Related papers: Pathway Realisability in Chemical Networks
Analysing and explaining relationships between entities in a graph is a fundamental problem associated with many practical applications. For example, a graph of biological pathways can be used for discovering a previously unknown…
We propose a method for checking generalized reachability properties in Petri nets that takes advantage of structural reductions and that can be used, transparently, as a pre-processing step of existing model-checkers. Our approach is based…
Time-Basic Petri nets, is a powerful formalism for model- ing real-time systems where time constraints are expressed through time functions of marking's time description associated with transition, representing possible firing times. We…
We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a…
Cellular ingredient concentrations can be stabilized by adjusting generation and consumption rates through multiple pathways. To explore the portion of cellular metabolism equipped with multiple pathways, we categorize individual metabolic…
Mechanistic interpretability aims to understand model behaviors in terms of specific, interpretable features, often hypothesized to manifest as low-dimensional subspaces of activations. Specifically, recent studies have explored subspace…
The goal of this paper is to gather and develop some necessary and sufficient criteria for injectivity and multistationarity in vector fields associated with a chemical reaction network under a variety of more or less general assumptions on…
Chord diagrams, under the name of Gauss diagrams, are used in low-dimensional topology as an important tool for studying curves or knots. Those Gauss diagrams that correspond to curves or knots are called realizable. The theme of our paper…
Approaches to understanding resilience from psychology and sociology emphasise individuals' agency but obscure systemic factors. Approaches to understanding resilience stemming from ecology emphasise system dynamics such as feedbacks but…
The concept of the limiting step is extended to the asymptotology of multiscale reaction networks. Complete theory for linear networks with well separated reaction rate constants is developed. We present algorithms for explicit…
Modern computer networks support interesting new routing models in which traffic flows from a source s to a destination t can be flexibly steered through a sequence of waypoints, such as (hardware) middleboxes or (virtualized) network…
Predicting the future motion of actors in a traffic scene is a crucial part of any autonomous driving system. Recent research in this area has focused on trajectory prediction approaches that optimize standard trajectory error metrics. In…
We introduce immediate observation Petri nets, a class of interest in the study of population protocols (a model of distributed computation), and enzymatic chemical networks. In these areas, relevant analysis questions translate into…
Reactive synthesis is a framework for modeling and automatically synthesizing strategies in robotics, typically through computing a \emph{winning} strategy in a 2-player game between the robot and the environment. Winning strategies,…
Interpretability aims to explain the behavior of deep neural networks. Despite rapid growth, there is mounting concern that much of this work has not translated into practical impact, raising questions about its relevance and utility. This…
We propose a reachability verification technique that combines the Petri net state equation (a linear algebraic overapproximation of the set of reachable states) with the concept of counterexample guided abstraction refinement. In essence,…
The pathway idea is a way of going from one family of functions to another family of functions and yet another family of functions through a parameter in the model so that a switching mechanism is introduced into the model through a…
The Feynman path integral does not allow a "one real path" interpretation, because amplitudes contribute to probabilities in a non-separable manner. The opposite extreme, "all paths happen", is not a useful or informative account. In this…
A well-known pitfall of molecular generative models is that they are not guaranteed to generate synthesizable molecules. Existing solutions for this problem often struggle to effectively navigate exponentially large combinatorial space of…
This work addresses the quantization of a self-interacting higher order time derivative theory using path integrals. To quantize this system and avoid the problems of energy not bounded from below and states of negative norm, we observe the…