DeepStack-DTIs: Predicting Drug-Target Interactions Using LightGBM Feature Selection and Deep-Stacked Ensemble Classifier

Rational Design of Lipid Nanoparticles for Enhanced mRNA Vaccine Delivery via Machine Learning

Since the coronavirus pandemic, mRNA vaccines have revolutionized the field of vaccinology. Lipid nanoparticles (LNPs) are proposed to enhance mRNA delivery efficiency; however, their design is suboptimal. Here, a rational method for designing LNPs is explored, focusing on the ionizable lipid composition and structural optimization using machine learning (ML) techniques. A total of 213 LNPs are analyzed using random forest regression models trained with 314 features to predict the mRNA expression efficiency. The models, which predict mRNA expression levels post-administration of intradermal injection in mice, identify phenol as the dominant substructure affecting mRNA encapsulation and expression. The specific phospholipids used as components of the LNPs, as well as the N/P ratio and mass ratio, are found to affect the efficacy of mRNA delivery. Structural analysis highlights the impact of the carbon chain length on the encapsulation efficiency and LNP stability. This integrated approach offers a framework for designing advanced LNPs and has the potential to unlock the full potential of mRNA therapeutics.

GSRF-DTI: a framework for drug-target interaction prediction based on a drug-target pair network and representation learning on a large graph

BACKGROUND

Identification of potential drug-target interactions (DTIs) with high accuracy is a key step in drug discovery and repositioning, especially concerning specific drug targets. Traditional experimental methods for identifying the DTIs are arduous, time-intensive, and financially burdensome. In addition, robust computational methods have been developed for predicting the DTIs and are widely applied in drug discovery research. However, advancing more precise algorithms for predicting DTIs is essential to meet the stringent standards demanded by drug discovery.

RESULTS

We proposed a novel method called GSRF-DTI, which integrates networks with a deep learning algorithm to identify DTIs. Firstly, GSRF-DTI learned the embedding representation of drugs and targets by integrating multiple drug association information and target association information, respectively. Then, GSRF-DTI considered the influence of drug-target pair (DTP) association on DTI prediction to construct a drug-target pair network (DTP-NET). Next, we utilized GraphSAGE on DTP-NET to learn the potential features of the network and applied random forest (RF) to predict the DTIs. Furthermore, we conducted ablation experiments to validate the necessity of integrating different types of network features for identifying DTIs. It is worth noting that GSRF-DTI proposed three novel DTIs.

CONCLUSIONS

GSRF-DTI not only considered the influence of the interaction relationship between drug and target but also considered the impact of DTP association relationship on DTI prediction. We initially use GraphSAGE to aggregate the neighbor information of nodes for better identification. Experimental analysis on Luo's dataset and the newly constructed dataset revealed that the GSRF-DTI framework outperformed several state-of-the-art methods significantly.

Artificial Intelligence in Drug Identification and Validation: A Scoping Review

The end-to-end process in the discovery of drugs involves therapeutic candidate identification, validation of identified targets, identification of hit compound series, lead identification and optimization, characterization, and formulation and development. The process is lengthy, expensive, tedious, and inefficient, with a large attrition rate for novel drug discovery. Today, the pharmaceutical industry is focused on improving the drug discovery process. Finding and selecting acceptable drug candidates effectively can significantly impact the price and profitability of new medications. Aside from the cost, there is a need to reduce the end-to-end process time, limiting the number of experiments at various stages. To achieve this, artificial intelligence (AI) has been utilized at various stages of drug discovery. The present study aims to identify the recent work that has developed AI-based models at various stages of drug discovery, identify the stages that need more concern, present the taxonomy of AI methods in drug discovery, and provide research opportunities. From January 2016 to September 1, 2023, the study identified all publications that were cited in the electronic databases including Scopus, NCBI PubMed, MEDLINE, Anthropology Plus, Embase, APA PsycInfo, SOCIndex, and CINAHL. Utilising a standardized form, data were extracted, and presented possible research prospects based on the analysis of the extracted data.

