Machine learning-guided design of potent darunavir analogs targeting HIV-1 proteases: A computational approach for antiretroviral drug discovery

In the pursuit of novel antiretroviral therapies for human immunodeficiency virus type-1 (HIV-1) proteases (PRs), recent improvements in drug discovery have embraced machine learning (ML) techniques to guide the design process. This study employs ensemble learning models to identify crucial substructures as significant features for drug development. Using molecular docking techniques, a collection of 160 darunavir (DRV) analogs was designed based on these key substructures and subsequently screened using molecular docking techniques. Chemical structures with high fitness scores were selected, combined, and one-dimensional (1D) screening based on beyond Lipinski's rule of five (bRo5) and ADME (absorption, distribution, metabolism, and excretion) prediction implemented in the Combined Analog generator Tool (CAT) program. A total of 473 screened analogs were subjected to docking analysis through convolutional neural networks scoring function against both the wild-type (WT) and 12 major mutated PRs. DRV analogs with negative changes in binding free energy (ΔΔ G bind ) compared to DRV could be categorized into four attractive groups based on their interactions with the majority of vital PRs. The analysis of interaction profiles revealed that potent designed analogs, targeting both WT and mutant PRs, exhibited interactions with common key amino acid residues. This observation further confirms that the ML model-guided approach effectively identified the substructures that play a crucial role in potent analogs. It is expected to function as a powerful computational tool, offering valuable guidance in the identification of chemical substructures for synthesis and subsequent experimental testing.

An Ensemble Learning Model for Detecting Soybean Seedling Emergence in UAV Imagery

Efficient detection and evaluation of soybean seedling emergence is an important measure for making field management decisions. However, there are many indicators related to emergence, and using multiple models to detect them separately makes data processing too slow to aid timely field management. In this study, we aimed to integrate several deep learning and image processing methods to build a model to evaluate multiple soybean seedling emergence information. An unmanned aerial vehicle (UAV) was used to acquire soybean seedling RGB images at emergence (VE), cotyledon (VC), and first node (V1) stages. The number of soybean seedlings that emerged was obtained by the seedling emergence detection module, and image datasets were constructed using the seedling automatic cutting module. The improved AlexNet was used as the backbone network of the growth stage discrimination module. The above modules were combined to calculate the emergence proportion in each stage and determine soybean seedlings emergence uniformity. The results show that the seedling emergence detection module was able to identify the number of soybean seedlings with an average accuracy of 99.92%, a R2 of 0.9784, a RMSE of 6.07, and a MAE of 5.60. The improved AlexNet was more lightweight, training time was reduced, the average accuracy was 99.07%, and the average loss was 0.0355. The model was validated in the field, and the error between predicted and real emergence proportions was up to 0.0775 and down to 0.0060. It provides an effective ensemble learning model for the detection and evaluation of soybean seedling emergence, which can provide a theoretical basis for making decisions on soybean field management and precision operations and has the potential to evaluate other crops emergence information.

Prediction of Cavity Length Using an Interpretable Ensemble Learning Approach

The cavity length, which is a vital index in aeration and corrosion reduction engineering, is affected by many factors and is challenging to calculate. In this study, 10-fold cross-validation was performed to select the optimal input configuration. Additionally, the hyperparameters of three ensemble learning models-random forest (RF), gradient boosting decision tree (GBDT), and extreme gradient boosting tree (XGBOOST)-were fine-tuned by the Bayesian optimization (BO) algorithm to improve the prediction accuracy and compare the five empirical methods. The XGBOOST method was observed to present the highest prediction accuracy. Further interpretability analysis carried out using the Sobol method demonstrated its ability to reasonably capture the varying relative significance of different input features under different flow conditions. The Sobol sensitivity analysis also observed two patterns of extracting information from the input features in ML models: (1) the main effect of individual features in ensemble learning and (2) the interactive effect between each feature in SVR. From the results, the models obtaining individual information both predict the cavity length more accurately than that using interactive information. Subsequently, the XGBOOST captures more correct information from features, which leads to the varied Sobol index in accordance with outside phenomena; meanwhile, the predicted results fit the experimental points best.

