Refactor ISIC fine-tuning code and restructure repo

.github/workflows/build-and-test.yml

@@ -0,0 +1,45 @@
+#
+# This source file is part of the ARPA-H CARE LLM project
+#
+# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md)
+#
+# SPDX-License-Identifier: MIT
+#
+
+name: Build and Test
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+  workflow_call:
+
+jobs:
+  pylint:
+    name: PyLint
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - name: Install Infrastructure
+        run: |
+          pip install -r requirements.txt
+          pip install pylint
+      - name: Analysing the code with pylint
+        run: |
+          pylint $(git ls-files '*.py')
+  black_lint:
+    name: Black Code Formatter Check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - name: Install Black
+        run: pip install black[jupyter]
+      - name: Check code formatting with Black
+        run: black . --exclude '\.ipynb$'

.github/workflows/pull_request.yml

@@ -0,0 +1,37 @@
+#
+# This source file is part of the ARPA-H CARE LLM project
+#
+# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md)
+#
+# SPDX-License-Identifier: MIT
+#
+
+name: Pull Request
+
+on:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  reuse_action:
+    name: REUSE Compliance Check
+    uses: DaneshjouLab/.github/.github/workflows/reuse.yml@main
+  markdown_link_check:
+    name: Markdown Link Check
+    uses: DaneshjouLab/.github/.github/workflows/markdown-link-check.yml@main
+  yamllint:
+    name: YAML Lint Check
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+
+      - name: Install yamllint
+        run: pip install yamllint
+
+      - name: Run yamllint with custom config
+        run: yamllint -c .yamllint .github/workflows/*.yml

README.md

@@ -0,0 +1,80 @@
+# Finetuning Pretrained Models for Compressed Dermatology Image Analysis
+
+This project explores how compressed and degraded dermatology images (from the ISIC 2019 dataset) affect classification performance using pretrained vision models. It compares fine-tuning vs. linear probing across multiple JPEG quality levels.
+
+## Project Goals
+
+- Evaluate model robustness to image compression (JPEG 90/50/20)
+- Compare pretrained models: ViT, DINOv2, and SimCLR
+- Benchmark fine-tuning vs. linear probing
+- Analyze FLOPs, GPU memory, and classification accuracy
+
+## Models
+
+- `ViT`: Vision Transformer from Hugging Face
+- `DINOv2`: Self-supervised ViT from Meta
+- `SimCLR`: Contrastive ResNet50 trained with linear classifier
+
+## Metrics Tracked
+
+- Accuracy, F1 Score, AUC
+- FLOPs (GFLOPs)
+- GPU memory usage
+- Training and evaluation time
+
+## Project Structure
+
+```
+CS231N/
+├── configs/                         
+│   └── example_config.yaml          # Configs for job submissions
+│
+├── scripts/                         # Lightweight utility or shell scripts
+│   ├── download_unpack_isic2019.sh  # Downloads and unpacks ISIC data
+│   └── submit_from_config.sh        # SLURM submission helper
+│
+├── jobs/                            # SLURM-related job definitions
+│   └── job_template.slurm
+│
+├── src/                             # Source code, logically grouped
+│   ├── __init__.py
+│   ├── finetune/                    # Fine-tuning workflows
+│   │   └── baseline_finetuning.py
+│   ├── evaluation/                  # Evaluation + plotting
+│   │   └── evaluate_isic_results.py
+│   └── models/                      # Model-related scripts
+│       ├── model_comparison.py      # Config file with constant strings
+│       ├── model_comparison.py
+│       └── model_comparison_2.py
+
+│
+├── results/                         # Auto-generated results
+│   ├── plots/                       # Accuracy/f1/AUC plots
+│   └── logs/                        # Training logs or SLURM outputs
+│
+├── requirements.txt
+├── .gitignore
+├── .github
+└── README.md   
+```
+
+## Quick Start
+
+1. Install requirements:
+   ```bash
+   pip install -r requirements.txt
+   ```
+
+2. Run training:
+   ```bash
+   python train_models.py
+   ```
+
+3. Run evaluation:
+   ```bash
+   python evaluate_isic_results.py
+   ```
+
+## 📦 Dataset
+
+- [ISIC 2019 (Hugging Face)](https://huggingface.co/datasets/MKZuziak/ISIC_2019_224)

requirements.txt.licence

@@ -0,0 +1 @@
+# MIT

submit_from_config.sh → scripts/submit_from_config.sh

@@ -39,7 +39,16 @@ for placeholder in "${!config_map[@]}"; do
   if [ -z "$value" ]; then
     echo "Warning: Config key '${config_map[$placeholder]}' is empty or missing"
   fi
-  sed -i '' "s|{{${placeholder}}}|${value}|g" "$JOB_FILE"
+
+  # Escape characters that might break sed (like slashes or ampersands)
+  value_escaped=$(printf '%s\n' "$value" | sed 's/[&/\]/\\&/g')
+
+  # Detect OS and use correct sed syntax
+  if [[ "$OSTYPE" == "darwin"* ]]; then
+      sed -i '' "s|{{${placeholder}}}|${value}|g" "$JOB_FILE"
+  else
+      sed -i "s|{{${placeholder}}}|${value}|g" "$JOB_FILE"
+  fi
 done
 
 # Submit the job