Analysis of the plant architecture via tree-structured statistical models: The hidden Markov tree models

New Phytologist

Volumn 166, Issue 3, 2005, Pages 813-825

  Durand, J B ^a   Guedon Y ^b   Caraglio, Y ^b   Costes, E ^c  

^a GRENOBLE INSTITUTE OF TECHNOLOGY   (France)

^b UNIV MONTPELLIER   (France)

^c INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

Author keywords

Apple tree; Bush willow; Clustering of tree structured entities; Differentiation of meristems; Hidden Markov tree models; Plant architecture modelling; Tree segmentation

Indexed keywords

MORPHOLOGY; PLANT ARCHITECTURE; TREE;

APPLE; ARTICLE; AUDIOVISUAL EQUIPMENT; COMBRETACEAE; COMPUTER SIMULATION; GROWTH, DEVELOPMENT AND AGING; PLANT; PROBABILITY; STATISTICAL MODEL;

COMBRETACEAE; COMPUTER SIMULATION; MALUS; MARKOV CHAINS; MODELS, STATISTICAL; MODELS, STRUCTURAL; PLANT COMPONENTS, AERIAL;

MALUS X DOMESTICA; SALIX;

EID: 19344366830     PISSN: 0028646X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2005.01405.x     Document Type: Article

References (26)

1. Adam B, Sinoquet H, Godin C, Dones N. 1999. 3A - A Software for the Acquisition of Plant Architecture, Version 2.0. Clermont-Ferrand, France: UMR PIAF INRA-UBP.
2. Barlow PW. 1994. From cell to system: repetitive units of growth in the development of roots and shoots. In: Iqbal M, ed. Growth Patterns in Vascular Plants. Portland, OR, USA: Dioscorides Press, 19-58.
3. Barthélémy D. 1991. Levels of organization and repetition phenomena in seed plants. Acta Biotheoretica 39: 309-323.
4. Barthélémy D, Caraglio Y, Costes E. 1997. Architecture, gradients morphogénétiques étage physiologique chez les végétaux. In: Bouchon J, de Reffye P, Barthélémy D, eds. Modélisation et Simulation de L'architecture des Végétaux. INRA Editions, 89-136.
5. Bell A. 1991. Plant Form - An Illustrated Guide to Flowering Plant Morphology. Oxford, New York, Tokyo: Oxford University Press.
6. Biernacki C, Celeux G, Govaert G. 2000. Assessing a mixture model for clustering with the integrated completed likelihood. IEEE Transactions on Pattern Analysis and Machine Intelligence 22: 719-725.
7. Bonnet P. 2002. Évaluation de la productivité du Combretum adenogonium Steud. ex. A. Rich à partir d'une approche architecturale. DESS Gestion des Systèmes Agro-Sylvo-Pastoraux en Zone Tropicale. Université Paris XII.
8. Bühlmann P, Wyner AJ. 1999. Variable length Markov chains. Annals of Statistics 27: 480-513.
9. Celeux G, Durand J-B. 2002. Choosing the order of a hidden Markov chain through cross-validated likelihood. In: Klinke S, Ahrend P, Richter L, eds. Compstat 2002. Berlin, Germany: Humboldt-Universität zu Berlin. http://ise.wiwi.hu-berlin.de/~sigbert/compstat2002/paper/short/C_02_celeux.pdf
10. Costes E, Guédon Y. 2002. Modelling branching patterns on 1-year-old trunks of six apple cultivars. Annals of Botany 89: 513-524.
11. Costes E, Sinoquet H, Keiner JJ, Godin C. 2003. Exploring within - tree architectural development of two apple tree cultivars over 6 years. Annals of Botany 91: 91-104.
12. Crabbé J, Escobedo-Alvarez JA. 1991. Activités méristématiques et cadre temporel assurant la transformation florale des bourgeons chez le pommier (Malus X domestica Borkh., cv. Golden Delicious). L'Arbre: Biologie et Développement. Naturalia Monspeliensia, 369-379.
13. Crouse MS, Nowak RD, Baraniuk RG. 1998. Wavelet-based signal processing using hidden Markov models. IEEE Transactions on Signal Processing 46: 886-902.
14. Durand J-B, Gonçalvès P, Guédon Y. 2004. Computational methods for hidden Markov trees - an application to wavelet trees. IEEE Transactions on Signal Processing 52: 2551-2560.
15. Ephraim Y, Merhav N. 2002. Hidden Markov processes. IEEE Transactions on Information Theory 48: 1518-1569.
16. Ferraro P, Godin C. 2000. A distance measure between plant architectures. Annals of Forest Sciences 57: 445-461.
17. Ferraro P, Godin C. 2003. An edit distance between quotiented trees. Algorithmica 36: 1-39.
18. Gatsuk LE, Smirnova OV, Vorontzova LI, Zaugolnova LB, Zhukova LA. 1980. Age states of plants of various growth forms: a review. Journal of Ecology 68: 675-696.
19. Geiger D, Heckerman D, King H, Mekk C. 2001. Stratified exponential families: graphical models and model selection. Annals of Statistics 29: 505-529.
20. Godin C, Caraglio Y. 1998. A multiscale model of plant topological structures. Journal of Theoretical Biology 191: 1-46.
21. Godin C, Guédon Y, Costes E, Caraglio Y. 1997. Measuring and analysing plants with the AMAPmod software. In: Michalewicz MT, ed. Plants to Ecosystems - Advances in Computational Life Sciences, Vol. I. Melbourne, Australia: CSIRO Publishing, 53-84.
22. Guédon Y, Barthélémy D, Caraglio Y, Costes E. 2001. Pattern analysis in branching and axillary flowering sequences. Journal of Theoretical Biology 212: 481-520.
23. Lauri PÉ, Térouanne É, Lespinasse JM. 1997. Relationship between the early development of apple fruiting branches and the regularity of bearing - an approach to the strategies of various cultivars. Journal of Horticultural Science 72: 519-530.
24. Nozeran R, Bancilhon L, Neville P. 1971. Intervention of internal correlations in the morphogenesis of higher plants. Advances in Morphology 9: 1-66.
25. Smyth P, Heckerman D, Jordan MI. 1997. Probabilistic independence networks for hidden Markov probability models. Neural Computation 9: 227-270.
26. White J. 1979. The plantas a metapopulation. Annual Review of Ecology and Systematics 10: 109-145.