1. JEREMY HADIDJOJO
(510)-604-5316 hjeremy@umich.edu
4485C Randall Lab, 450 Church St, Ann Arbor, MI 48109-1040
PROFILE
• Computational physics, expertise in mathematical modeling, simulation and data analysis
• Extensive experience in:
scientific programming (MATLAB, Python, C++, parallel/GPU/HPC computing)
machine learning (SVM, neural networks, clustering, regression analysis, decision trees, PCA)
interdisciplinary collaboration (biologists, mathematicians, computer scientists, engineers)
scientific communication across disciplines and to non-scientific audiences
• Passion in research, coding, validating algorithms for machine learning and data science
• Strong analytical skills, able to derive and understand complex math behind algorithms/models
• Passion in exploring new technologies, especially in machine learning/data science
EDUCATION
University of Michigan, Ann Arbor August 2011 – present
Ph.D. in Physics, GPA 3.8/4.0, graduating May 2017
Nanyang Technological University, Singapore 2007 – 2011
B.Sc. in Physics with first-class Honours, Minor in Mathematics, GPA: 4.8/5.0
PROGRAMMING SKILLS & PROJECTS
Advanced: MATLAB, Mathematica, C/C++
Intermediate: OpenMP, Python (NumPy, SciPy, TensorFlow, SciKit-Learn, Panda, Cython)
Beginner: Theano, Embedded programming (Arduino, STM32F4)
1. Deep Learning of handwritted digits (MATLAB, Python) 2016
Coded from scratch object-oriented convolutional network in MATLAB, tested with MNIST hand-
written digit data. Reaches 99.4% accuracy with Python + Theano (GPU computing)
2. Large-scale cell mechanics simulation (C++) 2012 – present
Physical simulation of 2D tissue capable of handling 10,000+ cells. Written in object-oriented C++
with 25,000+ lines of code using (1) GSL for ODE integration, (2) BLAS/LAPACK for fast linear
algebra, and (3) OpenMP for parallel computation. MATLAB used for pre/post-processing and GUI.
3. High-performace timeseries analysis (MATLAB, Python, C++) 2013 – present
Developed highly-optimized codes for fast timeseries correlation. First version is MATLAB (parallel,
GPU), and second is Python calling compiled C++ routines (parallel OpenMP).
RESEARCH EXPERIENCE
New mechanism of planar cell chirality 2012 – present
• Devised a new framework of generating planar cell chirality through protein interaction
Developed mathematical model (pen & paper, Mathematica), performed numerical anal-
ysis (MATLAB) and simulation (C++ with BLAS/LAPACK, OpenMP)
Pattern formation of retinal cone photoreceptors 2012 – present
• Uncovered mechanisms that made patterns in zebrafish retina (published in PLoS ONE 2014)
Developed physical model based on experimental data, performed statistical analyses and
numerical simulation, and made prediction based on model.
Statistical analysis of noisy timeseries cell trajectories 2013 – presentt
• Searched for non-trivial correlation and causality between large timeseries of cell movement

2. Analyzed big data (terabytes), applied advanced statistical methods and machine
learning (SVM, clutering, mean-shift)
PUBLICATIONS
Hadidjojo J, Salbreux G, Lubensky DK (2017) Spontaneous Chiral Symmetry Breaking in Planar
Polarized Epithelia, Physical Review Letters (in preparation)
Nagashima M, Hadidjojo J, Barthel LK, Lubensky DK, Raymond PA (2017) Anisotropic Glial Scaf-
folding Shapes a Multiplex Photoreceptor Mosaic in Zebrafish Retina, eLife (submitted)
Raymond PA, Hadidjojo J, et al. (2014) Patterning the Cone Mosaic Array in Zebrafish Retina
Requires Specification of Ultraviolet-Sensitive Cones, PLoS ONE
Hadidjojo J, Cheong SA (2011) Equal Graph Partitioning on Estimated Infection Network as an
Effective Epidemic Mitigation Measure, PLoS ONE
CONFERENCES AND WORKSHOPS
Big Data Image Processing & Analysis Workshop (UC Irvine) 2016
Americal Physical Society (APS) March Meeting 2016 2016
Contributed talk: Planar Cell Chirality (PCC) from spontaneous symmetry breaking
EMBO Multi-level Modeling of Morphogenesis Workshop (John Innes Centre, UK) 2015
AWARDS & FELLOWSHIPS
Physics Department Graduate Fellowship August 2013
Awarded to 3 students based on past research and academic performance
Norman E. and Mary E. Barnett Graduate Fellowship January 2012
Awarded to 1 student in early PhD based on past research and academic performance
Physics Department Graduate Fellowship August 2011
Awarded to select incoming graduate students with outstanding undergraduate work
RELEVANT CLASSES
EECS 545: Statistical Machine Learning Fall 2015
Mathematics 630: Applied Stochastic Processes (audit) Fall 2014
Complex Systems 541: Nonlinear Dynamics Fall 2012
Complex Systems 510: Intro to Adaptive Systems Fall 2012
Physics 510: Statistical Mechanics Fall 2011
Complex Systems 535: Network Theory Fall 2011
HOBBIES AND OTHER ACTIVITIES
Photography, drone/quadcopter building and flying, electronics (Arduino), DIY in general.
Current spare-time project: tinkering with TensorFlow and Hadoop.