Predicting the efficiency of arsenic immobilization in soils by biochar using machine learning.

Arsenic (As) pollution in soils is a pervasive environmental issue. Biochar immobilization offers a promising solution for addressing soil As contamination. The efficiency of biochar in immobilizing As in soils primarily hinges on the characteristics of both the soil and the biochar. However, the influence of a specific property on As immobilization varies among different studies, and the development and application of arsenic passivation materials based on biochar often rely on empirical knowledge. To enhance immobilization efficiency and reduce labor and time costs, a machine learning (ML) model was employed to predict As immobilization efficiency before biochar application. In this study, we collected a dataset comprising 182 data points on As immobilization efficiency from 17 publications to construct three ML models. The results demonstrated that the random forest (RF) model outperformed gradient boost regression tree and support vector regression models in predictive performance. Relative importance analysis and partial dependence plots based on the RF model were conducted to identify the most crucial factors influencing As immobilization. These findings highlighted the significant roles of biochar application time and biochar pH in As immobilization efficiency in soils. Furthermore, the study revealed that Fe-modified biochar exhibited a substantial improvement in As immobilization. These insights can facilitate targeted biochar property design and optimization of biochar application conditions to enhance As immobilization efficiency.

Rapid detection of colored and colorless macro- and micro-plastics in complex environment via near-infrared spectroscopy and machine learning.

To better understand the migration behavior of plastic fragments in the environment, development of rapid non-destructive methods for in-situ identification and characterization of plastic fragments is necessary. However, most of the studies had focused only on colored plastic fragments, ignoring colorless plastic fragments and the effects of different environmental media (backgrounds), thus underestimating their abundance. To address this issue, the present study used near-infrared spectroscopy to compare the identification of colored and colorless plastic fragments based on partial least squares-discriminant analysis (PLS-DA), extreme gradient boost, support vector machine and random forest classifier. The effects of polymer color, type, thickness, and background on the plastic fragments classification were evaluated. PLS-DA presented the best and most stable outcome, with higher robustness and lower misclassification rate. All models frequently misinterpreted colorless plastic fragments and its background when the fragment thickness was less than 0.1mm. A two-stage modeling method, which first distinguishes the plastic types and then identifies colorless plastic fragments that had been misclassified as background, was proposed. The method presented an accuracy higher than 99% in different backgrounds. In summary, this study developed a novel method for rapid and synchronous identification of colored and colorless plastic fragments under complex environmental backgrounds.

Gut microbiome dynamics and predictive value in hospitalized COVID-19 patients: a comparative analysis of shallow and deep shotgun sequencing.

The COVID-19 pandemic caused by SARS-CoV-2 has led to a wide range of clinical presentations, with respiratory symptoms being common. However, emerging evidence suggests that the gastrointestinal (GI) tract is also affected, with angiotensin-converting enzyme 2, a key receptor for SARS-CoV-2, abundantly expressed in the ileum and colon. The virus has been detected in GI tissues and fecal samples, even in cases with negative results of the reverse transcription polymerase chain reaction in the respiratory tract. GI symptoms have been associated with an increased risk of ICU admission and mortality. The gut microbiome, a complex ecosystem of around 40 trillion bacteria, plays a crucial role in immunological and metabolic pathways. Dysbiosis of the gut microbiota, characterized by a loss of beneficial microbes and decreased microbial diversity, has been observed in COVID-19 patients, potentially contributing to disease severity. We conducted a comprehensive gut microbiome study in 204 hospitalized COVID-19 patients using both shallow and deep shotgun sequencing methods. We aimed to track microbiota composition changes induced by hospitalization, link these alterations to clinical procedures (antibiotics administration) and outcomes (ICU referral, survival), and assess the predictive potential of the gut microbiome for COVID-19 prognosis. Shallow shotgun sequencing was evaluated as a cost-effective diagnostic alternative for clinical settings. Our study demonstrated the diverse effects of various combinations of clinical parameters, microbiome profiles, and patient metadata on the precision of outcome prognostication in patients. It indicates that microbiological data possesses greater reliability in forecasting patient outcomes when contrasted with clinical data or metadata. Furthermore, we established that shallow shotgun sequencing presents a viable and cost-effective diagnostic alternative to deep sequencing within clinical environments.

