Update spine_coder/spine_coder_core.py

spine_coder/spine_coder_core.py

@@ -1,5 +1,5 @@
 # spine_coder_core_pro.py
-# Vertebro FINAL-v2.2-PRO   (Block 1/4)
+# Vertebro FINAL-v2.2-PRO  (Block 1/5)
 # Core utilities, text normalization, level parsing, region classification
 
 import re, json
@@ -18,17 +18,16 @@ def _norm(s: str) -> str:
 def _has(text: str, pat: str) -> bool:
     return re.search(pat, text, flags=re.I) is not None
 
-
 # ─────────────────────────────────────────────
 # LEVEL AND REGION LOGIC
 # ─────────────────────────────────────────────
-_ORDER = ["C", "T", "L", "S"]
+_ORDER  = ["C", "T", "L", "S"]
 _MAXNUM = {"C": 7, "T": 12, "L": 5, "S": 5}
 
 def _level_sort_key(lv: str) -> Tuple[int, int]:
     band_rank = {"C": 100, "T": 200, "L": 300, "S": 400}
     band = band_rank.get(lv[0].upper(), 999)
-    num = int(re.sub(r"\D", "", lv) or 0)
+    num  = int(re.sub(r"\D", "", lv) or 0)
     return (band, num)
 
 _SPAN   = re.compile(r"\b([CTLS])\s?(\d{1,2})\s*[-–]\s*([CTLS])?\s?(\d{1,2})\b", re.I)
@@ -36,7 +35,7 @@ _SINGLE = re.compile(r"\b([CTLS])\s?(\d{1,2})\b", re.I)
 
 def _expand_across_regions(p1: str, n1: int, p2: str, n2: int) -> List[str]:
     p1, p2 = p1.upper(), p2.upper()
-    out, i, j, r, num = [], _ORDER.index(p1), _ORDER.index(p2), _ORDER.index(p1), n1
+    out, r, num = [], _ORDER.index(p1), n1
     while True:
         out.append(f"{_ORDER[r]}{num}")
         if _ORDER[r] == p2 and num == n2:
@@ -68,8 +67,7 @@ def _extract_levels(t: str) -> List[str]:
     return sorted(levels, key=_level_sort_key)
 
 def _count_interspaces(levels: List[str]) -> int:
-    if not levels:
-        return 0
+    if not levels: return 0
     lv_sorted = sorted(set(levels), key=_level_sort_key)
     return max(0, len(lv_sorted) - 1)
 
@@ -87,9 +85,9 @@ def _classify_region(levels: List[str]) -> str:
     if s and not (c or t or l): return "sacral"
     return "mixed"
 
-# laterality/modifiers stub (we handle real modifiers later at case level)
+# laterality/modifiers stub (real modifiers are detected case-level)
 def _laterality_and_modifiers(note: str) -> Tuple[str, List[str]]:
-    return "midline", []  # spine work is midline; real modifiers added by detector
+    return "midline", []
 
 # Base keyword groups
 FUSION_KW       = r"\b(arthrodesis|fusion|t?lif|alif|plif|xlif|interbody\s+cage|peek\s+cage|structural\s+cage)\b"
@@ -100,8 +98,8 @@ AUTO_LOCAL_KW   = r"\b(local\s+autograft|spinous\s+process\s+bone|lamina\s+bone\
 AUTO_SEP_KW     = r"\b(iliac\s+crest|separate\s+incision|rib\s+graft|iliac crest bone|icbg)\b"
 
 # spine_coder_core_pro.py
-# Vertebro FINAL-v2.2-PRO   (Block 2/4)
-# CPT reasoning engine + specialty packs
+# Vertebro FINAL-v2.2-PRO  (Block 2/5)
+# CPT reasoning engine (decompression, TLIF/PLIF, ALIF, fusion, instrumentation, grafts, nav, removal)
 
 def _inst_code_by_span(span: int, anterior: bool) -> str:
     if span <= 1: return ""
@@ -109,6 +107,17 @@ def _inst_code_by_span(span: int, anterior: bool) -> str:
         return "22845" if span <= 3 else ("22846" if span <= 7 else "22847")
     return "22842" if span <= 3 else ("22843" if span <= 7 else "22844")
 
