Mengfei Cao
 

Graduate Student
Dept. Computer Science
Tufts University
email: mcao01 [at] cs.tufts.edu

 


About Me | Research Interests | Papers | Presentations | Courses TAed | Awards | Links

About me:

Hello ^_^, I am a Ph.D (well, it feels quite good to omit the word "candidate" now). I am fortunate to be advised by Prof. Lenore J. Cowen.

I graduated from USTC with a B.E. (thesis advisor: Prof. Tianzi Jiang) in Electronic Engineering and Information Science and a dual B.A. (thesis advisor: Prof. Zun Wu) in Finance.

News!

  • (May 4th, 2015) I will move to Seattle this Summer for a machine learning scientist internship position in Amazon.
  • (Jan 22nd, 2015) Our paper "Clinical Vestibular Testing Assessed with Machine Learning Algorithms" is published in JAMA Otolaryngology-Head & Neck Surgery. See here for more details.
  • (July 15th, 2014) I presented our paper "New Directions for Diffusion-Based Network Prediction of Protein Function: Incorporating Pathways with Confidence" at ISMB 2014. See here for more details.
  • (April 9th, 2014) Our new DSD paper is conditionally accepted by ISMB 2014. See here for more details.
  • (Oct 23rd, 2013) Our DSD paper is published on PLoS ONE! See here for more details ^-^.
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    Research Interests:

    Conducting RESEARCH was an exciting experience to me and thus I am here to obtain more. Bio-informatics and machine learning are two fields I am involved the most, but to learn math and apply math should be more accurate definition of my work. The following are the topics I am interested in most recently:

  • metrics, applied in protein interaction networks
  • remote protein homology detection
  • template-free protein structure prediction

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    Papers:

  • When should we NOT transfer functional annotation between sequence paralogs? Pacific Symposium on Biocomputing (PSB), 2017
    Cao M, Cowen L
    supporting material

  • Designing Exit Frequency Distance Measures for Biological Networks. Abstract appears at SIAM workshop on Network Science, 2016 [pdf]
    Beveridge A, Cao M, Redlich A, Cowen L

  • Clinical Vestibular Testing Assessed with Machine Learning Algorithms. JAMA Otolaryngology-Head & Neck Surgery, Volume 141(4), 2015 [pdf]
    Priesol A, Cao M, Brodley C, Lewis R
    supporting material

  • New Directions for Diffusion-Based Network Prediction of Protein Function: Incorporating Pathways with Confidence. Bioinformatics, Volume 30(12), i219-i227, 2014 [pdf]
    Cao M, Pietras C.M, Feng X, Doroschak K, Schaffner T, Park J, Zhang H, Cowen L, Hescott B
    supporting website (a talk is given in International Conference on Intelligent Systems for Molecular Biology, July 2014)

  • Going the distance for protein function prediction. PLOS ONE, Volume 8, e76339, 2013 [pdf]
    Cao M, Zhang H, Daniels N, Park J, Crovella M, Cowen L, Hescott B
    supporting website (a poster is presented in Computational Aspects of Biological Information 2013 at Microsoft Research New England)

  • Remote homology detection on alpha-structural proteins using simulated evolution. In Proceeding ACM-BCB 2012 [pdf]
    Cao M and Cowen L
    supporting website (a talk is given in ACM-BCB 2012)

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    Presentations:

  • New Directions for Diffusion-Based Network Prediction of Protein Function: Incorporating Pathways with Confidence
    The 22nd Annual International Conference on Intelligent Systems for Molecular Biology 2014
  • Remote homology detection on alpha-structural proteins using simulated evolution
    The 5th ACM Conference on Bioinformatics, Computational Biology and Health Informatics 2012
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    Courses TAed:

  • COMP-135: Introduction to Machine Learning, Prof. Anselm Blumer, 2015 Spring
  • COMP-150: Advanced Topics in Machine Learning: Reinforcement Learning & COMP-135, Prof. Roni Khardon, 2014 Fall
  • COMP-170: Computation Theory, Prof. Anselm Blumer, 2014 Spring & 2013 Spring
  • COMP-15: Data Structures, Prof. Donna Slonim, 2011 Spring
  • COMP-11: Introduction to Computer Science, Prof. Benjamin Hescott, 2010 Fall
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    Awards:

  • 2014    ISCB Student Travel Fellowship Award
  • 2012    ACM-BCB Student Travel Grant
  • 2009    Excellent Undergraudate Research Award of USTC, "Correspondence Matching in Images Using Spectral Clustering"
  • 2009    First Prize of China Undergraduate Mathematical Competition
  • 2006    Hunan Provincial San Hao Student
  • 2004    First Prize in High School Student Mathmatical Competition
  • -1999  Several Prizes in National Chinese Calligraphy Contest
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    Links

  • Tufts BCB group website
  • Prof. Jinbo Xu, who I worked with as a Summer intern in 2013.
  • Graduate coursework: 2010 Fall, 2011 Spring, 2011 Fall, 2012, 2013, 2014
  • Sources
  • Photos: Chinese calligraphy, travelling
  • Anand Louis, my friend, who I built this site from.
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    Site last updated: Sept 30th, 2016 (More description of my projects with figures will be posted)