EfficientMaize: A Lightweight Dataset for Maize Classification on Resource-Constrained Devices.

Hyperspectral imaging, combined with deep learning techniques, has been employed to classify maize. However, the implementation of these automated methods often requires substantial processing and computing resources, presenting a significant challenge for deployment on embedded devices due to high GPU power consumption. Access to Ghanaian local maize data for such classification tasks is also extremely difficult in Ghana. To address these challenges, this research aims to create a simple dataset comprising three distinct types of local maize seeds in Ghana. The goal is to facilitate the development of an efficient maize classification tool that minimizes computational costs and reduces human involvement in the process of grading seeds for marketing and production. The dataset is presented in two parts: raw images, consisting of 4,846 images, are categorized into bad and good. Specifically, 2,211 images belong to the bad class, while 2,635 belong to the good class. Augmented images consist of 28,910 images, with 13,250 representing bad data and 15,660 representing good data. All images have been validated by experts from Heritage Seeds Ghana and are freely available for use within the research community.

Improving skin cancer detection by Raman spectroscopy using convolutional neural networks and data augmentation.

Background: Our previous studies have demonstrated that Raman spectroscopy could be used for skin cancer detection with good sensitivity and specificity. The objective of this study is to determine if skin cancer detection can be further improved by combining deep neural networks and Raman spectroscopy. Patients and methods: Raman spectra of 731 skin lesions were included in this study, containing 340 cancerous and precancerous lesions (melanoma, basal cell carcinoma, squamous cell carcinoma and actinic keratosis) and 391 benign lesions (melanocytic nevus and seborrheic keratosis). One-dimensional convolutional neural networks (1D-CNN) were developed for Raman spectral classification. The stratified samples were divided randomly into training (70%), validation (10%) and test set (20%), and were repeated 56 times using parallel computing. Different data augmentation strategies were implemented for the training dataset, including added random noise, spectral shift, spectral combination and artificially synthesized Raman spectra using one-dimensional generative adversarial networks (1D-GAN). The area under the receiver operating characteristic curve (ROC AUC) was used as a measure of the diagnostic performance. Conventional machine learning approaches, including partial least squares for discriminant analysis (PLS-DA), principal component and linear discriminant analysis (PC-LDA), support vector machine (SVM), and logistic regression (LR) were evaluated for comparison with the same data splitting scheme as the 1D-CNN. Results: The ROC AUC of the test dataset based on the original training spectra were 0.886±0.022 (1D-CNN), 0.870±0.028 (PLS-DA), 0.875±0.033 (PC-LDA), 0.864±0.027 (SVM), and 0.525±0.045 (LR), which were improved to 0.909±0.021 (1D-CNN), 0.899±0.022 (PLS-DA), 0.895±0.022 (PC-LDA), 0.901±0.020 (SVM), and 0.897±0.021 (LR) respectively after augmentation of the training dataset (p<0.0001, Wilcoxon test). Paired analyses of 1D-CNN with conventional machine learning approaches showed that 1D-CNN had a 1-3% improvement (p<0.001, Wilcoxon test). Conclusions: Data augmentation not only improved the performance of both deep neural networks and conventional machine learning techniques by 2-4%, but also improved the performance of the models on spectra with higher noise or spectral shifting. Convolutional neural networks slightly outperformed conventional machine learning approaches for skin cancer detection by Raman spectroscopy.

Elucidating the role of angiogenesis-related genes in colorectal cancer: a multi-omics analysis.