Application of Artificial Intelligence in Drug-Drug Interactions Prediction: A Review

Drug-drug interactions (DDI) are a critical aspect of drug research that can have adverse effects on patients and can lead to serious consequences. Predicting these events accurately can significantly improve clinicians' ability to make better decisions and establish optimal treatment regimens. However, manually detecting these interactions is time-consuming and labor-intensive. Utilizing the advancements in Artificial Intelligence (AI) is essential for achieving accurate forecasts of DDIs. In this review, DDI prediction tasks are classified into three types according to the type of DDI prediction: undirected DDI prediction, DDI events prediction, and Asymmetric DDI prediction. The paper then reviews the progress of AI for each of these three prediction tasks in DDI and provides a summary of the data sets used as well as the representative methods used in these three prediction directions. In this review, we aim to provide a comprehensive overview of drug interaction prediction. The first section introduces commonly used databases and presents an overview of current research advancements and techniques across three domains of DDI. Additionally, we introduce classical machine learning techniques for predicting undirected drug interactions and provide a timeline for the progression of the predicted drug interaction events. At last, we debate the difficulties and prospects of AI approaches at predicting DDI, emphasizing their potential for improving clinical decision-making and patient outcomes.

Predicting lncRNA-protein interactions through deep learning framework employing multiple features and random forest algorithm

RNA-protein interaction (RPI) is crucial to the life processes of diverse organisms. Various researchers have identified RPI through long-term and high-cost biological experiments. Although numerous machine learning and deep learning-based methods for predicting RPI currently exist, their robustness and generalizability have significant room for improvement. This study proposes LPI-MFF, an RPI prediction model based on multi-source information fusion, to address these issues. The LPI-MFF employed protein-protein interactions features, sequence features, secondary structure features, and physical and chemical properties as the information sources with the corresponding coding scheme, followed by the random forest algorithm for feature screening. Finally, all information was combined and a classification method based on convolutional neural networks is used. The experimental results of fivefold cross-validation demonstrated that the accuracy of LPI-MFF on RPI1807 and NPInter was 97.60% and 97.67%, respectively. In addition, the accuracy rate on the independent test set RPI1168 was 84.9%, and the accuracy rate on the Mus musculus dataset was 90.91%. Accordingly, LPI-MFF demonstrated greater robustness and generalization than other prevalent RPI prediction methods.

Practical guidelines for the use of gradient boosting for molecular property prediction

Decision tree ensembles are among the most robust, high-performing and computationally efficient machine learning approaches for quantitative structure-activity relationship (QSAR) modeling. Among them, gradient boosting has recently garnered particular attention, for its performance in data science competitions, virtual screening campaigns, and bioactivity prediction. However, different variants of gradient boosting exist, the most popular being XGBoost, LightGBM and CatBoost. Our study provides the first comprehensive comparison of these approaches for QSAR. To this end, we trained 157,590 gradient boosting models, which were evaluated on 16 datasets and 94 endpoints, comprising 1.4 million compounds in total. Our results show that XGBoost generally achieves the best predictive performance, while LightGBM requires the least training time, especially for larger datasets. In terms of feature importance, the models surprisingly rank molecular features differently, reflecting differences in regularization techniques and decision tree structures. Thus, expert knowledge must always be employed when evaluating data-driven explanations of bioactivity. Furthermore, our results show that the relevance of each hyperparameter varies greatly across datasets and that it is crucial to optimize as many hyperparameters as possible to maximize the predictive performance. In conclusion, our study provides the first set of guidelines for cheminformatics practitioners to effectively train, optimize and evaluate gradient boosting models for virtual screening and QSAR applications.

