Related papers: Pathway Realisability in Chemical Networks
Isocontours in road networks represent the area that is reachable from a source within a given resource limit. We study the problem of computing accurate isocontours in realistic, large-scale networks. We propose polygons with minimum…
Validating network paths taken by packets is critical for a secure Internet architecture. Any feasible solution must both enforce packet forwarding along endhost-specified paths and verify whether packets have taken those paths. However,…
We define catalytic networks as chemical reaction networks with an essentially catalytic reaction pathway: one which is on in the presence of certain catalysts and off in their absence. We show that examples of catalytic networks include…
A problem studied in Systems Biology is how to find shortest paths in metabolic networks. Unfortunately, simple (i.e., graph theoretic) shortest paths do not properly reflect biochemical facts. An approach to overcome this issue is to use…
The reachability semantics for Petri nets can be studied using open Petri nets. For us an "open" Petri net is one with certain places designated as inputs and outputs via a cospan of sets. We can compose open Petri nets by gluing the…
The discovery of transition pathways to unravel distinct reaction mechanisms and, in general, rare events that occur in molecular systems is still a challenge. Recent advances have focused on analyzing the transition path ensemble using the…
One of our long term research goals is to develop systems to answer realistic questions (e.g., some mentioned in textbooks) about biological pathways that a biologist may ask. To answer such questions we need formalisms that can model…
Place/transition Petri nets are a standard model for a class of distributed systems whose reachability spaces might be infinite. One of well-studied topics is the verification of safety and liveness properties in this model; despite the…
This paper proposes a novel approach for efficiently evaluating regular path queries over provenance graphs of workflows that may include recursion. The approach assumes that an execution g of a workflow G is labeled with query-agnostic…
In Petri net synthesis we ask whether a given transition system $A$ can be implemented by a Petri net $N$. Depending on the level of accuracy, there are three ways how $N$ can implement $A$: an embedding, the least accurate implementation,…
We investigate a framework of Krivine realizability with I/O effects, and present a method of associating realizability models to specifications on the I/O behavior of processes, by using adequate interpretations of the central concepts of…
We introduce a technique for reachability analysis of Time-Basic (TB) Petri nets, a powerful formalism for real- time systems where time constraints are expressed as intervals, representing possible transition firing times, whose bounds are…
Current directions in network routing research have not kept pace with the latest developments in network architectures, such as peer-to-peer networks, sensor networks, ad-hoc wireless networks, and overlay networks. A common characteristic…
Discovering new drug molecules is a pivotal yet challenging process due to the near-infinitely large chemical space and notorious demands on time and resources. Numerous generative models have recently been introduced to accelerate the drug…
We propose a novel, path-based reasoning approach for the multi-hop reading comprehension task where a system needs to combine facts from multiple passages to answer a question. Although inspired by multi-hop reasoning over knowledge…
Connectivity is a fundamental structural feature of a network that determines the outcome of any dynamics that happens on top of it. However, an analytical approach to obtain connection probabilities between nodes associated to paths of…
This paper develops some basic principles to study autocatalytic networks and exploit their structural properties in order to characterize their inherent fundamental limits and tradeoffs. In a dynamical system with autocatalytic structure,…
Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in practical applications in chemistry. The latter is made…
With the advance of efficient analytical methods for sensitivity analysis ofprobabilistic networks, the interest in the sensitivities revealed by real-life networks is rekindled. As the amount of data resulting from a sensitivity analysis…
Pathway enrichment analysis has become a key tool for biomedical researchers to gain insight into the underlying biology of differentially expressed genes, proteins and metabolites. It reduces complexity and provides a system-level view of…