Evolution of Support Vector Machine and Regression Modeling in Chemoinformatics and Drug Discovery

Artificial intelligence in antidiabetic drug discovery: The advances in QSAR and the prediction of α-glucosidase inhibitors

Artificial Intelligence is transforming drug discovery, particularly in the hit identification phase of therapeutic compounds. One tool that has been instrumental in this transformation is Quantitative Structure-Activity Relationship (QSAR) analysis. This computer-aided drug design tool uses machine learning to predict the biological activity of new compounds based on the numerical representation of chemical structures against various biological targets. With diabetes mellitus becoming a significant health challenge in recent times, there is intense research interest in modulating antidiabetic drug targets. α-Glucosidase is an antidiabetic target that has gained attention due to its ability to suppress postprandial hyperglycaemia, a key contributor to diabetic complications. This review explored a detailed approach to developing QSAR models, focusing on strategies for generating input variables (molecular descriptors) and computational approaches ranging from classical machine learning algorithms to modern deep learning algorithms. We also highlighted studies that have used these approaches to develop predictive models for α-glucosidase inhibitors to modulate this critical antidiabetic drug target.

Remotely sensed estimates of long-term biochemical oxygen demand over Hong Kong marine waters using machine learning enhanced by imbalanced label optimisation

In many coastal cities around the world, continuing water degradation threatens the living environment of humans and aquatic organisms. To assess and control the water pollution situation, this study estimated the Biochemical Oxygen Demand (BOD) concentration of Hong Kong's marine waters using remote sensing and an improved machine learning (ML) method. The scheme was derived from four ML algorithms (RBF, SVR, RF, XGB) and calibrated using a large amount (N > 1000) of in-situ BOD5 data. Based on labeled datasets with different preprocessing, i.e., the original BOD5, the log10(BOD5), and label distribution smoothing (LDS), three types of models were trained and evaluated. The results highlight the superior potential of the LDS-based model to improve BOD5 estimate by dealing with imbalanced training dataset. Additionally, XGB and RF outperformed RBF and SVR when the model was developed using log10(BOD5) or LDS(BOD5). Over two decades, the BOD5 concentration of Hong Kong marine waters in the autumn (Sep. to Nov.) shows a downward trend, with significant decreases in Deep Bay, Western Buffer, Victoria Harbour, Eastern Buffer, Junk Bay, Port Shelter, and the Tolo Harbour and Channel. Principal component analysis revealed that nutrient levels emerged as the predominant factor in Victoria Harbour and the interior of Deep Bay, while chlorophyll-related and physical parameters were dominant in Southern, Mirs Bay, Northwestern, and the outlet of Deep Bay. LDS provides a new perspective to improve ML-based water quality estimation by alleviating the imbalance in the labeled dataset. Overall, the remotely sensed BOD5 can offer insight into the spatial-temporal distribution of organic matter in Hong Kong coastal waters and valuable guidance for the pollution control.

Prediction of Mycobacterium tuberculosis cell wall permeability using machine learning methods

Tuberculosis (TB) caused by the bacteria Mycobacterium tuberculosis (M. tb), continues to pose a significant worldwide health threat. The advent of drug-resistant strains of the disease highlights the critical need for novel treatments. The unique cell wall of M. tb provides an extra layer of protection for the bacteria and hence only compounds that can penetrate this barrier can reach their targets within the bacterial cell wall. The creation of a reliable machine learning (ML) model to predict the mycobacterial cell wall permeability of small molecules is presented in this work and four ML algorithms, including Random Forest, Support Vector Machines (SVM), k-nearest Neighbour (k-NN) and Logistic Regression were trained on a dataset of 5368 compounds. RDKit and Mordred toolkits were used to calculate features. To determine the most effective model, various performance metrics were used such as accuracy, precision, recall, F1 score, and area under the receiver operating characteristic curve. The best-performing model was further refined with hyperparameter tuning and tenfold cross-validation. The SVM model with filtering outperformed the other machine learning models and demonstrated 80.26% and 81.13% accuracy on the test and validation datasets, respectively. The study also provided insights into the molecular descriptors that play the most important role in predicting the ability of a molecule to pass the M. tb cell wall, which could guide future compound design. The model is available at https://github.com/PGlab-NIPER/MTB_Permeability .

Rapid In Situ Near-Infrared Assessment of Tetrahydrocannabinolic Acid in Cannabis Inflorescences before Harvest Using Machine Learning

