Dr Matthieu Vignes staff profile picture

Contact details +64 (06) 356 9099  ext. 84654

Dr Matthieu Vignes PhD

Senior Lecturer in Statistical Genetics

Institute of Fundamental Sciences

Matthieu studied Applied Maths/Stats at the ENS Lyon (France) before doing his PhD in Grenoble (2007, INRIA Rhone-Alpes, France). He then joined BioSS in Dundee and Aberdeen (Scotland) from 2006 to 2009 as a Statistician. He then became a Research Fellow in the Maths and Comput. Sc. dpt of the INRA in Toulouse (France) in 2009 (present: detached position).

Matthieu is now a Senior Lecturer in Statistical Genetics at Massey University (New Zealand).

Matthieu's work focuses on deciphering relationships between entities in a complex (e.g. biological) system; please have a look at his research interests.

Professional

Contact details

  • Ph: +64 (06) 356 9099 ext. 84654
    Location: B3.06, Science Tower B
    Campus: Turitea

Qualifications

  • PhD in Applied Mathematics / Statistics - Universite Joseph Fourier - Grenoble 1 (France) (2007)
  • Agregation de Mathematiques (French competitive teaching exam) - Ministere de l'Education Nationale (2002)
  • M.Sc in Mathematics - ENS Lyon & Universite Claude Bernard - Lyon 1 (France) (2002)

Research Expertise

Research Interests

My research is motivated by the understanding of the structure(s) which govern(s) the behaviour of complex systems. Mostly, I have been working with high-throughput data generated by biological organims, regarded layers of components of different natures which interact with each other possibly fulfilling different goals.

To this end, I am interested in probabilistic graphical modelling as a convenient way of representing the system under study and how its constituting elements interact. I am often faced with high-dimensional data posing both statistical and computational challenges. Missingness in the data sets at hand can also be a hindrance. Data sets are heterogeneous (e.g. mixing discrete and continuous data), sampling is certainly not independent and identically distributed and off-equilibrium and measurements noisy.

Recently, I am moving towards a causal interpretation of learnt relationships, hopefully revealing realistic mechanisms which explain the inner functioning of the system.

Thematics

Future Food Systems

Area of Expertise

Field of research codes
Applied Mathematics (010200):
Artificial Intelligence and Image Processing (080100):
Biological Mathematics (010202): Biostatistics (010402):
Information And Computing Sciences (080000):
Mathematical Sciences (010000):
Neural, Evolutionary and Fuzzy Computation (080108):
Numerical and Computational Mathematics (010300): Optimisation (010303):
Pattern Recognition and Data Mining (080109):
Statistical Theory (010405): Statistics (010400)

Keywords

  • Probabilistic graphical models (Bayesian networks, GGM...)
  • High-dimensional (biological) data
  • Gene network inference
  • Causality
  • Data integration
  • Computational statistics

Research Outputs

Journal

Vignes, MCL. (2017). Book Review: Modern optimization with R (by P. Cortez). Australian & New Zealand Journal of Statistics. 59(2), 235-236
[Book Review]Authored by: Vignes, M.
Champion, M., Picheny, V., & Vignes, M. (2017). Inferring large graphs using ℓ1-penalized likelihood. Statistics and Computing. , 1-17
[Journal article]Authored by: Vignes, M.
Vignes, MCL. (2016). Book Review: Inference principles for biostatisticians by Ian C. Marschner. Australian and New Zealand Journal of Statistics. 57(4), 571-572
[Book Review]Authored by: Vignes, M.
Villa-Vialaneix, N., Vignes, M., Viguerie, N., & Cristobal, MS. (2014). Inferring networks from multiple samples with consensus LASSO. Quality Technology and Quantitative Management. 11(1), 39-60
[Journal article]Authored by: Vignes, M.
Marchand, G., Huynh-Thu, VA., Kane, NC., Arribat, S., Varès, D., Rengel, D., . . . Langlade, NB. (2014). Bridging physiological and evolutionary time-scales in a gene regulatory network. New Phytologist. 203(2), 685-696
[Journal article]Authored by: Vignes, M.
Champion, M., Cierco-Ayrolles, C., Gadat, S., & Vignes, M. (2014). Sparse regression and support recovery with L2-Boosting algorithms. Journal of Statistical Planning and Inference. 155, 19-41
[Journal article]Authored by: Vignes, M.
Vandel, J., Mangin, B., Vignes, M., Leroux, D., Loudet, O., Martin-Magniette, ML., . . . De Givry, S. (2012). Gene regulatory network inference with extended scores for Bayesian networks. Revue d'Intelligence Artificielle. 26(6), 679-708
[Journal article]Authored by: Vignes, M.
Dupuy, LX., & Vignes, M. (2012). An algorithm for the simulation of the growth of root systems on deformable domains. Journal of Theoretical Biology. 310, 164-174
[Journal article]Authored by: Vignes, M.
Vignes, M., Blanchet, J., Leroux, D., & Forbes, F. (2011). SpaCEM3: A software for biological module detection when data is incomplete, high dimensional and dependent. Bioinformatics. 27(6), 881-882
[Journal article]Authored by: Vignes, M.
Vignes, M., Vandel, J., Allouche, D., Ramadan-Alban, N., Cierco-Ayrolles, C., Schiex, T., . . . de Givry, S. (2011). Gene regulatory network reconstruction using bayesian networks, the dantzig selector, the lasso and their meta-analysis. PLoS ONE. 6(12)
[Journal article]Authored by: Vignes, M.
Dupuy, L., Vignes, M., Mckenzie, BM., & White, PJ. (2010). The dynamics of root meristem distribution in the soil. Plant, Cell and Environment. 33(3), 358-369
[Journal article]Authored by: Vignes, M.
Dupuy, L., White, PJ., McKenzie, B., & Vignes, M. (2009). Meristematic fronts: A new model of the plant architectural development?. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY. 153A(2), S219-S219
[Journal article]Authored by: Vignes, M.
Blanchet, J., & Vignes, M. (2009). A model-based approach to gene clustering with missing observation reconstruction in a Markov random field framework. Journal of Computational Biology. 16(3), 475-486
[Journal article]Authored by: Vignes, M.
Vignes, M., & Forbes, F. (2009). Gene clustering via integrated markov models combining individual and pairwise features. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 6(2), 260-270
[Journal article]Authored by: Vignes, M.

