Aurora Agent MCP server

AURORA Agent (bioprism)

Query-compiled inference for executable biology.

Context engineering, with receipts.

An MCP server and CLI built on the FIBER decision-context compiler: a typed decision query is compiled into the smallest decision-sufficient evidence region, delivered with a Context Certificate stating exactly what was omitted.

Implementation of the AURORA BioPRISM / OncoWorld / FIBER blueprint (v0.6, 935 registered spec modules). A Rust workspace whose central idea is that context assembly is a compiler pass: instead of retrieval plus summarisation plus vibes-based compaction, a typed decision query is compiled into the smallest decision-sufficient evidence region, delivered as a Decision Section, and accompanied by a Context Certificate that states exactly what was omitted and whether the omission could have changed the decision.

Compile the smallest decision-sufficient evidence region. Never traverse the whole knowledge

structure by default.

What the measurements actually say

The reference world ships 761 facts, 750 of them exploratory distractors that all consume the same protected cohortid hub. FIBER compiles the query down to 11 facts (1.45% of the world)** and the deterministic oracle still returns the correct verdict with all four leakage witnesses.

It is not alone in doing so. Under equal tuning, a 5-hop incidence walk and a BM25 retriever at k=11 select exactly the same eleven facts. The distribution's own compare_baselines.py measures the graph baseline only at depth 7 and unbounded — the two settings where it returns everything — and reports a 69× advantage that vanishes under equal tuning. That is a strawman comparison, and correcting it is what 43.38 and 43.41 require.

So the reference world cannot tell these methods apart. crates/worldgen makes the structure a parameter and builds one that can — distractors attached near the target instead of at a hub leaf, decisive facts behind a relay chain, and distractor tags camouflaged to tokenise into the protected vocabulary:

Three distinct failure modes appear. The graph walk has no usable depth: 5–10 pull in 98% of the world and still miss every decisive witness; 11 is the first sound setting and by then it has taken everything. BM25 reaches the right verdict from a 91% protected closure — right by luck, having dropped a protected fact that happened not to matter, and raising k to 50 never recovers it. FIBER is the only admissible strategy: right verdict and full closure, at 11 facts.

That last failure is why the harness ranks on admissibility rather than verdict alone — ranking on verdict would have crowned the strategy that violated the mandatory closure and got away with it.

Shortened. The full README is on GitHub.