Cannabis is cultivated for therapeutic and recreational purposes where delta-9 tetrahydrocannabinol (THC) is a main target for its therapeutic effects. As the global cannabis industry and research into cannabinoids expands, more efficient and cost-effective analysis methods for determining cannabinoid concentrations will be beneficial to increase efficiencies and maximize productivity. The utilization of machine learning tools to develop near-infrared (NIR) spectroscopy-based prediction models, which have been validated from accurate and sensitive chemical analysis, such as gas chromatography (GC) or liquid chromatography mass spectroscopy (LCMS), is essential. Previous research on cannabinoid prediction models targeted decarboxylated cannabinoids, such as THC, rather than the naturally occurring precursor, tetrahydrocannabinolic acid (THCA), and utilize finely ground cannabis inflorescence. The current study focuses on building prediction models for THCA concentrations in whole cannabis inflorescences prior to harvest, by employing non-destructive screening techniques so cultivators may rapidly characterize high-performing cultivars for chemotype in real time, thus facilitating targeted optimization of crossbreeding efforts. Using NIR spectroscopy and LCMS to create prediction models we can differentiate between high-THCA and even ratio classes with 100% prediction accuracy. We have also developed prediction models for THCA concentration with a R2 = 0.78 with a prediction error average of 13%. This study demonstrates the viability of a portable handheld NIR device to predict THCA concentrations on whole cannabis samples before harvest, allowing the evaluation of cannabinoid profiles to be made earlier, therefore increasing high-throughput and rapid capabilities.

The Evolution of Risk Assessment in Spine Surgery: A Narrative Review

BACKGROUND

Risk assessment is critically important in elective and high-risk interventions, particularly spine surgery. This narrative review describes the evolution of risk assessment from the earliest instruments focused on general surgical risk stratification, to more accurate and spine-specific risk calculators that quantified risk, to the current era of big data.

METHODS

The PubMed and SCOPUS databases were queried on October 11, 2023 using search terms to identify risk assessment tools (RATs) in spine surgery. A total of 108 manuscripts were included after screening with full-text review using the following inclusion criteria: 1) study population of adult spine surgical patients, 2) studies describing validation and subsequent performance of preoperative RATs, and 3) studies published in English.

RESULTS

Early RATs provided stratified patients into broad categories and allowed for improved communication between physicians. Subsequent risk calculators attempted to quantify risk by estimating general outcomes such as mortality, but then evolved to estimate spine-specific surgical complications. The integration of novel concepts such as invasiveness, frailty, genetic biomarkers, and sarcopenia led to the development of more sophisticated predictive models that estimate the risk of spine-specific complications and long-term outcomes.

CONCLUSIONS

RATs have undergone a transformative shift from generalized risk stratification to quantitative predictive models. The next generation of tools will likely involve integration of radiographic and genetic biomarkers, machine learning, and artificial intelligence to improve the accuracy of these models and better inform patients, surgeons, and payers.

Developing a machine learning model for predicting venlafaxine active moiety concentration: a retrospective study using real-world evidence

BACKGROUND

Venlafaxine is frequently prescribed for patients with depression. To control the concentration of venlafaxine within the therapeutic window for the best treatment effect, a model to predict venlafaxine concentration is necessary.

AIM

Our objective was to develop a prediction model for venlafaxine concentration using real-world evidence based on machine learning and deep learning techniques.

METHOD

Patients who underwent venlafaxine treatment between November 2019 and August 2022 were included in the study. Important variables affecting venlafaxine concentration were identified using a combination of univariate analysis, sequential forward selection, and machine learning techniques. Predictive performance of nine machine learning and deep learning algorithms were assessed, and the one with the optimal performance was selected for modeling. The final model was interpreted using SHapley Additive exPlanations.

RESULTS

A total of 330 eligible patients were included. Five influential variables that affect venlafaxine concentration were venlafaxine daily dose, sex, age, hyperlipidemia, and adenosine deaminase. The venlafaxine concentration prediction model was developed using the eXtreme Gradient Boosting algorithm (R2 = 0.65, mean absolute error = 77.92, root mean square error = 93.58). In the testing cohort, the accuracy of the predicted concentration within ± 30% of the actual concentration was 73.49%. In the subgroup analysis, the prediction accuracy was 69.39% within the recommended therapeutic range of venlafaxine concentration within ± 30% of the actual value.

CONCLUSION

The XGBoost model for predicting blood concentration of venlafaxine using real-world evidence was developed, guiding the adjustment of regimen in clinical practice.

Advances in artificial intelligence for drug delivery and development: A comprehensive review

Artificial intelligence (AI) has emerged as a powerful tool to revolutionize the healthcare sector, including drug delivery and development. This review explores the current and future applications of AI in the pharmaceutical industry, focusing on drug delivery and development. It covers various aspects such as smart drug delivery networks, sensors, drug repurposing, statistical modeling, and simulation of biotechnological and biological systems. The integration of AI with nanotechnologies and nanomedicines is also examined. AI offers significant advancements in drug discovery by efficiently identifying compounds, validating drug targets, streamlining drug structures, and prioritizing response templates. Techniques like data mining, multitask learning, and high-throughput screening contribute to better drug discovery and development innovations. The review discusses AI applications in drug formulation and delivery, clinical trials, drug safety, and pharmacovigilance. It addresses regulatory considerations and challenges associated with AI in pharmaceuticals, including privacy, data security, and interpretability of AI models. The review concludes with future perspectives, highlighting emerging trends, addressing limitations and biases in AI models, and emphasizing the importance of collaboration and knowledge sharing. It provides a comprehensive overview of AI's potential to transform the pharmaceutical industry and improve patient care while identifying further research and development areas.

