docs: update readme references and add modular trajectory harvester

.gitignore

@@ -47,6 +47,7 @@ wandb/
 .pytest_cache/
 .coverage
 htmlcov/
+tests/artifacts/
 
 # Streamlit
 .streamlit/

README.md

@@ -8,6 +8,8 @@
 
 DT-Circuits is a research framework for mechanistic interpretability of Decision Transformers, focused on causal analysis, sparse feature decomposition, and circuit-level understanding of sequential decision-making agents.
 
+**Live Interactive Demo:** [DT-Explorer on Hugging Face Spaces](https://huggingface.co/spaces/sadhumitha-s/DT-Explorer)
+
 ---
 
 ## Table of Contents
@@ -17,6 +19,7 @@ DT-Circuits is a research framework for mechanistic interpretability of Decision
 - [Project Structure](#project-structure)
 - [Installation and Usage](#installation-and-usage)
 - [Documentation](#documentation)
+- [Foundational Research & References](#foundational-research--references)
 - [Citation](#citation)
 - [License](#license)
 
@@ -167,49 +170,72 @@ sae:
 
 ---
 
-## Installation and Usage
+## Execution Modes: Installation and Usage
+
+There are two primary ways to run and interact with the **DT-Circuits** framework depending on your research needs:
+
+---
+
+### Way 1: Interactive Cloud Demo (Hugging Face Spaces)
+
+For instant visual exploration, path intervention, and alignment auditing without any local workspace preparation, launch the web dashboard directly:
+
+* **Demo Link:** [DT-Explorer on Hugging Face Spaces](https://huggingface.co/spaces/sadhumitha-s/DT-Explorer)
+
+> [!NOTE]
+> **Concise Demo Constraints:**
+> * **CPU-Bound Resources:** Runs on standard free-tier CPU instances (2 vCPUs, 16 GB RAM); high-overhead operations like ACDC scans may show higher latency than on a local GPU workspace.
+> * **Slices Dataset:** Trajectory datasets are dynamically sliced down to a lightweight demo set under a **10MB limit** (defined in [deploy.sh](file:///Users/sadhumitha/Documents/projects/DT-Circuits/scripts/deploy.sh#L19-L33)) for storage and memory footprint constraints.
+> * **Read-Only / Ephemeral Container:** Uses pre-baked static weights (`mini_dt.pt`) and pre-trained SAE checkpoints. Training new models or writing persistent states is disabled.
+
+---
+
+### Way 2: Clone and Run Locally (Full Pipeline)
+
+For full end-to-end research, customized hyperparameter tuning, local data harvesting, and GPU-accelerated model or SAE training, run the workspace on your machine.
 
-### Setup
+#### Local Environment Setup
+First, clone the repository, set up a virtual environment, and install dependencies:
 ```bash
+git clone https://github.com/sadhumitha-s/DT-Circuits
+cd DT-Circuits
+
 python -m venv venv
 source venv/bin/activate  
+
 pip install -r requirements.txt
 ```
 
-### Dashboard Execution
-You can access the hosted version on Hugging Face Spaces instantly, or run it locally:
+#### Option 2.1: Simple Workflows via Makefile
+The workspace includes a standardized [Makefile](file:///Users/sadhumitha/Documents/projects/DT-Circuits/Makefile) to orchestrate common research pipelines with single commands:
 
-* **Live Hosted Space:** [DT-Explorer Web App](https://sadhumitha-s-dt-explorer.hf.space) (No local installation needed!)
-* **Local Run:** Launch the dashboard on your machine (it will initialize with a random model if no trained weights are detected):
-  ```bash
-  streamlit run src/dashboard/app.py
-  ```
+```bash
+make setup      # Set up local environment & install requirements
+make train      # Run the full end-to-end pipeline (Data harvesting -> DT -> SAE training)
+make dashboard  # Run the Streamlit visualization dashboard locally
+```
 
-### Workflow
+#### Option 2.2: Granular Control via Bash & Python
+For research flexibility, execute each step of the pipeline manually using granular terminal scripts:
 
-1. **Data Harvesting & Model Training**
+1. **Trajectories & Model Training**
+   Harvest teacher trajectories and train the target Decision Transformer (`HookedDT`):
    ```bash
    python scripts/train_dt.py
    ```
 
