SAI · Scientific AI

WikiMemory

How agents rediscovered an old medium for persistent scientific memory

Charles F. Vardeman II
Center for Research Computing, University of Notre Dame
August 31, 2026
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March 25 → April 4, 2026

A memory complaint became an agentic design pattern

KARPATHY · MAR 25Memory distractsan incidental question resurfaces as a permanent “interest”
ELVIS SARAVIA · MAR 25Use simple filesbut tune relevance, discovery, structure, and context
KARPATHY · APR 2–4Let an agent maintain a wikicompile sources, answer questions, file outputs, and lint

The surprise was not that a model could remember—it was that an agent could maintain external memory.

Karpathy on distracting memory · Elvis Saravia on methodical file-based memory · Karpathy, “LLM Knowledge Bases” · the “LLM Wiki” idea file.

The LLM Wiki · TL;DR

Compile knowledge once; improve the artifact over time

RAW /immutable sourcespapers · notes · transcripts · code
agent reads + integrates
WIKI /persistent synthesispages · links · contradictions · index
agent searches + traverses
WORKquestions + artifactsanswers feed back into the wiki
SCHEMA / AGENTS.mdInstructions define ingest, query, citation, maintenance, and linting.

Andrej Karpathy, “LLM Wiki” · Harrison Chase, “Wiki Memory”.

The continuity problem

Every model call begins now; science began long ago

Research advances by carrying evidence, failed attempts, critique, decisions, and learned procedures across people and time.

Models are episodic

The active context is powerful but temporary. A new call does not inherit a research history by default.

Science is cumulative

Claims gain meaning through sources, revisions, contradictions, methods, and negative results.

The system must bridge them

Continuity has to live somewhere inspectable outside the model invocation.

A longer history

WikiMemory is a convergence—not a sudden invention

Augment thoughtMemexNLS / Augmentread–write Web
Maintain shared knowledgeWikiWikiWebWikipedialiving wiki
Own a second brainpersonal wikiMarkdown vaultknowledge graph
Agentic WikiMemoryA model can now navigate, write, refactor, audit, and learn through the medium.

Our synthesis: three historical lineages converge in a harness-operable knowledge substrate.

1945 · associative memory

Bush imagined trails—not a better filing cabinet

The process of tying two items together is the important thing.

Vannevar Bush · As We May Think
EVIDENCEpaper
IDEAclaim
TENSIONconflict
NEXTquestion

Vannevar Bush, “As We May Think”, 1945.

1960s · augmented knowledge work

Hypertext was designed as a cognitive environment

Engelbart · NLS

Augment the whole workshop

Structured text, links, views, collaborative editing, tools, and working procedures formed one environment for improving knowledge work.

Nelson · Xanadu

Make relationships first-class

Hypertext, bidirectional links, versioning, transclusion, and visible provenance challenged the document as an isolated page.

Doug Engelbart Institute, NLS / Augment · Project Xanadu history.

March 1989 · Information Management: A Proposal

The Web began as a continuity problem at CERN

Tim Berners-Lee's 1989 circles-and-arrows diagram connecting linked information, hypertext, projects, documents, people, software, and CERN systems
Berners-Lee’s original “circles and arrows” map · converted from the W3C archival GIF.

People rotated through. Projects evolved. Information existed—but could not be found.

Turnoverexpertise and project history left with short-term staff
Entanglementreal work crossed the formal organizational hierarchy
Changebooks and trees became stale as dependencies shifted

The proposal was for evolving organizational memory—not merely online publishing.

Tim Berners-Lee, “Information Management: A Proposal”, March 1989 / May 1990 · original W3C diagram.

1989 · the proposed information model
NODES COULD BE
peopleprojectsconceptsdocumentssoftwarehardware
linked by
LINKS COULD MEAN
depends onpart ofmaderefers tousesexample of
remoteheterogeneousnon-centralizedconnect existing datamachine-analyzable

Before the Web had pages at planetary scale, its proposal described a flexible, distributed knowledge graph.

Berners-Lee, “Information Management: A Proposal,” 1989 · sections: Linked information systems · CERN Requirements · Data analysis.

1989 → 1999 · from links to relationships
UNTYPED WEB LINK
document— href →claim

Useful for navigation; the machine learns only “links to.”

