MCPInstall

transformer-lens-interpretability

Provides guidance for mechanistic interpretability research using TransformerLens to inspect and manipulate transformer internals via HookPoints and activation caching. Use when reverse-engineering model algorithms, studying attention patterns, or performing activation patching experiments.

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Install

Works with every agent the skills CLI supports.

npx skills add https://github.com/orchestra-research/ai-research-skills --skill transformer-lens-interpretability
  1. 01

    Install

    Run the command in your project. The CLI asks which agents to install for.

  2. 02

    Describe the task

    Ask your agent for something this skill covers. It loads transformer-lens-interpretability automatically when relevant.

  3. 03

    Review the result

    The agent follows the SKILL.md steps, scripts and references bundled with the skill.

SKILL.md

The instructions your agent reads when the skill is triggered.

TransformerLens: Mechanistic Interpretability for Transformers

TransformerLens is the de facto standard library for mechanistic interpretability research on GPT-style language models. Created by Neel Nanda and maintained by Bryce Meyer, it provides clean interfaces to inspect and manipulate model internals via HookPoints on every activation.

GitHub: TransformerLensOrg/TransformerLens (2,900+ stars)

When to Use TransformerLens

Use TransformerLens when you need to:

  • Reverse-engineer algorithms learned during training
  • Perform activation patching / causal tracing experiments
  • Study attention patterns and information flow
  • Analyze circuits (e.g., induction heads, IOI circuit)
  • Cache and inspect intermediate activations
  • Apply direct logit attribution

Consider alternatives when:

  • You need to work with non-transformer architectures → Use nnsight or pyvene
  • You want to train/analyze Sparse Autoencoders → Use SAELens
  • You need remote execution on massive models → Use nnsight with NDIF
  • You want higher-level causal intervention abstractions → Use pyvene

Installation

pip install transformer-lens

For development version:

pip install git+https://github.com/TransformerLensOrg/TransformerLens

Core Concepts

HookedTransformer

The main class that wraps transformer models with HookPoints on every activation:

from transformer_lens import HookedTransformer

# Load a model
model = HookedTransformer.from_pretrained("gpt2-small")

# For gated models (LLaMA, Mistral)
import os
os.environ["HF_TOKEN"] = "your_token"
model = HookedTransformer.from_pretrained("meta-llama/Llama-2-7b-hf")

Supported Models (50+)

FamilyModels
GPT-2gpt2, gpt2-medium, gpt2-large, gpt2-xl
LLaMAllama-7b, llama-13b, llama-2-7b, llama-2-13b
EleutherAIpythia-70m to pythia-12b, gpt-neo, gpt-j-6b
Mistralmistral-7b, mixtral-8x7b
Othersphi, qwen, opt, gemma

Activation Caching

Run the model and cache all intermediate activations:

# Get all activations
tokens = model.to_tokens("The Eiffel Tower is in")
logits, cache = model.run_with_cache(tokens)

# Access specific activations
residual = cache["resid_post", 5]  # Layer 5 residual stream
attn_pattern = cache["pattern", 3]  # Layer 3 attention pattern
mlp_out = cache["mlp_out", 7]  # Layer 7 MLP output

# Filter which activations to cache (saves memory)
logits, cache = model.run_with_cache(
    tokens,
    names_filter=lambda name: "resid_post" in name
)

ActivationCache Keys

Key PatternShapeDescription
resid_pre, layer[batch, pos, d_model]Residual before attention
resid_mid, layer[batch, pos, d_model]Residual after attention
resid_post, layer[batch, pos, d_model]Residual after MLP
attn_out, layer[batch, pos, d_model]Attention output
mlp_out, layer[batch, pos, d_model]MLP output
pattern, layer[batch, head, q_pos, k_pos]Attention pattern (post-softmax)
q, layer[batch, pos, head, d_head]Query vectors
k, layer[batch, pos, head, d_head]Key vectors
v, layer[batch, pos, head, d_head]Value vectors

Workflow 1: Activation Patching (Causal Tracing)

Identify which activations causally affect model output by patching clean activations into corrupted runs.

