Deploy ENCODE backend (allowlisted runtime)

.dockerignore

@@ -0,0 +1,20 @@
+**
+!Dockerfile
+!README.md
+!src/
+!src/**
+src/frontend/demo/
+!artifacts/
+artifacts/**
+!artifacts/part_a_embeddings/
+!artifacts/part_a_embeddings/**
+!artifacts/part_a_canonical/
+!artifacts/part_a_canonical/canonical_phenotypes.jsonl
+!artifacts/part_a_canonical/code_descriptions.jsonl
+!artifacts/part_a_canonical/algorithm_components.jsonl
+!artifacts/part_a_canonical/cipher_links.jsonl
+!artifacts/part_a_canonical/med_ingredient_map.jsonl
+!artifacts/part_a_canonical/rxcui_ingredient_map.jsonl
+!artifacts/part_a_canonical/loinc_terms.jsonl
+!artifacts/vidul/
+!artifacts/vidul/**

.gitattributes

@@ -1,35 +1,5 @@
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-*.arrow filter=lfs diff=lfs merge=lfs -text
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+*.faiss filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
-*.zst filter=lfs diff=lfs merge=lfs -text
-*tfevents* filter=lfs diff=lfs merge=lfs -text
+artifacts/part_a_canonical/*.jsonl filter=lfs diff=lfs merge=lfs -text

Dockerfile

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+FROM python:3.12-slim
+
+RUN useradd -m -u 1000 user
+USER user
+
+ENV HOME=/home/user \
+    PATH=/home/user/.local/bin:$PATH \
+    PYTHONDONTWRITEBYTECODE=1 \
+    PYTHONUNBUFFERED=1 \
+    PIP_NO_CACHE_DIR=1 \
+    ENCODE_DEVICE=cpu \
+    ENCODE_VIDUL_ROOT=/home/user/app/artifacts/vidul \
+    ENCODE_PARTA_MODEL=/home/user/app/artifacts/vidul/BGE_FT_VA \
+    ENCODE_ANNOT_DIR=/tmp/encode-annotations \
+    OMP_NUM_THREADS=2 \
+    OPENBLAS_NUM_THREADS=2 \
+    MKL_NUM_THREADS=2 \
+    TOKENIZERS_PARALLELISM=false \
+    HF_HUB_DISABLE_TELEMETRY=1
+
+WORKDIR $HOME/app
+
+COPY --chown=user src/requirements.txt ./requirements.txt
+RUN python -m pip install --no-cache-dir --upgrade pip && \
+    python -m pip install --no-cache-dir \
+      --index-url https://download.pytorch.org/whl/cpu "torch==2.13.0" && \
+    python -m pip install --no-cache-dir -r requirements.txt
+
+COPY --chown=user artifacts/vidul ./artifacts/vidul
+
+COPY --chown=user src ./src
+COPY --chown=user artifacts/part_a_embeddings ./artifacts/part_a_embeddings
+COPY --chown=user artifacts/part_a_canonical ./artifacts/part_a_canonical
+
+EXPOSE 7860
+STOPSIGNAL SIGTERM
+
+HEALTHCHECK --interval=30s --timeout=3s --start-period=10s --retries=3 \
+    CMD python -c "import urllib.request; urllib.request.urlopen('http://127.0.0.1:7860/healthz', timeout=2).read()"
+
+CMD ["uvicorn", "src.backend.app:app", "--host", "0.0.0.0", "--port", "7860", "--workers", "1"]

README.md

@@ -1,10 +1,114 @@
 ---
-title: ENCODE
-emoji: ⚡
-colorFrom: purple
-colorTo: gray
+title: ENCODE Clinical Code Search
+emoji: 🩺
+colorFrom: blue
+colorTo: indigo
 sdk: docker
-pinned: false
+app_port: 7860
+suggested_hardware: cpu-basic
+startup_duration_timeout: 30m
+short_description: CPU clinical-code and phenotype retrieval with BGE_FT_VA
 ---
 
