Mengfei Cao's Homepage

Mengfei Cao

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

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 4^th, 2015) I will move to Seattle this Summer for a machine learning scientist internship position in Amazon.

(Jan 22^nd, 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 15^th, 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 9^th, 2014) Our new DSD paper is conditionally accepted by ISMB 2014. See here for more details.

(Oct 23^rd, 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-167: Introduction to Computational Biology, Prof. Donna Slonim, 2016 Spring

COMP-86: Object-Oriented Programming for Graphical User Interface, Prof. Robert Jacob, 2015 Fall

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