Manfred D. Laubichler

Nayely Vélez-Cruz, Manfred D. Laubichler

The ubiquity of multiscale interactions in complex systems is well-recognized, with development and heredity serving as a prime example of how processes at different temporal scales influence one another. This work introduces a novel multiscale state-space model to explore the dynamic interplay between systems interacting across different time scales, with feedback between each scale. We propose a Bayesian learning framework to estimate unknown states by learning the unknown process noise covariances within this multiscale model. We develop a Particle Gibbs with Ancestor Sampling (PGAS) algorithm for inference and demonstrate through simulations the efficacy of our approach.

Nayely Vélez-Cruz, Manfred D. Laubichler

In this work, we introduce a generalized framework for multiscale state-space modeling that incorporates nested nonlinear dynamics, with a specific focus on Bayesian learning under switching regimes. Our framework captures the complex interactions between fast and slow processes within systems, allowing for the analysis of how these dynamics influence each other across various temporal scales. We model these interactions through a hierarchical structure in which finer time-scale dynamics are nested within coarser ones, while facilitating feedback between the scales. To promote the practical application of our framework, we address the problem of identifying switching regimes and transient dynamics. In particular, we develop a Bayesian learning approach to estimate latent states and indicators corresponding to switching dynamics, enabling the model to adapt effectively to regime changes. We employ Sequential Monte Carlo, or particle filtering, for inference. We illustrate the utility of our framework through simulations. The results demonstrate that our Bayesian learning approach effectively tracks state transitions and achieves accurate identification of switching dynamics in multiscale systems.

David H. Wolpert, Michael H. Price, Stefani A. Crabtree et al.

Historical processes manifest remarkable diversity. Nevertheless, scholars have long attempted to identify patterns and categorize historical actors and influences with some success. A stochastic process framework provides a structured approach for the analysis of large historical datasets that allows for detection of sometimes surprising patterns, identification of relevant causal actors both endogenous and exogenous to the process, and comparison between different historical cases. The combination of data, analytical tools and the organizing theoretical framework of stochastic processes complements traditional narrative approaches in history and archaeology.

B. R. Erick Peirson, Erin Bottino, Julia L. Damerow et al.

Journal of the History of Biology provides a fifty-year long record for examining the evolution of the history of biology as a scholarly discipline. In this paper, we present a new dataset and preliminary quantitative analysis of the thematic content of JHB from the perspectives of geography, organisms, and thematic fields. The geographic diversity of authors whose work appears in JHB has increased steadily since 1968, but the geographic coverage of the content of JHB articles remains strongly lopsided toward the United States, United Kingdom, and western Europe and has diversified much less dramatically over time. The taxonomic diversity of organisms discussed in JHB increased steadily between 1968 and the late 1990s but declined in later years, mirroring broader patterns of diversification previously reported in the biomedical research literature. Finally, we used a combination of topic modeling and nonlinear dimensionality reduction techniques to develop a model of multi-article fields within JHB. We found evidence for directional changes in the representation of fields on multiple scales. The diversity of JHB with regard to the representation of thematic fields has increased overall, with most of that diversification occurring in recent years. Drawing on the dataset generated in the course of this analysis, as well as web services in the emerging digital history and philosophy of science ecosystem, we have developed an interactive web platform for exploring the content of JHB, and we provide a brief overview of the platform in this article. As a whole, the data and analyses presented here provide a starting-place for further critical reflection on the evolution of the history of biology over the past half-century.