DBGRU-SE: predicting drug-drug interactions based on double BiGRU and squeeze-and-excitation attention mechanism

The prediction of drug-drug interactions (DDIs) is essential for the development and repositioning of new drugs. Meanwhile, they play a vital role in the fields of biopharmaceuticals, disease diagnosis and pharmacological treatment. This article proposes a new method called DBGRU-SE for predicting DDIs. Firstly, FP3 fingerprints, MACCS fingerprints, Pubchem fingerprints and 1D and 2D molecular descriptors are used to extract the feature information of the drugs. Secondly, Group Lasso is used to remove redundant features. Then, SMOTE-ENN is applied to balance the data to obtain the best feature vectors. Finally, the best feature vectors are fed into the classifier combining BiGRU and squeeze-and-excitation (SE) attention mechanisms to predict DDIs. After applying five-fold cross-validation, The ACC values of DBGRU-SE model on the two datasets are 97.51 and 94.98%, and the AUC are 99.60 and 98.85%, respectively. The results showed that DBGRU-SE had good predictive performance for drug-drug interactions.

Integrating Structured and Unstructured EHR Data for Predicting Mortality by Machine Learning and Latent Dirichlet Allocation Method

An ICU is a critical care unit that provides advanced medical support and continuous monitoring for patients with severe illnesses or injuries. Predicting the mortality rate of ICU patients can not only improve patient outcomes, but also optimize resource allocation. Many studies have attempted to create scoring systems and models that predict the mortality of ICU patients using large amounts of structured clinical data. However, unstructured clinical data recorded during patient admission, such as notes made by physicians, is often overlooked. This study used the MIMIC-III database to predict mortality in ICU patients. In the first part of the study, only eight structured variables were used, including the six basic vital signs, the GCS, and the patient's age at admission. In the second part, unstructured predictor variables were extracted from the initial diagnosis made by physicians when the patients were admitted to the hospital and analyzed using Latent Dirichlet Allocation techniques. The structured and unstructured data were combined using machine learning methods to create a mortality risk prediction model for ICU patients. The results showed that combining structured and unstructured data improved the accuracy of the prediction of clinical outcomes in ICU patients over time. The model achieved an AUROC of 0.88, indicating accurate prediction of patient vital status. Additionally, the model was able to predict patient clinical outcomes over time, successfully identifying important variables. This study demonstrated that a small number of easily collectible structured variables, combined with unstructured data and analyzed using LDA topic modeling, can significantly improve the predictive performance of a mortality risk prediction model for ICU patients. These results suggest that initial clinical observations and diagnoses of ICU patients contain valuable information that can aid ICU medical and nursing staff in making important clinical decisions.

A Novel Autoencoder-Based Feature Selection Method for Drug-Target Interaction Prediction with Human-Interpretable Feature Weights

Drug-target interaction prediction provides important information that could be exploited for drug discovery, drug design, and drug repurposing. Chemogenomic approaches for predicting drug-target interaction assume that similar receptors bind to similar ligands. Capturing this similarity in so-called “fingerprints” and combining the target and ligand fingerprints provide an efficient way to search for protein-ligand pairs that are more likely to interact. In this study, we constructed drug and target fingerprints by employing features extracted from the DrugBank. However, the number of extracted features is quite large, necessitating an effective feature selection mechanism since some features can be redundant or irrelevant to drug-target interaction prediction problems. Although such feature selection methods are readily available in the literature, usually they act as black boxes and do not provide any quantitative information about why a specific feature is preferred over another. To alleviate this lack of human interpretability, we proposed a novel feature selection method in which we used an autoencoder as a symmetric learning method and compared the proposed method to some popular feature selection algorithms, such as Kbest, Variance Threshold, and Decision Tree. The results of a detailed performance study, in which we trained six Multi-Layer Perceptron (MLP) Networks of different sizes and configurations for prediction, demonstrate that the proposed method yields superior results compared to the aforementioned methods.

Ensemble Learning of Multiple Models Using Deep Learning for Multiclass Classification of Ultrasound Images of Hepatic Masses

Ultrasound (US) is often used to diagnose liver masses. Ensemble learning has recently been commonly used for image classification, but its detailed methods are not fully optimized. The purpose of this study is to investigate the usefulness and comparison of some ensemble learning and ensemble pruning techniques using multiple convolutional neural network (CNN) trained models for image classification of liver masses in US images. Dataset of the US images were classified into four categories: benign liver tumor (BLT) 6320 images, liver cyst (LCY) 2320 images, metastatic liver cancer (MLC) 9720 images, primary liver cancer (PLC) 7840 images. In this study, 250 test images were randomly selected for each class, for a total of 1000 images, and the remaining images were used as the training. 16 different CNNs were used for training and testing ultrasound images. The ensemble learning used soft voting (SV), weighted average voting (WAV), weighted hard voting (WHV) and stacking (ST). All four types of ensemble learning (SV, ST, WAV, and WHV) showed higher values of accuracy than the single CNN. All four types also showed significantly higher deep learning (DL) performance than ResNeXt101 alone. For image classification of liver masses using US images, ensemble learning improved the performance of DL over a single CNN.

