3 citations · 7 across the 16 of their papers we have counts for
17 papers
Automating Observable Closure Analysis for Graph Transformation Models with MolFoundry
Marcel Friedrichs, Addie Jordon, Juri Kolčák +1
Graph transformations model changing systems, with applications in software, biology and chemistry, among others. We introduce MolFoundry, a graph transformation framework, and pre…
Enumerating Chemical Structures, Stereoisomers, and Stereogenic Units with Analytic Combinatorics
Casper Asbjørn Eriksen, Daniel Merkle
The enumeration of chemical structures traditionally relies on graph- and group-theoretic techniques, including Pólya theory, in order to account for stereochemical symmetries. The…
Systematic pathway comparison on the powerset of rule-based biochemical systems
Anne-Susann Abel, Sissel Banke, Erika M. Herrera Machado +4
Computational pathway design often focuses on evaluating selected pathways or optimizing fluxes in a fixed network, but gives less direct access to the combinatorial question of wh…
On the realizability of abstract reaction networks with real molecules and reactions
Tuyet-Minh Phan, Daniel Merkle, Tieu-Long Phan +2
Abstract reaction networks appear not only as models of chemical reactions but also as models of complex systems, with applications in areas such as ecology and epidemiology, and a…
A Collision-based strategy for Network-free Exploration of Complex Molecular Networks
Adittya Pal, Rolf Fagerberg, Jakob Lykke Andersen +2
This work presents a stochastic exploration framework for large, implicitly defined chemical reaction spaces that are too large to be generated and stored as explicit molecular net…
CombOL: a Library for Practical Enumeration and Boltzmann Sampling of Combinatorial Classes
Casper Asbjørn Eriksen, Daniel Merkle
We present CombOL (Combinatorial Objects Library), an open-source library for the enumeration and Boltzmann sampling of combinatorial classes. Classes can be specified by a concise…
ChemRecon: a Consolidated Meta-Database Platform for Biochemical Data Integration
Casper Asbjørn Eriksen, Jakob Lykke Andersen, Rolf Fagerberg +1
In this paper, we present ChemRecon, a meta-database and Python interface for integrating and exploring biochemical data across multiple heterogeneous resources by consolidating co…
Saturation-Based Atom Provenance Tracing in Chemical Reaction Networks
Marcel Friedrichs, Daniel Merkle
Atom tracing is essential for understanding the fate of labeled atoms in biochemical reaction networks, yet existing computational methods either simplify label correlations or suf…
Continuous Petri Nets for Fast Yield Computation: Polynomial-Time and MILP Approaches
Addie Jordon, Juri Kolčák, Daniel Merkle
Petri nets provide accurate analogues to chemical reaction networks, with places representing individual molecules (the resources of the system) and transitions representing chemic…
A Sensitivity Analysis Methodology for Rule-Based Stochastic Chemical Systems
Erika M. Herrera Machado, Jakob L. Andersen, Rolf Fagerberg +1
In this study, we introduce a sensitivity analysis methodology for stochastic systems in chemistry, where dynamics are often governed by random processes. Our approach is based on…
Rule-Based Gillespie Simulation of Chemical Systems
Erika M. Herrera Machado, Jakob L. Andersen, Rolf Fagerberg +3
The MØD computational framework implements rule-based generative chemistries as explicit transformations of graphs representing chemical structural formulae. Here, we expand MØD by…
ChemReservoir -- An Open-Source Framework for Chemically-Inspired Reservoir Computing
Mehmet Aziz Yirik, Jakob Lykke Andersen, Rolf Fagerberg +1
Reservoir computing is a type of a recurrent neural network, mapping the inputs into higher dimensional space using fixed and nonlinear dynamical systems, called reservoirs. In the…
Assembly in Directed Hypergraphs
Christoph Flamm, Daniel Merkle, Peter F. Stadler
Assembly theory has received considerable attention in the recent past. Here we analyze the formal framework of this model and show that assembly pathways coincide with certain min…
Finding Pathways in Reaction Networks guided by Energy Barriers using Integer Linear Programming
Adittya Pal, Rolf Fagerberg, Jakob Lykke Andersen +2
Analyzing synthesis pathways for target molecules in a chemical reaction network annotated with information on the kinetics of individual reactions is an area of active study. This…
Finding Thermodynamically Favorable Pathways in Chemical Reaction Networks Using Flows in Hypergraphs and Mixed-Integer Linear Programming
Adittya Pal, Rolf Fagerberg, Jakob Lykke Andersen +3
The search for pathways that optimize the formation of a particular target molecule in a reaction network is a key problem in many settings, including reactor systems. Chemical rea…
Automated Inference of Graph Transformation Rules
Jakob L. Andersen, Akbar Davoodi, Rolf Fagerberg +6
The explosion of data available in life sciences is fueling an increasing demand for expressive models and computational methods. Graph transformation is a model for dynamic system…
Rewriting Theory for the Life Sciences: A Unifying Theory of CTMC Semantics (Long version)
Nicolas Behr, Jean Krivine, Jakob L. Andersen +1
The Kappa biochemistry and the MØD organic chemistry frameworks are amongst the most intensely developed applications of rewriting-based methods in the life sciences to date. A typ…