Knowledge layer
Notes are your working memory: dated, contextual, full of detail. The Knowledge layer is what Graphium distills out of them — a personal wiki of short, editable pages that each state one reusable point and cite the notes they came from. This page explains the three kinds of knowledge, how to add notes to it, and how to browse, maintain, and trust what the AI builds.
Needs AI
The Knowledge layer runs only with an AI backend, which ships inside the desktop app, with at least one model registered. See AI setup. In the browser preview the Knowledge section shows an upgrade notice instead.
Notes vs. knowledge
A lab note answers "what happened on Tuesday". A knowledge page answers "what do I now know". Graphium keeps both, linked in one direction: every knowledge page ends with a References section whose Source: entries link back to the notes it was distilled from, so you can always drop back into the original context.
Because knowledge is derived, regeneration is normal. When your notes change, the pages built from them can be rebuilt — knowledge follows your notes, not the other way around.
The three kinds
Graphium's knowledge follows an hourglass: context-rich notes narrow into short general statements, which then connect back outward across your work — notes → claims → insights. The reasoning model behind this is documented in Inference types in Graphium.
| Kind | What it is |
|---|---|
| Summaries | A short AI summary of a single note |
| Claims | A grounded assertion extracted from your notes |
| Insights | A pattern that recurs across two or more claims |
Each kind carries a semantic type badge. Claims have a role (Finding, Decision, Anomaly, Question, Setup, Interpretation, Issue); insights have a pattern type (Causal, Mechanistic, Conditional, and so on).
Adding a note to knowledge
The main entry point is the Add to Knowledge chip in the note editor header (it also appears in the side peek and in the note's header menu). Click it and the AI reads the note, then writes a summary and extracts claims from it.
Progress appears in a toast at the corner of the screen — Generating Knowledge (1/3) — which you can collapse with Minimize and reopen with Show details. While it runs, the toast header also has a Stop button (■): it interrupts the in-flight AI call, keeps whatever already finished, and marks the rest Stopped — useful when a slow model turns out to be slower than you expected. When it finishes you'll see Done: 2 generated, and the chip flips to In Knowledge; clicking it now jumps to the generated entry. Running it again on an updated note regenerates the existing entries rather than duplicating them.
Other routes into knowledge:
| From | How |
|---|---|
| Note list | Select multiple notes, then Add 3 to Knowledge. A Knowledge column shows which notes are already in |
| Materials | Select URLs / PDFs in the gallery, then Add 3 to Knowledge; memos can be ingested directly too |
| AI chat | Make Knowledge on an answer (see below) |
The Composer (⌘K, Ctrl+K on Windows/Linux) | The Add this note to Knowledge suggestion card |
TIP
Ingestion is always something you trigger — Graphium never turns notes into knowledge behind your back. Skills marked Auto-apply on Ingest let you inject your own standing instructions (terminology, style) into every run.
Two built-in skills define the default writing voice (Japanese / English). When an app update ships an improved default, skills you never edited pick it up automatically. If you have edited one, an Update available badge appears in the skill list instead, and Reset to default replaces your version with the new content. Added in v0.30.0 (2026-08-09)
Prompts take trial and error, so skills support the same manual version snapshots as notes: while editing a skill, press ⌘⇧S or click Save version in the History tab to pin the current prompt, and use Restore this version on any saved version to switch the skill back to it. The restore itself is recorded in the edit history. Added in v0.30.0 (2026-08-09)
Browsing knowledge
The sidebar has a Knowledge section (collapsed by default) listing Summaries, Claims, and Insights with counts. Click a kind to open its list view, which offers:
- Columns: Title, Type, Sources (how many source notes), Refs out / Refs in, Model, Created, Modified, and World (latest world-grounding verdict)
- Search, per-column type filters, sorting, and drag-to-range multi-select
- Bulk actions on selected rows: Regenerate 3, Move 3 to trash, Check world (3)
Claims also show an evidence status: ?candidate (used in only 1 note) or ✓verified (used in 2+ notes). A claim that gets corroborated by a second independent note is promoted automatically, and its page shows a Corroborated badge.