+def _infer_id_depth_code(t: str) -> str:
+    """
+    Heuristic for I&D depth CPT:
+    - 11044: bone
+    - 11043: fascia/muscle
+    - 11042: skin/subcut or unspecified
+    """
+    if _has(t, r"\b(bone|osteomyelitis|to bone|down to bone)\b"): return "11044"
+    if _has(t, r"\b(fascia|fascial|muscle|muscular|deep fascial)\b"): return "11043"
+    return "11042"
+
 def _infer_cpts(note: str, region: str, levels: List[str]) -> List[Dict[str, Any]]:
     t = _norm(note)
     out: List[Dict[str, Any]] = []
@@ -116,13 +125,21 @@ def _infer_cpts(note: str, region: str, levels: List[str]) -> List[Dict[str, Any
     span   = max(inters + 1, 2)
 
     def add(cpt: str, desc: str, rationale: str, cat: str, conf: float = 0.85, primary: bool = False):
-        out.append({"cpt": cpt, "desc": desc, "rationale": rationale, "category": cat,
-                    "confidence": round(conf, 2), "primary": primary})
+        out.append({
+            "cpt": cpt, "desc": desc, "rationale": rationale, "category": cat,
+            "confidence": round(conf, 2), "primary": primary
+        })
 
-    # Washout/I&D guard — prevents false fusion/instrumentation
+    # Washout/I&D guard — prevents false fusion/instrumentation on washout only
     washout_only = _has(t, r"(washout|irrigation and debridement|i\&d)") and not _has(t, FUSION_KW)
 
-    # 1) Decompression
+    # (A) I&D / Washout CPTs (always add if present)
+    if _has(t, r"\b(washout|irrigation and debridement|i\&d|incision and debridement|debridement)\b"):
+        id_code = _infer_id_depth_code(t)
+        add(id_code, "Irrigation & Debridement (depth-based)",
+            "Infection/washout documented.", "washout", 0.86, True)
+
+    # (B) Decompression
     if _has(t, r"laminectomy|decompression|facetectomy|foraminotomy"):
         base_map = {"cervical": "63045", "thoracic": "63046", "lumbar": "63047"}
         base = base_map.get(region, "63047")
@@ -132,12 +149,12 @@ def _infer_cpts(note: str, region: str, levels: List[str]) -> List[Dict[str, Any
             add("63048", f"Each additional level ×{inters}",
                 "Multi-level decompression inferred.", "decompression add-on", 0.82)
 
-    # 2) TLIF/PLIF (explicit or implicit via facetectomy + cage + screws)
+    # (C) TLIF/PLIF (explicit or implicit)
     tlif_like = (
-        _has(t, r"\btlif\b|\bplif\b|posterior interbody fusion")
-        or (_has(t, r"\bfacetectom(y|ies)\b|complete facetectomy|transforaminal")
-            and _has(t, r"\b(interbody (cage|device|spacer)|peek (cage|spacer)|titanium (cage|spacer)|allograft spacer)\b")
-            and _has(t, r"\bpedicle\s+screws?\b"))
+        _has(t, r"\btlif\b|\bplif\b|posterior interbody fusion") or
+        (_has(t, r"\bfacetectom(y|ies)\b|complete facetectomy|transforaminal") and
+         _has(t, r"\b(interbody (cage|device|spacer)|peek (cage|spacer)|titanium (cage|spacer)|allograft spacer)\b") and
+         _has(t, r"\bpedicle\s+screws?\b"))
     )
     if tlif_like and not washout_only and region in {"lumbar", "thoracic"}:
         add("22633", "Posterior/posterolateral + posterior interbody, single level",
@@ -152,7 +169,7 @@ def _infer_cpts(note: str, region: str, levels: List[str]) -> List[Dict[str, Any
                     "22844":"Posterior segmental instrumentation (8+ segments)"}[code]
             add(code, desc, "Posterior instrumentation detected.", "instrumentation", 0.83)
 
