Classification of nervous system withdrawn and approved drugs with ToxPrint features via machine learning strategies

Deep Learning Bridged Bioactivity, Structure, and GC-HRMS-Readable Evidence to Decipher Nontarget Toxicants in Sediments

Identifying causative toxicants in mixtures is critical, but this task is challenging when mixtures contain multiple chemical classes. Effect-based methods are used to complement chemical analyses to identify toxicants, yet conventional bioassays typically rely on an apical and/or single endpoint, providing limited diagnostic potential to guide chemical prioritization. We proposed an event-driven taxonomy framework for mixture risk assessment that relied on high-throughput screening bioassays and toxicant identification integrated by deep learning. In this work, the framework was evaluated using chemical mixtures in sediments eliciting aryl-hydrocarbon receptor activation and oxidative stress response. Mixture prediction using target analysis explained <10% of observed sediment bioactivity. To identify additional contaminants, two deep learning models were developed to predict fingerprints of a pool of bioactive substances (event driver fingerprint, EDFP) and convert these candidates to MS-readable information (event driver ion, EDION) for nontarget analysis. Two libraries with 121 and 118 fingerprints were established, and 247 bioactive compounds were identified at confidence level 2 or 3 in sediment extract using GC-qToF-MS. Among them, 12 toxicants were analytically confirmed using reference standards. Collectively, we present a "bioactivity-signature-toxicant" strategy to deconvolute mixtures and to connect patchy data sets and guide nontarget analysis for diverse chemicals that elicit the same bioactivity.

Artificial intelligence in the field of pharmacy practice: A literature review

Artificial intelligence (AI) is a transformative technology used in various industrial sectors including healthcare. In pharmacy practice, AI has the potential to significantly improve medication management and patient care. This review explores various AI applications in the field of pharmacy practice. The incorporation of AI technologies provides pharmacists with tools and systems that help them make accurate and evidence-based clinical decisions. By using AI algorithms and Machine Learning, pharmacists can analyze a large volume of patient data, including medical records, laboratory results, and medication profiles, aiding them in identifying potential drug-drug interactions, assessing the safety and efficacy of medicines, and making informed recommendations tailored to individual patient requirements. Various AI models have been developed to predict and detect adverse drug events, assist clinical decision support systems with medication-related decisions, automate dispensing processes in community pharmacies, optimize medication dosages, detect drug-drug interactions, improve adherence through smart technologies, detect and prevent medication errors, provide medication therapy management services, and support telemedicine initiatives. By incorporating AI into clinical practice, health care professionals can augment their decision-making processes and provide patients with personalized care. AI allows for greater collaboration between different healthcare services provided to a single patient. For patients, AI may be a useful tool for providing guidance on how and when to take a medication, aiding in patient education, and promoting medication adherence and AI may be used to know how and where to obtain the most cost-effective healthcare and how best to communicate with healthcare professionals, optimize the health monitoring using wearables devices, provide everyday lifestyle and health guidance, and integrate diet and exercise.

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.

Graph-Based Feature Selection Approach for Molecular Activity Prediction

In the construction of QSAR models for the prediction of molecular activity, feature selection is a common task aimed at improving the results and understanding of the problem. The selection of features allows elimination of irrelevant and redundant features, reduces the effect of dimensionality problems, and improves the generalization and interpretability of the models. In many feature selection applications, such as those based on ensembles of feature selectors, it is necessary to combine different selection processes. In this work, we evaluate the application of a new feature selection approach to the prediction of molecular activity, based on the construction of an undirected graph to combine base feature selectors. The experimental results demonstrate the efficiency of the graph-based method in terms of the classification performance, reduction, and redundancy compared to the standard voting method. The graph-based method can be extended to different feature selection algorithms and applied to other cheminformatics problems.

A review on machine learning approaches and trends in drug discovery

Drug discovery aims at finding new compounds with specific chemical properties for the treatment of diseases. In the last years, the approach used in this search presents an important component in computer science with the skyrocketing of machine learning techniques due to its democratization. With the objectives set by the Precision Medicine initiative and the new challenges generated, it is necessary to establish robust, standard and reproducible computational methodologies to achieve the objectives set. Currently, predictive models based on Machine Learning have gained great importance in the step prior to preclinical studies. This stage manages to drastically reduce costs and research times in the discovery of new drugs. This review article focuses on how these new methodologies are being used in recent years of research. Analyzing the state of the art in this field will give us an idea of where cheminformatics will be developed in the short term, the limitations it presents and the positive results it has achieved. This review will focus mainly on the methods used to model the molecular data, as well as the biological problems addressed and the Machine Learning algorithms used for drug discovery in recent years.