Step-by-Step

from transformer_lens import HookedTransformer, patching
import torch

model = HookedTransformer.from_pretrained("gpt2-small")

# 1. Define clean and corrupted prompts
clean_prompt = "The Eiffel Tower is in the city of"
corrupted_prompt = "The Colosseum is in the city of"

clean_tokens = model.to_tokens(clean_prompt)
corrupted_tokens = model.to_tokens(corrupted_prompt)

# 2. Get clean activations
_, clean_cache = model.run_with_cache(clean_tokens)

# 3. Define metric (e.g., logit difference)
paris_token = model.to_single_token(" Paris")
rome_token = model.to_single_token(" Rome")

def metric(logits):
    return logits[0, -1, paris_token] - logits[0, -1, rome_token]

# 4. Patch each position and layer
results = torch.zeros(model.cfg.n_layers, clean_tokens.shape[1])

for layer in range(model.cfg.n_layers):
    for pos in range(clean_tokens.shape[1]):
        def patch_hook(activation, hook):
            activation[0, pos] = clean_cache[hook.name][0, pos]
            return activation

        patched_logits = model.run_with_hooks(
            corrupted_tokens,
            fwd_hooks=[(f"blocks.{layer}.hook_resid_post", patch_hook)]
        )
        results[layer, pos] = metric(patched_logits)

# 5. Visualize results (layer x position heatmap)

Checklist

  • Define clean and corrupted inputs that differ minimally
  • Choose metric that captures behavior difference
  • Cache clean activations
  • Systematically patch each (layer, position) combination
  • Visualize results as heatmap
  • Identify causal hotspots

Workflow 2: Circuit Analysis (Indirect Object Identification)

Replicate the IOI circuit discovery from "Interpretability in the Wild".

Step-by-Step

from transformer_lens import HookedTransformer
import torch

model = HookedTransformer.from_pretrained("gpt2-small")

# IOI task: "When John and Mary went to the store, Mary gave a bottle to"
# Model should predict "John" (indirect object)

prompt = "When John and Mary went to the store, Mary gave a bottle to"
tokens = model.to_tokens(prompt)

# 1. Get baseline logits
logits, cache = model.run_with_cache(tokens)

john_token = model.to_single_token(" John")
mary_token = model.to_single_token(" Mary")

# 2. Compute logit difference (IO - S)
logit_diff = logits[0, -1, john_token] - logits[0, -1, mary_token]
print(f"Logit difference: {logit_diff.item():.3f}")

# 3. Direct logit attribution by head
def get_head_contribution(layer, head):
    # Project head output to logits
    head_out = cache["z", layer][0, :, head, :]  # [pos, d_head]
    W_O = model.W_O[layer, head]  # [d_head, d_model]
    W_U = model.W_U  # [d_model, vocab]

    # Head contribution to logits at final position
    contribution = head_out[-1] @ W_O @ W_U
    return contribution[john_token] - contribution[mary_token]

# 4. Map all heads
head_contributions = torch.zeros(model.cfg.n_layers, model.cfg.n_heads)
for layer in range(model.cfg.n_layers):
    for head in range(model.cfg.n_heads):
        head_contributions[layer, head] = get_head_contribution(layer, head)

# 5. Identify top contributing heads (name movers, backup name movers)

Checklist

  • Set up task with clear IO/S tokens
  • Compute baseline logit difference
  • Decompose by attention head contributions
  • Identify key circuit components (name movers, S-inhibition, induction)
  • Validate with ablation experiments

Workflow 3: Induction Head Detection

Find induction heads that implement [A][B]...[A] → [B] pattern.

from transformer_lens import HookedTransformer
import torch

model = HookedTransformer.from_pretrained("gpt2-small")

# Create repeated sequence: [A][B][A] should predict [B]
repeated_tokens = torch.tensor([[1000, 2000, 1000]])  # Arbitrary tokens

_, cache = model.run_with_cache(repeated_tokens)

# Induction heads attend from final [A] back to first [B]
# Check attention from position 2 to position 1
induction_scores = torch.zeros(model.cfg.n_layers, model.cfg.n_heads)

for layer in range(model.cfg.n_layers):
    pattern = cache["pattern", layer][0]  # [head, q_pos, k_pos]
    # Attention from pos 2 to pos 1
    induction_scores[layer] = pattern[:, 2, 1]

# Heads with high scores are induction heads
top_heads = torch.topk(induction_scores.flatten(), k=5)

Common Issues & Solutions

Issue: Hooks persist after debugging

# WRONG: Old hooks remain active
model.run_with_hooks(tokens, fwd_hooks=[...])  # Debug, add new hooks
model.run_with_hooks(tokens, fwd_hooks=[...])  # Old hooks still there!

