Add examples in the documentation

Author: sofiene-boutaj

docs/examples.md

@@ -0,0 +1,235 @@
+
+# Examples
+
+The general command format for running a benchmark is:
+```bash
+thunder benchmark <MODEL> <DATASET> <TASK> [OPTIONS]
+```
+
+In the following examples, we illustrate how to use THUNDER through both the **command-line interface (CLI)** and the **Python API**.
+As example, we will use **Hoptimus1** as the model, **MHIST** as the classification dataset, and **PanNuke** for segmentation.
+
+---
+
+## 1. View Benchmark Help
+
+### **CLI**
+
+```bash
+thunder benchmark --help
+```
+
+---
+
+## 2. Download Datasets
+
+### **CLI**
+
+```bash
+thunder download-datasets mhist pannuke
+```
+
+---
+
+## 3. Generate Data Splits
+
+### **CLI**
+
+```bash
+thunder generate-data-splits pannuke mhist
+```
+
+---
+
+## 4. Download Pretrained Models
+
+### **CLI**
+
+```bash
+thunder download-models hoptimus1
+```
+
+---
+
+# Benchmarking Examples
+
+Below are examples for multiple tasks using the **Hoptimus1** model.
+
+---
+
+## Pre-computing Embeddings
+
+### **CLI**
+
+```bash
+thunder benchmark hoptimus1 mhist pre_computing_embeddings
+thunder benchmark hoptimus1 pannuke pre_computing_embeddings
+
+```
+
+### **API**
+
+```python
+from thunder import benchmark
+
+benchmark(
+    "hoptimus1",
+    dataset="mhist",
+    task="pre_computing_embeddings",
+)
+
+benchmark(
+    "hoptimus1",
+    dataset="pannuke",
+    task="pre_computing_embeddings",
+)
+```
+
+---
+
+## 6. K-NN Classification
+
+### **CLI**
+
+```bash
+thunder benchmark hoptimus1 mhist knn
+```
+
+### **API**
+
+```python
+from thunder import benchmark
+
+benchmark(
+    "hoptimus1",
+    dataset="mhist",
+    task="knn",
+)
+```
+
+---
+
+## 7. Linear Probing
+
+Using pre-loaded embeddings.
+
+### **CLI**
+
+```bash
+thunder benchmark hoptimus1 mhist linear_probing --loading-mode=embedding_pre_loading
+```
+
+### **API**
+
+```python
+from thunder import benchmark
+
+benchmark(
+    "hoptimus1",
+    dataset="mhist",
+    task="linear_probing",
+    loading_mode="embedding_pre_loading",
+)
+```
+
+---
+
+## 8. Segmentation (PanNuke)
+
+### **CLI**
+
+```bash
+thunder benchmark hoptimus1 pannuke segmentation --loading-mode=embedding_pre_loading
+```
+
+### **API**
+
+```python
+from thunder import benchmark
+
+benchmark(
+    "hoptimus1",
+    dataset="pannuke",
+    task="segmentation",
+    loading_mode="embedding_pre_loading",
+)
+```
+
+---
+
+## 9. SimpleShot Classification
+
+### **CLI**
+
+```bash
+thunder benchmark hoptimus1 mhist simple_shot --loading-mode=embedding_pre_loading
+```
+
+### **API**
+
+```python
+from thunder import benchmark
+
+benchmark(
+    "hoptimus1",
+    dataset="mhist",
+    task="simple_shot",
+    loading_mode="embedding_pre_loading",
+)
+```
+
+---
+
+## 10. Transformation Invariance
+
+### **CLI**
+
+```bash
+thunder benchmark hoptimus1 mhist transformation_invariance
+```
+
+### **API**
+
+```python
+from thunder import benchmark
+
+benchmark(
+    "hoptimus1",
+    dataset="mhist",
+    task="transformation_invariance",
+)
+```
+
+---
+
+## 11. Adversarial Attack Robustness
+
+### **CLI**
+
+```bash
+thunder benchmark hoptimus1 mhist adversarial_attack
+```
+
+### **API**
+
+```python
+from thunder import benchmark
+
+benchmark(
+    "hoptimus1",
+    dataset="mhist",
+    task="adversarial_attack",
+)
+```
+
+---
+
+# 12. Results Summary
+
+### **CLI**
+
+To display all collected benchmark results, simply run the command below after your experiments have finished.
+
+```bash
+thunder results-summary
+```

mkdocs.yml

@@ -23,6 +23,7 @@ nav:
   - Leaderboards: leaderboards.md
   - Tutorials:
     - Getting Started: getting_started.md
+    - Examples: examples.md
     - Benchmarking a Custom Model: custom_model.md
     - Benchmarking on a Custom Dataset: custom_dataset.md
     - Overriding Configurations: custom_config.md