WYSIWYG: IoT Device Identification Based on WebUI Login Pages

With the improvement of intelligence and interconnection, Internet of Things (IoT) devices tend to become more vulnerable and exposed to many threats. Device identification is the foundation of many cybersecurity operations, such as asset management, vulnerability reaction, and situational awareness, which are important for enhancing the security of IoT devices. The more information sources and the more angles of view we have, the more precise identification results we obtain. This study proposes a novel and alternative method for IoT device identification, which introduces commonly available WebUI login pages with distinctive characteristics specific to vendors as the data source and uses an ensemble learning model based on a combination of Convolutional Neural Networks (CNN) and Deep Neural Networks (DNN) for device vendor identification and develops an Optical Character Recognition (OCR) based method for device type and model identification. The experimental results show that the ensemble learning model can achieve 99.1% accuracy and 99.5% F1-Score in the determination of whether a device is from a vendor that appeared in the training dataset, and if the answer is positive, 98% accuracy and 98.3% F1-Score in identifying which vendor it is from. The OCR-based method can identify fine-grained attributes of the device and achieve an accuracy of 99.46% in device model identification, which is higher than the results of the Shodan cyber search engine by a considerable margin of 11.39%.

Performance analysis and prediction of type 2 diabetes mellitus based on lifestyle data using machine learning approaches

Objective

Diabetes is a chronic fatal disease that has affected millions of people all over the globe. Type 2 Diabetes Mellitus (T2DM) accounts for 90% of the affected population among all types of diabetes. Millions of T2DM patients remain undiagnosed due to lack of awareness and under resourced healthcare system. So, there is a dire need for a diagnostic and prognostic tool that shall help the healthcare providers, clinicians and practitioners with early prediction and hence can recommend the lifestyle changes required to stop the progression of diabetes. The main objective of this research is to develop a framework based on machine learning techniques using only lifestyle indicators for prediction of T2DM disease. Moreover, prediction model can be used without visiting clinical labs and hospital readmissions.

Method

A proposed framework is presented and implemented based on machine learning paradigms using lifestyle indicators for better prediction of T2DM disease. The current research has involved different experts like Diabetologists, Endocrinologists, Dieticians, Nutritionists, etc. for selecting the contributing 1552 instances and 11 attributes lifestyle biological features to promote health and manage complications towards T2DM disease. The dataset has been collected through survey and google forms from different geographical regions.

Results

Seven machine learning classifiers were employed namely K-Nearest Neighbour (KNN), Linear Regression (LR), Support Vector Machine (SVM), Naive Bayes (NB), Decision Tree (DT), Random Forest (RF) and Gradient Boosting (GB). Gradient Boosting classifier outperformed best with an accuracy rate of 97.24% for training and 96.90% for testing separately followed by RF, DT, NB, SVM, LR, and KNN as 95.36%, 92.52%, 90.72%, 90.20%, 90.20% and 77.06% respectively. However, in terms of precision, RF achieved high performance (0.980%) and KNN performed the lowest (0.793%). As far as recall is being concerned, GB achieved the highest rate of 0.975% and KNN showed the worst rate of 0.774%. Also, GB is top performed in terms of f1-score. According to the ROCs, GB and NB had a better area under the curve compared to the others.

Conclusion

The research developed a realistic health management system for T2DM disease based on machine learning techniques using only lifestyle data for prediction of T2DM. To extend the current study, these models shall be used for different, large and real-time datasets which share the commonality of data with T2DM disease to establish the efficacy of the proposed system.

Predicting Monthly Community-Level Domestic Radon Concentrations in the Greater Boston Area with an Ensemble Learning Model

Inhaling radon and its progeny is associated with adverse health outcomes. However, previous studies of the health effects of residential exposure to radon in the United States were commonly based on a county-level temporally invariant radon model that was developed using measurements collected in the mid- to late 1980s. We developed a machine learning model to predict monthly radon concentrations for each ZIP Code Tabulation Area (ZCTA) in the Greater Boston area based on 363,783 short-term measurements by Spruce Environmental Technologies, Inc., during the period 2005-2018. A two-stage ensemble-based model was developed to predict radon concentrations for all ZCTAs and months. Stage one included 12 base statistical models that independently predicted ZCTA-level radon concentrations based on geological, architectural, socioeconomic, and meteorological factors for each ZCTA. Stage two aggregated the predictions of these 12 base models using an ensemble learning method. The results of a 10-fold cross-validation showed that the stage-two model has a good prediction accuracy with a weighted R² of 0.63 and root mean square error of 22.6 Bq/m³. The community-level time-varying predictions from our model have good predictive precision and accuracy and can be used in future prospective epidemiological studies in the Greater Boston area.