-    # 3) ALIF
+    # (D) ALIF
     if _has(t, r"\balif\b|anterior lumbar interbody fusion") and not washout_only:
         add("22558", "Anterior lumbar interbody fusion, single interspace",
             "ALIF detected.", "ALIF", 0.9, True)
@@ -167,7 +184,7 @@ def _infer_cpts(note: str, region: str, levels: List[str]) -> List[Dict[str, Any
                         "22847":"Anterior instrumentation (8+ segments)"}[code]
                 add(code, desc, "Anterior plate present; span estimated from levels.", "instrumentation", 0.8)
 
-    # 4) Posterolateral/posterior fusion (no interbody)
+    # (E) Posterolateral/posterior fusion (no interbody)
     if _has(t, r"posterolateral\b.*\bfusion|posterior\b.*\bfusion|in situ\b.*\bfusion") \
        and not _has(t, r"\btlif\b|\bplif\b|posterior interbody") and not washout_only:
         base_map = {"cervical":"22600", "thoracic":"22610", "lumbar":"22612", "lumbosacral":"22612", "cervicothoracic":"22600"}
@@ -185,7 +202,7 @@ def _infer_cpts(note: str, region: str, levels: List[str]) -> List[Dict[str, Any
                         "22844":"Posterior segmental instrumentation (8+ segments)"}[code]
                 add(code, desc, "Posterior instrumentation detected.", "instrumentation", 0.8)
 
-    # 5) Instrumentation w/o explicit fusion (posterior)
+    # (F) Instrumentation without explicit fusion (posterior)
     if _has(t, INSTR_KW) and not washout_only:
         code = _inst_code_by_span(span, anterior=False)
         if code and not any(r["category"] == "instrumentation" for r in out):
@@ -194,12 +211,12 @@ def _infer_cpts(note: str, region: str, levels: List[str]) -> List[Dict[str, Any
                     "22844":"Posterior segmental instrumentation (8+ segments)"}[code]
             add(code, desc, "Posterior instrumentation documented.", "instrumentation", 0.82)
 
-    # 6) Navigation (if not separately captured by facility)
+    # (G) Navigation
     if _has(t, NAV_KW):
         add("61783", "Intraoperative navigation (image-guided)",
             "Navigation terms detected (O-arm/3D spin/Stealth/7D).", "navigation", 0.82)
 
-    # 7) Bone grafts
+    # (H) Bone grafts
     if _has(t, AUTO_SEP_KW):
         add("20937", "Autograft (separate incision)", "Iliac crest or separate-site autograft.", "graft", 0.8)
     elif _has(t, AUTO_LOCAL_KW):
@@ -207,7 +224,7 @@ def _infer_cpts(note: str, region: str, levels: List[str]) -> List[Dict[str, Any
     if _has(t, ALLO_KW):
         add("20930", "Allograft, morselized / DBM", "Allograft/DBM used.", "graft", 0.8)
 
-    # 8) Hardware removal
+    # (I) Hardware removal
     if _has(t, r"(remov(ed|al)|explant).*(instrument|hardware|plate|rod|screw)"):
         if _has(t, r"\banterior\b|acdf|plate"):
             add("22855", "Removal of anterior instrumentation", "Anterior hardware removal.", "hardware_removal", 0.84, True)
@@ -216,13 +233,19 @@ def _infer_cpts(note: str, region: str, levels: List[str]) -> List[Dict[str, Any
 
     return out
 
+# spine_coder_core_pro.py
+# Vertebro FINAL-v2.2-PRO  (Block 3/5)
+# Specialty packs layered onto core CPT logic
+
 def _apply_specialty_packs(note: str, region: str, inters: int, levels: List[str]) -> List[Dict[str, Any]]:
     t = _norm(note)
     extra: List[Dict[str, Any]] = []
 
     def add(cpt, desc, rationale, cat, conf=0.84, primary=False):
-        extra.append({"cpt": cpt, "desc": desc, "rationale": rationale, "category": cat,
-                      "confidence": round(conf, 2), "primary": primary})
+        extra.append({
+            "cpt": cpt, "desc": desc, "rationale": rationale, "category": cat,
+            "confidence": round(conf, 2), "primary": primary
+        })
 
