Related papers: A Calculus of Located Entities
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
Intracellular transport processes are essential to the healthy development of many organisms as well as more generally to healthy cellular function. The complex dynamics and interactions between protein molecules and filaments on different…
We posit that hippocampal place cells encode information about future locations under a transition distribution observed as an agent explores a given (physical or conceptual) space. The encoding of information about the current location,…
There is a great need for accurate and efficient computational approaches that can account for both the discrete and stochastic nature of chemical interactions as well as spatial inhomogeneities and diffusion. This is particularly true in…
The Calculus of Wrapped Compartments (CWC) is a variant of the Calculus of Looping Sequences (CLS). While keeping the same expressiveness, CWC strongly simplifies the development of automatic tools for the analysis of biological systems.…
Entity alignment has always had significant uses within a multitude of diverse scientific fields. In particular, the concept of matching entities across networks has grown in significance in the world of social science as communicative…
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, meaning that the serial limit has already been reached in…
Particle-In-Cell codes are widely used for plasma physics simulations. It is often the case that particles within a computational cell need to be split to improve the statistics or, in the case of non-uniform meshes, to avoid the…
We present new algorithms and fast implementations to find efficient approximations for modelling stochastic processes. For many numerical computations it is essential to develop finite approximations for stochastic processes. While the…
Cell migration plays essential roles in development, wound healing, diseases, and in the maintenance of a complex body. Experiments in collective cell migration generally measure quantities such as cell displacement and velocity. The…
In the context of MDPs with high-dimensional states, downstream tasks are predominantly applied on a compressed, low-dimensional representation of the original input space. A variety of learning objectives have therefore been used to attain…
Agent-based models capture heterogeneity among individuals in a population and are widely used in studies of multi-cellular systems, disease, epidemics and demography to name a few. However, existing frameworks consider discrete time-step…
The equation which describes a particle diffusing in a logarithmic potential arises in diverse physical problems such as momentum diffusion of atoms in optical traps, condensation processes, and denaturation of DNA molecules. A detailed…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
Change point analyses are concerned with identifying positions of an ordered stochastic process that undergo abrupt local changes of some underlying distribution. When multiple processes are observed, it is often the case that information…
We introduce an approach to inferring the causal architecture of stochastic dynamical systems that extends rate distortion theory to use causal shielding---a natural principle of learning. We study two distinct cases of causal inference:…
Memories are stored, retained, and recollected through complex, coupled processes operating on multiple timescales. To understand the computational principles behind these intricate networks of interactions we construct a broad class of…
By estimating 3D shape and instances from a single view, we can capture information about an environment quickly, without the need for comprehensive scanning and multi-view fusion. Solving this task for composite scenes (such as object…
We survey different perspectives on the stochastic localization process of Eldan, a powerful construction that has had many exciting recent applications in high-dimensional probability and algorithm design. Unlike prior surveys on this…
We present local distributed, stochastic algorithms for \emph{alignment} in self-organizing particle systems (SOPS) on two-dimensional lattices, where particles occupy unique sites on the lattice, and particles can make spatial moves to…