Machine Learning for Exposure-Response Analysis: Methodological Considerations and Confirmation of Their Importance via Computational Experimentations

AI-Driven Applications in Clinical Pharmacology and Translational Science: Insights From the ASCPT 2024 AI Preconference

Artificial intelligence (AI) is driving innovation in clinical pharmacology and translational science with tools to advance drug development, clinical trials, and patient care. This review summarizes the key takeaways from the AI preconference at the American Society for Clinical Pharmacology and Therapeutics (ASCPT) 2024 Annual Meeting in Colorado Springs, where experts from academia, industry, and regulatory bodies discussed how AI is streamlining drug discovery, dosing strategies, outcome assessment, and patient care. The theme of the preconference was centered around how AI can empower clinical pharmacologists and translational researchers to make informed decisions and translate research findings into practice. The preconference also looked at the impact of large language models in biomedical research and how these tools are democratizing data analysis and empowering researchers. The application of explainable AI in predicting drug efficacy and safety, and the ethical considerations that should be applied when integrating AI into clinical and biomedical research were also touched upon. By sharing these diverse perspectives and real-world examples, this review shows how AI can be used in clinical pharmacology and translational science to bring efficiency and accelerate drug discovery and development to address patients' unmet clinical needs.

Applications of pharmacometrics in drug development

The last two decades have witnessed profound changes in how advanced computational tools can help leverage tons of data to improve our knowledge, and ultimately reduce cost and increase productivity in drug development. Pharmacometrics has demonstrated its impact through model-informed drug development (MIDD) approaches. It is now an indispensable component throughout the whole continuum of drug discovery, development, regulatory review, and approval. Today, applications of pharmacometrics are common in designing better trials and accelerating evidence-based decisions. Newly emerging technologies, especially those from data and computer sciences, are being integrated with existing computational tools used in the pharmaceutical industry at a remarkably fast pace. The new challenges faced by the pharmacometrics community are not what or how to contribute, but which optimal MIDD strategy should be adopted to maximize its value in the decision-making process. While we are embracing new innovative approaches and tools, this article discusses how a variety of existing modeling tools, with differentiated advantages and focus, can work in concert to inform drug development.

Practical guide to SHAP analysis: Explaining supervised machine learning model predictions in drug development

Despite increasing interest in using Artificial Intelligence (AI) and Machine Learning (ML) models for drug development, effectively interpreting their predictions remains a challenge, which limits their impact on clinical decisions. We address this issue by providing a practical guide to SHapley Additive exPlanations (SHAP), a popular feature-based interpretability method, which can be seamlessly integrated into supervised ML models to gain a deeper understanding of their predictions, thereby enhancing their transparency and trustworthiness. This tutorial focuses on the application of SHAP analysis to standard ML black-box models for regression and classification problems. We provide an overview of various visualization plots and their interpretation, available software for implementing SHAP, and highlight best practices, as well as special considerations, when dealing with binary endpoints and time-series models. To enhance the reader's understanding for the method, we also apply it to inherently explainable regression models. Finally, we discuss the limitations and ongoing advancements aimed at tackling the current drawbacks of the method.

Multi-output prediction of dose-response curves enables drug repositioning and biomarker discovery

Drug response prediction is hampered by uncertainty in the measures of response and selection of doses. In this study, we propose a probabilistic multi-output model to simultaneously predict all dose-responses and uncover their biomarkers. By describing the relationship between genomic features and chemical properties to every response at every dose, our multi-output Gaussian Process (MOGP) models enable assessment of drug efficacy using any dose-response metric. This approach was tested across two drug screening studies and ten cancer types. Kullback-leibler divergence measured the importance of each feature and identified EZH2 gene as a novel biomarker of BRAF inhibitor response. We demonstrate the effectiveness of our MOGP models in accurately predicting dose-responses in different cancer types and when there is a limited number of drug screening experiments for training. Our findings highlight the potential of MOGP models in enhancing drug development pipelines by reducing data requirements and improving precision in dose-response predictions.

