A vision transformer based approach for analysis of plasmodium vivax life cycle for malaria prediction using thin blood smear microscopic images

AI-powered microscopy image analysis for parasitology: integrating human expertise

Microscopy image analysis plays a pivotal role in parasitology research. Deep learning (DL), a subset of artificial intelligence (AI), has garnered significant attention. However, traditional DL-based methods for general purposes are data-driven, often lacking explainability due to their black-box nature and sparse instructional resources. To address these challenges, this article presents a comprehensive review of recent advancements in knowledge-integrated DL models tailored for microscopy image analysis in parasitology. The massive amounts of human expert knowledge from parasitologists can enhance the accuracy and explainability of AI-driven decisions. It is expected that the adoption of knowledge-integrated DL models will open up a wide range of applications in the field of parasitology.

The Impact of Artificial Intelligence on Microbial Diagnosis

Traditional microbial diagnostic methods face many obstacles such as sample handling, culture difficulties, misidentification, and delays in determining susceptibility. The advent of artificial intelligence (AI) has markedly transformed microbial diagnostics with rapid and precise analyses. Nonetheless, ethical considerations accompany AI adoption, necessitating measures to uphold patient privacy, mitigate biases, and ensure data integrity. This review examines conventional diagnostic hurdles, stressing the significance of standardized procedures in sample processing. It underscores AI's significant impact, particularly through machine learning (ML), in microbial diagnostics. Recent progressions in AI, particularly ML methodologies, are explored, showcasing their influence on microbial categorization, comprehension of microorganism interactions, and augmentation of microscopy capabilities. This review furnishes a comprehensive evaluation of AI's utility in microbial diagnostics, addressing both advantages and challenges. A few case studies including SARS-CoV-2, malaria, and mycobacteria serve to illustrate AI's potential for swift and precise diagnosis. Utilization of convolutional neural networks (CNNs) in digital pathology, automated bacterial classification, and colony counting further underscores AI's versatility. Additionally, AI improves antimicrobial susceptibility assessment and contributes to disease surveillance, outbreak forecasting, and real-time monitoring. Despite a few limitations, integration of AI in diagnostic microbiology presents robust solutions, user-friendly algorithms, and comprehensive training, promising paradigm-shifting advancements in healthcare.

From microscope to micropixels: A rapid review of artificial intelligence for the peripheral blood film

Artificial intelligence (AI) and its application in classification of blood cells in the peripheral blood film is an evolving field in haematology. We performed a rapid review of the literature on AI and peripheral blood films, evaluating the condition studied, image datasets, machine learning models, training set size, testing set size and accuracy. A total of 283 studies were identified, encompassing 6 broad domains: malaria (n = 95), leukemia (n = 81), leukocytes (n = 72), mixed (n = 25), erythrocytes (n = 15) or Myelodysplastic syndrome (MDS) (n = 1). These publications have demonstrated high self-reported mean accuracy rates across various studies (95.5% for malaria, 96.0% for leukemia, 94.4% for leukocytes, 95.2% for mixed studies and 91.2% for erythrocytes), with an overall mean accuracy of 95.1%. Despite the high accuracy, the challenges toward real world translational usage of these AI trained models include the need for well-validated multicentre data, data standardisation, and studies on less common cell types and non-malarial blood-borne parasites.

Enhancing medical image analysis with unsupervised domain adaptation approach across microscopes and magnifications

