ZB4199 Final Year Project:
Deep Learning and The Diffusion Partial Differential Equation from simulated data of Drosophila embryos.
The code repository for Python programmes used for the Final Year Project (FYP).
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Data_Generating_NoteBooks folder: Python notebooks to generate 2D datasets for DeepMod
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Diffusion_noisy.ipynb: Notebook to produce noisy 2D data for Diffusion
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Diffusion_clean.ipynb: Notebook to produce clean 2D data for Diffusion
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Diffusion_Decay_defaultBC.ipynb: Notebook to produce clean/noisy 2D data for Diffusion-Decay with default boundary condition as stated in the FYP thesis (sections 5.2.1 to 5.2.2 of thesis).
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Diffusion_Decay_bicoidSurge.ipynb: Notebook to produce clean/noisy 2D data for Diffusion-Decay with alternative boundary condition 1 as stated in the FYP thesis (section 5.2.3 of thesis).
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Diffusion_Decay_flux.ipynb: Notebook to produce clean/noisy 2D data for Diffusion-Decay with alternative boundary condition 2 as stated in the FYP thesis (section 5.2.3 of thesis).
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DeepMod_Training folder: Python programmes to train Deepmod algorithm
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deepmod_original.py: Software pipeline to load data to train DeepMod.
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gpu_util.py: Programme to search for GPU resources within MBI's computing infrastructure for Deep Learning.
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parameters.py: Programme containing DeepMod's neural network architecture and Deep/Machine Learning hyper-parameters.
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pde_util.py: Programme containing library of PDE terms for DeepMod and other relevant library parameters.
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result_util.py: Programme to store results after training DeepMod.
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Algorithm1.py: Python programme which contained an enhanced procedure of DeepMod's thresholding (section 5.3.1 of thesis).
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Figure31.png: Image of Figure 31 for section 6.1 of the FYP thesis.
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LR_expt folder: LR means Lasso Regression. Python notebook which discusses DeepMod's normalisation issues (section 5.3.2 of the thesis).
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LR_expts.ipynb: Demo for section 5.3.2 for the thesis.
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sparse_pattern_deepmod.npy: Bit mask generated by DeepMod.
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theta.npy: Theta matrix.
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time_deriv.npy: du_dt vector.
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- Python programming language version: 3.7.4.
- Tensorflow version: 1.14.0.
- Numpy version: 1.17.5.
- Scikit-learn version: 0.22.1.
- Pandas version: 1.0.0.
- DeepMod (written in Tensorflow, Python): https://github.com/PhIMaL/DeePyMoD.
Ho Wei Chin (National University of Singapore)
Tricia Loo, for the Forward-Time-Central-Space Python programme.
Gert-Jan Both et al, for their DeepMod algorithm.