batch-processing-clinical-text

name	batch-processing-clinical-text
description	Run large-scale batch NER, PII extraction, or de-identification over many clinical notes on-device with OpenMed, with sharding, checkpointing, resumability, and append-only JSONL output. Use when the user needs to process a corpus or folder of notes, de-identify a dataset, run NER over thousands of documents, build a resumable batch pipeline, or stream results to JSONL without holding everything in memory. Covers process_batch / BatchProcessor / BatchItem / BatchResult, the operation= selector (analyze_text | extract_pii | deidentify), iter_process streaming, the PHI-safe on_progress callback, chunking long documents, and no-PHI logging. Produces a resumable batch runner over an OpenMed model.
license	Apache-2.0
metadata	{"project":"OpenMed","category":"deployment-ops","pairs":"adjacent","version":"1.0"}

Batch processing clinical text

openmed.processing runs OpenMed over many documents efficiently, with progress tracking, per-item error isolation, and streaming. It runs fully on-device: the corpus, the model, and the output never leave the host. This skill shows a resumable runner — sharded, checkpointed, append-only JSONL — that you can restart without reprocessing.

When to use this skill

For corpora, folders, or datasets — anything beyond a handful of notes. For a single note, just call openmed.analyze_text / deidentify directly (extracting-clinical-entities, deidentifying-clinical-text). For an always-on HTTP service, see serving-openmed-rest-api.

Quick start

from openmed import process_batch

texts = ["Patient has type 2 diabetes.", "No acute distress. BP 120/80."]
result = process_batch(texts, model_name="disease_detection_superclinical")

print(result.summary())          # PHI-safe counts + timing
print(result.successful_items, "/", result.total_items)
for item in result.get_successful_results():
    print(item.id, item.result.to_dict()["entities"])   # spans only; avoid raw text in logs

process_batch(...) is a thin wrapper over BatchProcessor. Real signatures (openmed/processing/batch.py):

• process_batch(texts, model_name="disease_detection_superclinical", ids=None, config=None, progress_callback=None, on_progress=None, **kwargs) -> BatchResult
• BatchProcessor(model_name=..., operation="analyze_text", batch_size=8, continue_on_error=True, **analyze_kwargs) with operation ∈ {"analyze_text", "extract_pii", "deidentify"}.
• BatchItem(id, text, source=None, metadata=None)
• BatchResult — .items, .total_items, .successful_items, .failed_items, .success_rate, .average_processing_time, .summary(), .to_dict(), .get_successful_results(), .get_failed_results().
• BatchItemResult — .id, .result (a PredictionResult/DeidentificationResult), .error, .processing_time, .source, .success, .to_dict().

Choosing the operation

from openmed import BatchProcessor

# NER (default)
ner = BatchProcessor(model_name="disease_detection_superclinical")          # operation="analyze_text"
# Detect PHI spans
pii = BatchProcessor(operation="extract_pii", model_name="OpenMed/OpenMed-PII-SuperClinical-Small-44M-v1")
# De-identify (rewrites text)
deid = BatchProcessor(operation="deidentify", method="mask", confidence_threshold=0.7)

BatchProcessor reuses one model loader across items (and a cached privacy filter for PII ops), so a single processor over many texts is far cheaper than many one-off calls.

Streaming + PHI-safe progress

from openmed.processing import BatchProcessor, BatchProgress

proc = BatchProcessor(operation="deidentify", method="mask", batch_size=16)

def on_progress(p: BatchProgress) -> None:   # frozen record: completed/total/current_index/elapsed
    if p.completed % 500 == 0:
        print(f"{p.completed}/{p.total} ({p.elapsed:.1f}s)")   # NO PHI

for item in proc.iter_process(texts, ids=doc_ids, on_progress=on_progress):
    write_jsonl(item)   # one result at a time — constant memory for huge corpora

on_progress receives only counts/timing (never text), so it is safe to log. iter_process yields BatchItemResults without holding the whole corpus.