Developing a Semi-Supervised Approach Using a PU-Learning-Based Data Augmentation Strategy for Multitarget Drug Discovery

Multifactorial diseases demand therapeutics that can modulate multiple targets for enhanced safety and efficacy, yet the clinical approval of multitarget drugs remains rare. The integration of machine learning (ML) and deep learning (DL) in drug discovery has revolutionized virtual screening. This study investigates the synergy between ML/DL methodologies, molecular representations, and data augmentation strategies. Notably, we found that SVM can match or even surpass the performance of state-of-the-art DL methods. However, conventional data augmentation often involves a trade-off between the true positive rate and false positive rate. To address this, we introduce Negative-Augmented PU-bagging (NAPU-bagging) SVM, a novel semi-supervised learning framework. By leveraging ensemble SVM classifiers trained on resampled bags containing positive, negative, and unlabeled data, our approach is capable of managing false positive rates while maintaining high recall rates. We applied this method to the identification of multitarget-directed ligands (MTDLs), where high recall rates are critical for compiling a list of interaction candidate compounds. Case studies demonstrate that NAPU-bagging SVM can identify structurally novel MTDL hits for ALK-EGFR with favorable docking scores and binding modes, as well as pan-agonists for dopamine receptors. The NAPU-bagging SVM methodology should serve as a promising avenue to virtual screening, especially for the discovery of MTDLs.

PredCoffee: A binary classification approach specifically for coffee odor

Compared to traditional methods, using machine learning to assess or predict the odor of molecules can save costs in various aspects. Our research aims to collect molecules with coffee odor and summarize the regularity of these molecules, ultimately creating a binary classifier that can determine whether a molecule has a coffee odor. In this study, a total of 371 coffee-odor molecules and 9,700 non-coffee-odor molecules were collected. The Knowledge-guided Pre-training of Graph Transformer (KPGT), support vector machine (SVM), random forest (RF), multi-layer perceptron (MLP), and message-passing neural networks (MPNN) were used to train the data. The model with the best performance was selected as the basis of the predictor. The prediction accuracy value of the KPGT model exceeded 0.84 and the predictor has been deployed as a webserver PredCoffee.

An assessment of crucial structural contributors of HDAC6 inhibitors through fragment-based non-linear pattern recognition and molecular dynamics simulation approaches

Amidst the Zn2+-dependant isoforms of the HDAC family, HDAC6 has emerged as a potential target associated with an array of diseases, especially cancer and neuronal disorders like Rett's Syndrome, Alzheimer's disease, Huntington's disease, etc. Also, despite the availability of a handful of HDAC inhibitors in the market, their non-selective nature has restricted their use in different disease conditions. In this situation, the development of selective and potent HDAC6 inhibitors will provide efficacious therapeutic agents to treat different diseases. In this context, this study has been carried out to evaluate the potential structural contributors of quinazoline-cap-containing HDAC6 inhibitors via machine learning (ML), conventional classification-dependant QSAR, and MD simulation-based binding mode of interaction analysis toward HDAC6 binding. This combined conventional and modern molecular modeling study has revealed the significance of the quinazoline moiety, substitutions present at the quinazoline cap group, as well as the importance of molecular property, number of hydrogen bond donor-acceptor functions, carbon-chlorine distance that significantly affects the HDAC6 binding of these inhibitors, subsequently affecting their potency . Interestingly, the study also revealed that the substitutions such as the chloroethyl group, and bulky quinazolinyl cap group can affect the binding of the cap function with the amino acid residues present in the loops proximal to the catalytic site of HDAC6. Such contributions of cap groups can lead to both stabilization and destabilization of the cap function after occupying the hydrophobic catalytic site by the aryl hydroxamate linker-ZBG functions.

Machine Learning in Diagnosis and Prognosis of Lung Cancer by PET-CT

As a disease with high morbidity and high mortality, lung cancer has seriously harmed people's health. Therefore, early diagnosis and treatment are more important. PET/CT is usually used to obtain the early diagnosis, staging, and curative effect evaluation of tumors, especially lung cancer, due to the heterogeneity of tumors and the differences in artificial image interpretation and other reasons, it also fails to entirely reflect the real situation of tumors. Artificial intelligence (AI) has been applied to all aspects of life. Machine learning (ML) is one of the important ways to realize AI. With the help of the ML method used by PET/CT imaging technology, there are many studies in the diagnosis and treatment of lung cancer. This article summarizes the application progress of ML based on PET/CT in lung cancer, in order to better serve the clinical. In this study, we searched PubMed using machine learning, lung cancer, and PET/CT as keywords to find relevant articles in the past 5 years or more. We found that PET/CT-based ML approaches have achieved significant results in the detection, delineation, classification of pathology, molecular subtyping, staging, and response assessment with survival and prognosis of lung cancer, which can provide clinicians a powerful tool to support and assist in critical daily clinical decisions. However, ML has some shortcomings such as slightly poor repeatability and reliability.

