// AXRE ECOSYSTEM
A digital X-ray of clinical logic.
AXRE scans the reasoning behind every model output and renders it as structured, traceable evidence. These are the repositories that build it — extraction, graph, reasoning, atlas.
// REPOSITORIES
6 repositories- First stage
axre-extract
PrivateClinical NLP pipeline for axiomatic extraction. The first stage of the AXRE environment. axre-extract reads medical exam–style case vignettes and turns them into a typed, SNOMED CT / UMLS–grounded clinical hypergraph — every finding, anatomical site, procedure, medication, lab result, and candidate diagnosis, with negation, assertion status, and the relations between them. Each case is emitted as a sealed, self-contained hypergraph artifact (reasoner_input.json); downstream AXRE modules consume that artifact. ⚙️ Deterministic, not LLM-dependent — same input → same graph; the LLM is optional and off by default, contributing zero graph structure (concepts, relations, question types). 🔗 Typed predicate-logic hypergraphs — clinical facts as a queryable typed hypergraph artifact, not opaque embeddings or flat triples. 🩺 Grounded to UMLS/SNOMED — every concept resolved to a standard clinical CUI (MedCAT · SapBERT · SciSpaCy), not a free-text label. 🛑 Hard-fail, no silent degradation — a missing or degraded component aborts loudly and quarantines the case; it never emits a quietly corrupted graph. 🧱 Extraction ≠ inference — surface clinical facts only; diagnosis is left to downstream reasoning, never baked into the graph. 🔒 Answer-blind by construction — for exam-derived inputs the gold answer never enters the graph (structural firewall).
- information-extraction
- umls
- hypergraph
- entity-linking
- snomed-ct
- clinical-nlp
- concept-normalization
- biomedical-nlp
- medical-nlp
- gliner
Python · DockerfileUpdated 3 days ago - Extraction only
CaseGraph
Privatevignette2graph · clinical MCQ vignettes → UMLS-grounded typed hypergraphs (extraction only)
- python
- information-extraction
- knowledge-graph
- named-entity-recognition
- help-wanted
- umls
- hypergraph
- entity-linking
- snomed-ct
- predicate-logic
- medcat
- medical-qa
- scispacy
- typedb
- biomedical-nlp
- clinical-nlp
- concept-normalization
- medical-nlp
Python · DockerfileUpdated last week - Research phase
axre-reason
PrivateAXRE ecosystem module — research phase
Updated 3 days ago - Research phase
axre-graph
PrivateAXRE ecosystem module — research phase
Updated 3 days ago - Research phase
axre-atlas
PrivateAXRE ecosystem module — research phase
Updated 3 days ago - Org meta
.github
PrivateOrganization-level defaults and shared community health files for AXRE.
Updated 3 days ago