Trends of common laboratory biomarkers after SARS-CoV-2 infection.

BACKGROUND: Most studies that explore the long-term effects of COVID-19 are based on subjectively reported symptoms, while laboratory-measured biomarkers are mainly examined in studies of relatively small cohorts. This study investigates the long-term effects of SARS-CoV-2 infection on common laboratory biomarkers. METHODS: We utilized a retrospective cohort of SARS-CoV-2 infected individuals and rigorously matched controls based on demographic and clinical characteristics, examining 63 common laboratory biomarkers. Additional lab-specific cohorts were matched with an additional criterion of baseline biomarker values. Differences in biomarkers over a 12-month follow-up were analyzed using standardized mean difference-in-differences. RESULTS: The general cohort included 361,061 matched pairs, with 26M laboratory results. The effects on most biomarkers lasted 1-4 months and were consistent with anticipated changes after acute viral infections. Some biomarkers presented prolonged effects, consistent across the general and lab-specific cohorts. One group of such findings included a 7-8 month decrease in WBC counts, mainly driven by decreased counts of neutrophils, monocytes, and basophils. Potassium levels were decreased for 3-5 months. Vaccinated individuals' data suggested potentially smaller effects on WBCs, but cohort sizes limited this analysis. CONCLUSIONS: This study explores SARS-CoV-2 infection effects on common laboratory biomarkers, characterizing the direction and duration of these effects on the largest infected cohort to date. The effects of most biomarkers resolve in the first months following infection. The most notable longer-lasting effects involved the immune system. Further research is required to characterize the magnitude of these effects among specific individuals.

Eravacycline, an antibacterial drug, repurposed for pancreatic cancer therapy: insights from a molecular-based deep learning model.

BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) remains a serious threat to health, with limited effective therapeutic options, especially due to advanced stage at diagnosis and its inherent resistance to chemotherapy, making it one of the leading causes of cancer-related deaths worldwide. The lack of clear treatment directions underscores the urgent need for innovative approaches to address and manage this deadly condition. In this research, we repurpose drugs with potential anti-cancer activity using machine learning (ML). METHODS: We tackle the problem by using a neural network trained on drug-target interaction information enriched with drug-drug interaction information, which has not been used for anti-cancer drug repurposing before. We focus on eravacycline, an antibacterial drug, which was selected and evaluated to assess its anti-cancer effects. RESULTS: Eravacycline significantly inhibited the proliferation and migration of BxPC-3 cells and induced apoptosis. CONCLUSION: Our study highlights the potential of drug repurposing for cancer treatment using ML. Eravacycline showed promising results in inhibiting cancer cell proliferation, migration and inducing apoptosis in PDAC. These findings demonstrate that our developed ML drug repurposing models can be applied to a wide range of new oncology therapeutics, to identify potential anti-cancer agents. This highlights the potential and presents a promising approach for identifying new therapeutic options.

A simplified similarity-based approach for drug-drug interaction prediction.

Drug-drug interactions (DDIs) are a critical component of drug safety surveillance. Laboratory studies aimed at detecting DDIs are typically difficult, expensive, and time-consuming; therefore, developing in-silico methods is critical. Machine learning-based approaches for DDI prediction have been developed; however, in many cases, their ability to achieve high accuracy relies on data only available towards the end of the molecule lifecycle. Here, we propose a simple yet effective similarity-based method for preclinical DDI prediction where only the chemical structure is available. We test the model on new, unseen drugs. To focus on the preclinical problem setting, we conducted a retrospective analysis and tested the models on drugs that were added to a later version of the DrugBank database. We extend an existing method, adjacency matrix factorization with propagation (AMFP), to support unseen molecules by applying a new lookup mechanism to the drugs' chemical structure, lookup adjacency matrix factorization with propagation (LAMFP). We show that using an ensemble of different similarity measures improves the results. We also demonstrate that Chemprop, a message-passing neural network, can be used for DDI prediction. In computational experiments, LAMFP results in high accuracy, with an area under the receiver operating characteristic curve of 0.82 for interactions involving a new drug and an existing drug and for interactions involving only existing drugs. Moreover, LAMFP outperforms state-of-the-art, complex graph neural network DDI prediction methods.

