Cold-Start Problems in Data-Driven Prediction of Drug-Drug Interaction Effects

The future of medicine: an outline attempt using state-of-the-art business and scientific trends

Introduction

Currently, there is a lot of discussion about the future of medicine. From research and development to regulatory approval and access to patients until the withdrawal of a medicinal product from the market, there have been many challenges and a lot of barriers to overcome. In parallel, the business environment changes rapidly. So, the big question is how the pharma ecosystem will evolve in the future.

Methods

The current literature about the latest business and scientific evolutions and trends was reviewed.

Results

In the business environment, vast changes have taken place via the development of the internet as well as the Internet of Things. A new approach to production has emerged in a frame called Creative Commons; producer and consumer may be gradually identified in the context of the same process. As technology rapidly evolves, it is dominated by Artificial Intelligence (AI), its subset, Machine Learning, and the use of Big Data and Real-World Data (RWD) to produce Real-World Evidence (RWE). Nanotechnology is an inter-science field that gives new opportunities for the manufacturing of devices and products that have dimensions of a billionth of a meter. Artificial Neural Networks and Deep Learning (DL) are mimicking the use of the human brain, combining computer science with new theoretical foundations for complex systems. The implementation of these evolutions has already been initiated in the medicinal products' lifecycle, including screening of drug candidates, clinical trials, pharmacovigilance (PV), marketing authorization, manufacturing, and the supply chain. This has emerged as a new ecosystem which features characteristics such as free online tools and free data available online. Personalized medicine is a breakthrough field where tailor-made therapeutic solutions can be provided customized to the genome of each patient.

Conclusion

Various interactions take place as the pharma ecosystem and technology rapidly evolve. This can lead to better, safer, and more effective treatments that are developed faster and with a more solid, data-driven and evidence-concrete approach, which will drive the benefit for the patient.

Emerging drug interaction prediction enabled by a flow-based graph neural network with biomedical network

Drug-drug interactions (DDIs) for emerging drugs offer possibilities for treating and alleviating diseases, and accurately predicting these with computational methods can improve patient care and contribute to efficient drug development. However, many existing computational methods require large amounts of known DDI information, which is scarce for emerging drugs. Here we propose EmerGNN, a graph neural network that can effectively predict interactions for emerging drugs by leveraging the rich information in biomedical networks. EmerGNN learns pairwise representations of drugs by extracting the paths between drug pairs, propagating information from one drug to the other, and incorporating the relevant biomedical concepts on the paths. The edges of the biomedical network are weighted to indicate the relevance for the target DDI prediction. Overall, EmerGNN has higher accuracy than existing approaches in predicting interactions for emerging drugs and can identify the most relevant information on the biomedical network.

3D graph neural network with few-shot learning for predicting drug-drug interactions in scaffold-based cold start scenario

Understanding drug-drug interactions (DDI) of new drugs is critical for minimizing unexpected adverse drug reactions. The modeling of new drugs is called a cold start scenario. In this scenario, Only a few structural information or physicochemical information about new drug is available. The 3D conformation of drug molecules usually plays a crucial role in chemical properties compared to the 2D structure. 3D graph network with few-shot learning is a promising solution. However, the 3D heterogeneity of drug molecules and the discretization of atomic distributions lead to spatial confusion in few-shot learning. Here, we propose a 3D graph neural network with few-shot learning, Meta3D-DDI, to predict DDI events in cold start scenario. The 3DGNN ensures rotation and translation invariance by calculating atomic pairwise distances, and incorporates 3D structure and distance information in the information aggregation stage. The continuous filter interaction module can continuously simulate the filter to obtain the interaction between the target atom and other atoms. Meta3D-DDI further develops a FSL strategy based on bilevel optimization to transfer meta-knowledge for DDI prediction tasks from existing drugs to new drugs. In addition, the existing cold start setting may cause the scaffold structure information in the training set to leak into the test set. We design scaffold-based cold start scenario to ensure that the drug scaffolds in the training set and test set do not overlap. The extensive experiments demonstrate that our architecture achieves the SOTA performance for DDI prediction under scaffold-based cold start scenario on two real-world datasets. The visual experiment shows that Meta3D-DDI significantly improves the learning for DDI prediction of new drugs. We also demonstrate how Meta3D-DDI can reduce the amount of data required to make meaningful DDI predictions.

DSN-DDI: an accurate and generalized framework for drug-drug interaction prediction by dual-view representation learning

Drug-drug interaction (DDI) prediction identifies interactions of drug combinations in which the adverse side effects caused by the physicochemical incompatibility have attracted much attention. Previous studies usually model drug information from single or dual views of the whole drug molecules but ignore the detailed interactions among atoms, which leads to incomplete and noisy information and limits the accuracy of DDI prediction. In this work, we propose a novel dual-view drug representation learning network for DDI prediction ('DSN-DDI'), which employs local and global representation learning modules iteratively and learns drug substructures from the single drug ('intra-view') and the drug pair ('inter-view') simultaneously. Comprehensive evaluations demonstrate that DSN-DDI significantly improved performance on DDI prediction for the existing drugs by achieving a relatively improved accuracy of 13.01% and an over 99% accuracy under the transductive setting. More importantly, DSN-DDI achieves a relatively improved accuracy of 7.07% to unseen drugs and shows the usefulness for real-world DDI applications. Finally, DSN-DDI exhibits good transferability on synergistic drug combination prediction and thus can serve as a generalized framework in the drug discovery field.

