Related papers: Pathway Realisability in Chemical Networks
To better understand the structure and function of complex systems, researchers often represent direct interactions between components in complex systems with networks, assuming that indirect influence between distant components can be…
Rapid advances in high-throughput technologies have led to considerable interest in analyzing genome-scale data in the context of biological pathways, with the goal of identifying functional systems that are involved in a given phenotype.…
Computer-assisted methods have emerged as valuable tools for retrosynthesis analysis. However, quantifying the plausibility of generated retrosynthesis routes remains a challenging task. We introduce Retro-BLEU, a statistical metric adapted…
The shortest path problem is among the most fundamental combinatorial optimization problems to answer reachability queries. It is hard to deter-mine which vertices or edges are visited during shortest path traversals. In this paper, we…
Although decidable, the marking reachability problem for Petri nets is well-known to be intractable in general, and a non-elementary lower bound has been recently uncovered. In order to alleviate this difficulty, various structural and…
Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures has become possible. Various…
Understanding how and how far information, behaviors, or pathogens spread in social networks is an important problem, having implications for both predicting the size of epidemics, as well as for planning effective interventions. There are,…
A variety of natural phenomena comprises a huge number of competing reactions and short-lived intermediates. Any study of such processes requires the discovery and accurate modeling of their underlying reaction network. However, this task…
Graph transformation systems have the potential to be realistic models of chemistry, provided a comprehensive collection of reaction rules can be extracted from the body of chemical knowledge. A first key step for rule learning is the…
With the growing use of deep learning methods, particularly graph neural networks, which encode intricate interconnectedness information, for a variety of real tasks, there is a necessity for explainability in such settings. In this paper,…
Pathways-reduced analysis is one of the techniques used by the Fispact-II nuclear activation and transmutation software to study the sensitivity of the computed inventories to uncertainties in reaction cross-sections. Although deciding…
Petri networks and network models are two frameworks for the compositional design of systems of interacting entities. Here we show how to combine them using the concept of a "catalyst": an entity that is neither destroyed nor created by any…
Reachability queries ask whether there exists a path from the source vertex to the target vertex on a graph. Recently, several powerful reachability queries, such as Label-Constrained Reachability (LCR) queries and Regular Path Queries…
In this paper we investigate formal verification problems for Neural Network computations. Various reachability problems will be in the focus, such as: Given symbolic specifications of allowed inputs and outputs in form of Linear…
Real-world scenarios demand reasoning about process, more than final outcome prediction, to discover latent causal chains and better understand complex systems. It requires the learning algorithms to offer both accurate predictions and…
In this thesis a comprehensive verification framework is proposed to contend with some important issues in composability verification and a verification process is suggested to verify composability of different kinds of systems models, such…
A central decision problem in Petri net theory is reachability asking whether a given marking can be reached from the initial marking. Related is the covering problem (or sub-marking reachbility), which decides whether there is a reachable…
We survey graph reachability indexing techniques for efficient processing of graph reachability queries in two types of popular graph models: plain graphs and edge-labeled graphs. Reachability queries are Boolean in nature, determining…
Classical path search assumes complete graphs and scalar optimization metrics, yet real infrastructure networks are incomplete and require multi-dimensional evaluation. We introduce the concept of traversal: a generalization of paths that…
We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…