Workflow

1. De-identify upstream if the corpus has PHI, or key everything by stable internal ids so logs/output never carry identifiers.
2. Pick the operation + model — one BatchProcessor per operation (analyze_text / extract_pii / deidentify); reuse it across all items so the loader is shared.
3. Shard the corpus into independent partitions writing to separate JSONL files; run shards as separate processes for parallelism.
4. Stream with iter_process and append each BatchItemResult to JSONL (flush per item) — that append-only file is your checkpoint.
5. Track progress with the PHI-safe on_progress callback (counts/timing only).
6. Re-run to resume: skip ids already present in the output; with continue_on_error=True, failures are recorded, not raised.
7. Reconcile via result.get_failed_results() / a failures pass, then hand JSONL to the downstream consumer.

A resumable batch runner

import json
from pathlib import Path
from openmed.processing import BatchProcessor

def run_resumable(texts, ids, out_path: Path, *, operation="deidentify", **kw):
    out_path.parent.mkdir(parents=True, exist_ok=True)
    # 1) checkpoint = ids already written (append-only JSONL is the source of truth)
    done = set()
    if out_path.exists():
        with out_path.open() as f:
            done = {json.loads(line)["id"] for line in f if line.strip()}
    todo = [(i, t) for i, t in zip(ids, texts) if i not in done]
    if not todo:
        return
    pending_ids, pending_texts = zip(*todo)

    proc = BatchProcessor(operation=operation, continue_on_error=True, **kw)
    # 2) append each result as it completes -> safe to kill/restart anytime
    with out_path.open("a") as f:
        for item in proc.iter_process(list(pending_texts), ids=list(pending_ids)):
            record = {"id": item.id, "ok": item.success,
                      "result": item.result.to_dict() if item.success else None,
                      "error": item.error}            # item.error is a message, keep PHI out
            f.write(json.dumps(record) + "\n")
            f.flush()

Re-running skips finished ids (continue_on_error=True keeps one bad doc from killing the run; failures are recorded, not raised). Shard a corpus by writing to out/shard_000.jsonl, shard_001.jsonl, … and run shards in separate processes.

Chunking long documents

BatchProcessor does not split single documents. For notes longer than the model's max sequence length, pre-split into sentences/windows (openmed.processing.sentences) — or for analyze_text, rely on built-in sentence handling — then re-stitch entities by adding the chunk offset back to each entity's start/end so spans point into the original document.

Hand-off to / from OpenMed

• Per-item engine: each operation calls the same openmed.analyze_text / extract_pii / deidentify you'd call directly — same results, batched.
• Downstream: JSONL feeds building-patient-timelines, etl-to-omop-cdm, and exporting-to-fhir. De-id JSONL feeds evaluating-with-leakage-gates.
• Service vs batch: for request/response use serving-openmed-rest-api; for corpora use this batch path.

Edge cases & gotchas

• No PHI in logs/JSONL keys. Use stable ids (BatchItem.id), offsets, and labels. BatchItemResult.error is a message — keep raw text out of inputs to exceptions you log.
• continue_on_error=True is the default and recommended for corpora; check result.get_failed_results() afterward. Set False only when one failure should abort everything.
• batch_size is a throughput dial, not correctness — tune to memory/CPU. Larger isn't always faster on CPU.
• Append-only is the checkpoint. Don't buffer results in memory and write at the end; you lose progress on a crash. Append + flush per item.
• process_files/process_directory read files for you and set BatchItem.source; unreadable files become failed items (not crashes) under continue_on_error.
• Mixed languages: pass lang= per run for PII ops; don't run an English PII model across other languages (deidentifying-multilingual-text).

Standards & references

• JSON Lines (newline-delimited JSON): https://jsonlines.org/
• HIPAA de-identification (when batching PHI removal), 45 CFR 164.514(b): https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/index.html
• OpenMed source: openmed/processing/batch.py (process_batch, BatchProcessor, BatchItem, BatchItemResult, BatchResult, BatchProgress, iter_process).