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Anne Berry 
Publications, research reports, dissertations

DBLP Anne Berry

Journal papers    Conference papers   Reports and submitted papers  Dissertations  


See also the link to my DBLP

  1. Separability generalizes Dirac's theorem.
    A. Berry and  J.-P. Bordat.
    Discrete Applied Mathematics 84(1998)43-53.
    abstract 

  2. Orthotreillis de séparabilité dans un graphe non-orienté.
    A. Berry and J.-P. Bordat.
    Mathématiques, Informatique et Sciences Humaines 146(1999)5-17.
    abstract  

  3. Generating all the minimal separators of a graph.
    A. Berry, J.-P. Bordat and O.Cogis.
    International Journal of Foundations of Computer Science (IJFCS) 11(2000)397-404.

  4. Recognizing Weakly Triangulated Graphs by Edge Separability.
    A. Berry,  J-P.Bordat and Pinar Heggernes.
    Nordic Journal Computing, vol.7, no.3, pp. 164-177, 2000.

  5. Asteroidal Triples of Moplexes.
    A. Berry and  J-P.Bordat.
    Discrete Applied Mathematics, vol. 111 (2001), no. 3,  219-229.

  6. Maximum Cardinality Search for Computing Minimal Triangulations of Graphs.
    Anne Berry, Jean Blair, Pinar Heggernes and Barry Peyton.
    Algorithmica 39-4 (2004), pages 287 - 298.

  7. Representing a concept lattice by a graph.
    A. Berry and  A. Sigayret.
    Discrete Applied Mathematics, vol 144 (2004), no.1-2, 27-42
    (special issue on Discrete Maths for Data Mining)

  8. A wide-range algorithm for minimal triangulation from an arbitrary ordering.
    Anne Berry,  Jean-Paul Bordat, Pinar Heggernes, Genevieve Simonet, and Yngve Villanger.
    Journal of Algorithms, Volume 58, Issue 1, (2006), Pages 33-66.

  9. Maximal sub-triangulation in preprocessing phylogenetic data.
    A. Berry, A. Sigayret and C. Sinoquet.
    Soft Computing ( Springer-Verlag GmbH), special issue on Recent Advances in Knowledge Discovery, G. Govaert, R. Haenle and M. Nadif (eds). 1900:01 (2005)

  10. Generalized Domination in Closure Systems.
    A. Berry, E. SanJuan and A. Sigayret.
    Discrete Applied Mathematics, 154-7 (2006), Pages  1064-1084.

  11. A vertex incremental approach for maintaining chordality.
    A. Berry, P. Heggernes and Y. Villander.
    Discrete Mathematics,
    306-3 (2006), pages 318-336.
    (Research Report LIMOS/RR-03-04,
    An on-line incremental approach for dynamically maintaining chordal graphs)

  12. Preface to Special issue on Minimal Separation and Minimal Triangulation.
    A. Berry, J. R. S. Blair, G. Simonet.
    Discrete Mathematics, 306-3 (2006), Page 293.

  13. Recognizing Chordal Probe Graphs and Cycle-bicolorable Graphs.
    A. Berry,  M. C. Golumbic and M. Lipsteyn.
    (Research Report LIMOS/RR-03-14, Recognizing and triangulating chordal probe graphs).
     SIAM J. Discrete Math. 21(3): 573-591 (2007).

  14. Introduction to the special volume on Knowledge Discovery and Discrete Mathematics
    and a Tribute to the Memory of Peter L. Hammer.
    Anne Berry, Eric SanJuan, Maurice Pouzet  as Guest Editors, and Martin C. Golumbic as Editor-in-Chief.
    AMAI
      Ann. Math. Artif. Intell. 49(1-4): 1-4 (2007).

  15. A local Approach to Concept Generation.
    A. Berry, A. Sigayret and J-P.Bordat.
     (Research Report LIMOS/RR-03-03, Efficient Concept Generation)
    AMAI Ann. Math. Artif. Intell. 49(1-4): 117-136 (2007).