Pretrained transformer models for predicting the withdrawal of drugs from the market.

MOTIVATION: The process of drug discovery is notoriously complex, costing an average of 2.6 billion dollars and taking ∼13 years to bring a new drug to the market. The success rate for new drugs is alarmingly low (around 0.0001%), and severe adverse drug reactions (ADRs) frequently occur, some of which may even result in death. Early identification of potential ADRs is critical to improve the efficiency and safety of the drug development process. RESULTS: In this study, we employed pretrained large language models (LLMs) to predict the likelihood of a drug being withdrawn from the market due to safety concerns. Our method achieved an area under the curve (AUC) of over 0.75 through cross-database validation, outperforming classical machine learning models and graph-based models. Notably, our pretrained LLMs successfully identified over 50% drugs that were subsequently withdrawn, when predictions were made on a subset of drugs with inconsistent labeling between the training and test sets. AVAILABILITY AND IMPLEMENTATION: The code and datasets are available at https://github.com/eyalmazuz/DrugWithdrawn.

TTANAD: Test-Time Augmentation for Network Anomaly Detection.

Machine learning-based Network Intrusion Detection Systems (NIDS) are designed to protect networks by identifying anomalous behaviors or improper uses. In recent years, advanced attacks, such as those mimicking legitimate traffic, have been developed to avoid alerting such systems. Previous works mainly focused on improving the anomaly detector itself, whereas in this paper, we introduce a novel method, Test-Time Augmentation for Network Anomaly Detection (TTANAD), which utilizes test-time augmentation to enhance anomaly detection from the data side. TTANAD leverages the temporal characteristics of traffic data and produces temporal test-time augmentations on the monitored traffic data. This method aims to create additional points of view when examining network traffic during inference, making it suitable for a variety of anomaly detector algorithms. Our experimental results demonstrate that TTANAD outperforms the baseline in all benchmark datasets and with all examined anomaly detection algorithms, according to the Area Under the Receiver Operating Characteristic (AUC) metric.

Molecule generation using transformers and policy gradient reinforcement learning.

Generating novel valid molecules is often a difficult task, because the vast chemical space relies on the intuition of experienced chemists. In recent years, deep learning models have helped accelerate this process. These advanced models can also help identify suitable molecules for disease treatment. In this paper, we propose Taiga, a transformer-based architecture for the generation of molecules with desired properties. Using a two-stage approach, we first treat the problem as a language modeling task of predicting the next token, using SMILES strings. Then, we use reinforcement learning to optimize molecular properties such as QED. This approach allows our model to learn the underlying rules of chemistry and more easily optimize for molecules with desired properties. Our evaluation of Taiga, which was performed with multiple datasets and tasks, shows that Taiga is comparable to, or even outperforms, state-of-the-art baselines for molecule optimization, with improvements in the QED ranging from 2 to over 20 percent. The improvement was demonstrated both on datasets containing lead molecules and random molecules. We also show that with its two stages, Taiga is capable of generating molecules with higher biological property scores than the same model without reinforcement learning.

Predicting drug characteristics using biomedical text embedding.

