Deduplication and symbol resolution

Parsing one file at a time only gets you halfway. A call to load_config() in app.py is useful only when it points at the load_config defined in config.py, and a concept your docs call “Auth Service” should be the same node as the one another doc calls “auth service”. Graphify Local does both before it writes the graph, and it labels how sure it is.

Read this page when you want to know whether to trust an edge, why two nodes merged, or why a call you expected isn’t in the graph.

How it works

Symbol resolution

Index

Every file’s definitions, imports, and exports are indexed with tree-sitter.

Resolve across files

Calls and references are matched to definitions through imports, re-exports, and language-specific passes (receiver types, qualified member calls, framework conventions). New languages plug in through a resolver registry.

Tag confidence

Each edge gets a tag, so you and your agent know what was read and what was worked out.

Tag	Meaning
`EXTRACTED`	Written explicitly in the source, such as an import or a method on a class.
`INFERRED`	Derived by resolution, such as a call matched to its definition through imports.
`AMBIGUOUS`	Several targets were possible. Kept, but down-weighted in clustering.

Resolution is conservative. When Graphify can’t tell which of several definitions a call means, it records an AMBIGUOUS edge or no edge, rather than guessing.

Deduplication

Entity deduplication runs on every build, before the graph is written:

Exact match

Labels are normalised (case, punctuation, Unicode marks) and identical ones merge.

Candidate pairs

MinHash with locality-sensitive hashing finds labels that might be the same, so Graphify never compares every pair.

Verify

Each candidate is scored with Jaro-Winkler similarity. Pairs in the same community get a 5-point bonus. A score of 92 or more merges.

Guard rails

Short labels only merge on a single-character typo, and labels that differ only in an embedded number (ADR 0011 and ADR 0012) never merge.

Rewire

Edges and hyperedges are moved to the surviving node. Genuine ID collisions across files stay separate and are reported.

See it in action

explain shows the tag on every connection:

graphify explain "APIRoute"

  --> RequestValidationError [uses] [INFERRED]
  --> Dependant [uses] [INFERRED]
  --> .get() [method] [EXTRACTED]
  <-- __init__.py [imports] [EXTRACTED]

Configure

To	Do this
Treat an extension as another language for resolution	Add `language.<ext>=...` to `.graphifyrc`.
Change how much `AMBIGUOUS` edges affect communities	Set `GRAPHIFY_AMBIGUOUS_SCALE` (`1.0` = full weight, `0` = ignore).
Check for edges collapsed between the same two nodes	Run `graphify diagnose multigraph`.

Verify and troubleshoot

Symptom	Fix
A call is missing	The target was probably ambiguous. Run `graphify explain` on the caller and look for `AMBIGUOUS` edges.
Two different things merged	Rename one label, or report it with both labels on GitHub.
Calls between repositories are missing	Merge the graphs. Cross-repository member calls are completed after merging. See Multiple repositories.

Does deduplication change code nodes?

Code symbols mostly have unique IDs from their file and name, so they rarely merge. Deduplication matters most for concepts pulled from docs and papers.

Can my agent rely on INFERRED edges?

Yes for navigation. For a change that must be correct, confirm the edge by opening the file and line the node points to.

Run it on a second repository

These examples come from a code-only graph of the open-source httpx repository, built with Graphify Local 0.9.97. Your counts will differ. The dedup step reports what it merged:

[graphify] Deduplicated 32 node(s) (28 exact, 4 fuzzy).
[graphify extract] wrote .../graphify-out/graph.json: 1883 nodes, 3960 edges, 106 communities

diagnose multigraph on the same graph found no edges collapsed between the same endpoints:

$ graphify diagnose multigraph
nodes: 1883
raw_edges: 3960
self_loop_edges: 5
exact_duplicate_edges: 0
directed_same_endpoint_collapsed_edges: 0
undirected_same_endpoint_collapsed_edges: 0
post_build_edges: 3960
note: normal graph.json is post-build; raw producer loss must be measured earlier.

FAQ

Can I see merges as JSON? Pass --json to diagnose multigraph, and --max-examples N to see more examples. Same name in two files? Those stay separate nodes. Commands such as explain report the ambiguity and list each ID, with exit code 3.

What’s next

Community detection

How resolved edges become communities.

Supported inputs

Languages and file types.

Try it in Graphify

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Features

Configuration

Support

Deduplication and symbol resolution

How it works

Symbol resolution

Deduplication

See it in action

Configure

Verify and troubleshoot

Run it on a second repository

FAQ

What’s next

Community detection

Supported inputs

Try it in Graphify

​How it works

​Symbol resolution

​Deduplication

​See it in action

​Configure

​Verify and troubleshoot

​Run it on a second repository

​FAQ

​What’s next

Community detection

Supported inputs

Try it in Graphify

How it works

Symbol resolution

Deduplication

See it in action

Configure

Verify and troubleshoot

Run it on a second repository

FAQ

What’s next