Adapting Deep Learning QSPR Models to Specific Drug Discovery Projects

Medicinal chemistry and drug design efforts can be assisted by machine learning (ML) models that relate the molecular structure to compound properties. Such quantitative structure-property relationship models are generally trained on large data sets that include diverse chemical series (global models). In the pharmaceutical industry, these ML global models are available across discovery projects as an "out-of-the-box" solution to assist in drug design, synthesis prioritization, and experiment selection. However, drug discovery projects typically focus on confined parts of the chemical space (e.g., chemical series), where global models might not be applicable. Local ML models are sometimes generated to focus on specific projects or series. Herein, ML-based global models, local models, and hybrid global-local strategies were benchmarked. Analyses were done for more than 300 drug discovery projects at Novartis and ten absorption, distribution, metabolism, and excretion (ADME) assays. In this work, hybrid global-local strategies based on transfer learning approaches were proposed to leverage both historical ADME data (global) and project-specific data (local) to adapt model predictions. Fine-tuning a pretrained global ML model (used for weights' initialization, WI) was the top-performing method. Average improvements of mean absolute errors across all assays were 16% and 27% compared with global and local models, respectively. Interestingly, when the effect of training set size was analyzed, WI fine-tuning was found to be successful even in low-data scenarios (e.g., ∼10 molecules per project). Taken together, this work highlights the potential of domain adaptation in the field of molecular property predictions to refine existing pretrained models on a new compound data distribution.

Prediction of matrilineal specific patatin-like protein governing in-vivo maternal haploid induction in maize using support vector machine and di-peptide composition

The mutant matrilineal (mtl) gene encoding patatin-like phospholipase activity is involved in in-vivo maternal haploid induction in maize. Doubling of chromosomes in haploids by colchicine treatment leads to complete fixation of inbreds in just one generation compared to 6-7 generations of selfing. Thus, knowledge of patatin-like proteins in other crops assumes great significance for in-vivo haploid induction. So far, no online tool is available that can classify unknown proteins into patatin-like proteins. Here, we aimed to optimize a machine learning-based algorithm to predict the patatin-like phospholipase activity of unknown proteins. Four different kernels [radial basis function (RBF), sigmoid, polynomial, and linear] were used for building support vector machine (SVM) classifiers using six different sequence-based compositional features (AAC, DPC, GDPC, CTDC, CTDT, and GAAC). A total of 1170 protein sequences including both patatin-like (585 sequences) from various monocots, dicots, and microbes; and non-patatin-like proteins (585 sequences) from different subspecies of Zea mays were analyzed. RBF and polynomial kernels were quite promising in the prediction of patatin-like proteins. Among six sequence-based compositional features, di-peptide composition attained > 90% prediction accuracies using RBF and polynomial kernels. Using mutual information, most explaining dipeptides that contributed the highest to the prediction process were identified. The knowledge generated in this study can be utilized in other crops prior to the initiation of any experiment. The developed SVM model opened a new paradigm for scientists working in in-vivo haploid induction in commercial crops. This is the first report of machine learning of the identification of proteins with patatin-like activity.

Ultrasound-Based Radiomics for the Classification of Henoch-Schönlein Purpura Nephritis in Children

Henoch-Schönlein purpura nephritis (HSPN) is one of the most common kidney diseases in children. The current diagnosis and classification of HSPN depend on pathological biopsy, which is seriously limited by its invasive and high-risk nature. The aim of the study was to explore the potential of radiomics model for evaluating the histopathological classification of HSPN based on the ultrasound (US) images. A total of 440 patients with Henoch-Schönlein purpura nephritis proved by biopsy were analyzed retrospectively. They were grouped according to two histopathological categories: those without glomerular crescent formation (ISKDC grades I-II) and those with glomerular crescent formation (ISKDC grades III-V). The patients were randomly assigned to either a training cohort (n = 308) or a validation cohort (n = 132) with a ratio of 7:3. The sonologist manually drew the regions of interest (ROI) on the ultrasound images of the right kidney including the cortex and medulla. Then, the ultrasound radiomics features were extracted using the Pyradiomics package. The dimensions of radiomics features were reduced by Spearman correlation coefficients and least absolute shrinkage and selection operator (LASSO) method. Finally, three radiomics models using k-nearest neighbor (KNN), logistic regression (LR), and support vector machine (SVM) were established, respectively. The predictive performance of such classifiers was assessed with receiver operating characteristic (ROC) curve. 105 radiomics features were extracted from derived US images of each patient and 14 features were ultimately selected for the machine learning analysis. Three machine learning models including k-nearest neighbor (KNN), logistic regression (LR), and support vector machine (SVM) were established for HSPN classification. Of the three classifiers, the SVM classifier performed the best in the validation cohort [area under the curve (AUC) =0.870 (95% CI, 0.795-0.944), sensitivity = 0.706, specificity = 0.950]. The US-based radiomics had good predictive value for HSPN classification, which can be served as a noninvasive tool to evaluate the severity of renal pathology and crescentic formation in children with HSPN.

Prediction of intraoperative red blood cell transfusion in valve replacement surgery: machine learning algorithm development based on non-anemic cohort

Background

Our study aimed to develop machine learning algorithms capable of predicting red blood cell (RBC) transfusion during valve replacement surgery based on a preoperative dataset of the non-anemic cohort.