Book

Allouche, D., Cierco-Ayrolles, C., Givry, SD., Guillermin, G., Mangin, B., Schiex, T., . . . Vignes, M. (2013). A panel of learning methods for the reconstruction of gene regulatory networks in a systems genetics context. In Gene Network Inference: Verification of Methods for Systems Genetics Data. (pp. 9 - 31).
[Chapter]Authored by: Vignes, M.

Thesis

Vignes, M. (2007). Modèles markoviens graphiques pour la fusion de données individuelles et d'interactions : application à la classification de gènes. (Doctoral Thesis, Université Joseph Fourier - Grenoble 1, France)
[Doctoral Thesis]Authored by: Vignes, M.

Report

Champion, M., Picheny, V., & Vignes, M.Inferring large graphs with an l1-penalized likelihood formulation and a hybrid genetic algorithm.
[Technical Report]Authored by: Vignes, M.
Peyrard, N., Givry, SD., Franc, A., Robin, S., Sabbadin, R., Schiex, T., . . . Vignes, M.Exact and approximate inference in graphical models: variable elimination and beyond.
[Technical Report]Authored by: Vignes, M.

Conference

Schrefheere, A., Campbell, M., Tate, J., Cox, M., & Vignes, MCL.Statistical modelling of expression patterns in hybrid species. Paper presented at the meeting of JOURNÉES OUVERTES DE BIOLOGIE INFORMATIQUE & MATHÉMATIQUES. Lyon, France
[Conference Paper]Authored by: Cox, M., Tate, J., Vignes, M.
Sammarro, M., Friedrich, A., Marshall, J., Biggs, P., French, N., & Vignes, MCL.Revealing the genetic basis for host-pathogen interaction using machine learning. Paper presented at the meeting of JOURNÉES OUVERTES DE BIOLOGIE INFORMATIQUE & MATHÉMATIQUES. Lyon, France
[Conference Paper]Authored by: Biggs, P., French, N., Marshall, J., Vignes, M.
Vignes, MCL. (2016, November). Disease module detection (via graph clustering). Presented at 2016 Joint NZSA+ORSNZ Conference. Auckland, New Zealand.
[Conference Oral Presentation]Authored by: Vignes, M.
Sammarro, M., Schrefheere, A., Biggs, P., marshall, J., Tate, J., Cox, M., . . . Vignes, MCL. (2016). Challenges and leads for modelling complex molecular biological systems. Poster session presented at the meeting of Complex Networks and Applications 2016 workshop. Marseilles, France
[Conference Poster]Authored by: Biggs, P., Cox, M., French, N., Marshall, J., Marsland, S., Vignes, M.
Champion, M., Picheny, V., & Vignes, M. (2014, November). Statistical causal inference in a complex system - an hybrid convex-genetic algorithm. Presented at NZSA conference. Wellington, NZ.
[Conference Oral Presentation]Authored by: Vignes, M.
Picheny, V., Vandel, J., Vignes, M., & Villa-Vialaneix, N. (2014). Reconstruction quality of a biological network when its constituting elements are partially observed. Poster session presented at the meeting of AISTAT 2014. Reykjavik, Iceland
[Conference Poster]Authored by: Vignes, M.
Champion, M., Gadat, S., Cierco-Ayrolles, C., & Vignes, MCL.Sparse multivariate regression with L2 -Boosting algorithm.
[Conference Paper]Authored by: Vignes, M.
Allouche, D., CIerco-Ayrolles, C., de Givry, S., Guillermin, G., Mangin, B., Schiex, T., . . . Vignes, M. (2013, March). A panel of learning methods for the reconstruction of gene regulatory networks in a systems genetics context. Presented at StatSeq workshop
[Conference Oral Presentation]Authored by: Vignes, M.
Marchand, G., Huynh-Thu, VA., Kane, N., Arribat, S., Vares, D., Rengel, D., . . . Langlade, .Bridging physiological and evolutionary time scales in a gene regulatory network.
[Conference Paper]Authored by: Vignes, M.