LGBMDF: A cascade forest framework with LightGBM for predicting drug-target interactions

Prediction of drug-target interactions (DTIs) plays an important role in drug development. However, traditional laboratory methods to determine DTIs require a lot of time and capital costs. In recent years, many studies have shown that using machine learning methods to predict DTIs can speed up the drug development process and reduce capital costs. An excellent DTI prediction method should have both high prediction accuracy and low computational cost. In this study, we noticed that the previous research based on deep forests used XGBoost as the estimator in the cascade, we applied LightGBM instead of XGBoost to the cascade forest as the estimator, then the estimator group was determined experimentally as three LightGBMs and three ExtraTrees, this new model is called LGBMDF. We conducted 5-fold cross-validation on LGBMDF and other state-of-the-art methods using the same dataset, and compared their Sn, Sp, MCC, AUC and AUPR. Finally, we found that our method has better performance and faster calculation speed.

DrugSim2DR: systematic prediction of drug functional similarities in the context of specific disease for drug repurposing

BACKGROUND

Traditional approaches to drug development are costly and involve high risks. The drug repurposing approach can be a valuable alternative to traditional approaches and has therefore received considerable attention in recent years.

FINDINGS

Herein, we develop a previously undescribed computational approach, called DrugSim2DR, which uses a network diffusion algorithm to identify candidate anticancer drugs based on a drug functional similarity network. The innovation of the approach lies in the drug-drug functional similarity network constructed in a manner that implicitly links drugs through their common biological functions in the context of a specific disease state, as the similarity relationships based on general states (e.g., network proximity or Jaccard index of drug targets) ignore disease-specific molecular characteristics. The drug functional similarity network may provide a reference for prediction of drug combinations. We describe and validate the DrugSim2DR approach through analysis of data on breast cancer and lung cancer. DrugSim2DR identified some US Food and Drug Administration-approved anticancer drugs, as well as some candidate drugs validated by previous studies in the literature. Moreover, DrugSim2DR showed excellent predictive performance, as evidenced by receiver operating characteristic analysis and multiapproach comparisons in various cancer datasets.

CONCLUSIONS

DrugSim2DR could accurately assess drug-drug functional similarity within a specific disease context and may more effectively prioritize disease candidate drugs. To increase the usability of our approach, we have developed an R-based software package, DrugSim2DR, which is freely available on CRAN (https://CRAN.R-project.org/package=DrugSim2DR).

A Novel Combined Model for Predicting Humidity in Sheep Housing Facilities

Accurately predicting humidity changes in sheep barns is important to ensure the healthy growth of the animals and to improve the economic returns of sheep farming. In this study, to address the limitations of conventional methods in establishing accurate mathematical models of dynamic changes in humidity in sheep barns, we propose a method to predict humidity in sheep barns based on a machine learning model combining a light gradient boosting machine with gray wolf optimization and support-vector regression (LightGBM-CGWO-SVR). Influencing factors with a high contribution to humidity were extracted using LightGBM to reduce the complexity of the model. To avoid the local extremum problem, the CGWO algorithm was used to optimize the required hyperparameters in SVR and determine the optimal hyperparameter combination. The combined algorithm was applied to predict the humidity of an intensive sheep-breeding facility in Manas, Xinjiang, China, in real time for the next 10 min. The experimental results indicated that the proposed LightGBM-CGWO-SVR model outperformed eight existing models used for comparison on all evaluation metrics. It achieved minimum values of 0.0662, 0.2284, 0.0521, and 0.0083 in terms of mean absolute error, root mean square error, mean squared error, and normalized root mean square error, respectively, and a maximum value of 0.9973 in terms of the R² index.