Methods

A total of 423 patients who underwent valvular replacement surgery from January 2015 to December 2020 were enrolled. A comprehensive database that incorporated demographic characteristics, clinical conditions, and results of preoperative biochemistry tests was used for establishing the models. A range of machine learning algorithms were employed, including decision tree, random forest, extreme gradient boosting (XGBoost), categorical boosting (CatBoost), support vector classifier and logistic regression (LR). Subsequently, the area under the receiver operating characteristic curve (AUC), accuracy, recall, precision, and F1 score were used to determine the predictive capability of the algorithms. Furthermore, we utilized SHapley Additive exPlanation (SHAP) values to explain the optimal prediction model.

Results

The enrolled patients were randomly divided into training set and testing set according to the 8:2 ratio. There were 16 important features identified by Sequential Backward Selection for model establishment. The top 5 most influential features in the RF importance matrix plot were hematocrit, hemoglobin, ALT, fibrinogen, and ferritin. The optimal prediction model was CatBoost algorithm, exhibiting the highest AUC (0.752, 95% CI: 0.662-0.780), which also got relatively high F1 score (0.695). The CatBoost algorithm also showed superior performance over the LR model with the AUC (0.666, 95% CI: 0.534-0.697). The SHAP summary plot and the SHAP dependence plot were used to visually illustrate the positive or negative effects of the selected features attributed to the CatBoost model.

Conclusions

This study established a series of prediction models to enhance risk assessment of intraoperative RBC transfusion during valve replacement in no-anemic patients. The identified important predictors may provide effective preoperative interventions.

Generalizability Improvement of Interpretable Symbolic Regression Models for Quantitative Structure-Activity Relationships

In the pursuit of optimal quantitative structure-activity relationship (QSAR) models, two key factors are paramount: the robustness of predictive ability and the interpretability of the model. Symbolic regression (SR) searches for the mathematical expressions that explain a training data set. Thus, the models provided by SR are globally interpretable. We previously proposed an SR method that can generate interpretable expressions by humans. This study introduces an enhanced symbolic regression method, termed filter-induced genetic programming 2 (FIGP2), as an extension of our previously proposed SR method. FIGP2 is designed to improve the generalizability of SR models and to be applicable to data sets in which cost-intensive descriptors are employed. The FIGP2 method incorporates two major improvements: a modified domain filter to eradicate diverging expressions based on optimal calculation and the introduction of a stability metric to penalize expressions that would lead to overfitting. Our retrospective comparative analysis using 12 structure-activity relationship data sets revealed that FIGP2 surpassed the previously proposed SR method and conventional modeling methods, such as support vector regression and multivariate linear regression in terms of predictive performance. Generated mathematical expressions by FIGP2 were relatively simple and not divergent in the domain of function. Taken together, FIGP2 can be used for making interpretable regression models with predictive ability.

Distinguishing brain tumors by Label-free confocal micro-Raman spectroscopy

BACKGROUND

Brain tumors have serious adverse effects on public health and social economy. Accurate detection of brain tumor types is critical for effective and proactive treatment, and thus improve the survival of patients.

METHODS

Four types of brain tumor tissue sections were detected by Raman spectroscopy. Principal component analysis (PCA) has been used to reduce the dimensionality of the Raman spectra data. Linear discriminant analysis (LDA) and quadratic discriminant analysis (QDA) methods were utilized to discriminate different types of brain tumors.

RESULTS

Raman spectra were collected from 40 brain tumors. Variations in intensity and shift were observed in the Raman spectra positioned at 721, 854, 1004, 1032, 1128, 1248, 1449 cm-1 for different brain tumor tissues. The PCA results indicated that glioma, pituitary adenoma, and meningioma are difficult to differentiate from each other, whereas acoustic neuroma is clearly distinguished from the other three tumors. Multivariate analysis including QDA and LDA methods showed the classification accuracy rate of the QDA model was 99.47 %, better than the rate of LDA model was 95.07 %.

CONCLUSIONS

Raman spectroscopy could be used to extract valuable fingerprint-type molecular and chemical information of biological samples. The demonstrated technique has the potential to be developed to a rapid, label-free, and intelligent approach to distinguish brain tumor types with high accuracy.

Assessment of machine learning-based methods predictive suitability for migration pollutants from microplastics degradation

The aim of the work was to assess the usefulness of machine learning in predicting the migration of pollutants from microplastics. The search for methods to reduce unnecessary laboratory analyzes is a necessary action both to protect the environment and from an economic perspective. Multiple regression, artificial neural networks, support vector method and random forest regression were used in the study to predict leaching of plasticizers and other contaminants from microplastics. The development of the methods were based on the results of laboratory tests obtained by the GC-MS method. The results obtained confirm the potential of artificial neural networks and the support vector method for effective modelling and prediction of chemical compounds leached from microplastics. Correlation results were obtained for the analyzed parameters between the data obtained in the model and laboratory data in the range of 0.96-0.98 and 0.93-0.99 for artificial neural networks and the support vector method, respectively. Multiple regression showed the lowest performance in all cases in predicting plastic phthalic acid esters (coefficient of determination (R2) in the range of 0.03-0.24). ENVIRONMENTAL IMPLICATION: The results presented in this paper will provide new insight into the influence of different parameters and factors on the leaching of plastic additives. This information is necessary to assess the harmfulness of these materials. The collected data is unique on a global scale. For the first time, machine learning were used to predict the leaching rate of plasticizers from different polymers under different environmental conditions. The use of machine learning allows to reduce unnecessary laboratory tests and reduce costs and protect the environment. Currently, there are no research results in this field in the scientific literature.

