References and thesis
TL;DR
MENoBiS implements the theoretical framework of Oleguer Sagarra's doctoral
thesis on non-binary maximum-entropy network ensembles, extended with
exact microcanonical samplers. Cite the software (via CITATION.cff) and
the scientific references relevant to your use.
Primary thesis
O. Sagarra, Non-binary maximum entropy network ensembles and their application to the study of urban mobility, PhD thesis, 2015.
https://hdl.handle.net/10803/400560
A copy of the thesis PDF ships with the repository at
docs/concepts/OSP_PhD_THESIS.pdf.
This is the primary scientific reference for the model ontology: the ME/B/W occupation families, the grand-canonical constraint framework, and the urban-mobility applications.
Core papers
| Topic | Reference |
|---|---|
| Multi-edge framework | O. Sagarra, C. J. Pérez Vicente, A. Díaz-Guilera, Statistical mechanics of multiedge networks, Phys. Rev. E 88, 062806. DOI: 10.1103/PhysRevE.88.062806 |
| Fixed-strength magnitudes | O. Sagarra, F. Font-Clos, C. J. Pérez-Vicente, A. Díaz-Guilera, The configuration multi-edge model, EPL 107, 38002. DOI: 10.1209/0295-5075/107/38002 |
| Urban mobility reconstruction | O. Sagarra, M. Szell, P. Santi, A. Díaz-Guilera, C. Ratti, Supersampling and Network Reconstruction of Urban Mobility, PLOS ONE. DOI: 10.1371/journal.pone.0134508 |
| Event nature and statistics | O. Sagarra, C. J. Pérez Vicente, A. Díaz-Guilera, Role of adjacency-matrix degeneracy in maximum-entropy-weighted network models, Phys. Rev. E 92, 052816. DOI: 10.1103/PhysRevE.92.052816 |
Complementary microcanonical references
| Topic | Reference |
|---|---|
| Tailored graph ensembles | A. Annibale, A. C. C. Coolen, L. P. Fernandes, F. Fraternali, J. Kleinjung, Tailored graph ensembles as proxies for biological network data, J. Phys. A: Math. Theor. 42, 485001 (2009). DOI: 10.1088/1751-8113/42/48/485001 — foundational microcanonical null modelling for binary networks |
Citation instructions
The repository ships a CITATION.cff; GitHub renders it through the
Cite this repository button. When publishing results obtained with
MENoBiS, cite the software and the scientific references above that ground
the models you used (at minimum the primary thesis, plus the papers matching
the families/constraints you employed).
Historical terminology
The thesis and related literature call MENoBiS objects weighted networks and speak of edge weights. Within the MENoBiS documentation the terminology is non-binary networks, occupation numbers, and occupied pairs; the historical wording is literature terminology, not the current canonical vocabulary (see Notation).
Mapping to the current ontology
The thesis concepts map one-to-one onto the current model ontology, which is documented in these pages rather than in a stale mapping table:
- families ME / B / W → Event families;
- constraints → Constraints;
- ensembles → Ensembles;
- filtering → Filtering statistics;
- supported combinations → Supported models.