In the domain of medical image analysis, deep learning models are heralding a revolution, especially in detecting complex and nuanced features characteristic of diseases like tumors and cancers. However, the robustness and adaptability of these models across varied imaging conditions and magnifications remain a formidable challenge. This paper introduces the Fourier Adaptive Recognition System (FARS), a pioneering model primarily engineered to address adaptability in malarial parasite recognition. Yet, the foundational principles guiding FARS lend themselves seamlessly to broader applications, including tumor and cancer diagnostics. FARS capitalizes on the untapped potential of transitioning from bounding box labels to richer semantic segmentation labels, enabling a more refined examination of microscopy slides. With the integration of adversarial training and the Color Domain Aware Fourier Domain Adaptation (F2DA), the model ensures consistent feature extraction across diverse microscopy configurations. The further inclusion of category-dependent context attention amplifies FARS's cross-domain versatility. Evidenced by a substantial elevation in cross-magnification performance from 31.3% mAP to 55.19% mAP and a 15.68% boost in cross-domain adaptability, FARS positions itself as a significant advancement in malarial parasite recognition. Furthermore, the core methodologies of FARS can serve as a blueprint for enhancing precision in other realms of medical image analysis, especially in the complex terrains of tumor and cancer imaging. The code is available at; https://github.com/Mr-TalhaIlyas/FARS.

Harnessing of Artificial Intelligence for the Diagnosis and Prevention of Hospital-Acquired Infections: A Systematic Review

Healthcare-associated infections (HAIs) are the most common adverse events in healthcare and constitute a major global public health concern. Surveillance represents the foundation for the effective prevention and control of HAIs, yet conventional surveillance is costly and labor intensive. Artificial intelligence (AI) and machine learning (ML) have the potential to support the development of HAI surveillance algorithms for the understanding of HAI risk factors, the improvement of patient risk stratification as well as the prediction and timely detection and prevention of infections. AI-supported systems have so far been explored for clinical laboratory testing and imaging diagnosis, antimicrobial resistance profiling, antibiotic discovery and prediction-based clinical decision support tools in terms of HAIs. This review aims to provide a comprehensive summary of the current literature on AI applications in the field of HAIs and discuss the future potentials of this emerging technology in infection practice. Following the PRISMA guidelines, this study examined the articles in databases including PubMed and Scopus until November 2023, which were screened based on the inclusion and exclusion criteria, resulting in 162 included articles. By elucidating the advancements in the field, we aim to highlight the potential applications of AI in the field, report related issues and shortcomings and discuss the future directions.

Interactive content-based image retrieval with deep learning for CT abdominal organ recognition

Objective.Recognizing the most relevant seven organs in an abdominal computed tomography (CT) slice requires sophisticated knowledge. This study proposed automatically extracting relevant features and applying them in a content-based image retrieval (CBIR) system to provide similar evidence for clinical use.Approach.A total of 2827 abdominal CT slices, including 638 liver, 450 stomach, 229 pancreas, 442 spleen, 362 right kidney, 424 left kidney and 282 gallbladder tissues, were collected to evaluate the proposed CBIR in the present study. Upon fine-tuning, high-level features used to automatically interpret the differences among the seven organs were extracted via deep learning architectures, including DenseNet, Vision Transformer (ViT), and Swin Transformer v2 (SwinViT). Three images with different annotations were employed in the classification and query.Main results.The resulting performances included the classification accuracy (94%-99%) and retrieval result (0.98-0.99). Considering global features and multiple resolutions, SwinViT performed better than ViT. ViT also benefited from a better receptive field to outperform DenseNet. Additionally, the use of hole images can obtain almost perfect results regardless of which deep learning architectures are used.Significance.The experiment showed that using pretrained deep learning architectures and fine-tuning with enough data can achieve successful recognition of seven abdominal organs. The CBIR system can provide more convincing evidence for recognizing abdominal organs via similarity measurements, which could lead to additional possibilities in clinical practice.

WBC YOLO-ViT: 2 Way - 2 stage white blood cell detection and classification with a combination of YOLOv5 and vision transformer

Accurate detection and classification of white blood cells, otherwise known as leukocytes, play a critical role in diagnosing and monitoring various illnesses. However, conventional methods, such as manual classification by trained professionals, must be revised in terms of accuracy, efficiency, and potential bias. Moreover, applying deep learning techniques to detect and classify white blood cells using microscopic images is challenging owing to limited data, resolution noise, irregular shapes, and varying colors from different sources. This study presents a novel approach integrating object detection and classification for numerous type-white blood cell. We designed a 2-way approach to use two types of images: WBC and nucleus. YOLO (fast object detection) and ViT (powerful image representation capabilities) are effectively integrated into 16 classes. The proposed model demonstrates an exceptional 96.449% accuracy rate in classification.