NAMED RELATIONSHIP
paper— supports →claim

The predicate carries reusable intent.

ExplainHumans see whether a source supports, criticizes, defines, or depends on another page.
QueryAsk “what supports this claim?” instead of searching for pages that mention its words.
InferDirection and inverse relations expose dependencies, evidence paths, and affected neighbors.
GovernA shared predicate vocabulary can be documented, validated, linted, and evolved.

Dan Brickley, “Nodes and Arcs 1989–1999: The WWW Proposal and RDF: Then and Now” · informal W3C discussion, 1999.

1990 · WorldWideWeb implementation

The Web began as a read–write medium

humanreadwrite
WORLDWIDEWEB · 1990browser + editorfollow links · create pages · create links
sharedinformation space

Wikis did not invent read–write hypertext; they recovered an ambition the mainstream Web largely left behind.

1989 client/server proposal · W3C, “WorldWideWeb: the first web client” · Berners-Lee, “Realising the Full Potential of the Web”.

1995 · WikiWikiWeb

Wiki made knowledge maintenance a social process

Openreaders may repair
Incrementallink what is not written yet
Organicstructure grows with use
WIKIwrite · link · refactor
Observablechanges can be reviewed
Convergentduplication is reconciled
Mundanefew conventions suffice

Ward Cunningham, “Design Principles of Wiki”, WikiSym 2006.

2001 · wiki at social scale
EARLY WIKICamelCaselightweight page creation
FREE LINKS[[any phrase]]concepts become addressable
MEDIAWIKIhistory + watchlistsrevision becomes governable
namespacesbacklinksdiscussionrecent changesrevertmaintenance reports

MediaWiki history · Wikipedia launched in January 2001; double-bracket “free links” emerged in the early Wikipedia toolchain.

2001–2008 · file-native knowledge

Plain text became both prose and data

YAML · 2001human-readable structurestatus: contested
+
MARKDOWN · 2004readable source text## A claim
+
JEKYLL + GIT · 2008versioned content workflowdiff → review → publish
A note can be read as prose, queried as structure, reviewed as a change, and moved without losing its meaning.

YAML specification history · Gruber, “Introducing Markdown” · Preston-Werner, “Blogging Like a Hacker”.

2004–2020 · personal networked thought

The wiki became a personal knowledge graph

2004TiddlyWikipersonal nonlinear notebook
2019Roamnetworked thought + backlinks
2020Obsidianlocal Markdown + graph

PKM “knowledge graph”

Notes, backlinks, tags, graph views, and emergent associations.

Academic personal KG

Structured entities, attributes, and relations personally relevant to an individual.

The Story of TiddlyWiki · Roam Research · Obsidian · Balog & Kenter, 2019.

1950s–1990s · Zettelkasten

Luhmann built a network of arguments—not a filing system

ADDRESS1/1a2every note has a stable place
BRANCHinsert nearbyextend an argument without reorganizing it
REFERcross-linkconnect distant trains of thought

Entry points, not a master taxonomy

A selective keyword index and overview cards opened routes into the collection.

Serendipity by construction

Following references resurfaced ideas in new contexts and helped generate manuscripts.

Johannes F. K. Schmidt, “Niklas Luhmann’s Card Index” · “The Fabrication of Serendipity”.

Zettelkasten → personal knowledge graph

A digital PKG preserves the mechanics—not the furniture

Card-index mechanism
File-native implementation
Card + permanent slip address
Markdown note + stable filename, ID, or URI
Branch beside an existing thought
Link a note into the argument it extends
Cross-reference distant cards
[[wikilink]]—ideally with the reason for the relation
Keyword index + overview cards
Index notes, Maps of Content, properties, and queries
Separate bibliographic apparatus
Source notes with citation and provenance metadata
Re-encounter by following trails
Backlinks, local graph, search, and deliberate resurfacing

The graph view displays a network; the linking practice creates one worth traversing.

Niklas Luhmann Archive · Obsidian internal links.

The file-native substrate

Obsidian makes the substrate inspectable

pagesMarkdown files

Human-readable, local, portable, scriptable.

edges[[wikilinks]]

Cheap references, backlinks, and unfinished destinations.

schemaYAML properties

Types, status, dates, provenance, and controlled vocabulary.

viewsFolders + queries + graph

Hierarchy, indexes, neighborhoods, and task-specific projections.