The Use of Artificial Intelligence in Pharmacovigilance: A Systematic Review of the Literature

INTRODUCTION

Artificial intelligence through machine learning uses algorithms and prior learnings to make predictions. Recently, there has been interest to include more artificial intelligence in pharmacovigilance of products already in the market and pharmaceuticals in development.

OBJECTIVE

The aim of this study was to identify and describe the uses of artificial intelligence in pharmacovigilance through a systematic literature review.

METHODS

Embase and MEDLINE database searches were conducted for articles published from January 1, 2015 to July 9, 2021 using search terms such as 'pharmacovigilance,' 'patient safety,' 'artificial intelligence,' and 'machine learning' in the title or abstract. Scientific articles that contained information on the use of artificial intelligence in all modalities of patient safety or pharmacovigilance were reviewed and synthesized using a pre-specified data extraction template. Articles with incomplete information and letters to editor, notes, and commentaries were excluded.

RESULTS

Sixty-six articles were identified for evaluation. Most relevant articles on artificial intelligence focused on machine learning, and it was used in patient safety in the identification of adverse drug events (ADEs) and adverse drug reactions (ADRs) (57.6%), processing safety reports (21.2%), extraction of drug-drug interactions (7.6%), identification of populations at high risk for drug toxicity or guidance for personalized care (7.6%), prediction of side effects (3.0%), simulation of clinical trials (1.5%), and integration of prediction uncertainties into diagnostic classifiers to increase patient safety (1.5%). Artificial intelligence has been used to identify safety signals through automated processes and training with machine learning models; however, the findings may not be generalizable given that there were different types of data included in each source.

CONCLUSION

Artificial intelligence allows for the processing and analysis of large amounts of data and can be applied to various disease states. The automation and machine learning models can optimize pharmacovigilance processes and provide a more efficient way to analyze information relevant to safety, although more research is needed to identify if this optimization has an impact on the quality of safety analyses. It is expected that its use will increase in the near future, particularly with its role in the prediction of side effects and ADRs.

Language-agnostic pharmacovigilant text mining to elicit side effects from clinical notes and hospital medication records

We sought to craft a drug safety signalling pipeline associating latent information in clinical free text with exposures to single drugs and drug pairs. Data arose from 12 secondary and tertiary public hospitals in two Danish regions, comprising approximately half the Danish population. Notes were operationalised with a fastText embedding, based on which we trained 10,720 neural-network models (one for each distinct single-drug/drug-pair exposure) predicting the risk of exposure given an embedding vector. We included 2,905,251 admissions between May 2008 and June 2016, with 13,740,564 distinct drug prescriptions; the median number of prescriptions was 5 (IQR: 3-9) and in 1,184,340 (41%) admissions patients used ≥5 drugs concomitantly. 10,788,259 clinical notes were included, with 179,441,739 tokens retained after pruning. Of 345 single-drug signals reviewed, 28 (8.1%) represented possibly undescribed relationships; 186 (54%) signals were clinically meaningful. 16 (14%) of the 115 drug-pair signals were possible interactions and 2 (1.7%) were known. In conclusion, we built a language-agnostic pipeline for mining associations between free-text information and medication exposure without manual curation, predicting not the likely outcome of a range of exposures, but the likely exposures for outcomes of interest. Our approach may help overcome limitations of text mining methods relying on curated data in English and can help leverage non-English free text for pharmacovigilance.

A smart hospital-driven approach to precision pharmacovigilance

Researchers, regulatory agencies, and the pharmaceutical industry are moving towards precision pharmacovigilance as a comprehensive framework for drug safety assessment, at the service of the individual patient, by clustering specific risk groups in different databases. This article explores its implementation by focusing on: (i) designing a new data collection infrastructure, (ii) exploring new computational methods suitable for drug safety data, and (iii) providing a computer-aided framework for distributed clinical decisions with the aim of compiling a personalized information leaflet with specific reference to a drug's risks and adverse drug reactions. These goals can be achieved by using 'smart hospitals' as the principal data sources and by employing methods of precision medicine and medical statistics to supplement current public health decisions.

On the road to explainable AI in drug-drug interactions prediction: A systematic review

Over the past decade, polypharmacy instances have been common in multi-diseases treatment. However, unwanted drug-drug interactions (DDIs) that might cause unexpected adverse drug events (ADEs) in multiple regimens therapy remain a significant issue. Since artificial intelligence (AI) is ubiquitous today, many AI prediction models have been developed to predict DDIs to support clinicians in pharmacotherapy-related decisions. However, even though DDI prediction models have great potential for assisting physicians in polypharmacy decisions, there are still concerns regarding the reliability of AI models due to their black-box nature. Building AI models with explainable mechanisms can augment their transparency to address the above issue. Explainable AI (XAI) promotes safety and clarity by showing how decisions are made in AI models, especially in critical tasks like DDI predictions. In this review, a comprehensive overview of AI-based DDI prediction, including the publicly available source for AI-DDIs studies, the methods used in data manipulation and feature preprocessing, the XAI mechanisms to promote trust of AI, especially for critical tasks as DDIs prediction, the modeling methods, is provided. Limitations and the future directions of XAI in DDIs are also discussed.