Background: Angiogenesis plays a pivotal role in colorectal cancer (CRC), yet its underlying mechanisms demand further exploration. This study aimed to elucidate the significance of angiogenesis-related genes (ARGs) in CRC through comprehensive multi-omics analysis. Methods: CRC patients were categorized according to ARGs expression to form angiogenesis-related clusters (ARCs). We investigated the correlation between ARCs and patient survival, clinical features, consensus molecular subtypes (CMS), cancer stem cell (CSC) index, tumor microenvironment (TME), gene mutations, and response to immunotherapy. Utilizing three machine learning algorithms (LASSO, Xgboost, and Decision Tree), we screen key ARGs associated with ARCs, further validated in independent cohorts. A prognostic signature based on key ARGs was developed and analyzed at the scRNA-seq level. Validation of gene expression in external cohorts, clinical tissues, and blood samples was conducted via RT-PCR assay. Results: Two distinct ARC subtypes were identified and were significantly associated with patient survival, clinical features, CMS, CSC index, and TME, but not with gene mutations. Four genes (S100A4, COL3A1, TIMP1, and APP) were identified as key ARCs, capable of distinguishing ARC subtypes. The prognostic signature based on these genes effectively stratified patients into high- or low-risk categories. scRNA-seq analysis showed that these genes were predominantly expressed in immune cells rather than in cancer cells. Validation in two external cohorts and through clinical samples confirmed significant expression differences between CRC and controls. Conclusion: This study identified two ARG subtypes in CRC and highlighted four key genes associated with these subtypes, offering new insights into personalized CRC treatment strategies.

A simple and effective machine learning model for predicting the stability of intracranial aneurysms using CT angiography.

Background: It is vital to accurately and promptly distinguish unstable from stable intracranial aneurysms (IAs) to facilitate treatment optimization and avoid unnecessary treatment. The aim of this study is to develop a simple and effective predictive model for the clinical evaluation of the stability of IAs. Methods: In total, 1,053 patients with 1,239 IAs were randomly divided the dataset into training (70%) and internal validation (30%) datasets. One hundred and ninety seven patients with 229 IAs from another hospital were evaluated as an external validation dataset. The prediction models were developed using machine learning based on clinical information, manual parameters, and radiomic features. In addition, a simple model for predicting the stability of IAs was developed, and a nomogram was drawn for clinical use. Results: Fourteen machine learning models exhibited excellent classification performance. Logistic regression Model E (clinical information, manual parameters, and radiomic shape features) had the highest AUC of 0.963 (95% CI 0.943-0.980). Compared to manual parameters, radiomic features did not significantly improve the identification of unstable IAs. In the external validation dataset, the simplified model demonstrated excellent performance (AUC = 0.950) using only five manual parameters. Conclusion: Machine learning models have excellent potential in the classification of unstable IAs. The manual parameters from CTA images are sufficient for developing a simple and effective model for identifying unstable IAs.

Forecasting West Nile Virus With Graph Neural Networks: Harnessing Spatial Dependence in Irregularly Sampled Geospatial Data.

Machine learning methods have seen increased application to geospatial environmental problems, such as precipitation nowcasting, haze forecasting, and crop yield prediction. However, many of the machine learning methods applied to mosquito population and disease forecasting do not inherently take into account the underlying spatial structure of the given data. In our work, we apply a spatially aware graph neural network model consisting of GraphSAGE layers to forecast the presence of West Nile virus in Illinois, to aid mosquito surveillance and abatement efforts within the state. More generally, we show that graph neural networks applied to irregularly sampled geospatial data can exceed the performance of a range of baseline methods including logistic regression, XGBoost, and fully-connected neural networks.

Machine learning algorithms to predict healthcare-seeking behaviors of mothers for acute respiratory infections and their determinants among children under five in sub-Saharan Africa.