Applying an Improved Stacking Ensemble Model to Predict the Mortality of ICU Patients with Heart Failure

Cardiovascular diseases have been identified as one of the top three causes of death worldwide, with onset and deaths mostly due to heart failure (HF). In ICU, where patients with HF are at increased risk of death and consume significant medical resources, early and accurate prediction of the time of death for patients at high risk of death would enable them to receive appropriate and timely medical care. The data for this study were obtained from the MIMIC-III database, where we collected vital signs and tests for 6699 HF patient during the first 24 h of their first ICU admission. In order to predict the mortality of HF patients in ICUs more precisely, an integrated stacking model is proposed and applied in this paper. In the first stage of dataset classification, the datasets were subjected to first-level classifiers using RF, SVC, KNN, LGBM, Bagging, and Adaboost. Then, the fusion of these six classifier decisions was used to construct and optimize the stacked set of second-level classifiers. The results indicate that our model obtained an accuracy of 95.25% and AUROC of 82.55% in predicting the mortality rate of HF patients, which demonstrates the outstanding capability and efficiency of our method. In addition, the results of this study also revealed that platelets, glucose, and blood urea nitrogen were the clinical features that had the greatest impact on model prediction. The results of this analysis not only improve the understanding of patients' conditions by healthcare professionals but allow for a more optimal use of healthcare resources.

Machine Learning Algorithms: Prediction and Feature Selection for Clinical Refracture after Surgically Treated Fragility Fracture

BACKGROUND

The number of patients with fragility fracture has been increasing. Although the increasing number of patients with fragility fracture increased the rate of fracture (refracture), the causes of refracture are multifactorial, and its predictors are still not clarified. In this issue, we collected a registry-based longitudinal dataset that contained more than 7000 patients with fragility fractures treated surgically to detect potential predictors for clinical refracture.

METHODS

Based on the fact that machine learning algorithms are often used for the analysis of a large-scale dataset, we developed automatic prediction models and clarified the relevant features for patients with clinical refracture. Formats of input data containing perioperative clinical information were table data. Clinical refracture was documented as the primary outcome if the diagnosis of fracture was made at postoperative outpatient care. A decision-tree-based model, LightGBM, had moderate accuracy for the prediction in the test and the independent dataset, whereas the other models had poor accuracy or worse.

RESULTS

From a clinical perspective, rheumatoid arthritis (RA) and chronic kidney disease (CKD) were noted as the relevant features for patients with clinical refracture, both of which were associated with secondary osteoporosis.

CONCLUSION

The decision-tree-based algorithm showed the precise prediction of clinical refracture, in which RA and CKD were detected as the potential predictors. Understanding these predictors may improve the management of patients with fragility fractures.

Drug repurposing in silico screening platforms

Over the last decade, for the first time, substantial efforts have been directed at the development of dedicated in silico platforms for drug repurposing, including initiatives targeting cancers and conditions as diverse as cryptosporidiosis, dengue, dental caries, diabetes, herpes, lupus, malaria, tuberculosis and Covid-19 related respiratory disease. This review outlines some of the exciting advances in the specific applications of in silico approaches to the challenge of drug repurposing and focuses particularly on where these efforts have resulted in the development of generic platform technologies of broad value to researchers involved in programmatic drug repurposing work. Recent advances in molecular docking methodologies and validation approaches, and their combination with machine learning or deep learning approaches are continually enhancing the precision of repurposing efforts. The meaningful integration of better understanding of molecular mechanisms with molecular pathway data and knowledge of disease networks is widening the scope for discovery of repurposing opportunities. The power of Artificial Intelligence is being gainfully exploited to advance progress in an integrated science that extends from the sub-atomic to the whole system level. There are many promising emerging developments but there are remaining challenges to be overcome in the successful integration of the new advances in useful platforms. In conclusion, the essential component requirements for development of powerful and well optimised drug repurposing screening platforms are discussed.