Computational Tools and Data Integration to Accelerate Vaccine Development: Challenges, Opportunities, and Future Directions

Lindsey N Anderson ^1* Charles Tapley Hoyt ² Jeremy Zucker ¹ Jeremy R Teuton ^1* Andrew D Mcnaughton ¹ Klas Karis ² Natasha N Arokium-Christian ^1* Zachary R Stromberg ¹ Jackson T Warley ^1* Benjamin M Gyori ^2,3* Neeraj Kumar ^1*

• ¹ Pacific Northwest National Laboratory (DOE), Richland, United States
• ² Khoury College of Computer Sciences, Northeastern University, Boston, Massachusetts, United States
• ³ Department of Bioengineering, College of Engineering, Northeastern University, Boston, Massachusetts, United States

The development of effective vaccines is crucial for combating current and emerging pathogens. Despite significant advances in the field of vaccine development there remain numerous challenges including the lack of standardized data reporting and curation practices, making it difficult to determine correlates of protection from experimental and clinical studies. Significant gaps in data and knowledge integration can hinder vaccine development which relies on a comprehensive understanding of the interplay between pathogens and the host immune system. In this review, we explore the current landscape of vaccine development, highlighting the computational challenges, limitations, and opportunities associated with integrating diverse data types for leveraging artificial intelligence (AI) and machine learning (ML) techniques in vaccine design. We discuss the role of natural language processing, semantic integration, and causal inference in extracting valuable insights from published literature and unstructured data sources, as well as the computational modeling of immune responses. Furthermore, we highlight specific challenges associated with uncertainty quantification in vaccine development and emphasize the importance of establishing standardized data formats and ontologies to facilitate the integration and analysis of heterogeneous data. Through data harmonization and integration, the development of safe and effective vaccines can be accelerated to improve public health outcomes. Looking to the future, we highlight the need for collaborative efforts among researchers, data scientists, and public health experts to realize the full potential of AI-assisted vaccine design and streamline the vaccine development process.