Code

Matlab Code for Gene Expression modeling with counting grids (Code by Pietro Lovato): link
Related papers:
  • P. Lovato, M. Bicego, M. Kesa, N. Jojic, V. Murino, A. Perina: "Traveling on discrete embeddings of gene expression", Artificial Intelligence in Medicine, vol. 70, pp. 1-11, (2016)
  • A. Perina, M. Kesa, M. Bicego: "Expression Microarray data classification using Counting Grids and Fisher Kernel", Proc. Int. Conf on Pattern Recognition (ICPR2014), 1770-1775, (2014)
  • P. Lovato, M. Bicego, M. Cristani, N. Jojic, A. Perina: "Feature selection using Counting Grids: application to microarray data", Proc. Int. Workshop on Statistical Techniques in Pattern Recognition (SPR2012), (2012)
  • Matlab Code for the multimodal approach for Protein Remote Homology Detection (Code by Pietro Lovato): download
    Related papers:
  • P. Lovato, A. Giorgetti, M. Bicego: "A multimodal approach for protein remote homology detection", IEEE/ACM Transactions on Computational Biology and Bioinformatics, accepted, (2015)
  • P. Lovato, A. Giorgetti, M. Bicego: "A multimodal approach to protein remote homology detection", poster at the European Conference on Computational Biology (ECCB2014), (2014)
  • Matlab Code for the Componential Counting grid model (Code by Alessandro Perina): download
    Related paper:
  • A. Perina, N. Jojic, M. Bicego, A. Truski: "Documents as multiple overlapping windows into grids of counts", Proc. Advances in Neural Information Processing Systems (NIPS2013), (2013)
  • NOTE: You may be interested also in the code of the Counting Grid Model (N. Jojic, A. Perina: "Multidimensional counting grids: Inferring word order from disordered bags of words", UAI 2011): download

    Matlab Code for the Bag of Peaks Representation for NMR spectrometry: download
    Related papers:
  • G. Brelstaff, M. Bicego, N. Culeddu, M. Chessa: "Bag of Peaks: interpretation of NMR spectrometry", Bioinformatics, vol. 25, pp 258-264, (2009)
  • M. Bicego, G. Brelstaff, N. Culeddu, M. Chessa: "Bag of Peaks: Interpretation of NMR Spectroscopy", poster at the 7th European Conference on Computational Biology, (2008)
  • Matlab Code for Gene Expression classification with topic models and IT kernels (Code by Pietro Lovato): link
    Related papers:
  • M. Bicego, P. Lovato, A. Perina, M. Fasoli, M. Delledonne, M. Pezzotti, A. Polverari, V. Murino: "Investigating topic models' capabilities in expression microarray data classification", IEEE/ACM Trans. on Computational Biology and Bioinformatics, vol. 9(6), pp. 1831-1836, (2012)
  • M. Bicego, P. Lovato, B. Oliboni, A. Perina "Expression microarray classification using topic models", Proc. of ACM SAC - Bioinformatics and Computational Biology track (SAC-BIO2010), pp. 1516-1520, (2010)
  • Matlab Code for C-link, a hierarchical Clustering Approach to large-scale Coalition Formation: download
    Related paper:
  • A. Farinelli, M. Bicego, S.D. Ramchurn, M. Zucchelli: "C-Link: A Hierarchical Clustering Approach to Large-scale Near-optimal Coalition Formation", Proc. Int. Joint Conf. on Artificial Intelligence (IJCAI2013), (2013)
  • Matlab Code for the Weighted One Class Support Vector Machine (version of Tax and Duin - SVDD): download
    Related paper:
  • M. Bicego, M.A.T. Figueiredo: "Soft Clustering using Weighted One Class Support Vector Machines", Pattern Recognition, vol. 42(1), pp. 27-32, (2009)
  • NOTE: You need to install the dd_tools library of David Tax

    Matlab Code for the Pruning Model Selection scheme for Hidden Markov Models: download
    Related paper:
  • M. Bicego, V. Murino, M.A.T. Figueiredo: "A sequential pruning strategy for the selection of the number of states in Hidden Markov Models". Pattern Recognition Letters , vol. 24(9-10), pp. 1395-1407, (2003).