Predictive stroke risk model with vision transformer-based Doppler features

BACKGROUND

Acute stroke is the leading cause of death and disability globally, with an estimated 16 million cases each year. The progression of carotid stenosis reduces blood flow to the intracranial vasculature, causing stroke. Early recognition of ischemic stroke is crucial for disease treatment and management.

PURPOSE

A computer-aided diagnosis (CAD) system was proposed in this study to rapidly evaluate ischemic stroke in carotid color Doppler (CCD).

METHODS

Based on the ground truth from the clinical examination report, the vision transformer (ViT) features extracted from all CCD images (513 stroke and 458 normal images) were combined in machine learning classifiers to generate the likelihood of ischemic stroke for each image. The pretrained weights from ImageNet reduced the time-consuming training process. The accuracy, sensitivity, specificity, and area under the receiver operating characteristic curve were calculated to evaluate the stroke prediction model. The chi-square test, DeLong test, and Bonferroni correction for multiple comparisons were applied to deal with the type-I error. Only p values equal to or less than 0.00125 were considered to be statistically significant.

RESULTS

The proposed CAD system achieved an accuracy of 89%, a sensitivity of 94%, a specificity of 84%, and an area under the receiver operating characteristic curve of 0.95, outperforming the convolutional neural networks AlexNet (82%, p < 0.001), Inception-v3 (78%, p < 0.001), ResNet101 (84%, p < 0.001), and DenseNet201 (85%, p < 0.01). The computational time in model training was only 30 s, which would be efficient and practical in clinical use.

CONCLUSIONS

The experiment shows the promising use of CCD images in stroke estimation. Using the pretrained ViT architecture, the image features can be automatically and efficiently generated without human intervention. The proposed CAD system provides a rapid and reliable suggestion for diagnosing ischemic stroke.

YOLO-PAM: Parasite-Attention-Based Model for Efficient Malaria Detection

Malaria is a potentially fatal infectious disease caused by the Plasmodium parasite. The mortality rate can be significantly reduced if the condition is diagnosed and treated early. However, in many underdeveloped countries, the detection of malaria parasites from blood smears is still performed manually by experienced hematologists. This process is time-consuming and error-prone. In recent years, deep-learning-based object-detection methods have shown promising results in automating this task, which is critical to ensure diagnosis and treatment in the shortest possible time. In this paper, we propose a novel Transformer- and attention-based object-detection architecture designed to detect malaria parasites with high efficiency and precision, focusing on detecting several parasite sizes. The proposed method was tested on two public datasets, namely MP-IDB and IML. The evaluation results demonstrated a mean average precision exceeding 83.6% on distinct Plasmodium species within MP-IDB and reaching nearly 60% on IML. These findings underscore the effectiveness of our proposed architecture in automating malaria parasite detection, offering a potential breakthrough in expediting diagnosis and treatment processes.

Expression, Purification, and Characterization of Plasmodium vivax Lactate Dehydrogenase from Bacteria without Codon Optimization

Plasmodium vivax is the most widespread cause of malaria, especially in subtropical and temperate regions such as Asia-Pacific and America. P. vivax lactate dehydrogenase (PvLDH), an essential enzyme in the glycolytic pathway, is required for the development and reproduction of the parasite. Thus, LDH from these parasites has garnered attention as a diagnostic biomarker for malaria and as a potential molecular target for developing antimalarial drugs. In this study, we prepared a transformed Escherichia coli strain for the overexpression of PvLDH without codon optimization. We introduced this recombinant plasmid DNA prepared by insertion of the PvLDH gene in the pET-21a(+) expression vector, into the Rosetta(DE3), an E. coli strain suitable for eukaryotic protein expression. The time, temperature, and inducer concentration for PvLDH expression from this E. coli Rosetta(DE3), containing the original PvLDH gene, were optimized. We obtained PvLDH with a 31.0 mg/L yield and high purity (>95%) from this Rosetta(DE3) strain. The purified protein was characterized structurally and functionally. The PvLDH expressed and purified from transformed bacteria without codon optimization was successfully demonstrated to exhibit its potential tetramer structure and enzyme activity. These findings are expected to provide valuable insights for research on infectious diseases, metabolism, diagnostics, and therapeutics for malaria caused by P. vivax.