Recent trends in artificial intelligence-driven identification and development of anti-neurodegenerative therapeutic agents

Neurological disorders affect various aspects of life. Finding drugs for the central nervous system is a very challenging and complex task due to the involvement of the blood-brain barrier, P-glycoprotein, and the drug's high attrition rates. The availability of big data present in online databases and resources has enabled the emergence of artificial intelligence techniques including machine learning to analyze, process the data, and predict the unknown data with high efficiency. The use of these modern techniques has revolutionized the whole drug development paradigm, with an unprecedented acceleration in the central nervous system drug discovery programs. Also, the new deep learning architectures proposed in many recent works have given a better understanding of how artificial intelligence can tackle big complex problems that arose due to central nervous system disorders. Therefore, the present review provides comprehensive and up-to-date information on machine learning/artificial intelligence-triggered effort in the brain care domain. In addition, a brief overview is presented on machine learning algorithms and their uses in structure-based drug design, ligand-based drug design, ADMET prediction, de novo drug design, and drug repurposing. Lastly, we conclude by discussing the major challenges and limitations posed and how they can be tackled in the future by using these modern machine learning/artificial intelligence approaches.

Research on fuzzy English automatic recognition and human-computer interaction based on machine learning

Fuzzy English recognition is affected by many factors, which leads to certain accuracy problems in intelligent recognition results. In order to improve the automatic recognition efficiency of fuzzy English, based on machine learning technology, this study constructs a neural network model. At the same time, this paper analyzes the research status and existing problems of handwritten character recognition, analyzes the model, and adopts multiple modules for automatic English recognition. In addition, the system is built on the basis of algorithms and model support, which makes fuzzy English recognition intelligent. Finally, in order to study the algorithm and model performance, the fuzzy English recognition is carried out through experiments. The research shows that the model constructed in this paper has certain recognition effect, which can be applied to practice, and can provide theoretical reference for subsequent related research.

Role of Artificial Intelligence in Patient Safety Outcomes: Systematic Literature Review

BACKGROUND

Artificial intelligence (AI) provides opportunities to identify the health risks of patients and thus influence patient safety outcomes.

OBJECTIVE

The purpose of this systematic literature review was to identify and analyze quantitative studies utilizing or integrating AI to address and report clinical-level patient safety outcomes.

METHODS

We restricted our search to the PubMed, PubMed Central, and Web of Science databases to retrieve research articles published in English between January 2009 and August 2019. We focused on quantitative studies that reported positive, negative, or intermediate changes in patient safety outcomes using AI apps, specifically those based on machine-learning algorithms and natural language processing. Quantitative studies reporting only AI performance but not its influence on patient safety outcomes were excluded from further review.

RESULTS

We identified 53 eligible studies, which were summarized concerning their patient safety subcategories, the most frequently used AI, and reported performance metrics. Recognized safety subcategories were clinical alarms (n=9; mainly based on decision tree models), clinical reports (n=21; based on support vector machine models), and drug safety (n=23; mainly based on decision tree models). Analysis of these 53 studies also identified two essential findings: (1) the lack of a standardized benchmark and (2) heterogeneity in AI reporting.

CONCLUSIONS

This systematic review indicates that AI-enabled decision support systems, when implemented correctly, can aid in enhancing patient safety by improving error detection, patient stratification, and drug management. Future work is still needed for robust validation of these systems in prospective and real-world clinical environments to understand how well AI can predict safety outcomes in health care settings.

Influence of feature rankers in the construction of molecular activity prediction models

In the construction of activity prediction models, the use of feature ranking methods is a useful mechanism for extracting information for ranking features in terms of their significance to develop predictive models. This paper studies the influence of feature rankers in the construction of molecular activity prediction models; for this purpose, a comparative study of fourteen rankings methods for feature selection was conducted. The activity prediction models were constructed using four well-known classifiers and a wide collection of datasets. The ranking algorithms were compared considering the performance of these classifiers using different metrics and the consistency of the ranked features.