J. Carr, D. Mazauric, F. Cazals, and D. J. Wales, Energy landscapes and persistent minima, The Journal of Chemical Physics, vol.144, issue.5, p.2016
DOI : 10.1063/1.4941052

URL : https://hal.archives-ouvertes.fr/hal-01423280

F. Cazals and T. Dreyfus, The structural bioinformatics library: modeling in biomolecular science and beyond, Bioinformatics, p.2016
DOI : 10.1093/bioinformatics/btw752

URL : https://hal.archives-ouvertes.fr/hal-01379635

F. Cazals, T. Dreyfus, D. Mazauric, A. Roth, and C. H. Robert, Conformational ensembles and sampled energy landscapes: Analysis and comparison, Journal of Computational Chemistry, vol.32, issue.16, pp.1213-1231, 2015.
DOI : 10.1002/jcc.23913

URL : https://hal.archives-ouvertes.fr/hal-01076317

F. Chazal, L. Guibas, S. Oudot, and P. Skraba, Persistence-Based Clustering in Riemannian Manifolds, Journal of the ACM, vol.60, issue.6, pp.1-38, 2013.
DOI : 10.1145/2535927

URL : https://hal.archives-ouvertes.fr/hal-01094872

Y. Cheng, Mean shift, mode seeking, and clustering, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.17, issue.8, pp.790-799, 1995.
DOI : 10.1109/34.400568

G. B. Dantzig, Application of the simplex method to a transportation problem Activity Analysis of Production and Allocation, pp.359-373, 1951.

M. R. Garey and D. S. Johnson, Computers and Intractability: A Guide to the Theory of NP-Completeness, 1979.

A. Genevay, M. Cuturi, G. Peyré, and F. Bach, Stochastic optimization for large-scale optimal transport, Proc. NIPS'16, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01321664

F. Hillier and G. Lieberman, Introduction to mathematical programming, 1977.

L. Jaillet, F. J. Corcho, J. Pérez, and J. Cortés, Randomized tree construction algorithm to explore energy landscapes, Journal of Computational Chemistry, vol.319, issue.16, pp.3464-3474, 2011.
DOI : 10.1002/jcc.21931

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.589.7111

E. Levina and P. Bickel, The Earth Mover's distance is the Mallows distance: some insights from statistics, Proceedings Eighth IEEE International Conference on Computer Vision. ICCV 2001, pp.251-256, 2001.
DOI : 10.1109/ICCV.2001.937632

G. Monge, Mémoire sur la théorie des déblais et des remblais, Histoire de l'Académie Royale des Sciences de Paris, pp.666-704

M. T. Oakley, D. J. Wales, and R. L. Johnston, Energy Landscape and Global Optimization for a Frustrated Model Protein, The Journal of Physical Chemistry B, vol.115, issue.39, pp.11525-11529, 2011.
DOI : 10.1021/jp207246m

URL : http://doi.org/10.1021/jp207246m

A. Roth, T. Dreyfus, C. H. Robert, and F. Cazals, Hybridizing rapidly exploring random trees and basin hopping yields an improved exploration of energy landscapes, Journal of Computational Chemistry, vol.124, issue.8, pp.739-752, 2016.
DOI : 10.1002/jcc.24256

URL : https://hal.archives-ouvertes.fr/hal-01497994

Y. Rubner, C. Tomasi, and L. J. Guibas, The earth mover's distance as a metric for image retrieval, International Journal of Computer Vision, vol.40, issue.2, pp.99-121, 2000.
DOI : 10.1023/A:1026543900054

J. Solomon, F. De-goes, G. Peyré, M. Cuturi, A. Butscher et al., Convolutional wasserstein distances, ACM Transactions on Graphics, vol.34, issue.4, p.66, 2015.
DOI : 10.1145/2766963

URL : https://hal.archives-ouvertes.fr/hal-01188953

C. Villani, Topics in optimal transportation. Number 58, 2003.

D. J. Wales, Energy Landscapes, 2003.
DOI : 10.1017/CBO9780511721724

URL : https://hal.archives-ouvertes.fr/hal-01423280