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e419e45
Added gitignore file
retinotopyproject Oct 16, 2023
2d23cd1
Added python file and README stubs
retinotopyproject Oct 16, 2023
cfb7ce8
Fixed incorrect file import
retinotopyproject Oct 16, 2023
9f868fe
added file and readme stubs for 2D transformer
retinotopyproject Oct 22, 2023
a548211
implemented multi-head-attention class/module
retinotopyproject Oct 22, 2023
b38da5f
implemented Feed-Forward module/component
retinotopyproject Oct 22, 2023
1822bde
added class for combining FF and Attention modules
retinotopyproject Oct 22, 2023
003959f
added helper function for positional encoding
retinotopyproject Oct 22, 2023
16ad862
added ViT model implementation
retinotopyproject Oct 22, 2023
12ab005
added dataset/model saving dirs to gitignore
retinotopyproject Oct 22, 2023
6a22cc6
added dir to gitignore
retinotopyproject Oct 23, 2023
33c17fb
added ADNI dataset dir to gitignore
retinotopyproject Oct 23, 2023
a0e06c9
added basic class for ADNI dataset init
retinotopyproject Oct 23, 2023
cb4b793
changed ADNI data load to use ImageFolder (torch)
retinotopyproject Oct 23, 2023
0c14c94
added basic training code for benchmark dataset
retinotopyproject Oct 23, 2023
de1986b
Added testing for benchmark data (Imagenette)
retinotopyproject Oct 23, 2023
8032def
fixed bugs with matmul and einops formatting
retinotopyproject Oct 23, 2023
c232ef8
added patient-based stratified train-val split
retinotopyproject Oct 23, 2023
9c57aa5
removed some commented out code
retinotopyproject Oct 23, 2023
b99bdcc
changed train/test scripts to use ADNI dataset
retinotopyproject Oct 23, 2023
1020b17
added saving/output of basic model loss/metrics
retinotopyproject Oct 23, 2023
dfefe2f
modified docstrings in ViT modules
retinotopyproject Oct 24, 2023
74feab3
added opening PIL images, img transforms
retinotopyproject Oct 24, 2023
4eb1d47
fixed bugs with multiprocessing (Windows devices)
retinotopyproject Oct 24, 2023
af3a607
fixed issues with loading model/data for training
retinotopyproject Oct 24, 2023
9982e84
fixed more bugs with multiprocessing on Windows
retinotopyproject Oct 24, 2023
4d3bde5
added method for plotting ground truth images
retinotopyproject Oct 24, 2023
34365ec
saves predictions/empirical class values (testing)
retinotopyproject Oct 25, 2023
f5fb21a
saving of predicted & empirical classes (training)
retinotopyproject Oct 25, 2023
688d11a
added dependencies info to README
retinotopyproject Oct 25, 2023
4f5e36f
added training loss plotting
retinotopyproject Oct 25, 2023
e906308
fixed LR scheduler to step after each epoch
retinotopyproject Oct 25, 2023
93be092
minor refactoring/added number rounding in testing
retinotopyproject Oct 25, 2023
42c776a
added eval for validation set in training loop
retinotopyproject Oct 25, 2023
74cbf82
added plotting for validation set loss
retinotopyproject Oct 25, 2023
bc3098a
added dir to gitigore
retinotopyproject Oct 25, 2023
0b488f2
removed VQVAE files
retinotopyproject Oct 25, 2023
0a4a452
added train test split info to README
retinotopyproject Oct 26, 2023
d45511c
added train test split info to README
retinotopyproject Oct 26, 2023
ffd418d
added more preprocessing info to README
retinotopyproject Oct 26, 2023
8016a15
fixed bugs with dataset load; modifying comments
retinotopyproject Oct 26, 2023
a769a7a
fixed bugs with test set loading for predictions
retinotopyproject Oct 26, 2023
ed37c08
fixed bugs with train/val split & validation set
retinotopyproject Oct 26, 2023
575d830
added to examples & improvements sections (README)
retinotopyproject Oct 26, 2023
9d49fdd
added basic READMEs to subdirs
retinotopyproject Oct 26, 2023
e5e08d0
excluded READMEs from gitignore
retinotopyproject Oct 26, 2023
1e6e2cc
added validation accuracy plot
retinotopyproject Oct 26, 2023
5877dd3
modified comments/docstrings
retinotopyproject Oct 26, 2023
c1077b3
added model info, etc to README
retinotopyproject Oct 26, 2023
d8bc747
fixed issue with array elements not sent to cpu
retinotopyproject Oct 26, 2023
acf9ed8
fixed issue with incorrect validation accuracy
retinotopyproject Oct 26, 2023
fe7b59c
added reproducibility info, some results to README
retinotopyproject Oct 26, 2023
5eacdac
added confusion matrix plots for test set
retinotopyproject Oct 27, 2023
a6bb88a
added plot for precision-recall curve (test set)
retinotopyproject Oct 27, 2023
aa3ad35
removed precision-recall plotting method
retinotopyproject Oct 27, 2023
9fb287c
added more plots and results to readme
retinotopyproject Oct 27, 2023
336a505
minor tweaks/changes to train and test scripts
retinotopyproject Oct 27, 2023
a2aa69b
Merge branch 'topic-recognition' into topic-recognition
retinotopyproject Nov 21, 2023
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2 changes: 1 addition & 1 deletion .gitignore
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@@ -1,2 +1,2 @@

*.pyc
*.pyc
300 changes: 300 additions & 0 deletions recognition/TRANSFORMER_43909856/README.md

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422 changes: 422 additions & 0 deletions recognition/TRANSFORMER_43909856/dataset.py

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22 changes: 22 additions & 0 deletions recognition/TRANSFORMER_43909856/dataset/README.md
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# dataset:

The ADNI dataset should be placed in this directory.

To ensure that the model and dataset loading works correctly, the dataset should
be added such that it conforms to the following directory structure:

```
- dataset/:
- 'test/'
- 'AD/
- ...
- 'NC/'
- ...
- 'train/'
- 'AD/'
- ...
- 'NC/'
- ...
```

'...' represents the ADNI image JPEG files.
9 changes: 9 additions & 0 deletions recognition/TRANSFORMER_43909856/models/README.md
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# models

After model training has completed, the trained model will be saved to this directory location.

This location will also contain saved metrics for the train, validation, and test set performance.

These metrics include the train and validation loss throughout the training process,
the validation set accuracy, and the predictions and observed classes for the validation
and test set.
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