Closed, one-stop intelligent and accurate particle characterization based on micro-Raman spectroscopy and digital microfluidics

Monoclonal antibodies are prone to form protein particles through aggregation, fragmentation, and oxidation under varying stress conditions during the manufacturing, shipping, and storage of parenteral drug products. According to pharmacopeia requirements, sub-visible particle levels need to be controlled throughout the shelf life of the product. Therefore, in addition to determining particle counts, it is crucial to accurately characterize particles in drug product to understand the stress condition of exposure and to implement appropriate mitigation actions for a specific formulation. In this study, we developed a new method for intelligent characterization of protein particles using micro-Raman spectroscopy on a digital microfluidic chip (DMF). Several microliters of protein particle solutions induced by stress degradation were loaded onto a DMF chip to generate multiple droplets for Raman spectroscopy testing. By training multiple machine learning classification models on the obtained Raman spectra of protein particles, eight types of protein particles were successfully characterized and predicted with high classification accuracy (93%-100%). The advantages of the novel particle characterization method proposed in this study include a closed system to prevent particle contamination, one-stop testing of morphological and chemical structure information, low sample volume consumption, reusable particle droplets, and simplified data analysis with high classification accuracy. It provides great potential to determine the probable root cause of the particle source or stress conditions by a single testing, so that an accurate particle control strategy can be developed and ultimately extend the product shelf-life.

Machine learning in Alzheimer's disease drug discovery and target identification

Alzheimer's disease (AD) stands as a formidable neurodegenerative ailment that poses a substantial threat to the elderly population, with no known curative or disease-slowing drugs in existence. Among the vital and time-consuming stages in the drug discovery process, disease modeling and target identification hold particular significance. Disease modeling allows for a deeper comprehension of disease progression mechanisms and potential therapeutic avenues. On the other hand, target identification serves as the foundational step in drug development, exerting a profound influence on all subsequent phases and ultimately determining the success rate of drug development endeavors. Machine learning (ML) techniques have ushered in transformative breakthroughs in the realm of target discovery. Leveraging the strengths of large dataset analysis, multifaceted data processing, and the exploration of intricate biological mechanisms, ML has become instrumental in the quest for effective AD treatments. In this comprehensive review, we offer an account of how ML methodologies are being deployed in the pursuit of drug discovery for AD. Furthermore, we provide an overview of the utilization of ML in uncovering potential intervention strategies and prospective therapeutic targets for AD. Finally, we discuss the principal challenges and limitations currently faced by these approaches. We also explore the avenues for future research that hold promise in addressing these challenges.

Supra-Quantum Dot Assemblies to Maximize Color-Based Multiplexed Fluorescence Detection with a Smartphone Camera

Photoluminescence (PL) imaging and bioanalysis with smartphone-based devices are of growing interest for point-of-care/point-of-need diagnostics. Strategies for maximizing sensitivity have been explored in this context, but color multiplexing has been very limited, with its maximum level unexplored. Here, we evaluated color multiplexing with smartphone-based PL imaging by using supra-nanoparticle assemblies of quantum dots (supra-QDs). These materials were prepared as composite colors that were tailored to the red-green-blue (RGB) color space of smartphone cameras by coassembling different ratios of R-, G-, and B-emitting QDs on a silica nanoparticle scaffold. The supra-QDs were characterized and used to label cell-sized objects that were measured under flow with a smartphone-based device. Each color followed an approximately linear trajectory in the RGB space, and training of support vector machine models enabled color classification with overall accuracies ≥87% for 10-color multiplexing and better accuracies for fewer colors. Most misclassification occurred at low signal levels, such that establishing a nonclassifiable zone near the origin of RGB color space improved the overall 10-color classification accuracy to ≥94%. Similar improvements in accuracy with greater retention of data were possible with a probabilistic rather than a radial threshold. Simulations that were parameterized by experimental data suggested that ≥14-color multiplexing with accuracies ≥90% should be possible with an optimized supra-QD color set. This study is an important foundation for advancing RGB color-based multiplexing for imaging and analyses with smartphone cameras and related charge-coupled device and CMOS color image sensor technologies.