BACKGROUND: Drug-drug interactions (DDIs) are preventable causes of medical injuries and often result in doctor and emergency room visits. Previous research demonstrates the effectiveness of using matrix completion approaches based on known drug interactions to predict unknown Drug-drug interactions. However, in the case of a new drug, where there is limited or no knowledge regarding the drug's existing interactions, such an approach is unsuitable, and other drug's preferences can be used to accurately predict new Drug-drug interactions. METHODS: We propose adjacency biomedical text embedding (ABTE) to address this limitation by using a hybrid approach which combines known drugs' interactions and the drug's biomedical text embeddings to predict the DDIs of both new and well known drugs. RESULTS: Our evaluation demonstrates the superiority of this approach compared to recently published DDI prediction models and matrix factorization-based approaches. Furthermore, we compared the use of different text embedding methods in ABTE, and found that the concept embedding approach, which involves biomedical information in the embedding process, provides the highest performance for this task. Additionally, we demonstrate the effectiveness of leveraging biomedical text embedding for additional drugs' biomedical prediction task by presenting text embedding's contribution to a multi-modal pregnancy drug safety classification. CONCLUSION: Text and concept embeddings created by analyzing a domain-specific large-scale biomedical corpora can be used for predicting drug-related properties such as Drug-drug interactions and drug safety prediction. Prediction models based on the embeddings resulted in comparable results to hand-crafted features, however text embeddings do not require manual categorization or data collection and rely solely on the published literature.

CDCDB: A large and continuously updated drug combination database.

In recent years, due to the complementary action of drug combinations over mono-therapy, the multiple-drugs for multiple-targets paradigm has received increased attention to treat bacterial infections and complex diseases. Although new drug combinations screening has benefited from experimental tests like automated high throughput screening, it is limited due to the large number of possible drug combinations. The task of drug combination screening can be streamlined through computational methods and models. Such models require up-to-date databases; however, existing databases are static and consist of the data collected at the time of their creation. This paper introduces the Continuous Drug Combination Database (CDCDB), a continuously updated drug combination database. The CDCDB includes over 40,795 drug combinations, of which 17,107 are unique combinations consisting of more than 4,129 individual drugs, curated from ClinicalTrials.gov, the FDA Orange Book®, and patents. To create CDCDB, we use various methods, including natural language processing techniques, to improve the process of drug combination discovery, ensuring that our database can be used for drug synergy prediction. Website: https://icc.ise.bgu.ac.il/medical_ai/CDCDB/ .

Explainable multimodal machine learning model for classifying pregnancy drug safety.

MOTIVATION: Teratogenic drugs can cause severe fetal malformation and therefore have critical impact on the health of the fetus, yet the teratogenic risks are unknown for most approved drugs. This article proposes an explainable machine learning model for classifying pregnancy drug safety based on multimodal data and suggests an orthogonal ensemble for modeling multimodal data. To train the proposed model, we created a set of labeled drugs by processing over 100 000 textual responses collected by a large teratology information service. Structured textual information is incorporated into the model by applying clustering analysis to textual features. RESULTS: We report an area under the receiver operating characteristic curve (AUC) of 0.891 using cross-validation and an AUC of 0.904 for cross-expert validation. Our findings suggest the safety of two drugs during pregnancy, Varenicline and Mebeverine, and suggest that Meloxicam, an NSAID, is of higher risk; according to existing data, the safety of these three drugs during pregnancy is unknown. We also present a web-based application that enables physicians to examine a specific drug and its risk factors. AVAILABILITY AND IMPLEMENTATION: The code and data is available from https://github.com/goolig/drug_safety_pregnancy_prediction.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Using Machine Learning to Predict Rehabilitation Outcomes in Postacute Hip Fracture Patients.

