More specifically, we’re going to discuss how to build a knowledge base system inspired by Andrej Karpathy

One of the biggest problems with large language models is having to repeatedly upload and reprocess the same raw files over and over againLLMs waste huge amounts of tokens re-reading documents, lose context between files, sometimes miss important relationships, and often produce less accurate answers because of itKarpathy’s solution is the Wiki Layer (LLM Wiki)Don’t forget to bookmark this article so you can read it later or come back to it whenever you need itThe idea is simple, but incredibly powerful:The LLM cleans, structures, and links all of your data once, then stops working with raw files entirely and instead operates on a clean, organized knowledge baseAs a result, you get:

• massive token savings (up to 70-90% on repeated queries)
• significantly better answer quality and relevance
• automatic links between documents
• a visual knowledge graph
• a system that continuously grows and updates itself over time

The Structure of the Wiki Layer

The entire system is built around three core folders:

1. raw/ - immutable source files

This is where all original materials are stored: HTML pages, PDFs, text notes, screenshots, spreadsheets, and any other raw dataThis folder is never edited manually, it remains the single source of truth2. wiki/ - the main knowledge baseClean, well-structured Markdown files generated and maintained by the LLM itselfThis becomes the primary workspace the model interacts with going forward3. Instructions and templatesSeparate files that define all the rules: How data should be cleaned, which templates to use, how links are created, what metadata should be added, and how the knowledge base should be updated over time

Step-by-Step Guide to Building a Wiki Layer

1. Set Up the Project

Create a root project folder and place all your existing materials inside a raw/ subfolder2. Launch the Structuring AgentIn Claude (or any powerful LLM with file and code support), provide a dedicated system promptThe agent will automatically:

• clean files from technical junk, ads, and unnecessary formatting
• convert everything into clean, readable Markdown
• apply predefined templates
• create internal wiki links ([[Page_Name]])
• add metadata and establish relationships between documents

3. Open the Knowledge Base

in ObsidianSimply open the project folder in ObsidianYou’ll instantly get:

• a visual knowledge graph with automatic links
• powerful full-text search
• the ability to jump between connected notes in seconds

4. Work With the Finished Knowledge Base

Now, instead of uploading dozens of files every time, you simply tell the model: “Work with my Wiki database inside the wiki/ folder” The LLM can then instantly retrieve information from a clean, structured, and interconnected knowledge system

Why a Wiki Layer Is Better Than the Traditional Approach

• token efficiency - the model no longer has to repeatedly re-read raw files every time you ask a question
• higher accuracy - all information is already cleaned, structured, and interconnected
• scalability - the knowledge base can easily grow to hundreds or even thousands of documents
• better workflow - obsidian turns the entire system into a visual “second brain”
• privacy - everything stays on your local machine, nothing needs to be uploaded to the cloud

When You Should Start Using a Wiki Layer

• you already have more than 10-20 documents on the same topic
• your data is constantly being updated or expanded
• you regularly generate content, reports, research or ideas
• you work with personal, business, or confidential information

Adapting the System to Your Own Needs

The agent prompt is fully customizableInside the instruction files, you can define:

• which templates should be used for different document types
• which metadata fields are required (date, author, tags, summary, etc.)
• the rules for creating links between notes
• how the agent should handle updates and conflicts

This makes the Wiki Layer useful for almost any field: marketing, software development, learning, health, business analytics, and much more

Final Thoughts

Karpathy’s Wiki Layer transforms a chaotic collection of files into a true AI knowledge baseOnce you spend time setting it up, you get a powerful, constantly evolving system that dramatically improves both the quality and speed of working with any LLMIf you enjoyed this article or found it useful:

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