Knowledge pages are editable notes
A knowledge page opens like any other note, and you can edit it like one. What makes it special is the banner at the top:
- Regenerate — rebuild the page from its current sources with your configured model
- Derived from — the page's provenance: source Notes, Source claims (for insights), and Related insights
- Check world — locate the statement against external knowledge (see World grounding)
- Epistemic status — how firmly the statement is grounded, from speculation to established
The body ends with a References section linking back to sources. Keep in mind that Regenerate rewrites the body from the sources — so make lasting corrections in the source notes where you can, and treat hand-edits to knowledge pages as provisional.
Log and Health
Two buttons at the bottom of the sidebar's Knowledge section open maintenance views:
- Log — an activity log of every knowledge operation (ingest, merge, cross-update, regenerate, delete), grouped by day, each entry linking to the affected page.
- Health — the Knowledge Health Check. Press Run Check and choose Quick (local only), which finds stale and orphaned entries without any LLM call, or Full (AI analysis), which also finds Contradiction, Gap, and Redundant issues. Each issue offers one-click fixes: Regenerate, Archive, or Open.
Discovering insights from claims
Insights are found by scanning claims for patterns that recur across two or more of them. This happens incrementally during ingestion, and you can run it across your whole corpus from Settings → Knowledge → Discover Insights from Claims → Discover Insights. Existing insights are sent to the model so duplicates aren't recreated — when a new claim supports an insight you already have, the insight is reinforced instead of duplicated.
Every scan reports how much it looked at Added in v0.45.0 (2026-08-25). Claims are scanned cluster by cluster, and the result reports the coverage it measured — covered n/m after an ingest, Claims in view: n/m in the corpus-wide run — meaning how many of your claims were in view at least once. So "no new insights" is never ambiguous: you can see whether the scan looked at everything and found nothing new, or simply hasn't reached the rest of your corpus yet. The corpus-wide run continues until every claim has been in view, and tells you up front how many LLM calls that takes; ingest-time scanning is capped by Scans per ingest in Settings → AI, so you decide what each ingest costs. If Insights are rare, the FAQ walks through how to tell whether it's your material or your model.
Bulk regeneration and re-embedding
The Settings → Knowledge tab holds corpus-wide maintenance:
| Tool | When to use it |
|---|---|
| Bulk regenerate Knowledge | After changing models — rebuild pages by kind (Target kinds), with an optional Model override (optional), progress display, cancel, and Retry failed only |
| Re-embed all Knowledge | When AI-chat citation search stops finding your knowledge — rebuilds the embeddings for every page |
Both show a confirmation with the count first; regeneration issues LLM calls and consumes tokens.
Saving chat findings as knowledge Added in v0.16.8 (2026-07-02)
When an AI chat answer contains something worth keeping, press Make Knowledge under the answer. Instead of saving the whole reply, Graphium proposes discrete candidates in a picker titled Knowledge candidates (select to save) — each with a Claims or Insights badge, a title, and a preview. Check the ones you want (or Select all) and press Save selected (2). Only what you pick enters your knowledge.
Knowledge in the global graph
Open Global Graph from the sidebar to see your whole workspace as three layers: Sources at the bottom, Notes in the middle, and Claim · Insight on top. Knowledge sits at the crystallized tip — you can watch clusters of notes funnel into a few claims and insights, and spot notes that haven't been distilled yet.
Provenance of knowledge Added in v0.17.3 (2026-07-13)
Knowledge is held to the same provenance standard as everything else in Graphium:
- Every page's Derived from panel and References section cite its sources; insights additionally record which claims they were lifted from.
- Growth events — ingest, merge, reinforcement, regeneration — are recorded as first-class activities in the page's history, so the history panel shows which sources fed each revision.
- Deleted pages go to the trash, and merged ones are archived rather than destroyed, so existing citations keep resolving.
You can also cite knowledge back into your notes: type / in the editor and pick Claims or Insights under the Existing knowledge group to insert references to existing pages (multi-select supported).