Machine Learning-Based Quantification of Patient Factors Impacting Remission in Patients With Ulcerative Colitis: Insights from Etrolizumab Phase III Clinical Trials

Etrolizumab, an investigational anti-β7 integrin monoclonal antibody, has undergone evaluation for safety and efficacy in phase III clinical trials on patients with moderate to severe ulcerative colitis (UC). Etrolizumab was terminated because mixed efficacy results were shown in the induction and maintenance phase in patients with UC. In this post hoc analysis, we characterized the impact of explanatory variables on the probability of remission using XGBoost machine learning (ML) models alongside with the SHapley Additive exPlanations framework for explainability. We used patient-level data encompassing demographics, physiology, disease history, clinical questionnaires, histology, serum biomarkers, and etrolizumab drug exposure to develop ML models aimed at predicting remission. Baseline covariates and early etrolizumab exposure at week 4 in the induction phase were utilized to develop an induction ML model, whereas covariates from the end of the induction phase and early etrolizumab exposure at week 4 in the maintenance phase were used to develop a maintenance ML model. Both the induction and maintenance ML models exhibited good predictive performance, achieving an area under the receiver operating characteristic curve (AUROC) of 0.74 ± 0.03 and 0.75 ± 0.06 (mean ± SD), respectively. Compared with placebo, the highest tertile of etrolizumab exposure contributed to 15.0% (95% confidence interval (CI): 9.7-19.9) and 17.0% (95% CI: 8.1-26.4) increases in remission probability in the induction and maintenance phases, respectively. Additionally, the key covariates that predicted remission were CRP, MAdCAM-1, and stool frequency for the induction phase and white blood cells, fecal calprotectin and age for the maintenance phase. These findings hold significant implications for establishing stratification factors in the design of future clinical trials.

Artificial Intelligence for Quantitative Modeling in Drug Discovery and Development: An Innovation and Quality Consortium Perspective on Use Cases and Best Practices

Recent breakthroughs in artificial intelligence (AI) and machine learning (ML) have ushered in a new era of possibilities across various scientific domains. One area where these advancements hold significant promise is model-informed drug discovery and development (MID3). To foster a wider adoption and acceptance of these advanced algorithms, the Innovation and Quality (IQ) Consortium initiated the AI/ML working group in 2021 with the aim of promoting their acceptance among the broader scientific community as well as by regulatory agencies. By drawing insights from workshops organized by the working group and attended by key stakeholders across the biopharma industry, academia, and regulatory agencies, this white paper provides a perspective from the IQ Consortium. The range of applications covered in this white paper encompass the following thematic topics: (i) AI/ML-enabled Analytics for Pharmacometrics and Quantitative Systems Pharmacology (QSP) Workflows; (ii) Explainable Artificial Intelligence and its Applications in Disease Progression Modeling; (iii) Natural Language Processing (NLP) in Quantitative Pharmacology Modeling; and (iv) AI/ML Utilization in Drug Discovery. Additionally, the paper offers a set of best practices to ensure an effective and responsible use of AI, including considering the context of use, explainability and generalizability of models, and having human-in-the-loop. We believe that embracing the transformative power of AI in quantitative modeling while adopting a set of good practices can unlock new opportunities for innovation, increase efficiency, and ultimately bring benefits to patients.

Advancing Precision Medicine: A Review of Innovative In Silico Approaches for Drug Development, Clinical Pharmacology and Personalized Healthcare

The landscape of medical treatments is undergoing a transformative shift. Precision medicine has ushered in a revolutionary era in healthcare by individualizing diagnostics and treatments according to each patient's uniquely evolving health status. This groundbreaking method of tailoring disease prevention and treatment considers individual variations in genes, environments, and lifestyles. The goal of precision medicine is to target the "five rights": the right patient, the right drug, the right time, the right dose, and the right route. In this pursuit, in silico techniques have emerged as an anchor, driving precision medicine forward and making this a realistic and promising avenue for personalized therapies. With the advancements in high-throughput DNA sequencing technologies, genomic data, including genetic variants and their interactions with each other and the environment, can be incorporated into clinical decision-making. Pharmacometrics, gathering pharmacokinetic (PK) and pharmacodynamic (PD) data, and mathematical models further contribute to drug optimization, drug behavior prediction, and drug-drug interaction identification. Digital health, wearables, and computational tools offer continuous monitoring and real-time data collection, enabling treatment adjustments. Furthermore, the incorporation of extensive datasets in computational tools, such as electronic health records (EHRs) and omics data, is also another pathway to acquire meaningful information in this field. Although they are fairly new, machine learning (ML) algorithms and artificial intelligence (AI) techniques are also resources researchers use to analyze big data and develop predictive models. This review explores the interplay of these multiple in silico approaches in advancing precision medicine and fostering individual healthcare. Despite intrinsic challenges, such as ethical considerations, data protection, and the need for more comprehensive research, this marks a new era of patient-centered healthcare. Innovative in silico techniques hold the potential to reshape the future of medicine for generations to come.