Background: Acute respiratory infections (ARIs) are the leading cause of death in children under the age of 5 globally. Maternal healthcare-seeking behavior may help minimize mortality associated with ARIs since they make decisions about the kind and frequency of healthcare services for their children. Therefore, this study aimed to predict the absence of maternal healthcare-seeking behavior and identify its associated factors among children under the age 5 in sub-Saharan Africa (SSA) using machine learning models. Methods: The sub-Saharan African countries' demographic health survey was the source of the dataset. We used a weighted sample of 16,832 under-five children in this study. The data were processed using Python (version 3.9), and machine learning models such as extreme gradient boosting (XGB), random forest, decision tree, logistic regression, and Naïve Bayes were applied. In this study, we used evaluation metrics, including the AUC ROC curve, accuracy, precision, recall, and F-measure, to assess the performance of the predictive models. Result: In this study, a weighted sample of 16,832 under-five children was used in the final analysis. Among the proposed machine learning models, the random forest (RF) was the best-predicted model with an accuracy of 88.89%, a precision of 89.5%, an F-measure of 83%, an AUC ROC curve of 95.8%, and a recall of 77.6% in predicting the absence of mothers' healthcare-seeking behavior for ARIs. The accuracy for Naïve Bayes was the lowest (66.41%) when compared to other proposed models. No media exposure, living in rural areas, not breastfeeding, poor wealth status, home delivery, no ANC visit, no maternal education, mothers' age group of 35-49 years, and distance to health facilities were significant predictors for the absence of mothers' healthcare-seeking behaviors for ARIs. On the other hand, undernourished children with stunting, underweight, and wasting status, diarrhea, birth size, married women, being a male or female sex child, and having a maternal occupation were significantly associated with good maternal healthcare-seeking behaviors for ARIs among under-five children. Conclusion: The RF model provides greater predictive power for estimating mothers' healthcare-seeking behaviors based on ARI risk factors. Machine learning could help achieve early prediction and intervention in children with high-risk ARIs. This leads to a recommendation for policy direction to reduce child mortality due to ARIs in sub-Saharan countries.

Prediction of Listeria monocytogenes Clonal Complexes from Multilocus Variable Number Tandem Repeat Analysis Patterns Using a Machine Learning Approach.

Multilocus variable number tandem repeat analysis (MLVA) is a molecular subtyping technique that remains useful for those without the resources to access whole genome sequencing for the tracking and tracing of bacterial contaminants. Unlike techniques such as multilocus sequence typing (MLST) and pulsed-field gel electrophoresis, MLVA did not emerge as a standardized subtyping method for Listeria monocytogenes, and as a result, there is no reference database of virulent or food-associated MLVA subtypes as there is for MLST-based clonal complexes (CCs). Having previously shown the close congruence of a 5-loci MLVA scheme with MLST, a predictive model was created using the XGBoost machine learning (ML) technique, which enabled the prediction of CCs from MLVA patterns with ∼85% (±4%) accuracy. As well as validating the model on existing data, a straightforward update protocol was simulated for if and when previously unseen subtypes might arise. This article illustrates how ML techniques can be applied with elementary coding skills to add value to previous-generation molecular subtyping data in-built food processing environments.

Gamified Crowdsourcing as a Novel Approach to Lung Ultrasound Data Set Labeling: Prospective Analysis.

BACKGROUND: Machine learning (ML) models can yield faster and more accurate medical diagnoses; however, developing ML models is limited by a lack of high-quality labeled training data. Crowdsourced labeling is a potential solution but can be constrained by concerns about label quality. OBJECTIVE: This study aims to examine whether a gamified crowdsourcing platform with continuous performance assessment, user feedback, and performance-based incentives could produce expert-quality labels on medical imaging data. METHODS: In this diagnostic comparison study, 2384 lung ultrasound clips were retrospectively collected from 203 emergency department patients. A total of 6 lung ultrasound experts classified 393 of these clips as having no B-lines, one or more discrete B-lines, or confluent B-lines to create 2 sets of reference standard data sets (195 training clips and 198 test clips). Sets were respectively used to (1) train users on a gamified crowdsourcing platform and (2) compare the concordance of the resulting crowd labels to the concordance of individual experts to reference standards. Crowd opinions were sourced from DiagnosUs (Centaur Labs) iOS app users over 8 days, filtered based on past performance, aggregated using majority rule, and analyzed for label concordance compared with a hold-out test set of expert-labeled clips. The primary outcome was comparing the labeling concordance of collated crowd opinions to trained experts in classifying B-lines on lung ultrasound clips. RESULTS: Our clinical data set included patients with a mean age of 60.0 (SD 19.0) years; 105 (51.7%) patients were female and 114 (56.1%) patients were White. Over the 195 training clips, the expert-consensus label distribution was 114 (58%) no B-lines, 56 (29%) discrete B-lines, and 25 (13%) confluent B-lines. Over the 198 test clips, expert-consensus label distribution was 138 (70%) no B-lines, 36 (18%) discrete B-lines, and 24 (12%) confluent B-lines. In total, 99,238 opinions were collected from 426 unique users. On a test set of 198 clips, the mean labeling concordance of individual experts relative to the reference standard was 85.0% (SE 2.0), compared with 87.9% crowdsourced label concordance (P=.15). When individual experts' opinions were compared with reference standard labels created by majority vote excluding their own opinion, crowd concordance was higher than the mean concordance of individual experts to reference standards (87.4% vs 80.8%, SE 1.6 for expert concordance; P<.001). Clips with discrete B-lines had the most disagreement from both the crowd consensus and individual experts with the expert consensus. Using randomly sampled subsets of crowd opinions, 7 quality-filtered opinions were sufficient to achieve near the maximum crowd concordance. CONCLUSIONS: Crowdsourced labels for B-line classification on lung ultrasound clips via a gamified approach achieved expert-level accuracy. This suggests a strategic role for gamified crowdsourcing in efficiently generating labeled image data sets for training ML systems.