Disease Diagnosis Based on Improved Gray Wolf Optimization (IGWO) and Ensemble Classification

This paper introduces a simple strategy for diagnosing disease, which is called improved gray wolf optimization (IGWO) and ensemble classification. The proposed strategy consists of two sequential phases, which are; (i) Feature Selection Phase (FSP) and (ii) Ensemble Classification Phase (ECP). During the former, the most effective features for diagnosing disease are selected, while during the latter, the actual diagnosis takes place depending on voting of five different classifiers. The main contribution of this paper is a suggested modification for the traditional Gray Wolf Optimization (GWO), which is called Improved Gray Wolf Optimization (IGWO). As an optimization technique, the proposed IGWO is employed in the FSP for selecting the effective features. For evaluating, IGWO has been implemented using recent feature selection techniques as well as the proposed method. To accomplish the classification phase; ensemble classification has been used which uses several classification techniques such as; Naïve Bayes (NB), Support Vector Machines (SVM), Deep Neural Network (DNN), Decision Tree (DT), and K-Nearest Neighbors (KNN). Ensemble classification integrate several classifiers for improving prediction performance. Experimental results have shown that employing IGWO promotes the performance of the diagnosing strategy of different diseases in terms of precision, recall, and accuracy.

Identification of a prognostic evaluator from glutamine metabolic heterogeneity studies within and between tissues in hepatocellular carcinoma

Background: The liver is the major metabolic organ of the human body, and abnormal metabolism is the main factor influencing hepatocellular carcinoma (HCC). This study was designed to determine the effect of glutamine metabolism on HCC heterogeneity and to develop a prognostic evaluator based on the heterogeneity study of glutamine metabolism within HCC tumors and between tissues. Methods: Single-cell transcriptome data were extracted from the GSE149614 dataset and processed using the Seurat package in R for quality control of these data. HCC subtypes in the Cancer Genome Atlas and the GSE14520 dataset were identified via consensus clustering based on glutamine family amino acid metabolism (GFAAM) process genes. The machine learning algorithms gradient boosting machine, support vector machine, random forest, eXtreme gradient boosting, decision trees, and least absolute shrinkage and selection operator were utilized to develop the prognosis model of differentially expressed genes among the molecular gene subtypes. Results: The samples in the GSE149614 dataset included 10 cell types, and there was no significant difference in the GFAAM pathway. HCC was classified into three molecular subtypes according to GFAAM process genes, showing molecular heterogeneity in prognosis, clinicopathological features, and immune cell infiltration. C1 showed the worst survival rate and the highest immune score and immune cell infiltration. A six-gene model for prognostic and immunotherapy responses was constructed among subtypes, and the calculated high-risk score was significantly correlated with poor prognosis, high immune abundance, and a low response rate of immunotherapy in HCC. Conclusion: Our discovery of GFAAM-associated marker genes may help to further decipher the role in HCC occurrence and progression. In particular, this six-gene prognostic model may serve as a predictor of treatment and prognosis in HCC patients.

Revolutionizing Medicinal Chemistry: The Application of Artificial Intelligence (AI) in Early Drug Discovery

Artificial intelligence (AI) has permeated various sectors, including the pharmaceutical industry and research, where it has been utilized to efficiently identify new chemical entities with desirable properties. The application of AI algorithms to drug discovery presents both remarkable opportunities and challenges. This review article focuses on the transformative role of AI in medicinal chemistry. We delve into the applications of machine learning and deep learning techniques in drug screening and design, discussing their potential to expedite the early drug discovery process. In particular, we provide a comprehensive overview of the use of AI algorithms in predicting protein structures, drug-target interactions, and molecular properties such as drug toxicity. While AI has accelerated the drug discovery process, data quality issues and technological constraints remain challenges. Nonetheless, new relationships and methods have been unveiled, demonstrating AI's expanding potential in predicting and understanding drug interactions and properties. For its full potential to be realized, interdisciplinary collaboration is essential. This review underscores AI's growing influence on the future trajectory of medicinal chemistry and stresses the importance of ongoing synergies between computational and domain experts.

Artificial Intelligence and Machine Learning in Pharmacological Research: Bridging the Gap Between Data and Drug Discovery

Artificial intelligence (AI) has transformed pharmacological research through machine learning, deep learning, and natural language processing. These advancements have greatly influenced drug discovery, development, and precision medicine. AI algorithms analyze vast biomedical data identifying potential drug targets, predicting efficacy, and optimizing lead compounds. AI has diverse applications in pharmacological research, including target identification, drug repurposing, virtual screening, de novo drug design, toxicity prediction, and personalized medicine. AI improves patient selection, trial design, and real-time data analysis in clinical trials, leading to enhanced safety and efficacy outcomes. Post-marketing surveillance utilizes AI-based systems to monitor adverse events, detect drug interactions, and support pharmacovigilance efforts. Machine learning models extract patterns from complex datasets, enabling accurate predictions and informed decision-making, thus accelerating drug discovery. Deep learning, specifically convolutional neural networks (CNN), excels in image analysis, aiding biomarker identification and optimizing drug formulation. Natural language processing facilitates the mining and analysis of scientific literature, unlocking valuable insights and information. However, the adoption of AI in pharmacological research raises ethical considerations. Ensuring data privacy and security, addressing algorithm bias and transparency, obtaining informed consent, and maintaining human oversight in decision-making are crucial ethical concerns. The responsible deployment of AI necessitates robust frameworks and regulations. The future of AI in pharmacological research is promising, with integration with emerging technologies like genomics, proteomics, and metabolomics offering the potential for personalized medicine and targeted therapies. Collaboration among academia, industry, and regulatory bodies is essential for the ethical implementation of AI in drug discovery and development. Continuous research and development in AI techniques and comprehensive training programs will empower scientists and healthcare professionals to fully exploit AI's potential, leading to improved patient outcomes and innovative pharmacological interventions.

