Daniel Haehn PRO
Hi, I am a biomedical imaging and visualization researcher who investigates how computational methods can accelerate biological and medical research.
2/7
2/21
2/28
5/22
Team Selection
Client Presentations
Project Proposal
Revised Project Proposal
Final Project Documentation
No class
No class
No class
Project Presentations
5/04
No class
Implementation / Testing / Deployment
29 Days
Full-Power
in the next 2 weeks
4/28 Project Status Meeting
Project Presentations
5/4
5/6
5/8
5/11
5/13
5/15
or?
5/22
Everything needs to be done
and you might have exams!
Bonus C++ Assignment (15% of final grade)
Bonus
100%
9
Training Data
Inference Phase
Testing Data
0 0 0
1 1 1
2 2 2
3 3 3
4 4 4
5 5 5
6 6 6
7 7 7
8 8 8
9 9 9
Training Phase
Learn weights to reduce loss!
Use weights from training to predict!
cat
Convolutional Neural Network
Original Dataset
CS410 Dataset
VGG19
Functions, Classes
Arrays, Vectors
Templates
GIBBS Cluster
Cython
Run our C++ code in Python using Cython
and compare timing against NumPy
Analyze a bunch of numbers and calculate min, max, mean, stddev.
Elastic Compute Cloud (EC2)
Start an Ubuntu Virtual Machine
SSH into it
Copy our Cython code over
Write and run tests to measure speed
pytest
pytest
$ pytest
=========================== test session starts ============================
platform linux -- Python 3.x.y, pytest-5.x.y, py-1.x.y, pluggy-0.x.y
cachedir: $PYTHON_PREFIX/.pytest_cache
rootdir: $REGENDOC_TMPDIR
collected 1 item
test_sample.py F [100%]
================================= FAILURES =================================
_______________________________ test_answer ________________________________
def test_answer():
> assert inc(3) == 5
E assert 4 == 5
E + where 4 = inc(3)
test_sample.py:6: AssertionError
========================= short test summary info ==========================
FAILED test_sample.py::test_answer - assert 4 == 5
============================ 1 failed in 0.12s =============================
# content of test_sample.py
def inc(x):
return x + 1
def test_answer():
assert inc(3) == 5
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
conda create --name CS410 python=3
conda activate CS410
conda install numpy
conda install cython
conda install pytest
python setup.py build_ext --inplace
Install Miniconda
Setup Environment
Get C++/Cython code and compile
git clone https://github.com/haehn/cs410fullrun.git
By Daniel Haehn
Hi, I am a biomedical imaging and visualization researcher who investigates how computational methods can accelerate biological and medical research.