Efficient diagnosis of hematologic malignancies using bone marrow microscopic images: A method based on MultiPathGAN and MobileViTv2

BACKGROUND AND OBJECTIVES

Hematologic malignancies, including the associated multiple subtypes, are critically threatening to human health. The timely detection of malignancies is crucial for their effective treatment. In this regard, the examination of bone marrow smears constitutes a crucial step. Nonetheless, the conventional approach to cell identification and enumeration is laborious and time-intensive. Therefore, the present study aimed to develop a method for the efficient diagnosis of these malignancies directly from bone marrow microscopic images.

METHODS

A deep learning-based framework was developed to facilitate the diagnosis of common hematologic malignancies. First, a total of 2033 microscopic images of bone marrow analysis, including the images for 6 disease types and 1 healthy control, were collected from two Chinese medical websites. Next, the collected images were classified into the training, validation, and test datasets in the ratio of 7:1:2. Subsequently, a method of stain normalization to multi-domains (stain domain augmentation) based on the MultiPathGAN model was developed to equalize the stain styles and expand the image datasets. Afterward, a lightweight hybrid model named MobileViTv2, which integrates the strengths of both CNNs and ViTs, was developed for disease classification. The resulting model was trained and utilized to diagnose patients based on multiple microscopic images of their bone marrow smears, obtained from a cohort of 61 individuals.

RESULTS

MobileViTv2 exhibited an average accuracy of 94.28% when applied to the test set, with multiple myeloma, acute lymphocytic leukemia, and lymphoma revealed as the three diseases diagnosed with the highest accuracy values of 98%, 96%, and 96%, respectively. Regarding patient-level prediction, the average accuracy of MobileViTv2 was 96.72%. This model outperformed both CNN and ViT models in terms of accuracy, despite utilizing only 9.8 million parameters. When applied to two public datasets, MobileViTv2 exhibited accuracy values of 99.75% and 99.72%, respectively, and outperformed previous methods.

CONCLUSIONS

The proposed framework could be applied directly to bone marrow microscopic images with different stain styles to efficiently establish the diagnosis of common hematologic malignancies.

Deep learning-based assessment of knee septic arthritis using transformer features in sonographic modalities

PURPOSE

Septic arthritis is an infectious disease. Conventionally, the diagnosis of septic arthritis can only be based on the identification of causal pathogens taken from synovial fluid, synovium or blood samples. However, the cultures require several days for the isolation of pathogens. A rapid assessment performed through computer-aided diagnosis (CAD) would bring timely treatment.

METHODS

A total of 214 non-septic arthritis and 64 septic arthritis images generated by gray-scale (GS) and Power Doppler (PD) ultrasound modalities were collected for the experiment. A deep learning-based vision transformer (ViT) with pre-trained parameters were used for image feature extraction. The extracted features were then combined in machine learning classifiers with ten-fold cross validation in order to evaluate the abilities of septic arthritis classification.

RESULTS

Using a support vector machine, GS and PD features can achieve an accuracy rate of 86% and 91%, with the area under the receiver operating characteristic curves (AUCs) being 0.90 and 0.92, respectively. The best accuracy (92%) and best AUC (0.92) was obtained by combining both feature sets.

CONCLUSIONS

This is the first CAD system based on a deep learning approach for the diagnosis of septic arthritis as seen on knee ultrasound images. Using pre-trained ViT, both the accuracy and computation costs improved more than they had through convolutional neural networks. Additionally, automatically combining GS and PD generates a higher accuracy to better assist the physician's observations, thus providing a timely evaluation of septic arthritis.