  16. Clustering gene expression data using graph separators
    B. Kaba, N. Pinet, G. Lelandais, A. Sigayret, A. Berry.
     In Silico Biol. 2007;7(4-5):433-52.

  17. Sequential and parallel triangulating algorithms for Elimination Game and new insights on Minimum Degree.
    A. Berry, E. Dahlhaus, P. Heggernes, G. Simonet.
    Theoretical Computer Science, Vol.409,3(2008), pp601-616.

  18. Maximal Label Search algorithms to compute perfect and minimal elimination orderings.
    A. Berry, R. Krueger and G. Simonet.
    SIAM Journ. Discrete Math., Vol.23(2009), pp428-446.

  19. A General Label Search to investigate classical graph search algorithms.
    R. Krueger, G. Simonet and A. Berry.
    Discrete Applied Mathematics,
    59(2-3): 128-142 (2011)

  20. Graph extremities defined by search algorithms.
    A. Berry,  J.R.S. Blair,  J-P.Bordat and G. Simonet.
    Algorithms, Volume 3, Issue 2 (June 2010), Pages 100-124.

    http://www.mdpi.com/1999-4893/3/2/

  21. An introduction to Clique Minimal Separator Decomposition.
    A. Berry, R. Pogorelcnik and G. Simonet.

    Algorithms 3(2): 197-215 (2010).
    http://www.mdpi.com/1999-4893/3/2/197/

  22. A simple algorithm to generate the minimal separators and the maximal cliques of a chordal graph.
    A. Berry, R. Pogorelcnik.
    Information Processing Letters: 111(11): 508-511 (2011)
    .

  23. MosaicFinder: Identification of fused gene families in sequence similarity networks
    P.-A Jachiet, R. Pogorelcnik, A. Berry, P. Lopez, E. Bapteste.
    Bioinformatics: 29(7):837-44
    (2013).

  24. Organizing the atoms of the clique separator decomposition into an atom tree.
    A. Berry, G. Simonet and R. Pogorelcnik.
    Discrete Applied Math., 177:1-13 (2014).

  25. Hermes: a simple and efficient algorithm for building the AOC-poset of a binary relation.
    A. Berry, A. Gutierrez, M. Huchard, A. Napoli, A. Sigayret.
    Annals of Mathematics and Artificial Intelligence (AMAI), 72:45-71 (2014). 
  26. The Dilworth number of Auto-chordal Bipartite Graphs.
    A. Berry, A. Brandstädt , K. Engel.
    CoRR abs/1309.5787.

    Graphs and Combinatorics 31:1463-1471 (2015).

  27. Efficiently decomposing, recognizing and triangulating hole-free graphs without diamonds.
    A. Berry, A. Brandstädt , V. Giakoumakis, F. Maffray.
    Discrete Applied Math., 184:50-61 (2015).


    Conference papers

    back to top of page

  28. A Wide-Range Efficient Algorithm for Minimal Triangulation.
    Anne Berry.
    Proceedings of the Tenth Annual Symposium on Discrete Algorithms (SODA'99), pp 860-861, Jan. 1999. 

  29. Generating all the minimal separators of a graph.
    A. Berry, J.-P. Bordat and O.Cogis.
    Proceedings of the 25th International Workshop on Graph-Theoretic Concepts in Computer Science (WG'99).

  30. Local LexBFS Properties in an Arbitrary Graph.
    A. Berry and J.-P. Bordat.
    Proceedings of  Journées Informatiques Messines (JIM 2000).
    postscript of full version

  31. Recognizing Weakly Triangulated Graphs by Edge Separability.
    A. Berry,  J-P.Bordat and Pinar Heggernes.
    Proceedings of the Seventh Scandinavian Workshop on Algorithm Theory (SWAT'2000).

