What's New: 

• I am co-organizing NIPS 2009 MLCB Workshop. We have an exciting program this year and invited three top researchers in the field. 

Selected Publications: 

• Y. Qi, HK. Dhiman, et al, Z. Bar-Joseph, J. Klein-Seetharaman,(2009) 
  "Systematic prediction of human membrane receptor interactions" (PROTEOMICS 2009 (Accepted) (SupportingWeb) (Impact Factor 5.479)
  


• Y. Qi, P. Kuksa, R. Collobert, K. Sadamasa, K. Kavukcuoglu, J. Weston,(2009)
  "Semi-Supervised Sequence Labeling with Self-Learned Feature" IEEE ICDM 2009 (regular paper acceptance rate: 9% = 70/786)
  


• Y. Qi, R. Collobert, P. Kuksa, K. Kavukcuoglu, J. Weston,(2009) 
  "Combining Labeled and Unlabeled Data for Word-Class Distribution" CIKM 2009  (short paper acceptance rate: 20% = (171 + 123)/847)
  


• O. Tastan, Y. Qi, J.G. Carbonell, J. Klein-Seetharaman, (2009);
  “Prediction of Interactions between HIV-1 and Human Proteins by Information Integration“, Pacific Symposium on Biocomputing 14: (PSB-2009 Jan. 2009 (Supplementary Web)
  


• B. Bai, J.Weston. D. Grangier, R. Collobert, K. Sadamasa, Y. Qi, C.  Cortes, M.  Mohri, (2009)
  "Polynomial Semantic Indexing", NIPS 2009(acceptance rate: 23% = 263/1105)


• B. Bai, J.Weston. D. Grangier, R. Collobert, K. Sadamasa, Y. Qi, O. Chapelle, Kilian Weinberger, (2009)
  "Supervised Semantic Indexing", CIKM 2009 (regular paper acceptance rate: 15% = 123/847)


• B. Bai, J.Weston. D. Grangier, R. Collobert, K. Sadamasa, Y. Qi, O. Chapelle, Kilian Weinberger, (2009)
  "Learning to Rank with (a Lot of) Word Features", the special issue on Learning to Rank of the Information Retrieval Journal.
  


• B. Bai, J.Weston. D. Grangier, R. Collobert, K. Sadamasa, Y. Qi, O. Chapelle, Kilian Weinberger,(2009)
  "Learning to Rank with Low Rank", SIGIR 09 workshop: Learning to Rank for Information Retrieval
  


• Y. Qi, (2008) Learning of Protein Interaction Networks. Ph.D. Dissertation (also CMU Technical Report: CMU-LTI-08-06), Carnegie MellonUniversity, School of Computer Science, May 2008 (PDF) (Dissertation Committee: Ziv Bar-Joseph, Judith Klein-Seetharaman, Christos Faloutsos, Jaime Carbonell, Baldo Oliva)
  


• Y. Qi, F. Balem, C. Faloutsos, J. Klein-Seetharaman, Z. Bar-Joseph, (2008)
  “Protein Complex Identification by Supervised Graph Clustering”, Bioinformatics 2008 24(13), i250-i268 (The 16th Annual International Conference Intelligent Systems for Molecular Biology (ISMB), July 2008, (>Online)(PDF)(Supplementary Web)(TalkSlide) (Impact Factor 4.328) (acceptance rate of ISMB08: 17% = 49/292)
  


• L. Pena-Castillo, et al, Y. Qi, et al, F.P. Roth,(2008)
  “A Critical Assessment of M. Musculus Gene Function Prediction using Integrated Genomic Evidence”, Genome Biology 2008, 9(S1):S2, June 2008 (Online) (Impact Factor 6.15)
  


• H. Nozawa,G. Howell, S. Suzuki, Q. Zhang, Y. Qi, J. Klein-Seetharaman, A. Wells, J.R. Grandis, S.M. Thomas,(2008)
  “Combined inhibition of PLCγ-1 and c-Src abrogates Epidermal Growth Factor Receptor-mediated head and neck squamous cell carcinoma invasion”, Clinical Cancer Research, 14:4336-43,  2008 (online) (Impact Factor 6.488)
  


• Y. Qi, J. Klein-Seetharaman, Z. Bar-Joseph, (2007)
  "A mixture of feature experts approach for protein-protein interaction prediction", BMC Bioinformatics 8 (S10):S6, 2007 (Online) (Supporting Web)(PDF) (Impact Factor 3.78)
  


• Y. Qi, Z. Bar-Joseph, J. Klein-Seetharaman,(2006) 
  "Evaluation of different biological data and computational classification methods for use in protein interaction prediction", PROTEINS: Structure, Function, and Bioinformatics. 63(3):490-500. 2006 (Online) (Supplementary Web) (PDF) (Impact Factor 3.39)
  


• Y. Qi, J. Klein-Seetharaman, Z. Bar-Joseph, (2005)
  "A mixture of experts approach for protein-protein interaction prediction", Proceedings of Neural Information Processing Systems (NIPS): The workshop on Computational Biology and the Analysis of Heterogeneous Data, Dec 2005. (PDF), (talk PDF).  (Supplementary Web)
  


• Y. Qi, J. Klein-Seetharaman, Z. Bar-Joseph, (2005)
  “Random Forest Similarity for Protein-Protein Interaction Prediction from Multiple source”, Pacific Symposium on Biocomputing 10: (PSB 2005) Jan. 2005. (Supplementary Web)(PDF)
  


• A.G. Hauptmann, J. Gao, R. Yan, Y. Qi and J. Yang, (2004)
  “Automated Analysis of Nursing Home Observations”, IEEE Pervasive Computing, Special Issue on Pervasive Computing for Successful Aging, 3(2):15-21, April-June, 2004 (PDF)
  


• Y.Qi, A.Hauptman, T. Liu, (2003)
  "Supervised Classification for Video Shot Segmentation",  Proceeding of 2003 IEEE International Conference on Multimedia & Expo (ICME 2003), July 2003, Baltimore MD, USA.  (PDF) (TalkSlide)
  


• Jin, R. ,Y. Qi, Hauptman,A.,(2002) 
  “Probabilistic Model for Camera Zoom Detection”, Proceedings of the sixteenth conference of the International Association for Pattern Recognition (ICPR 2002) Québec City, Canada August 11-15,2002 (PDF)
  


• Hauptmann, A., R.Yan, Y.Qi, Jin, R., M.Christel, M.Derthick,M.-Y.Chen, R.Baron, W.H.Lin, and T.D.Ng,(2002) 
  "Video Classification and Retrieval with the Informedia Digital Video Library System", the Eleventh Text Retrieval Conference (TREC-2002), Nov 2002 
  


• Hauptmann, A., Jin, R., N. Papernick, D. Ng, Y. Qi, Houghton, RThornton, S. (2001)  “
  Video Retrieval with the Informedia Digital Video Library System”, Proceedings of the Tenth Text Retrieval Conference (TREC-2001), Nov 2001