-2. **SAE Training**
+2. **TopK Sparse Autoencoder (SAE) Training**
+   Train sparse autoencoders on target activation layers:
    ```bash
    python scripts/train_sae.py
    ```
 
-3. **Interpretability Analysis**
+3. **Interactive Analysis**
+   Launch the Streamlit visualization engine locally to run audits with custom weights:
    ```bash
    streamlit run src/dashboard/app.py
    ```
 
-### Alternative: Makefile
-Common tasks can also be executed via `make`:
-```bash
-make setup      # Install dependencies
-make train      # Run full training pipeline (DT + SAE)
-make dashboard  # Launch DT-Explorer
-```
-
 ---
 
 ## Documentation
@@ -222,6 +248,19 @@ Detailed technical documentation for specific modules:
 
 ---
 
+## Foundational Research & References
+
+This framework implements and builds upon the following foundational methodologies:
+
+*   **Decision Transformers**: [Chen et al., 2021](https://arxiv.org/abs/2106.01345) — Reinforcement learning as sequence modeling.
+*   **Transformer Circuits**: [Elhage et al., 2021](https://transformer-circuits.pub/2021/framework/index.html) — Mathematical foundations of mechanistic interpretability.
+*   **ACDC (Automated Circuit Discovery)**: [Conmy et al., 2023](https://arxiv.org/abs/2304.14997) — Algorithmic discovery of subgraphs.
+*   **Sparse Autoencoders (SAEs)**: [Bricken et al., 2023](https://transformer-circuits.pub/2023/monosemantic-features/index.html) (monosemantic features) & [Gao et al., 2024](https://arxiv.org/abs/2406.04096) (TopK SAEs).
+*   **Activation Steering**: [Turner et al., 2023](https://arxiv.org/abs/2308.10248) — Control via residual stream vector additions.
+*   **Path Patching**: [Goldowsky-Dill et al., 2023](https://arxiv.org/abs/2304.05969) — Inter-component causal mediation.
+
+---
+
 ## Citation
 
 ```bibtex

src/data/harvester.py

@@ -0,0 +1,64 @@
+import os
+import gymnasium as gym
+import torch
+import numpy as np
+from minigrid.wrappers import FlatObsWrapper
+from stable_baselines3 import PPO
+from tqdm import tqdm
+
+class PPOHarvester:
+    """
+    Utility to run a 'Teacher' PPO agent to collect high-quality state-action-reward triplets.
+    """
+    def __init__(self, env_id="MiniGrid-Empty-8x8-v0", model_path=None):
+        self.env_id = env_id
+        self.env = FlatObsWrapper(gym.make(env_id, render_mode="rgb_array"))
+        if model_path and os.path.exists(model_path):
+            self.model = PPO.load(model_path, env=self.env)
+        else:
+            print(f"No model found at {model_path}. Training a new one for collection...")
+            self.model = PPO("MlpPolicy", self.env, verbose=1)
+            self.model.learn(total_timesteps=20000)
+            if model_path:
+                self.model.save(model_path)
+
+    def collect_trajectories(self, num_episodes=100):
+        trajectories = []
+        for i in tqdm(range(num_episodes), desc="Collecting trajectories"):
+            obs, _ = self.env.reset(seed=42 + i)
+            done = False
+            truncated = False
+            episode = {
+                "observations": [],
+                "actions": [],
+                "rewards": [],
+                "dones": []
+            }
+            while not (done or truncated):
+                action, _states = self.model.predict(obs, deterministic=False)
+                next_obs, reward, done, truncated, info = self.env.step(action)
+                
+                episode["observations"].append(obs)
+                episode["actions"].append(action)
+                episode["rewards"].append(reward)
+                episode["dones"].append(done)
+                
+                obs = next_obs
+            
+            # Convert to numpy arrays
+            for key in episode:
+                episode[key] = np.array(episode[key])
+            
+            trajectories.append(episode)
+        
+        return trajectories
+
+    def save_trajectories(self, trajectories, file_path):
+        os.makedirs(os.path.dirname(file_path), exist_ok=True)
+        torch.save(trajectories, file_path)
+        print(f"Saved {len(trajectories)} trajectories to {file_path}")
+
+if __name__ == "__main__":
+    harvester = PPOHarvester(model_path="ppo_minigrid_teacher.zip")
+    trajs = harvester.collect_trajectories(num_episodes=50)
+    harvester.save_trajectories(trajs, "data/trajectories.pt")