# RIGHT: Always reset hooks
model.reset_hooks()
model.run_with_hooks(tokens, fwd_hooks=[...])

Issue: Tokenization gotchas

# WRONG: Assuming consistent tokenization
model.to_tokens("Tim")  # Single token
model.to_tokens("Neel")  # Becomes "Ne" + "el" (two tokens!)

# RIGHT: Check tokenization explicitly
tokens = model.to_tokens("Neel", prepend_bos=False)
print(model.to_str_tokens(tokens))  # ['Ne', 'el']

Issue: LayerNorm ignored in analysis

# WRONG: Ignoring LayerNorm
pre_activation = residual @ model.W_in[layer]

# RIGHT: Include LayerNorm
ln_scale = model.blocks[layer].ln2.w
ln_out = model.blocks[layer].ln2(residual)
pre_activation = ln_out @ model.W_in[layer]

Issue: Memory explosion with large models

# Use selective caching
logits, cache = model.run_with_cache(
    tokens,
    names_filter=lambda n: "resid_post" in n or "pattern" in n,
    device="cpu"  # Cache on CPU
)

Key Classes Reference

ClassPurpose
HookedTransformerMain model wrapper with hooks
ActivationCacheDictionary-like cache of activations
HookedTransformerConfigModel configuration
FactoredMatrixEfficient factored matrix operations

Integration with SAELens

TransformerLens integrates with SAELens for Sparse Autoencoder analysis:

from transformer_lens import HookedTransformer
from sae_lens import SAE

model = HookedTransformer.from_pretrained("gpt2-small")
sae = SAE.from_pretrained("gpt2-small-res-jb", "blocks.8.hook_resid_pre")

# Run with SAE
tokens = model.to_tokens("Hello world")
_, cache = model.run_with_cache(tokens)
sae_acts = sae.encode(cache["resid_pre", 8])

Reference Documentation

For detailed API documentation, tutorials, and advanced usage, see the references/ folder:

FileContents
references/README.mdOverview and quick start guide
references/api.mdComplete API reference for HookedTransformer, ActivationCache, HookPoints
references/tutorials.mdStep-by-step tutorials for activation patching, circuit analysis, logit lens

External Resources

Tutorials

Papers

Official Documentation

Version Notes

  • v2.0: Removed HookedSAE (moved to SAELens)
  • v3.0 (alpha): TransformerBridge for loading any nn.Module

FAQ

What does the transformer-lens-interpretability skill do?

Provides guidance for mechanistic interpretability research using TransformerLens to inspect and manipulate transformer internals via HookPoints and activation caching. Use when reverse-engineering model algorithms, studying attention patterns, or performing activation patching experiments.

How do I install transformer-lens-interpretability?

Run npx skills add https://github.com/orchestra-research/ai-research-skills --skill transformer-lens-interpretability in your project. The skills CLI detects the agents you use and copies the skill into the right folder. For Claude Code you can also place the skill folder at ~/.claude/skills/transformer-lens-interpretability/ (personal) or .claude/skills/transformer-lens-interpretability/ (project).

Which AI agents can use transformer-lens-interpretability?

Any agent that supports the open Agent Skills format (a folder with a SKILL.md file), including Claude Code, Codex, Cursor, GitHub Copilot, Gemini CLI, Windsurf, Cline, OpenCode and more.

Is transformer-lens-interpretability safe to install?

No partner security audit is available yet. Skills can run commands and scripts, so read the SKILL.md and any bundled files before installing.

Who maintains transformer-lens-interpretability?

It is published by orchestra-research in orchestra-research/ai-research-skills. It has 959 recorded installs.

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