The vault supplies the medium; linking and maintenance practices turn it into memory.

Obsidian internal links · Obsidian properties.

2026 · a new division of labour

The new actor is not another reader—it is a maintainer

PERSONAL WIKI

The human

writesfileslinksrefactorsreviews
AGENTIC WIKI

Human + agent

sourcecompilecross-linklintchallenge

WikiMemory is not a new storage idea. It is a new actor in an old medium.

The shift became widely visible through Karpathy’s “LLM Wiki”, April 2026.

Compiled memory

RAG retrieves fragments; WikiMemory preserves synthesis

RAG

Rediscover at query time

chunksretrieveanswer

Relationships assembled for one response usually disappear with it.

WikiMemory

Compile and maintain

sourceswikiwork

Entities, tensions, and cross-source synthesis become reusable structure.

Not a replacement: raw-source retrieval remains essential for evidence, verification, and details lost in compilation.

WiCER finds blind compilation can discard critical facts; one or two evaluate–refine iterations recover much of the lost quality.

Why wiki affordances matter

Structure turns a folder into an operable knowledge space

Stable identityA page gives a concept an address that agents and humans can revisit.
Traversable relationsLinks create explicit paths for search, context expansion, and synthesis.
Structured metadataProperties expose type, status, provenance, ownership, and lifecycle.
Hierarchical scopeFolders and indexes bound domains and support progressive disclosure.
RevisionDiffs and history make memory editable without becoming unaccountable.
Human legibilityThe same artifact can be inspected, challenged, and repaired directly.

Design synthesis. Plain links remain the navigation baseline; add typed predicates when the relation changes query, validation, explanation, or workflow.

Progressive disclosure

index.md turns hierarchy into a context budget

# Scientific WikiMemory
  • Claims
    Synthesized claims, evidence, and status.
  • Methods
    Procedures, assumptions, and validation.
  • Experiments
    Runs, outcomes, failures, and decisions.
  • Sources
    Papers, data, code, and conversations.
Surveysee the available scopes cheaply
Selectchoose a branch for the present task
Expandopen its index, then relevant pages
Groundreopen raw sources only when needed

Context grows with relevance—not with the size of the corpus.

Google Cloud, Open Knowledge Format v0.2, §8 “Index files”.

A maintained neighborhood

A WikiMemory document is a typed node—not an isolated page

SOURCE · PAPERpaper-17reported result
supports
CLAIMclaim-7contestable assertion
contradicts
EXPERIMENT · RUNrun-042conflicting result
motivates
OPEN QUESTIONquestion-3what changed?
revises
NEXT ACTION · RUNrun-043revised experiment
METHOD · PROTOCOLprotocol-03tests the runs under a declared procedure
CONCEPT NOTE · HUBCompilation gaporganizes meaning, scope, and navigation across the neighborhoodconcerns ↑ the highlighted trail
ASSERTION BOUNDARYClaims stay separateContestable assertions keep their own evidence, contradictions, maturity, and review lifecycle.

Design synthesis: typed note roles and edges make the inquiry path inspectable; the concept note coordinates the neighborhood rather than absorbing every assertion.

Claim-note zoom · illustrative fields

A claim note keeps maturity separate from epistemic status

---
type: claim
maturity: draft
epistemic_status: contested
creator: researcher-or-agent-id
context: inquiry/compilation-gap
supported_by: ["[[paper-17]]"]
contradicted_by: ["[[run-042]]"]
review_after: 2026-10-01
---
CLAIMCompiled knowledge reduces rediscovery.
EVIDENCEpaper-17 supports the claim under the reported study conditions.
TENSIONSrun-042 contradicts the expected effect in a new evaluation.
OPEN QUESTIONWhich omitted details explain the disagreement?
NEXT INQUIRYRevise the protocol, run run-043, then review this claim.

Maturity asks how developed the note is. Epistemic status asks how well the claim is currently supported.

Illustrative Obsidian-compatible claim note—not a canonical schema for llm-wiki-colab or every vault.

