Yanjun Qi’s Selected Publications:                               Home                 (recent papers @ here )                       

 

Publications

·        Y. Qi, HK. Dhiman, N. Bhola, et al, Z. Bar-Joseph, J. Klein-Seetharaman, "Systematic prediction of human membrane receptor interactions" PROTEOMICS  2009 (SupportingWeb) (code / reference sets / features sets / predictions shared!)

  • Y. Qi, P. Kuksa, R. Collobert, 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, “Prediction of Interactions between HIV-1 and Human Proteins by Information Integration“, Pacific Symposium on Biocomputing 14: (PSB-2009) Jan. 2009 (Supplementary Web)

·        Y. Qi, Learning of Protein Interaction Networks. Ph.D. Dissertation (also CMU Technical Report: CMU-LTI-08-006), Carnegie Mellon University, School of Computer Science, May 2008 (PDF)

  • Y. Qi, F. Balem, C. Faloutsos, J. Klein-Seetharaman, Z. Bar-Joseph, “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)
  • L. Pena-Castillo, et al, Y. Qi, et al, F.P. Roth, “A Critical Assessment of M. Musculus Gene Function Prediction using Integrated Genomic Evidence”, Genome Biology 2008, 9(S1):S2, June 2008 (Online)
  • H. Nozawa, G. Howell, S. Suzuki, Q. Zhang, Y. Qi, J. Klein-Seetharaman, A. Wells, J.R. Grandis, S.M. Thomas, “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)
  • Y. Qi, J. Klein-Seetharaman, Z. Bar-Joseph, "A mixture of feature experts approach for protein-protein interaction prediction", BMC Bioinformatics 8 (S10):S6, 2007 (Online) (Supporting Web)(PDF)
  • Y. Qi, Z. Bar-Joseph, J. Klein-Seetharaman, "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)
  • Y. Qi, J. Klein-Seetharaman, Z. Bar-Joseph, "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, “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, “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, "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., “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,           "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. “Video Retrieval with the Informedia Digital Video Library System”, Proceedings of the Tenth Text Retrieval Conference (TREC-2001), Nov 2001

 

 

 

Published Abstracts

  • H.K. Dhiman, Y. Qi, A. Dutta, K. Tirupula, Z. Bar-Joseph and J. Klein-Seetharaman, "Validation of predicted protein-protein interaction partners of the EGFR", The 51st Annual Meeting of the Biophysical Society in Baltimore, Maryland, March 3-7, 2007. (Selected Oral Talk)
  • E. Gardner, Y. Tung, Y. Qi, N. Yanamala, K. Tirupula, D. Man, T. Reinhart, Z. Bar-Joseph and J.  Klein-Seetharaman, "Rhodopsin interacts with chemokines", The 51st Annual  Meeting of the Biophysical Society in Baltimore, Maryland, March 3-7, 2007. (Selected Oral Talk)
  • Y. Qi, Z. Bar-Joseph and J.  Klein-Seetharaman, “Predicting Protein-Protein Interactions from Labeled and Unlabeled Data”, the Cold Spring Harbor Meeting of Systems Biology: Genomics Approaches to Transcriptional Regulation, in CSHL, NY, March 4-7, 2004.

 

 

 

Invited Talks

  • Y. Qi, J. Klein-Seetharaman, Z. Bar-Joseph, " Predicting Protein-Protein Interactions from Multiple Biological Sources”, Biological Language Conference 2005. (BLC2005)
  • Y. Qi,  “Learning of Protein Interaction Networks”, Molecular Biophysics and Structural Biology Data and Literature Club, Sep. 2006

 

 

 

Reviewer for:  Bioinformatics, JMLR, PROTEINS, BMC Bioinformatics, ISBRA, NESCAI, ICML, ISMB, GIW, IEEE-TITB, IEEE-TCBB, PLOS, NIPS, NIPS-comBio-workshop, GHS, PSB, MachineLearning, Recomb

 

 

 

 

Some surveys: (I summarized before ), they might be useful to you

1.      Did a literature survey about semi-supervised learning in my IR-Lab course project (2004 Fall).

2.      Did a literature survey about imbalanced problems in classification in my IR-Lab project (2004 Fall).

3.      A brief introduction slide I summarized about Sampling Selection Bias topic.