Related papers: Pathway Realisability in Chemical Networks
Informally, a chemical reaction network is "atomic" if each reaction may be interpreted as the rearrangement of indivisible units of matter. There are several reasonable definitions formalizing this idea. We investigate the computational…
Among all characteristics exhibited by natural and man-made networks the small-world phenomenon is surely the most relevant and popular. But despite its significance, a reliable and comparable quantification of the question `how small is a…
For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive…
We explain how recent developments in the fields of realisability models for linear logic -- or geometry of interaction -- and implicit computational complexity can lead to a new approach of implicit computational complexity. This…
In graph theory and its practical networking applications, e.g., telecommunications and transportation, the problem of finding paths has particular importance. Selecting paths requires giving scores to the alternative solutions to drive a…
SMPT (for Satisfiability Modulo Petri Net) is a model checker for reachability problems in Petri nets. It started as a portfolio of methods to experiment with symbolic model checking, and was designed to be easily extended. Some distinctive…
Reasoning paths are reliable information in knowledge graph completion (KGC) in which algorithms can find strong clues of the actual relation between entities. However, in real-world applications, it is difficult to guarantee that…
Optimizing paths on networks is crucial for many applications, from subway traffic to Internet communication. As global path optimization that takes account of all path-choices simultaneously is computationally hard, most existing routing…
The logical connectives typically found in programming languages are similar to their mathematical counterparts, yet different due to their short-circuit behaviour -- when evaluating them, the second argument is only evaluated if the first…
It is often said that in relativistic quantum physics, a fundamental particle ontology is not viable. However, previous works have shown that certain relativistic quantum field theories can be reformulated as path integrals over particle…
Numerous tasks in program analysis and synthesis reduce to deciding reachability in possibly infinite graphs such as those induced by Petri nets. However, the Petri net reachability problem has recently been shown to require non-elementary…
Networks are a powerful tool to model the structure and dynamics of complex systems across scales. Direct connections between system components are often represented as edges, while paths and walks capture indirect interactions. This…
Chemical reactions occur in energy, environmental, biological, and many other natural systems, and the inference of the reaction networks is essential to understand and design the chemical processes in engineering and life sciences. Yet,…
Neural pathways as model explanations consist of a sparse set of neurons that provide the same level of prediction performance as the whole model. Existing methods primarily focus on accuracy and sparsity but the generated pathways may…
We describe some necessary conditions for the existence of a Hamiltonian path in any graph (in other words, for a graph to be traceable). These conditions result in a linear time algorithm to decide the Hamiltonian path problem for cactus…
Reaction networks, or equivalently Petri nets, are a general framework for describing processes in which entities of various kinds interact and turn into other entities. In chemistry, where the reactions are assigned "rate constants", any…
Reachability analysis, in general, is a fundamental method that supports formally-correct synthesis, robust model predictive control, set-based observers, fault detection, invariant computation, and conformance checking, to name but a few.…
A significant challenge in wet lab experiments with current drug design generative models is the trade-off between pharmacological properties and synthesizability. Molecules predicted to have highly desirable properties are often difficult…
Network reliability is a well-studied problem that requires to measure the probability that a target node is reachable from a source node in a probabilistic (or uncertain) graph, i.e., a graph where every edge is assigned a probability of…
Quantification is well known to be a major obstacle in the construction of a probabilistic network, especially when relying on human experts for this purpose. The construction of a qualitative probabilistic network has been proposed as an…