Vandel, J., de Givry, S., Leroux, D., Vignes, MCL., Loudet, O., Martin-Magniette, ML., . . . Mangin, B. (2012, April). Towards Arabidopsis thaliana genetic regulatory network using discrete Bayesian network. Presented at Statseq workshop
[Conference Oral Presentation]Authored by: Vignes, M.
Denoyes, B., Petit, A., Schwab, W., Vignes, M., Munoz-Blanco, J., Lerceteau-Kohler, E., . . . Rothan, C. (2012, February). Genetic dissection of fruit quality traits In the octoploid cultivated strawberry. Presented at VII International strawberry symposium. Beijing, China.
[Conference Oral Presentation]Authored by: Vignes, M.
Fouche, M., Denoyes, B., Rothan, C., Vignes, M., Mangin, B., Petit, A., . . . Villatoro, C. (2012). The role of MYB factor in fruit strawberry color. Poster session presented at the meeting of Sixth Rosaceous Genomics Conference. Mezzocorona, Italy
[Conference Poster]Authored by: Vignes, M.
Dupuy, L., & Vignes, M. (2010). Simplified root architectural models using continuous deformable domains. Plant Growth Modeling, Simulation, Visualization and Applications, Proceedings - PMA09. (pp. 142 - 148).
[Conference Paper in Published Proceedings]Authored by: Vignes, M.
Blanchet, J., & Vignes, M. (2007). Combined expression data with missing values and gene interaction network analysis: A Markovian integrated approach. Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE. (pp. 366 - 373).
[Conference Paper in Published Proceedings]Authored by: Vignes, M.

Other

Champion, M., Picheny, V., & Vignes, M. (2017). GADAG R package (A Genetic Algorithm for Learning Directed Acyclic Graphs).
[Other]Contributed to by: Vignes, M.

Consultancy and Languages

Languages

  • English
    Last used: today
    Spoken ability: Excellent
    Written ability: Excellent
  • French
    Last used: today
    Spoken ability: Excellent
    Written ability: Excellent
  • German
    Last used: few years ago
    Spoken ability: Average
    Written ability: Average

Supervision and Teaching

Summary of Doctoral Supervision

Position Current Completed
Supervisor 1 0
Co-supervisor 1 0

Teaching

Papers taught: (at Massey)

  • 161.331 Biostatistics (with Geoff Jones)
  • 161.705 Statistical Inference (with Mark Bebbington)
  • 161.729 Topics in Applied Statistics (with Chris Jewell)

Old teaching:

  • Statistics and learning at SupAero (with Emmanuel Rachelson) and Probability (with Jeremie Bigot) at ISAE SupAero, Toulouse, France, 2012-2014.
  • Statistics: basics to advanced subjects to undergraduates in Biology or Economics (2002-2006), to PhD students and scientists from research institutes (2007-2008).
  • General mathematics: Algebra and Analysis to undergraduates in Mathematics and Physics (2003-2005).
  • General science courses to high-school pupils (2005-2006).

Student supervision:

  • Co-supervision of Magali Champion PhD (2011-2014, Universite Paul Sabatier Toulouse 3), "Contribution to the modelling and inference of gene regulatory networks"

Current Doctoral Supervision

Supervisor of:

  • Olivia Angelin-Bonnet - Doctor of Philosophy
    Investigation of genotype and phenotype interactions using computational statistics

Co-supervisor of:

  • Luca Panizzi - Doctor of Philosophy
    Biomarker profiling of biologic fluids and tissues from horses with induced carpal osteoarthritis

Media and Links

Other Links

Massey Contact Centre Mon - Fri 8:30am to 5:00pm 0800 MASSEY (+64 6 350 5701) TXT 5222 contact@massey.ac.nz Web chat Staff Alumni News Māori @ Massey