Bayesian Networks for Prescreening in Depression: Algorithm Development and Validation.

BACKGROUND: Identifying individuals with depressive symptomatology (DS) promptly and effectively is of paramount importance for providing timely treatment. Machine learning models have shown promise in this area; however, studies often fall short in demonstrating the practical benefits of using these models and fail to provide tangible real-world applications. OBJECTIVE: This study aims to establish a novel methodology for identifying individuals likely to exhibit DS, identify the most influential features in a more explainable way via probabilistic measures, and propose tools that can be used in real-world applications. METHODS: The study used 3 data sets: PROACTIVE, the Brazilian National Health Survey (Pesquisa Nacional de Saúde [PNS]) 2013, and PNS 2019, comprising sociodemographic and health-related features. A Bayesian network was used for feature selection. Selected features were then used to train machine learning models to predict DS, operationalized as a score of ≥10 on the 9-item Patient Health Questionnaire. The study also analyzed the impact of varying sensitivity rates on the reduction of screening interviews compared to a random approach. RESULTS: The methodology allows the users to make an informed trade-off among sensitivity, specificity, and a reduction in the number of interviews. At the thresholds of 0.444, 0.412, and 0.472, determined by maximizing the Youden index, the models achieved sensitivities of 0.717, 0.741, and 0.718, and specificities of 0.644, 0.737, and 0.766 for PROACTIVE, PNS 2013, and PNS 2019, respectively. The area under the receiver operating characteristic curve was 0.736, 0.801, and 0.809 for these 3 data sets, respectively. For the PROACTIVE data set, the most influential features identified were postural balance, shortness of breath, and how old people feel they are. In the PNS 2013 data set, the features were the ability to do usual activities, chest pain, sleep problems, and chronic back problems. The PNS 2019 data set shared 3 of the most influential features with the PNS 2013 data set. However, the difference was the replacement of chronic back problems with verbal abuse. It is important to note that the features contained in the PNS data sets differ from those found in the PROACTIVE data set. An empirical analysis demonstrated that using the proposed model led to a potential reduction in screening interviews of up to 52% while maintaining a sensitivity of 0.80. CONCLUSIONS: This study developed a novel methodology for identifying individuals with DS, demonstrating the utility of using Bayesian networks to identify the most significant features. Moreover, this approach has the potential to substantially reduce the number of screening interviews while maintaining high sensitivity, thereby facilitating improved early identification and intervention strategies for individuals experiencing DS.

Machine learning methods in automated detection of CT enterography findings in Crohn's disease: A feasibility study.