Behavioural Models of Risk-Taking in Human-Robot Tactile Interactions

Touch can have a strong effect on interactions between people, and as such, it is expected to be important to the interactions people have with robots. In an earlier work, we showed that the intensity of tactile interaction with a robot can change how much people are willing to take risks. This study further develops our understanding of the relationship between human risk-taking behaviour, the physiological responses by the user, and the intensity of the tactile interaction with a social robot. We used data collected with physiological sensors during the playing of a risk-taking game (the Balloon Analogue Risk Task, or BART). The results of a mixed-effects model were used as a baseline to predict risk-taking propensity from physiological measures, and these results were further improved through the use of two machine learning techniques-support vector regression (SVR) and multi-input convolutional multihead attention (MCMA)-to achieve low-latency risk-taking behaviour prediction during human-robot tactile interaction. The performance of the models was evaluated based on mean absolute error (MAE), root mean squared error (RMSE), and R squared score (R2), which obtained the optimal result with MCMA yielding an MAE of 3.17, an RMSE of 4.38, and an R2 of 0.93 compared with the baseline of 10.97 MAE, 14.73 RMSE, and 0.30 R2. The results of this study offer new insights into the interplay between physiological data and the intensity of risk-taking behaviour in predicting human risk-taking behaviour during human-robot tactile interactions. This work illustrates that physiological activation and the intensity of tactile interaction play a prominent role in risk processing during human-robot tactile interaction and demonstrates that it is feasible to use human physiological data and behavioural data to predict risk-taking behaviour in human-robot tactile interaction.

O-GlyThr: Prediction of human O-linked threonine glycosites using multi-feature fusion

O-linked glycosylation is one of the most complex post-translational modifications (PTM) of human proteins modulating various cellular metabolic and signaling pathways. Unlike N-glycosylation, the O-glycosylation has nonspecific sequence features and nonstable glycan core structure, which makes identification of O-glycosites more challenging either by experimental or computational methods. Biochemical experiments to identify O-glycosites in batches are technically and economically demanding. Therefore, development of computation-based methods is greatly warranted. This study constructed a prediction model based on feature fusion for O-glycosites linked to the threonine residues in Homo sapiens. In the training model, we collected and sorted out high-quality human protein data with O-linked threonine glycosites. Seven feature coding methods were fused to represent the sample sequence. By comparison of different algorithms, random forest was selected as the final classifier to construct the classification model. Through 5-fold cross-validation, the proposed model, namely O-GlyThr, performed satisfactorily on both training set (AUC: 0.9308) and independent validation dataset (AUC: 0.9323). Compared with previously published predictors, O-GlyThr achieved the highest ACC of 0.8475 on the independent test dataset. These results demonstrated the high competency of our predictor in identifying O-glycosites on threonine residues. Furthermore, a user-friendly webserver named O-GlyThr (http://cbcb.cdutcm.edu.cn/O-GlyThr/) was developed to assist glycobiologists in the research associated with glycosylation structure and function.

Multimodal striatal neuromarkers in distinguishing parkinsonian variant of multiple system atrophy from idiopathic Parkinson's disease

AIMS

To develop an automatic method of classification for parkinsonian variant of multiple system atrophy (MSA-P) and Idiopathic Parkinson's disease (IPD) in early to moderately advanced stages based on multimodal striatal alterations and identify the striatal neuromarkers for distinction.

METHODS

77 IPD and 75 MSA-P patients underwent 3.0 T multimodal MRI comprising susceptibility-weighted imaging, resting-state functional magnetic resonance imaging, T1-weighted imaging, and diffusion tensor imaging. Iron-radiomic features, volumes, functional and diffusion scalars of bilateral 10 striatal subregions were calculated and provided to the support vector machine for classification RESULTS: A combination of iron-radiomic features, function, diffusion, and volumetric measures optimally distinguished IPD and MSA-P in the testing dataset (accuracy 0.911 and area under the receiver operating characteristic curves [AUC] 0.927). The diagnostic performance further improved when incorporating clinical variables into the multimodal model (accuracy 0.934 and AUC 0.953). The most crucial factor for classification was the functional activity of the left dorsolateral putamen.

CONCLUSION

The machine learning algorithm applied to multimodal striatal dysfunction depicted dorsal striatum and supervening prefrontal lobe and cerebellar dysfunction through the frontostriatal and cerebello-striatal connections and facilitated accurate classification between IPD and MSA-P. The dorsolateral putamen was the most valuable neuromarker for the classification.