  32. Decomposition by clique minimal separators.     
    A. Berry and  J-P.Bordat.
    Dagstuhl Seminar No. 01251  Report No. 312
    17.06.2001-22.06.2001on Graph Decompositions and Algorithmic Applications
    postscript version

  33. Moplex Elimination Orderings.
    A. Berry and  J-P.Bordat.
    First Cologne-Twente Workshop on Graphs and Combinatorial Optimization
    Cologne (Germany), June 6-8, 2001
    Electronic Notes in Discrete Mathematics Volume 8, pages 6-9 (May 2001)

    Edited by Johann Hurink, Stefan Pickl, Hajo Broersma and Ulrich Faigle
    postscript extended abstract

  34. Representing a concept lattice by a graph.
    A. Berry and  A. Sigayret.    
    Proceedings of Workshop on Discrete Mathematics and Data Mining (DM & DM 2002), Organizer: Peter Hammer, Second SIAM Conference on Data Mining.  

  35. Obtaining and maintaining polynomial-sized concept lattices.
    A. Berry and A. Sigayret.
    Proceedings Workshop FCAKDD (Formal Concept Analysis for Knowledge Discovery in Data bases), ECCAI 02.

  36. Maximum Cardinality Search for Computing Minimal Triangulations.
    Anne Berry,  Jean Blair and Pinar Heggernes.
    Proceedings WG 2002 - 28th Workshop on Graph Theoretical Concepts in Computer Science, Cesky Krumlov, Czech Rebublic, June 2002.
    Springer Verlag, Lecture Notes in Computer Science 2573, pages 1-12.

  37. Maintaining class membership information. A. Berry and A. Sigayret.
    Workshop MASPEGHI (MAnaging of SPEcialization/Generalization HIerarchies).
    LNCS proceedings of OOIS 02  (Object-Oriented Information Systems).

  38. Generalized Domination in Closure Systems. A. Berry, E. SanJuan and A. Sigayret.
    Proceedings of the Workshop on Discrete Mathematics and Data Mining (DM & DM 2003), Third SIAM Conference on Data Mining.

  39. The Minimum Degree Heuristic and the Minimal Triangulation Process.
    A. Berry, G. Simonet and P. Heggernes.
    Proceedings WG 2003 - 29th Workshop on Graph Theoretic Concepts in Computer Science,
    June 2003, Elspeet, the Netherlands. Springer Verlag, Lecture Notes in Computer Science 2880, pages 58 - 70.
    (Research Report LIMOS/RR-03-01).

  40. Génération des Chaînes Maximales d'un treillis.
    A. Berry, J.-P. Bordat, E. SanJuan et A. Sigayret.
    Atelier Usage des Treillis de Galois pour l' Intelligence Artificielle, (Plateforme AFIA 2003), Laval, France, juillet 2003.
    postscript

  41. Maximal sub-triangulation as improving phylogenetic data.
    A. Berry, A. Sigayret and C. Sinoquet.
    Proceedings of JIM 2003, INIST.

  42. Concepts  Can't Afford to Stammer.
    A. Berry, A. Sigayret and J-P.Bordat.
    Proceedings of JIM 2003, INIST.

  43. Graph extremities and minimal separation.
    Anne Berry.
    Invited talk.
    Proceedings of JIM 2003,
    INIST.

  44. A vertex- incremental approach for dynamically maintaining chordal graphs.
    A. Berry, P. Heggernes and Y. Villander.
    LNCS Proceedings ISAAC 2003, pp. 47-57.

  45. Two tricks to Triangulate Chordal Probe Graphs in Polynomial Time.
    A. Berry,  M. C. Golumbic and M. Lipsteyn.
    Proceedings SODA 2004.
    Also presented Dagstuhl Seminar Nº 04221, Robust and Approximative Algorithms on Particular Graph Classes.
    postscript extended abstract   postscript full version

  46. Classification et désarticulation de graphes de termes.
    A. Berry, B. Kaba, M. Nadif, E. SanJuan et A. Sigayret.
    Proceedings JADT' 2004, Louvain-la-Neuve, Belgium, 10-12 March 2004, 589-600.

  47. Efficiently Computing a Linear Extension of the Sub-hierarchy of a Concept Lattice.
    A. Berry, M. Huchard, R.M. McConnell, A. Sigayret and J. Spinrad.
    Proceedings of  ICFCA '05, LNCS,  Vol 3404/2005. 

