystem layer, a proposed approach is the utilization of process graphs from the chemical engineering field, in order to understand a whole system and what constitute the most crucial aspects of a One Health issue in ecosystem level. Here P-graphs are focused alongside their combinatorial algorithms, implemented in R, and their application researched in an effort to extract information and plan interventions.

The Application of Artificial Intelligence in the Diagnosis and Drug Resistance Prediction of Pulmonary Tuberculosis

With the increasing incidence and mortality of pulmonary tuberculosis, in addition to tough and controversial disease management, time-wasting and resource-limited conventional approaches to the diagnosis and differential diagnosis of tuberculosis are still awkward issues, especially in countries with high tuberculosis burden and backwardness. In the meantime, the climbing proportion of drug-resistant tuberculosis poses a significant hazard to public health. Thus, auxiliary diagnostic tools with higher efficiency and accuracy are urgently required. Artificial intelligence (AI), which is not new but has recently grown in popularity, provides researchers with opportunities and technical underpinnings to develop novel, precise, rapid, and automated implements for pulmonary tuberculosis care, including but not limited to tuberculosis detection. In this review, we aimed to introduce representative AI methods, focusing on deep learning and radiomics, followed by definite descriptions of the state-of-the-art AI models developed using medical images and genetic data to detect pulmonary tuberculosis, distinguish the infection from other pulmonary diseases, and identify drug resistance of tuberculosis, with the purpose of assisting physicians in deciding the appropriate therapeutic schedule in the early stage of the disease. We also enumerated the challenges in maximizing the impact of AI in this field such as generalization and clinical utility of the deep learning models.

Drug resistance prediction and resistance genes identification in Mycobacterium tuberculosis based on a hierarchical attentive neural network utilizing genome-wide variants

Prediction of antimicrobial resistance based on whole-genome sequencing data has attracted greater attention due to its rapidity and convenience. Numerous machine learning-based studies have used genetic variants to predict drug resistance in Mycobacterium tuberculosis (MTB), assuming that variants are homogeneous, and most of these studies, however, have ignored the essential correlation between variants and corresponding genes when encoding variants, and used a limited number of variants as prediction input. In this study, taking advantage of genome-wide variants for drug-resistance prediction and inspired by natural language processing, we summarize drug resistance prediction into document classification, in which variants are considered as words, mutated genes in an isolate as sentences, and an isolate as a document. We propose a novel hierarchical attentive neural network model (HANN) that helps discover drug resistance-related genes and variants and acquire more interpretable biological results. It captures the interaction among variants in a mutated gene as well as among mutated genes in an isolate. Our results show that for the four first-line drugs of isoniazid (INH), rifampicin (RIF), ethambutol (EMB) and pyrazinamide (PZA), the HANN achieves the optimal area under the ROC curve of 97.90, 99.05, 96.44 and 95.14% and the optimal sensitivity of 94.63, 96.31, 92.56 and 87.05%, respectively. In addition, without any domain knowledge, the model identifies drug resistance-related genes and variants consistent with those confirmed by previous studies, and more importantly, it discovers one more potential drug-resistance-related gene.