Joint trajectory and network inference via reference fitting

Network inference, the task of reconstructing interactions in a complex system from experimental observables, is a central yet extremely challenging problem in systems biology. While much progress has been made in the last two decades, network inference remains an open problem. For systems observed at steady state, limited insights are available since temporal information is unavailable and thus causal information is lost. Two common avenues for gaining causal insights into system behaviour are to leverage temporal dynamics in the form of trajectories, and to apply interventions such as knock-out perturbations. We propose an approach for leveraging both dynamical and perturbational single cell data to jointly learn cellular trajectories and power network inference. Our approach is motivated by min-entropy estimation for stochastic dynamics and can infer directed and signed networks from time-stamped single cell snapshots.

Geometry of the Space of Partitioned Networks: A Unified Theoretical and Computational Framework

Interactions and relations between objects may be pairwise or higher-order in nature, and so network-valued data are ubiquitous in the real world. The "space of networks", however, has a complex structure that cannot be adequately described using conventional statistical tools. We introduce a measure-theoretic formalism for modeling generalized network structures such as graphs, hypergraphs, or graphs whose nodes come with a partition into categorical classes. We then propose a metric that extends the Gromov-Wasserstein distance between graphs and the co-optimal transport distance between hypergraphs. We characterize the geometry of this space, thereby providing a unified theoretical treatment of generalized networks that encompasses the cases of pairwise, as well as higher-order, relations. In particular, we show that our metric is an Alexandrov space of non-negative curvature, and leverage this structure to define gradients for certain functionals commonly arising in geometric data analysis tasks. We extend our analysis to the setting where vertices have additional label information, and derive efficient computational schemes to use in practice. Equipped with these theoretical and computational tools, we demonstrate the utility of our framework in a suite of applications, including hypergraph alignment, clustering and dictionary learning from ensemble data, multi-omics alignment, as well as multiscale network alignment.