  48. Faster Dynamic Algorithms for Chordal Graphs, and an Application to Phylogeny
    A. Berry, A. Sigayret and J. Spinrad.
    Proceedings of the 31st International Workshop on Graph-Theoretic Concepts in Computer Science 2005 (WG 2005), LNCS 3787, pp. 445-455, Springer-Verlag, 2005.

  49. Ultimate Generalizations of LexBFS and LEX M.
    A. Berry, R. Krueger and G. Simonet.
    Proceedings of the 31st International Workshop on Graph-Theoretic Concepts in Computer Science 2005 (WG 2005), LNCS 3787, pp 199-213, Springer-Verlag, 2005.

  50. Extremities and orderings defined by generalized graph search algorithms.
    A. Berry, J.R.S. Blair, J-P.Bordat, R. Krueger and G. Simonet.
    Proceedings of 7th International Colloquium on Graph Theory (ICGT 05),
    Electronic Notes in Discrete Mathematics, Volume 22, Pages 413-420.

  51. Very Fast Instances for Concept Generation.
    A. Berry, R. McConnell, A. Sigayret and J. Spinrad.
    Proceedings of ICFCA 06,

    LNAI 3874 (2006) 119-129.

  52. Performances of Galois Sub-hierarchy-building algorithms
    Gabriela Arevalo, Anne Berry, Marianne Huchard, Guillaume Perrot and Alain Sigayret.
    Proceedings of ICFCA 07, LNCS, 166-180.

  53. Vertical decomposition of a lattice using clique separators
    A. Berry, R. Pogorelcnik and A. Sigayret.
    Proceedings of CLA 2011.

  54. A peep through the looking glass: articulation points in lattices
    A. Berry, and A. Sigayret.
    LNCS proceedings of ICFCA 2012 (10th International Conference on Formal Concept Analysis)
    LNAI 7278 (2012) 45-60.

  55. Triangulation and clique separator decomposition of claw-free graphs
    A. Berry and A. Wagler.
    WG 2012, Lecture Notes in Computer Science, 7551 (2012) 7-21.

  56. Hermes: an efficient algorithm for building Galois Sub-hierarchies.
    A. Berry, M. Huchard, A. Napoli, A. Sigayret.
    On-line proceedings of CLA 2012.

  57. Dismantlable lattices in the mirror
    A. Berry, A. Sigayret.
    ICFCA 2013, LNAI 7880, pp. 44-59.

  58. The Normal Graph Conjecture for classes of sparse graphs.
    A. Berry and A. Wagler.
    WG 2013, LNCS 8165 (2013) 64-75.


    Research Reports and submitted papers 
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  59. Towards improving phylogeny reconstruction with combinatorial-based constraints on an underlying family of graphs.
    A. Berry, A. Sigayret and C. Sinoquet.
    February 14, 2002.
    Research report LIMOS/RR-02-02.
    postscript

  60. Concept lattices and undirected graphs. A. Berry.
    postscript

  61. Efficient Algorithms for Minimal Subtriangulation and Minimum Degree Ordering
    A. Berry, G. Simonet and J. Spinrad.

  62. Efficient clique decomposition of a graph into its atom graph.
    A. Berry, G. Simonet and R. Pogorelcnik.
    Research Report LIMOS RR-10-07.

  63. Impact of the distance choice on clustering gene expression data using graph decompositions
    Marie Defay, Romain Pogorelcnik, Annegret Wagler, Anne Berry.
    Archive ouvertes HAL.


    Dissertations
  64. Treillis de Galois des Séparateurs Minimaux d'un graphe non-orienté
    Anne Berry.
    Mémoire de DEA, (Master's Dissertation), septembre 1995, LIRMM,
    Directeur de Recherche : Michel Habib.
    postscript version (in French, 1900K).

  65. Désarticulation d'un graphe
    Anne Berry.
    Thèse (PhD Dissertation), LIRMM, Montpellier, décembre 1998.
    Directeur de Thèse : Jean-Paul Bordat.

  66. Weaving Through a Crowd of Minimal Separators
    Anne Berry.
    HDR (Habilitation à diriger les recherches).

    LIMOS, Clermont-Ferrand, December 2003.
    postscript