Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add cyborg-garden/hermes-agent-mt --skill saelensgit clone --depth 1 https://github.com/cyborg-garden/hermes-agent-mtWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/cyborg-garden/hermes-agent-mt/saelens)<a href="https://agentmods.dev/skills/cyborg-garden/hermes-agent-mt/saelens"><img src="https://agentmods.dev/badge/skills/cyborg-garden/hermes-agent-mt/saelens/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/cyborg-garden/hermes-agent-mt/saelens"><img src="https://agentmods.dev/badge/skills/cyborg-garden/hermes-agent-mt/saelens.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00058 | $0.03290 |
| Opus 5 | $0.00029 | $0.01645 |
| Sonnet 5 | $0.00012 | $0.00658 |
| Haiku 4.5 | $0.00006 | $0.00329 |
Grade A, and why
sparse-autoencoder-training scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
This is a copy
92% identical to saelens — 110 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 391 lines — stays where its author put it; the contents beside it link to each section on GitHub.
SAELens: Sparse Autoencoders for Mechanistic Interpretability
SAELens is the primary library for training and analyzing Sparse Autoencoders (SAEs) - a technique for decomposing polysemantic neural network activations into sparse, interpretable features. Based on Anthropic's groundbreaking research on monosemanticity.
GitHub: jbloomAus/SAELens (1,100+ stars)
The Problem: Polysemanticity & Superposition
Individual neurons in neural networks are polysemantic - they activate in multiple, semantically distinct contexts. This happens because models use superposition to represent more features than they have neurons, making interpretability difficult.
SAEs solve this by decomposing dense activations into sparse, monosemantic features - typically only a small number of features activate for any given input, and each feature corresponds to an interpretable concept.
When to Use SAELens
Use SAELens when you need to:
- Discover interpretable features in model activations
- Understand what concepts a model has learned
- Study superposition and feature geometry
- Perform feature-based steering or ablation
- Analyze safety-relevant features (deception, bias, harmful content)
Consider alternatives when:
- You need basic activation analysis → Use TransformerLens directly
- You want causal intervention experiments → Use pyvene or TransformerLens
- You need production steering → Consider direct activation engineering
Installation
pip install sae-lens
Requirements: Python 3.10+, transformer-lens>=2.0.0
Core Concepts
What SAEs Learn
SAEs are trained to reconstruct model activations through a sparse bottleneck:
Input Activation → Encoder → Sparse Features → Decoder → Reconstructed Activation
(d_model) ↓ (d_sae >> d_model) ↓ (d_model)
sparsity reconstruction
penalty loss
What ships with it
3 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 9d ago First seen · 391 lines · 58 tokens per session scan A 2d9ffce4734c
sparse-autoencoder-training is a skill published in the GitHub repository cyborg-garden/hermes-agent-mt (13 stars, last pushed 4d ago), licensed MIT. It adds 58 tokens to every session and 3,290 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. It is 92% identical to saelens, differing in 110 lines, and is treated as a copy.
Other skills, from other repositories
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mnemosyne
Persistent cross-session memory via Mnemosyne — store, recall, and consolidate facts, preferences, and context.
tooluniverse-single-cell
Single-cell RNA-seq analysis with scanpy/anndata — h5ad data loading, scRNA-seq quality control and QC gating (ngenesbycounts, totalcounts, mitochondrial percent / pctcountsmt, pctcountsribo, doublet detection with Scrublet/scDblFinder, ambient RNA / SoupX awareness, empty-droplet filtering, MAD-based thresholds)…
tooluniverse-protein-sae-variant-interpretation
Interpret a missense variant via ESMC-6B Sparse Autoencoder (SAE) feature activations. For a given protein + variant, computes which interpretable SAE features (catalytic, ligand-binding, PTM, structural motif, domain, etc.) are lost or gained at the mutation site. Use when standard pathogenicity scores…
tooluniverse-protein-structure-prediction
Protein 3D structure prediction from sequence — ESMFold de novo prediction, AlphaFold database retrieval, experimental structures from RCSB, ProtVar variant impact assessment, ProtParam sequence properties. Use for structure prediction when no experimental structure exists, fold-confidence scoring, and…
tooluniverse-spatial-omics-analysis
Spatial multi-omics interpretation pipeline. Transforms spatially variable genes (SVGs), domain annotations, and tissue context into biological insights via domain-by-domain characterization, cell-type composition, spatial gene expression patterns, RNA+protein+metabolite integration. Use for Visium, MERFISH, seqFISH…