Formal Methods for the Informal Engineer: Workshop Recommendations

Abstract: Formal Methods for the Informal Engineer (FMIE) was a workshop held at the Broad Institute of MIT and Harvard in 2021 to explore the potential role of verified software in the biomedical software ecosystem. The motivation for organizing FMIE was the recognition that the life sciences and medicine are undergoing a transition from being […]

Physiology as a Lingua Franca for Clinical Machine Learning

Abstract: The intersection of medicine and machine learning (ML) has the potential to transform healthcare. We describe how physiology, a foundational discipline of medical training and practice with a rich quantitative history, could serve as a starting point for the development of a common language between clinicians and ML experts, thereby accelerating real-world impact. Gopal […]

The physician-scientist, 75 years after Vannevar Bush–rethinking the ‘bench’ and ‘bedside’ dichotomy

Abstract: Vannevar Bush enshrined the ‘basic’ and ‘applied’ research dichotomy on which much of science policy is still built 75 years later. However, it is time to assess whether this vision for science best serves the purposes of medical research and physician-scientists in the 21st century. Gopal P. Sarma, Allan Levey, and Victor Faundez, “The […]

Re-examining physician-scientist training through the prism of the discovery-invention cycle

Abstract: The training of physician-scientists lies at the heart of future medical research. In this commentary, we apply Narayanamurti and Odumosu’s framework of the “discovery-invention cycle” to analyze the structure and outcomes of the integrated MD/PhD program. We argue that the linear model of “bench-to-bedside” research, which is also reflected in the present training of […]

Integrative Biological Simulation, Neuropsychology, and AI Safety

Abstract: We describe a biologically-inspired research agenda with parallel tracks aimed at AI and AI safety. The bottom-up component consists of building a sequence of biophysically realistic simulations of simple organisms such as the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the zebrafish Danio rerio to serve as platforms for research into AI […]

OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans

Abstract: The adoption of powerful software tools and computational methods from the software industry by the scientific research community has resulted in a renewed interest in integrative, large-scale biological simulations. These typically involve the development of computational platforms to combine diverse, process-specific models into a coherent whole. The OpenWorm Foundation is an independent research organization […]

Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices

Abstract: Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems, a diverse array of biological systems have been the target of large-scale computational modeling efforts. Nonetheless, these research agendas have yet to prove […]

Unit Testing, Model Validation, and Biological Simulation

Abstract: The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the management of modern software. As computational models and methods have become increasingly common in […]