Agentic graph navigation · Markov analogy

The neighborhood is the transition space; the realized sequence is the trail

Harness externalization

The harness turns a writable vault into a memory system

MODELinterpret · propose · synthesize
HARNESSselect · authorize · validate · observe · rollback
MEMORYstate + knowledge
SKILLSreusable procedure
PROTOCOLSinteraction rules

Persistence is an externalized capability; reliability comes from how the harness governs it.

Zhou et al., “Externalization in LLM Agents” · “The Living Wiki” treats the vault schema as a procedural Skill.

Governed write · graph change set

A WikiMemory write changes a neighborhood—not just one file

01 · INTAKENew evidencepaper · data · run · conversation
02 · ORIENTDeduplicate + routefind the existing neighborhood and note role
03 · WRITECreate or revise typed notespreserve evidence and contestable claims
04 · INTEGRATEAdd typed + reciprocal linksrepair both sides of consequential relations
05 · COORDINATEUpdate concept · index · logkeep navigation and change history coherent
06 · VERIFYCheck provenance + structurescope · links · evidence · structure
07 · AUTHORIZEReview + commitapply the profile’s write and Git controls
08 · DERIVERebuild graph · permit rollbackwhen the profile defines derived RDF / SHACL
GENERIC · llm-wiki-colabGoverned wiki lifecycleorientation · explicit ingest skills · verification gate · index/log integration · Git coordination
SPECIALIZATION · VAULT /encodeStronger typed transactiontype routing · maturity + epistemic state · creator/context provenance · review · commit · RDF/SHACL rebuild

LA3D-LLM-Agents, llm-wiki-colab · Saboia Moreira et al., “Beyond Memory”.

Our implementation · typed edges

Readable predicates compile into an operable graph

AUTHOR IN ORDINARY MARKDOWN
Page-level · YAML
supports: "[[Claim-X]]"
dependsOn: "[[Dataset-Y]]"
Contextual · visible inline annotation
[Claim X](Claim-X)
([*supports*](Edge-Types#supports))
COMPILE + CHECK
Markdown + YAMLforward predicates + plain mentions
↓ extract
JSON-LD / RDFstable page and predicate IRIs
↓ materialize
Graph operationsinverse edges · SHACL · SPARQL
Evidencesource · supports · criticizes
Semanticsconcept · defines · related · mentions
Structureup · partOf · outOfScopeFor
Evolutionextends · precedes · incorporatedInto
DependencydependsOn · feedsInto · resolvedBy

Edge-Types.md vocabulary · KG build pipeline · forward predicates are authored; inverses are materialized.

Our implementation · executable methodology

Skills make scientific maintenance explicit

wiki-source

Integrate external evidence

Create a source summary, update the existing conceptual neighborhood, record typed relations, repair backlinks, and verify before commit.

wiki-experiment

File results honestly

Preserve configuration, measured metrics, comparison, surprise, negative results, affected claims, code paths, and commit identity.

wiki-lint

Maintain corpus integrity

Surface orphans, dead links, stale claims, missing metadata, one-way references, index gaps, and naming drift.

SUPPORTING SKILLSbootstrap: wiki-init · diagnose: wiki-doctor · collaborate: wiki-ask / wiki-enroll

Skills in llm-wiki-colab · each write procedure delegates to a shared Verification Gate.

Our implementation · LA3D-LLM-Agents

A federation keeps memory local—and expertise reachable

PROJECT AGENTrepo + wiki + Agent Cardsource of truth for one research domain
publish capability metadata
FEDERATION INDEXdiscover who knows whattopics · capabilities · contact
select + consult
PEER AGENTask · message · postcross-project collaboration through files

Share an honest capability description; consult the source wiki; avoid copying every project into private context.

LA3D LLM Agents organization profile · federation index.

Artifact federation · linked-data preview

One knowledge space, many artifacts

authoritative source object generated semantic projection discovery catalog
LIVE NOW · WEB ANNOTATIONPresentation AnnotationPageslide targets + learning context
OWNED WIKIMEMORY SOURCESConcept page + claim pagestable IRIs · typed relations · epistemic stategenerated JSON-LD / RDF view
PUBLICATIONDOI / articleCiTO relation
DATA OBJECTdataset / releaseidentifier · license
EXPERIMENTrun / immutable commitPROV-O lineage
TARGET · GENERATED PROJECTIONRepository manifestowner · scope · access · endpoints
TARGET · DISCOVERY LAYERFederation catalogfind identifiers—not copied corpora

Stable IRIs connect what each owner keeps authoritative; projections and catalogs carry links—not duplicate copies of every artifact.

