Related papers: Defining Pathway Assembly and Exploring its Applic…
Evolution is often understood through genetic mutations driving changes in an organism's fitness, but there is potential to extend this understanding beyond the genetic code. We propose that natural products - complex molecules central to…
Archetypal analysis represents a set of observations as convex combinations of pure patterns, or archetypes. The original geometric formulation of finding archetypes by approximating the convex hull of the observations assumes them to be…
The monography examines the problem of constructing a group of automorphisms of a graph. A graph automorphism is a mapping of a set of vertices onto itself that preserves adjacency. The set of such automorphisms forms a vertex group of a…
Autonomous systems, like vehicles or robots, require reliable, accurate, fast, resource-efficient, scalable, and low-latency trajectory predictions to get initial knowledge about future locations and movements of surrounding objects for…
Transition path theory computes statistics from ensembles of reactive trajectories. A common strategy for sampling reactive trajectories is to control the branching and pruning of trajectories so as to enhance the sampling of low…
Physically disentangling entangled objects from each other is a problem encountered in waste segregation or in any task that requires disassembly of structures. Often there are no object models, and, especially with cluttered irregularly…
Although many successful ensemble clustering approaches have been developed in recent years, there are still two limitations to most of the existing approaches. First, they mostly overlook the issue of uncertain links, which may mislead the…
We consider a general concept of composition and decomposition of objects, and discuss a few natural properties one may expect from a reasonable choice thereof. It will be demonstrated how this leads to multiplication and co- multiplication…
This paper begins with a description of methods for estimating image probability density functions that reflects the observation that such data is usually constrained to lie in restricted regions of the high-dimensional image space-not…
Models of complex networks are generally defined as graph stochastic processes in which edges and vertices are added or deleted over time to simulate the evolution of networks. Here, we define a unifying framework - probabilistic inductive…
We introduce and analyze the problem of the compilation of decision models from a decision-theoretic perspective. The techniques described allow us to evaluate various configurations of compiled knowledge given the nature of evidential…
We introduce a simple dynamical rule in which each particle locates a particle that is farthest from it and moves towards it. Repeated application of this algorithm results in the formation of unusual dynamical patterns: during the process…
We present a general mathematical framework for trajectory stratification for simulating rare events. Trajectory stratification involves decomposing trajectories of the underlying process into fragments limited to restricted regions of…
We demonstrate that the assembly pathway method underlying assembly theory (AT) is an encoding scheme widely used by popular statistical compression algorithms. We show that in all cases (synthetic or natural) AT performs similarly to other…
This article reviews the concepts and methods of variational path sampling. These methods allow computational studies of rare events in systems driven arbitrarily far from equilibrium. Based upon a statistical mechanics of trajectory space…
To date, most probabilistic reasoning systems have relied on a fixed belief network constructed at design time. The network is used by an application program as a representation of (in)dependencies in the domain. Probabilistic inference…
Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined as the spontaneous organization of multiple subunits (e.g. macromolecules, particles) into ordered multi-unit structures. The vast majority of…
Assembly Theory, as developed by Cronin and co-workers, assigns to an object an assembly index: the minimal number of binary join operations required to build at least one copy of the object from a specified set of basic building blocks,…
Combinatorial assembly uses standardized unit primitives to build objects that satisfy user specifications. This paper studies assembly sequence planning (ASP) for physical combinatorial assembly. Given the shape of the desired object, the…
Biclustering involves the simultaneous clustering of objects and their attributes, thus defining local two-way clustering models. Recently, efficient algorithms were conceived to enumerate all biclusters in real-valued datasets. In this…