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+# ENCODE
+
+ENCODE is a CPU-only FastAPI application packaged as a Hugging Face Docker
+Space. The runtime uses Vidul's `BGE_FT_VA` weights and prebuilt dense indexes.
+
+The exact proposed fresh-history file set is listed in
+[COMMIT_CONTENTS.md](COMMIT_CONTENTS.md).
+
+## Current retrieval path
+
+- Medical-code search reproduces Vidul's original convention: mean pooling,
+  `passage: ` query prefix, normalized vectors, and exact FAISS inner-product
+  search. Diagnosis, medication, NDC, lab, and procedure indexes load lazily.
+- Phenotype discovery uses the same fine-tuned weights with the CLS-pooling
+  convention recorded beside its prebuilt metadata and code-evidence vectors.
+- Ranking is dense retrieval only. Canonical sidecars supply source-grounded
+  display metadata and do not change result order.
+
+## Medication mapping coverage
+
+The packaged RxNorm sidecars remain the first source for medication ingredient
+graphs. When a medication is missing there, ENCODE can supplement the graph
+from the public RxNAV/RxNorm API:
+
+- NDC package codes use RxNAV's NDC-status mapping.
+- VA-local drug results use RxNAV exact-or-normalized name matching only.
+- Ambiguous, approximate, unavailable, and failed lookups produce no graph
+  rather than a best-guess relationship.
+
+Every live graph identifies its source as `RxNAV / RxNorm live lookup`. Only the
+selected medication identifier or display name is sent to RxNAV; no patient or
+annotation data is sent there.
+
+## Repository contents
+
+```text
+Dockerfile                         CPU-only Space image
+src/backend/                      FastAPI and retrieval engines
+src/frontend/                     Static browser UI
+tests/                            Focused retrieval tests
+artifacts/part_a_embeddings/      Runtime phenotype vectors
+artifacts/part_a_canonical/       Runtime phenotype/detail records
+artifacts/vidul/                  Vidul model and original FAISS indexes
+```
+
+Raw VA inputs, source ZIP archives, LOINC/RxNorm archives, prior experiment
+outputs, model-training
+artifacts, profiling output, generated demos, retired scripts, and historical
+docs are intentionally excluded by `.gitignore`. Large runtime files are marked
+for Git LFS in `.gitattributes`.
+
+## Run locally
+
+```bash
+docker build -t encode-space .
+docker run --rm --memory=16g --cpus=2 -p 7860:7860 encode-space
+```
+
+Open <http://localhost:7860>. The readiness endpoint is
+<http://localhost:7860/healthz>.
+
+## Push to a Hugging Face Space
+
+Install Git LFS before staging the repository:
+
+```bash
+git lfs install
+git add -A
+git commit -m "Prepare ENCODE CPU Space"
+git remote add space https://huggingface.co/spaces/OWNER/SPACE_NAME
+git push space HEAD:main
+```
+
+Replace `OWNER/SPACE_NAME` with the target Space. Hugging Face reads the YAML
+metadata at the top of this file and exposes the container on port 7860. The
+image runs one Uvicorn worker so model and index memory are not duplicated.
+
+## Deploy the Netlify Drop frontend
+
+The static frontend uses same-origin `/api/*` requests. Netlify proxies those
+requests to the Hugging Face Space, so the browser does not need a separate CORS
+configuration. First deploy the backend and substitute its public origin below:
+
+```bash
+ENCODE_BACKEND_ORIGIN=https://OWNER-SPACE.hf.space \
+  sh deploy/netlify-build.sh --package dist/netlify
+```
+
+Drag the resulting `dist/netlify` folder into Netlify Drop. For a Netlify
+site connected to this repository, set `ENCODE_BACKEND_ORIGIN` to that same
+origin; `netlify.toml` runs the equivalent build automatically. The build
+rejects non-Hugging Face origins and packages redirects plus security headers.
+
+The Hugging Face container still serves the UI directly for local use and
+backwards compatibility; Netlify is the public static frontend in the split
+deployment.
+
+## Persistence
+
+Submitted annotations default to `/tmp/encode-annotations` and are ephemeral.
+For durable writes, attach a Hugging Face Storage Bucket at `/data` and set the
+Space variable `ENCODE_ANNOT_DIR=/data/annotations`.

