Single-cell (sc)RNA-seq, together with RNA velocity and metabolic labeling, reveals cellular states and transitions at unprecedented resolution. Fully exploiting these data, however, requires kinetic models capable of unveiling governing regulatory functions. Here, we introduce an analytical framework dynamo (https://github.com/aristoteleo/dynamo-release), which infers absolute RNA velocity, reconstructs continuous vector fields that predict cell fates, employs differential geometry to extract underlying regulations, and ultimately predicts optimal reprogramming paths and perturbation outcomes. We highlight dynamo’s power to overcome fundamental limitations of conventional splicing-based RNA velocity analyses to enable accurate velocity estimations on a metabolically labeled human hematopoiesis scRNA-seq dataset. Furthermore, differential geometry analyses reveal mechanisms driving early megakaryocyte appearance and elucidate asymmetrical regulation within the PU.1-GATA1 circuit. Leveraging the least-action-path method, dynamo accurately predicts drivers of numerous hematopoietic transitions. Finally, in silico perturbations predict cell-fate diversions induced by gene perturbations. Dynamo, thus, represents an important step in advancing quantitative and predictive theories of cell-state transitions.

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We study a certain discrete differentiation of piecewise-constant functions on the adjoint of the braid hyperplane arrangement, defined by taking finite-differences across hyperplanes. In terms of Aguiar-Mahajan's Lie theory of hyperplane arrangements, we show that this structure is equivalent to the action of Lie elements on faces. We use layered binary trees to encode flags of adjoint arrangement faces, allowing for the representation of certain Lie elements by antisymmetrized layered binary forests. This is dual to the well-known use of (delayered) binary trees to represent Lie elements of the braid arrangement. The discrete derivative then induces an action of layered binary forests on piecewise-constant functions, which we call the forest derivative. Our main result states that forest derivatives of functions factorize as external products of functions precisely if one restricts to functions which satisfy the Steinmann relations, which are certain four-term linear relations appearing in the foundations of axiomatic quantum field theory. We also show that the forest derivative satisfies the Lie properties of antisymmetry the Jacobi identity. It follows from these Lie properties, and also crucially factorization, that functions which satisfy the Steinmann relations form a left comodule of the Lie cooperad, with the coaction given by the forest derivative. Dually, this endows the adjoint braid arrangement modulo the Steinmann relations with the structure of a Lie algebra internal to the category of vector species. This work is a first step towards describing new connections between Hopf theory in species and quantum field theory.