Posts by Vara Lakshmi Bayanagari
Finalized experiments using both datasets: Week 12 & Week13
- 21 August 2023
Monai’s VQVAE results on T1-weighted NFBS dataset, 125 samples, for batch size of 5 were qualitatively and quantitatively superior to all previous results. I continued the same experiments on the T1-weighted CC359(Calgary-Campinas-359) public dataset consisting of 359 anatomical MRI volumes of healthy individuals. Preprocessed the data using existing transform_img function -
Carbonate issues, GPU availability, Tensorflow errors: Week 10 & Week 11
- 07 August 2023
Recently, I’ve been an assigned RP(Research Project) account on University of Bloomington’s HPC cluster - Carbonate. This account lets me access multiple GPUs for my experiments in a dedicated account.
VQVAE MONAI models & checkerboard artifacts: Week 8 & Week 9
- 24 July 2023
We observed in our previous results that the Diffusion Model’s performance may depend on better and effective latents from VQVAE. After playing around with convolutional & residual components in the existing architecture that yielded unsatisfactory results, we decided to move to a more proven model on 3D MRIs. It is not necessary that a model that worked well on MNIST dataset would also deliver similarly on 3D MRI datasets, owing to the differences in complexity of the data distributions. Changing the convolutions to 3D filters alone clearly did not do the job.
Diffusion Model results on pre-trained VQVAE latents of NFBS MRI Dataset: Week 6 & Week 7
- 10 July 2023
My current code for VQVAE & DM is well tested on MNIST dataset as shown in the previous blog posts. I extended the current codebase for MRI dataset by using 3D convolutions instead of 2D ones, which resulted in 600k parameters for VQVAE for a downsampling factor f=3. I used a preprocess function to transform MRI volumes to the desired shape (128,128,128,1) through DIPY’s reslice and scipy’s affine_transform functions, followed by MinMax normalization. I trained the VQVAE architecture for batch_size=10, Adam optimizer’s lr=2e-4, 100 epochs. I followed suit for downsampling factor f=2 as well and got the following training curves-
Carbonate Account Setup, Experiment, Debug and Repeat: Week 5
- 26 June 2023
I finally got my hands on IU’s HPC - Carbonate & Big Red 200. I quickly set up a virtual remote connection to Carbonate’s Slate on VS Code with Jong’s help. Later, I started looking up on Interactive jobs on Carbonate to have GPUs on the go for coding and testing. I spent a ton of time reading up on Carbonate’s Interactive SLURM jobs information. Using X11 forwarding, I was able to spin up an interactive job inside the login node using command prompt. It popped up a Firefox browser window from the login node ending up slow and not very user friendly. Same goes for the Big Red 200 as well. Eventually my efforts were in vain and I resorted to installing a jupyter notebook server on my home directory. Although I can’t request a GPU with this notebook, it allows me to debug syntax errors, output visualization, plotting loss values etc.
Diffusion research continues: Week 4
- 19 June 2023
As discussed last week, I completed researching on StableDiffusion(SD). Currently we’re looking for unconditional image reconstruction/denoising/generation using SD. I completed putting together keras implementation of unconditional SD. Since I couldn’t find an official implementation of unconditional SD code, I collated the DDPM diffusion model codebase, VQ-VAE codebase separately.
VQ-VAE results and study on Diffusion models : Week 3
- 12 June 2023
I continued my experiments with VQ-VAE on MNIST data to see the efficacy of the Prior training in the generated outputs. The output of the encoder for every input image delivers a categorical index of a latent vector for every pixel in the output. As discussed in the previous blog post, the Prior has been trained separately using PixelCNN (without any conditioning) in the latent space.
Deep Dive into VQ-VAE : Week 2
- 05 June 2023
This week I took a deep dive into VQ-VAE code. Here’s a little bit about VQ-VAE -
Community bonding and Project kickstart : Week 1
- 29 May 2023
Community Bonding period ended last week and my first blog is based on the work carried out in the last week. My meeting with GSOC mentors at the start of the week helped me chalk out an agenda for the week. As the first step, I familiarized myself with Tensorflow operations, functions and distribution strategies. My previous experience with PyTorch as well as website tutorials on basic Deep Learning models helped me quickly learn Tensorflow. As the next step, I read VQ-VAE paper & understood the tensorflow open source implementation. VQ-VAE addresses ‘posterior collapse’ seen in traditional VAEs and overcomes it by discretizing latent space. This in turn also improved the generative capability by producing less blurrier images than before. Familiarizing about VQ-VAE early on helps in understanding the latents used in Diffusion models in later steps. I also explored a potential dataset - IXI (T1 images) - and performed some exploratory data analysis, such as age & sex distribution. The images contain entire skull information, it may require brain extraction & registration. It maybe more useful to use existing preprocessed datasets & align them to a template. For next week, I’ll be conducting further literature survey on Diffusion models.
Journey of GSOC application & acceptance : Week 0
- 19 May 2023
While applying for the GSOC 2023 DIPY sub-project titled “Creating Synthetic MRI”, I knew this would be the right one for me for two reasons. Keep reading to know more!