artifacts/part_a_canonical/build_report.md

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+# ENCODE Part A Canonical Data Build Report
+
+Generated by `scripts/build_part_a_canonical.py`.
+
+## Inputs
+
+- `Data source/all_phenotypes.zip`
+- `Data source/VA_CDW_Code_dimensions_tables (1).zip`
+
+## Output Contract
+
+- Schema version: `encode_part_a_v1`
+- Canonical phenotype records: `canonical_phenotypes.jsonl`
+- Embedding documents: `embedding_documents.jsonl`
+- Embedding document chunk cap: 4000 characters
+
+## Profile
+
+- Phenotypes: 8013
+- Embedding documents: 36681
+- Missing phenotype descriptions: 1665
+- Missing algorithm descriptions: 0
+- CIPHER enum sidecar parsed cleanly: False
+
+## Embedding Documents By View
+
+- code_evidence: 28668
+- phenotype_metadata: 8013
+
+## Code Entries By Type
+
+- Healthcare Common Procedure Coding System (HCPCS): 3
+- ICD-10 Diagnostic Codes: 6468
+- ICD-10 Procedure Codes: 21
+- ICD-9 Diagnostic Codes: 5995
+- ICD-9 Procedure Codes: 25
+- Laboratory Tests: 235
+- Medications: 156
+- Observational Medical Outcomes Partnership (OMOP) Concept: 28
+- Other: 1690
+- SNOMED CT, US Edition: 276
+- Text snippets: 1802
+- VA Clinic Stop Codes: 44
+
+## Code Label Status
+
+- exact: 395795
+- label_missing: 10186
+- prefix_expanded: 86799
+- unsupported_code_system: 140337
+
+## Notes
+
+- `prefix_expanded` labels are retrieval evidence only; the original CIPHER code is preserved as provenance.
+- Unsupported medication/lab/SNOMED/OMOP/CUI labels remain explicit instead of being guessed.
+- The malformed enum sidecar should still be replaced for production use.

artifacts/part_a_canonical/canonical_phenotypes.jsonl

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artifacts/part_a_canonical/code_descriptions_report.md

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+# Code Description Resolution Report (professor feedback 1.1)
+
+Generated by `scripts/resolve_code_descriptions.py`. Sidecar: `code_descriptions.jsonl`.
+
+- Unsupported code occurrences in corpus: **140,337**
+- Distinct unsupported codes: **77,233**
+- Distinct codes resolved to a description: **4,756** (6%)
+
+## Resolved by source
+
+- `va_dim_exact`: 2,166
+- `cipher_name`: 2,108
+- `va_labname`: 482
+
+## Left unresolved (honest gaps)
+
+- `study_specific`: 66,856
+- `needs_vocab:OMOP`: 4,322
+- `needs_vocab:LOINC`: 806
+- `needs_vocab:VA_STOP`: 255
+- `needs_vocab:NDC`: 238
+
+## Notes
+
+- `va_dim_exact`: code matched a VA ICD/CPT dictionary (often a code CIPHER
+  filed under "Other").
+- `cipher_name`: Medication codes are the drug name itself (generic/brand).
+- `va_labname`: Lab `%PATTERN%` SQL-LIKE test-name, wildcards stripped.
+- `needs_vocab:*`: resolvable once that vocabulary is added (LOINC, OMOP/Athena,
+  RxNorm/NDC, VA stop-code table) — none require guessing.
+- `study_specific`: author-defined variables (e.g. `PDI`, `hPDI`) with no
+  standard-vocabulary description; surfaced as-is, never fabricated.

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artifacts/part_a_embeddings/config.json

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+  "model": "artifacts/models/bge_ft_va",
+  "pooling": "cls",
+  "query_prefix": "",
+  "doc_prefix": "",
+  "max_seq_length": 512,
+  "dim": 1024,
+  "n_metadata": 8013,
+  "n_code": 28668
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artifacts/vidul/BGE_FT_VA/config.json

@@ -0,0 +1,31 @@
+{
+  "architectures": [
+    "BertModel"
+  ],
+  "attention_probs_dropout_prob": 0.1,
+  "classifier_dropout": null,
+  "dtype": "float16",
+  "gradient_checkpointing": false,
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 1024,
+  "id2label": {
+    "0": "LABEL_0"
+  },
+  "initializer_range": 0.02,
+  "intermediate_size": 4096,
+  "label2id": {
+    "LABEL_0": 0
+  },
+  "layer_norm_eps": 1e-12,
+  "max_position_embeddings": 512,
+  "model_type": "bert",
+  "num_attention_heads": 16,
+  "num_hidden_layers": 24,
+  "pad_token_id": 0,
+  "position_embedding_type": "absolute",
+  "transformers_version": "4.56.1",
+  "type_vocab_size": 2,
+  "use_cache": true,
+  "vocab_size": 30522
+}