PURPOSE: Qualitative findings in Crohn's disease (CD) can be challenging to reliably report and quantify. We evaluated machine learning methodologies to both standardize the detection of common qualitative findings of ileal CD and determine finding spatial localization on CT enterography (CTE). MATERIALS AND METHODS: Subjects with ileal CD and a CTE from a single center retrospective study between 2016 and 2021 were included. 165 CTEs were reviewed by two fellowship-trained abdominal radiologists for the presence and spatial distribution of five qualitative CD findings: mural enhancement, mural stratification, stenosis, wall thickening, and mesenteric fat stranding. A Random Forest (RF) ensemble model using automatically extracted specialist-directed bowel features and an unbiased convolutional neural network (CNN) were developed to predict the presence of qualitative findings. Model performance was assessed using area under the curve (AUC), sensitivity, specificity, accuracy, and kappa agreement statistics. RESULTS: In 165 subjects with 29,895 individual qualitative finding assessments, agreement between radiologists for localization was good to very good (κ = 0.66 to 0.73), except for mesenteric fat stranding (κ = 0.47). RF prediction models had excellent performance, with an overall AUC, sensitivity, specificity of 0.91, 0.81 and 0.85, respectively. RF model and radiologist agreement for localization of CD findings approximated agreement between radiologists (κ = 0.67 to 0.76). Unbiased CNN models without benefit of disease knowledge had very similar performance to RF models which used specialist-defined imaging features. CONCLUSION: Machine learning techniques for CTE image analysis can identify the presence, location, and distribution of qualitative CD findings with similar performance to experienced radiologists.

scDrug+: predicting drug-responses using single-cell transcriptomics and molecular structure.

Predicting drug responses based on individual transcriptomic profiles holds promise for refining prognosis and advancing precision medicine. Although many studies have endeavored to predict the responses of known drugs to novel transcriptomic profiles, research into predicting responses for newly discovered drugs remains sparse. In this study, we introduce scDrug+, a comprehensive pipeline that seamlessly integrates single-cell analysis with drug-response prediction. Importantly, scDrug+ is equipped to predict the response of new drugs by analyzing their molecular structures. The open-source tool is available as a Docker container, ensuring ease of deployment and reproducibility. It can be accessed at https://github.com/ailabstw/scDrugplus.

Prospective multicenter study of continuous tonic-clonic seizure monitoring on Apple Watch in epilepsy monitoring units and ambulatory environments.

OBJECTIVE: Evaluate the performance of a custom application developed for tonic-clonic seizure (TCS) monitoring on a consumer-wearable (Apple Watch) device. METHODS: Participants with a history of convulsive epileptic seizures were recruited for either Epilepsy Monitoring Unit (EMU) or ambulatory (AMB) monitoring; participants without epilepsy (normal controls [NC]) were also enrolled in the AMB group. Both EMU and AMB participants wore an Apple Watch with a research app that continuously recorded accelerometer and photoplethysmography (PPG) signals, and ran a fixed-and-frozen tonic-clonic seizure detection algorithm during the testing period. This algorithm had been previously developed and validated using a separate training dataset. All EMU convulsive events were validated by video-electroencephalography (video-EEG); AMB events were validated by caregiver reporting and follow-ups. Device performance was characterized and compared to prior monitoring devices through sensitivity, false alarm rate (FAR; false-alarms per 24 h), precision, and detection delay (latency). RESULTS: The EMU group had 85 participants (4,279 h, 19 TCS from 15 participants) enrolled across four EMUs; the AMB group had 21 participants (13 outpatient, 8 NC, 6,735 h, 10 TCS from 3 participants). All but one AMB participant completed the study. Device performance in the EMU group included a sensitivity of 100 % [95 % confidence interval (CI) 79-100 %]; an FAR of 0.05 [0.02, 0.08] per 24 h; a precision of 68 % [48 %, 83 %]; and a latency of 32.07 s [standard deviation (std) 10.22 s]. The AMB group had a sensitivity of 100 % [66-100 %]; an FAR of 0.13 [0.08, 0.24] per 24 h; a precision of 22 % [11 %, 37 %]; and a latency of 37.38 s [13.24 s]. Notably, a single AMB participant was responsible for 8 of 31 false alarms. The AMB FAR excluding this participant was 0.10 [0.07, 0.14] per 24 h. DISCUSSION: This study demonstrates the practicability of TCS monitoring on a popular consumer wearable (Apple Watch) in daily use for people with epilepsy. The monitoring app had a high sensitivity and a substantially lower FAR than previously reported in both EMU and AMB environments.

