Related papers: Coarse-graining and compounding as monads
The free algebra adjunction, between the category of algebras of a monad and the underlying category, induces a comonad on the category of algebras. The coalgebras of this comonad are the topic of study in this paper (following earlier…
The large deviation principle is proved for a class of $L^2$-valued processes that arise from the coarse-graining of a random field. Coarse-grained processes of this kind form the basis of the analysis of local mean-field models in…
The experimentally measured multiplicity distributions exhibit, after closer inspection, peculiarly enhanced void probability and oscillatory behavior of the modified combinants. We show that both these features can be used as additional…
Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation. However, such CG procedure induces information losses, which makes…
We present a dynamic coarse-graining technique that allows to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSM), which we construct from…
We study a formalization of the grammar induction problem that models sentences as being generated by a compound probabilistic context-free grammar. In contrast to traditional formulations which learn a single stochastic grammar, our…
The common idea behind complexity reduction in physical systems is separation of information into "physically meaningful" and "safely ignorable". Here we consider a generic notion of such separation -- implemented by coarse-graining the…
The presence of interparticle cohesion can drastically change the behavior of granular materials. For instance, powders are challenging to handle, and one can make a sandcastle using wet grains. In this study, we report experimental results…
Continuous-time generative models have achieved remarkable success in image restoration and synthesis. However, controlling the composition of multiple pre-trained models remains an open challenge. Current approaches largely treat…
Three fundamental segregation and pattern formation processes are known in granular mixtures in a rotating cylindrical drum: radial segregation, axial banding, and coarsening of the band pattern. While the mechanism for the first effect is…
The simplest prescription for building a patterned structure from its constituents is to add particles, one at a time, to an appropriate template. However, self-organizing molecular and colloidal systems in nature can evolve in much more…
The automated construction of coarse-grained models represents a pivotal component in computer simulation of physical systems and is a key enabler in various analysis and design tasks related to uncertainty quantification. Pertinent methods…
The algebraic properties of the combination of probabilistic choice and nondeterministic choice have long been a research topic in program semantics. This paper explains a formalization in the Coq proof assistant of a monad equipped with…
The partitioning of small molecules in cell membranes---a key parameter for pharmaceutical applications---typically relies on experimentally-available bulk partitioning coefficients. Computer simulations provide a structural resolution of…
Nested nonparametric processes are vectors of random probability measures widely used in the Bayesian literature to model the dependence across distinct, though related, groups of observations. These processes allow a two-level clustering,…
Self-organized pattern formation is vital for many biological processes. Reaction-diffusion models have advanced our understanding of how biological systems develop spatial structures, starting from homogeneity. However, biological…
Understanding the structure and dynamics of liquids is pivotal for the study of larger spatiotemporal processes, especially in glass-forming materials at low temperatures. Density scaling, observed in many molecular systems through…
We consider Coulomb gas models for which the empirical measure typically concentrates, when the number of particles becomes large, on an equilibrium measure minimizing an electrostatic energy. We study the behavior when the gas is…
This paper compares theory and experiment for the kinetics of time-dependent sedimentation. We discuss non-interacting suspensions and colloids which may exhibit behavior similar to the one-dimensional motion of compressible gas. The…
In-context learning has shown great success in i.i.d semantic parsing splits, where the training and test sets are drawn from the same distribution. In this setup, models are typically prompted with demonstrations that are similar to the…