MaMIClass

Classifying mammalian brains using supervised and unsupervised contrastive learning. Originally used for classifying MRI scans from the MaMI dataset (). See Mammalian_Brain_Classification.pdf for the full report.

Data Processing

To get access to the data, please contact me. To process the data using crop augmentations, run the cells under the "Data Processing" section in mami.ipynb. More specifically, the function process_raw_images should be used.

Training

All training should be run through main.py. For pretraining, pass the flag --mode pretraining, for finetuning - --mode finetuning. Furthermore, pass the flag --dir DIR to input a directory that contains the labels and processed data (default is "data"). The hyperparameters and all configuration for pretraining and finetuning are in config.py. Commented out are some example configurations that have been used in the project. For example:

python main.py --mode finetuning

Inference

For inference use inference.py. This file is responsible for outputing the losses graph, confusion matrix and latent space visualization. For example:

python inference.py checkpoint\fine_tune_epoch_10.pt

Trained models

Different model checkpoints are saved under checkpoint.

Models trained on 5 mammalian families:

• fine_tune_epoch_84_base.pth - A base model trained only on the MaMI data using cross entropy loss.
• fine_tune_epoch_83_pretrained.pth - Pretrained on data from BHB10K, NIMH and MultiRat_rest.
• fine_tune_epoch_77_pretrained_supcon.pth - Taking the pretrained model and training it on the MaMI data using SupCon loss, only then finetuning it using cross entropy loss.

Model trained on all 12 available mammalian families:

• fine_tune_epoch_199_all.pth - Trained in the same manner as pretrained + SupCon, using batch size 32 instead of 10 on the SupCon training stage.