An exploration of descriptive machine learning approaches for antimicrobial resistance: Multidrug resistance patterns in Salmonella enterica.

Salmonellosis is one of the most common foodborne diseases worldwide, with the ability to infect humans and animals. Antimicrobial resistance (AMR) and, particularly, multidrug resistance (MDR) among Salmonella enterica poses a risk to human health. Antimicrobial use (AMU) regulations in livestock have been implemented to reduce AMR and MDR in foodborne pathogens. In this study, we used an integrated machine learning approach to investigate Salmonella AMR and MDR patterns before and after the implementation of AMU restrictions in agriculture in the United States. For this purpose, Salmonella isolates from cattle in the National Antimicrobial Resistance Monitoring System (NARMS) dataset were analysed using three descriptive models consisting of hierarchical clustering, network analysis, and association rule mining. The analysis showed the impact of the United States' 2012 extra-label cephalosporin regulations on AMR trends and revealed a distinctive MDR pattern in the Dublin serotype. The results also indicated that each descriptive model provides insights on a specific aspect of resistance patterns and, therefore, combining these approaches make it possible to gain a deeper understanding of AMR.

Current strategies to address data scarcity in artificial intelligence-based drug discovery: A comprehensive review.

Artificial intelligence (AI) has played a vital role in computer-aided drug design (CADD). This development has been further accelerated with the increasing use of machine learning (ML), mainly deep learning (DL), and computing hardware and software advancements. As a result, initial doubts about the application of AI in drug discovery have been dispelled, leading to significant benefits in medicinal chemistry. At the same time, it is crucial to recognize that AI is still in its infancy and faces a few limitations that need to be addressed to harness its full potential in drug discovery. Some notable limitations are insufficient, unlabeled, and non-uniform data, the resemblance of some AI-generated molecules with existing molecules, unavailability of inadequate benchmarks, intellectual property rights (IPRs) related hurdles in data sharing, poor understanding of biology, focus on proxy data and ligands, lack of holistic methods to represent input (molecular structures) to prevent pre-processing of input molecules (feature engineering), etc. The major component in AI infrastructure is input data, as most of the successes of AI-driven efforts to improve drug discovery depend on the quality and quantity of data, used to train and test AI algorithms, besides a few other factors. Additionally, data-gulping DL approaches, without sufficient data, may collapse to live up to their promise. Current literature suggests a few methods, to certain extent, effectively handle low data for better output from the AI models in the context of drug discovery. These are transferring learning (TL), active learning (AL), single or one-shot learning (OSL), multi-task learning (MTL), data augmentation (DA), data synthesis (DS), etc. One different method, which enables sharing of proprietary data on a common platform (without compromising data privacy) to train ML model, is federated learning (FL). In this review, we compare and discuss these methods, their recent applications, and limitations while modeling small molecule data to get the improved output of AI methods in drug discovery. Article also sums up some other novel methods to handle inadequate data.

Machine Learning-based Cerebral Venous Thrombosis Diagnosis with Clinical Data.

OBJECTIVES: Cerebral Venous Thrombosis (CVT) poses diagnostic challenges due to the variability in disease course and symptoms. The prognosis of CVT relies on early diagnosis. Our study focuses on developing a machine learning-based screening algorithm using clinical data from a large neurology referral center in southern Iran. METHODS: The Iran Cerebral Venous Thrombosis Registry (ICVTR code: 9001013381) provided data on 382 CVT cases from Namazi Hospital. The control group comprised of adult headache patients without CVT as confirmed by neuroimaging and was retrospectively selected from those admitted to the same hospital. We collected 60 clinical and demographic features for model development and validation. Our modeling pipeline involved imputing missing values and evaluating four machine learning algorithms: generalized linear model, random forest, support vector machine, and extreme gradient boosting. RESULTS: A total of 314 CVT cases and 575 controls were included. The highest AUROC was reached when imputation was used to estimate missing values for all the variables, combined with the support vector machine model (AUROC=0.910, Recall=0.73, Precision=0.88). The best recall was achieved also by the support vector machine model when only variables with less than 50% missing rate were included (AUROC=0.887, Recall=0.77, Precision=0.86). The random forest model yielded the best precision by using variables with less than 50% missing rate (AUROC=0.882, Recall=0.61, Precision=0.94). CONCLUSION: The application of machine learning techniques using clinical data showed promising results in accurately diagnosing CVT within our study population. This approach offers a valuable complementary assistive tool or an alternative to resource-intensive imaging methods.