OBJECTIVE: To use machine learning-based methods in designing a predictive model of rehabilitation outcomes for postacute hip fracture patients. DESIGN: A retrospective analysis using linear models, AdaBoost, CatBoost, ExtraTrees, K-Nearest Neighbors, RandomForest, Support vector machine, XGBoost, and voting of all models to develop and validate a predictive model. SETTING: A university-affiliated 300-bed major postacute geriatric rehabilitation center. PARTICIPANTS: Consecutive hip fracture patients (N=1625) admitted to an postacute rehabilitation department. MAIN OUTCOME MEASURES: The FIM instrument, motor FIM (mFIM), and the relative functional gain on mFIM (mFIM effectiveness) as a continuous and binary variable. Ten predictive models were created: base models (linear/logistic regression), and 8 machine learning models (AdaBoost, CatBoost, ExtraTrees, K-Nearest Neighbors, RandomForest, Support vector machine, XGBoost, and a voting ensemble). R2 was used to evaluate their performance in predicting a continuous outcome variable, and the area under the receiver operating characteristic curve was used to evaluate the binary outcome. A paired 2-tailed t test compared the results of the different models. RESULTS: Machine learning-based models yielded better results than the linear and logistic regression models in predicting rehabilitation outcomes. The 3 most important predictors of the mFIM effectiveness score were the Mini Mental State Examination (MMSE), prefracture mFIM scores, and age. The 3 most important predictors of the discharge mFIM score were the admission mFIM, MMSE, and prefracture mFIM scores. The most contributing factors for favorable outcomes (mFIM effectiveness > median) with higher prediction confidence level were high MMSE (25.7±2.8), high prefacture mFIM (81.5±7.8), and high admission mFIM (48.6±8) scores. We present a simple prediction instrument for estimating the expected performance of postacute hip fracture patients. CONCLUSIONS: The use of machine learning models to predict rehabilitation outcomes of postacute hip fracture patients is superior to linear and logistic regression models. The higher the MMSE, prefracture mFIM, and admission mFIM scores are, the higher the confidence levels of the predicted parameters.

Detecting drug-drug interactions using artificial neural networks and classic graph similarity measures.

Drug-drug interactions are preventable causes of medical injuries and often result in doctor and emergency room visits. Computational techniques can be used to predict potential drug-drug interactions. We approach the drug-drug interaction prediction problem as a link prediction problem and present two novel methods for drug-drug interaction prediction based on artificial neural networks and factor propagation over graph nodes: adjacency matrix factorization (AMF) and adjacency matrix factorization with propagation (AMFP). We conduct a retrospective analysis by training our models on a previous release of the DrugBank database with 1,141 drugs and 45,296 drug-drug interactions and evaluate the results on a later version of DrugBank with 1,440 drugs and 248,146 drug-drug interactions. Additionally, we perform a holdout analysis using DrugBank. We report an area under the receiver operating characteristic curve score of 0.807 and 0.990 for the retrospective and holdout analyses respectively. Finally, we create an ensemble-based classifier using AMF, AMFP, and existing link prediction methods and obtain an area under the receiver operating characteristic curve of 0.814 and 0.991 for the retrospective and the holdout analyses. We demonstrate that AMF and AMFP provide state of the art results compared to existing methods and that the ensemble-based classifier improves the performance by combining various predictors. Additionally, we compare our methods with multi-source data-based predictors using cross-validation. In the multi-source data comparison, our methods outperform various ensembles created using 29 different predictors based on several data sources. These results suggest that AMF, AMFP, and the proposed ensemble-based classifier can provide important information during drug development and regarding drug prescription given only partial or noisy data. Additionally, the results indicate that the interaction network (known DDIs) is the most useful data source for identifying potential DDIs and that our methods take advantage of it better than the other methods investigated. The methods we present can also be used to solve other link prediction problems. Drug embeddings (compressed representations) created when training our models using the interaction network have been made public.

The effectiveness of a training method using self-modeling webcam photos for reducing musculoskeletal risk among office workers using computers.

An intervention study was conducted to examine the effectiveness of an innovative self-modeling photo-training method for reducing musculoskeletal risk among office workers using computers. Sixty workers were randomly assigned to either: 1) a control group; 2) an office training group that received personal, ergonomic training and workstation adjustments or 3) a photo-training group that received both office training and an automatic frequent-feedback system that displayed on the computer screen a photo of the worker's current sitting posture together with the correct posture photo taken earlier during office training. Musculoskeletal risk was evaluated using the Rapid Upper Limb Assessment (RULA) method before, during and after the six weeks intervention. Both training methods provided effective short-term posture improvement; however, sustained improvement was only attained with the photo-training method. Both interventions had a greater effect on older workers and on workers suffering more musculoskeletal pain. The photo-training method had a greater positive effect on women than on men.