Live now: this presentation’s AnnotationPage. Prospective: deployed WikiMemory manifests and a cross-project discovery catalog.

Web Annotation · PROV-O · SKOS · CiTO · DCMI Terms.

Agent traversal · FAIR preview
MARKOV-STYLE BRIDGE states resources·possible transitions typed links·policy signal task + evidence contextrealized trail the neighborhoods actually loaded
FAIR PREVIEW ALONG THE TRAIL
F · Findable manifests · catalog · stable IDs A · Accessible HTTPS / Git · access controls I · Interoperable JSON-LD · shared vocabularies R · Reusable provenance · versions · licenses · epistemic status

JSON-LD alone is not FAIR. Private knowledge stays private; shared semantics, access policy, provenance, licensing, and governance determine what can travel.

Wilkinson et al., FAIR Guiding Principles · W3C Data on the Web Best Practices · standards: Web Annotation · PROV-O · SKOS · CiTO · DCMI Terms.

A field crystallizes · 2026

Recent work is filling in different parts of the system

RepresentationKarpathyLiving Wikipersistent, linked, inspectable synthesis
CompilationWiCERDeepRefinediagnose loss; iteratively repair the artifact
NavigationLLM-WikiWikiLoopsearch, read, traverse, and learn from downstream use
ProvenanceTrajWikiBeyond Memorypreserve evolution, failures, and source-grounded revision
LearningWikiSkillskillscompile experience into reusable procedures

Chase, 2026 · WiCER · LLM-Wiki · WikiLoop · TrajWiki · Beyond Memory · WikiSkill.

Memory needs epistemology

An agent-maintained wiki can compound error, too

Weak sourceenters the corpus
Unsupported claimlooks more settled than its evidence
Concept synthesisdrops the qualification
Central pagegains links and apparent authority
Later agentsrepeat and reinforce it

Evidence

Claim-level provenance + explicit contradictory evidence.

State + review

Maturity ≠ epistemic status · scheduled re-examination.

Revision

Supersession + controlled writes preserve what changed and why.

Evaluation

Probes detect entrenchment; failed changes can roll back.

“Memory as Metabolism” highlights entrenchment and contradictory evidence · TrajWiki uses immutable snapshots plus ADD / REVISE / DEPRECATE operations.

From memory to learning

WikiSkill compiles experience into validated procedure

RAWexecution tracessuccesses + failures
WIKIpersistent patternsdiagnoses + history
SKILLScandidate procedureinstructions + resources
validate
acceptor rollback

Key result: persistent wiki knowledge materially improves skill evolution; accepted skills can transfer across models.

Tang et al., “WikiSkill: Compiling Agent Experience into Persistent Knowledge for Skill Evolution”, Google Research, Aug. 2026.

Scientific WikiMemory

Scientific memory must preserve why we believe—or doubt

RAW EVIDENCEpapers · data · code · runs · conversationsimmutable or independently recoverable
↑ grounded by
WIKI KNOWLEDGEclaims · entities · methods · tensions · provenancemaintained, linked, revisioned
↑ operationalized as
SCIENTIFIC PROCEDUREworkflows · checks · skills · decision protocolstested, gated, and inspectable

A scientific second brain should not only remember conclusions; it should preserve the routes by which conclusions remain contestable.

SAI research agenda

What would make WikiMemory scientifically trustworthy?

Representation

Which page types and relations earn their complexity?

Compilation

What is safe to synthesize—and what must remain raw?

Retrieval

When should an agent traverse the wiki or reopen evidence?

Maintenance

How do we detect staleness, contradiction, and conceptual drift?

Governance

Which writes are autonomous, reviewed, gated, or prohibited?

Evaluation

Does the system improve work without hiding failure?

Can an inspectable wiki become the shared memory substrate through which scientists and agents learn together?

SAI · Scientific AI