What Influences the Close Contact between healthcare workers and patients? An Observational Study in a Hospital Dental Outpatient Department.

BACKGROUND: Dental outpatient departments, characterized by close proximity and unmasked patients, present a considerable risk of respiratory infections for healthcare workers (HCWs). However, the lack of comprehensive data on close contact (<1.5m) between HCWs and patients poses a significant obstacle to the development of targeted control strategies. METHODS: An observation study was conducted at a hospital in Shenzhen, China, utilizing depth cameras with machine learning to capture close contact behaviors of patients with HCWs. Additionally, questionnaires were administered to collect patient demographics. RESULTS: The study included 200 patients, 10 dental practitioners and 10 nurses. Patients had significantly higher close contact rates with dental practitioners (97.5%) compared to nurses (72.8%; P<0.001). The reason for the visit significantly influenced patient-practitioner (P=0.018) and patient-nurse (P=0.007) close contact time, with the highest values observed in prosthodontics and orthodontics patients. Furthermore, patient age also significantly impacted the close contact rate with nurses (P=0.024), with the highest rate observed in patients below 14 years old at 85% [IQR:70-93]. CONCLUSION: Dental outpatient departments exhibit high HCW-patient close contact rates, influenced by visit purpose and patient age. Enhanced infection control measures are warranted, particularly for prosthodontics and orthodontics patients or those below 14 years old.

MR-Based Radiomics Predicts CDK6 Expression and Prognostic Value in High-grade Glioma.

RATIONALE AND OBJECTIVES: This study aims to assess the prognostic value of Cyclin-dependent kinases 6 (CDK6) expression levels and establish a machine learning-based radiomics model for predicting the expression levels of CDK6 in high-grade gliomas (HGG). MATERIALS AND METHODS: Clinical parameters and genomic data were extracted from 310 HGG patients in the Cancer Genome Atlas (TCGA) database and 27 patients in the Repository of Molecular Brain Neoplasia Data (REMBRANDT) database. Univariate and multivariate Cox regression, as well as Kaplan-Meier analysis, were performed for prognosis analysis. The correlation between immune cell Infiltration with CDK6 was assessed using spearman correlation analysis. Radiomic features were extracted from contrast-enhanced magnetic resonance imaging (CE-MRI) in the Cancer Imaging Archive (TCIA) database (n = 82) and REMBRANDT database (n = 27). Logistic regression (LR) and support vector machine (SVM) were employed to establish the radiomics model for predicting CDK6 expression. Receiver operating characteristic curve (ROC), calibration curve, and decision curve analysis (DCA) were utilized to assess the predictive performance of the radiomics model. Generate radiomic scores (RS) based on the LR model. An RS-based nomogram was constructed to predict the prognosis of HGG. RESULTS: CDK6 was significantly overexpressed in HGG tissues and was related to lower overall survival. A significant elevation in infiltrating M0 macrophages was observed in the CDK6 high group (P < 0.001). The LR radiomics model for the prediction of CDK6 expression levels (AUC=0.810 in the training cohort, AUC = 0.784 after cross-validation, AUC=0.750 in the testing cohort) was established utilizing three radiomic features. The predictive efficiencies of the RS-based nomogram, as measured by AUC, were 0.769 for 1-year, 0.815 for 3-year, and 0.780 for 5-year, respectively. CONCLUSION: The expression level of CDK6 can impact the prognosis of patients with HGG. The expression level of HGG can be noninvasively prognosticated utilizing a radiomics model.