Lessons learned and recommendations for data coordination in collaborative research: The CSER consortium experience

Integrating data across heterogeneous research environments is a key challenge in multi-site, collaborative research projects. While it is important to allow for natural variation in data collection protocols across research sites, it is also important to achieve interoperability between datasets in order to reap the full benefits of collaborative work. However, there are few standards to guide the data coordination process from project conception to completion. In this paper, we describe the experiences of the Clinical Sequence Evidence-Generating Research (CSER) consortium Data Coordinating Center (DCC), which coordinated harmonized survey and genomic sequencing data from seven clinical research sites from 2020 to 2022. Using input from multiple consortium working groups and from CSER leadership, we first identify 14 lessons learned from CSER in the categories of communication, harmonization, informatics, compliance, and analytics. We then distill these lessons learned into 11 recommendations for future research consortia in the areas of planning, communication, informatics, and analytics. We recommend that planning and budgeting for data coordination activities occur as early as possible during consortium conceptualization and development to minimize downstream complications. We also find that clear, reciprocal, and continuous communication between consortium stakeholders and the DCC is equally important to maintaining a secure and centralized informatics ecosystem for pooling data. Finally, we discuss the importance of actively interrogating current approaches to data governance, particularly for research studies that straddle the research-clinical divide

Geometric generalisation of surrogate model based optimisation to combinatorial spaces

Abstract. In continuous optimisation, Surrogate Models (SMs) are often indispensable components of optimisation algorithms aimed at tackling real-world problems whose candidate solutions are very expensive to evaluate. Because of the inherent spatial intuition behind these models, they are naturally suited to continuous problems but they do not seem applicable to combinatorial problems except for the special case when solutions are naturally encoded as integer vectors. In this paper, we show that SMs can be naturally generalised to encompass combinatorial spaces based in principle on any arbitrarily complex underlying solution representation by generalising their geometric interpretation from continuous to general metric spaces. As an initial illustrative example, we show how Radial Basis Function Networks (RBFNs) can be used successfully as surrogate models to optimise combinatorial problems defined on the Hamming space associated with binary strings.