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.

It is known that many (upper) cluster algebras possess different kinds of good bases which contain the cluster monomials and are parametrized by the tropical points of cluster Poisson varieties. For a large class of upper cluster algebras (injective-reachable ones with full rank coefficients), we describe all of its bases with these properties. Moreover, we show the existence of the generic basis for them. In addition, we prove that Bridgeland's representation theoretic formula is effective for their theta functions (weak genteelness). Our results apply to (almost) all well-known cluster algebras arising from representation theory or higher Teichmüller theory, including quantum affine algebras, unipotent cells, double Bruhat cells, skein algebras over surfaces, where we change the coefficients if necessary so that the full rank assumption holds.

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Let $G$ be a simple simply connected algebraic group and let $\mathfrak{g}_*$ be a $\mathbf{Z}/m$-grading on its Lie algebra $\mathfrak{g}$. G. Lusztig and Z. Yun, in a recent series of articles, studied the classification of simple $G_0$-equivariant perverse sheaves on the nilpotent cone of $\mathfrak{g}_i$ for $i\in \mathbf{Z}/m$, where $G_0$ is the exponentiation of the degree zero piece $\mathfrak{g}_0$. They proved a decomposition of the equivariant derived category of $\ell$-adic sheaves on the nilpotent cone of $\mathfrak{g}_i$ into blocks, each generated by a certain cuspidal local system via the procedure of {\itshape spiral inductions}. We prove a conjecture of them, stating that there is a bijection between 1) the set of simple perverse sheaves in a fixed block and 2) the set of simple modules of a block of a (trigonometric) degenerate double affine Hecke algebra (dDAHA). This is a dDAHA analogue of the Deligne--Langlands correspondence for affine Hecke algebras proven by Kazhdan--Lusztig. Our results generalise a previous work of E. Vasserot, where the perverse sheaves in the principal block were considered.