Co-occurrence & Matrix
Co-occurrence is a plain fact: two nodes appearing in the same note. The moment you write [[A]] and [[B]] together, they have co-occurred once.
The graph draws that as a line; the matrix lays it out as a grid — one dataset, two readings.
Connection Strength
A cell's depth is the strength of the relationship: how much of the time two concepts turn up together.
- Two concepts that always appear together → a deep cell
- Each appearing often, together rarely → a pale cell
The important part is that it measures what proportion of the time, not how many times. A pair appearing 100 times each and 5 times together comes out weak — those 5 were probably incidental. That is what makes cells comparable: a deep cell in a busy corner of your notes means the same thing as a deep cell anywhere else.
The colour language holds across the app: deeper blue = stronger, so moving between the matrix and the graph needs no relearning.
Reading the Structure
| What you see | What it means |
|---|---|
| Bright blocks on the diagonal | A cluster — these concepts all relate strongly; brackets mark its bounds |
| Bright cells between blocks | A bridge — a relationship joining two otherwise separate clusters |
| Largely empty rows/columns | Isolated nodes, barely co-occurring with anything |
Open a cell and the panel says whether the pair sits in the same cluster or different clusters. Strong cross-cluster relationships are often the most interesting — they join two lines of thought.
The High-Similarity Warning
The very strongest cells are flagged High Similarity in the warning colour. Overlap that heavy usually means one thing:
These may be two names for the same concept.
"User retention" and "retention rate", say. The right move there is usually not to link them but to merge the nodes.
Filtering the Noise Down
With many nodes the matrix turns to mush. The filter panel offers three dials:
| Filter | Use |
|---|---|
| Minimum co-occurrences | Pairs that co-occurred once are mostly incidental; 2 or 3 clears things up |
| Strength range | Raise the floor for strong relationships only, or lower the ceiling to hunt weak ones |
| By badge | Restrict to Core / Bridge / Emerging |
Using It
- Go to Node view and switch to Matrix (on iOS, the segmented capsule at the bottom toggles Graph / Matrix)
- Hover (macOS) or tap (iOS) a cell for that pair's details
- The panel also lists each node's strongest partners, so you can keep following the thread
When the matrix starts paying off
Patterns begin to surface at around 10 notes with backlinks — the more links, the clearer the structure. With Pro and a key, you can also have the AI explain what is behind a bright cell.
It Sees the Current Project Only
The matrix, the graph and the network summary all cover the currently selected project.
Next Steps
- Link Predictions — Pairs that never co-occurred but might belong together
- Knowledge Graph — The same data as a network
- AI Interpretation — Having the AI explain a strong relationship