Assembly in Directed Hypergraphs
Fuente:
arXiv
Saved in:
| Main Authors: | , , |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1866909626486751232 |
|---|---|
| author | Flamm, Christoph Merkle, Daniel Stadler, Peter F. |
| author_facet | Flamm, Christoph Merkle, Daniel Stadler, Peter F. |
| contents | 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 minimal hyperpaths in B-hypergraphs. This makes it possible to generalize the notion of assembly to general chemical reaction systems and to make explicit the connection to rule based models of chemistry, in particular DPO graph rewriting. We observe, furthermore, that assembly theory is closely related to retrosynthetic analysis in chemistry. The assembly index fits seamlessly into a large family of cost measures for directed hyperpath problems that also encompasses cost functions used in computational synthesis planning. This allows to devise a generic approach to compute complexity measures derived from minimal hyperpaths in rule-derived directed hypergraphs using integer linear programming. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2505_22826 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Assembly in Directed Hypergraphs Flamm, Christoph Merkle, Daniel Stadler, Peter F. Discrete Mathematics 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 minimal hyperpaths in B-hypergraphs. This makes it possible to generalize the notion of assembly to general chemical reaction systems and to make explicit the connection to rule based models of chemistry, in particular DPO graph rewriting. We observe, furthermore, that assembly theory is closely related to retrosynthetic analysis in chemistry. The assembly index fits seamlessly into a large family of cost measures for directed hyperpath problems that also encompasses cost functions used in computational synthesis planning. This allows to devise a generic approach to compute complexity measures derived from minimal hyperpaths in rule-derived directed hypergraphs using integer linear programming. |
| title | Assembly in Directed Hypergraphs |
| topic | Discrete Mathematics |
| url | https://arxiv.org/abs/2505.22826 |