     # Tumor / corpectomy
     if _has(t, r"corpectomy|tumou?r|metastatic|metastasis|en bloc"):
@@ -264,7 +287,7 @@ def _apply_specialty_packs(note: str, region: str, inters: int, levels: List[str
     return extra
 
 # spine_coder_core_pro.py
-# Vertebro FINAL-v2.2-PRO   (Block 3/4)
+# Vertebro FINAL-v2.2-PRO  (Block 4/5)
 # Case-level modifiers & complications detector
 
 def _detect_case_modifiers_and_complications(note: str) -> Tuple[List[Dict[str, str]], Dict[str, bool], List[str]]:
@@ -273,36 +296,44 @@ def _detect_case_modifiers_and_complications(note: str) -> Tuple[List[Dict[str,
     complications_map: Dict[str, bool] = {}
     complications_list: List[str] = []
 
-    # ——— Modifiers (-50 and -59 intentionally suppressed for spine billing) ———
+    # Modifiers (-50 / -59 intentionally suppressed for spine)
     mod_patterns = [
         ("22", r"(complex|technically (difficult|demanding)|difficult dissection|extensive adhesiolysis|"
                r"severe deformity|morbid obesity|revision (case|exposure)|re-?operative field|"
                r"dense scar tissue|prolonged (exposure|procedure)|ossified p(?:l|ll)\b)",
                "Increased procedural service (complexity)."),
-        ("52", r"\b(partial|limited|reduced (service|extent))\b", "Reduced service performed."),
+
+        # 52 — reduced service (guarded)
+        ("52", r"\b(partial|limited|reduced (service|extent))\b",
+               "Reduced service performed."),
+
         ("53", r"\b(aborted|terminated|discontinued|stopped prior to completion)\b",
                "Procedure discontinued for patient safety."),
+
         ("62", r"\b(co[- ]?surgeon|two surgeons|co-surgeons)\b",
                "Two surgeons (co-surgeons) documented."),
+
         ("76", r"\brepeat(ed)? procedure\b.*\b(same (surgeon|physician))\b",
                "Repeat procedure/service by the same physician."),
         ("77", r"\brepeat(ed)? procedure\b.*\b(another|different) (surgeon|physician)\b",
                "Repeat procedure by another physician."),
-        ("78", r"(\bunplanned return\b.*\b(operating|op)\s*room\b)"
-               r"|(\breturn to (the )?(operating|op)\s*room\b.*\b(postoperative|global period)\b)",
+
+        # 78 — broadened phrasing for Jason-style notes
+        ("78", r"(\btake[- ]?back\b|\bunplanned return\b).*\b(operating|op)\s*room\b"
+               r"|(\breturn to (the )?(operating|op)\s*room\b.*\b(postop|post[- ]?operative|global period)\b)",
                "Unplanned return to OR during postoperative period."),
-        ("79", r"\bunrelated procedure\b.*\b(postoperative|global period)\b",
+
+        ("79", r"\bunrelated procedure\b.*\b(postop|post[- ]?operative|global period)\b",
                "Unrelated procedure during postoperative period."),
-        # -50, -59 suppressed to avoid noise in spine
     ]
     for code, pat, reason in mod_patterns:
         if _has(t, pat):
             modifiers.append({"modifier": code, "reason": reason})
 
-    # Assistant logic: AS vs -80 (mutually exclusive); -82 supersedes -80
+    # Assistant logic: AS vs -80 (mutually exclusive); -82 supersedes -80; PA/NP beats -80
     has_pa_np = _has(t, r"\b(pa[- ]?c|physician assistant|pa-c|nurse practitioner|np|advanced practice provider|app)\b")
     has_md_do = _has(t, r"\b(dr\.?|m\.?d\.?|d\.?o\.?)\b") or _has(t, r"\bassistant surgeon\b")
-    if _has(t, r"assistant\(s\):") or _has(t, r"\bassistant(s)?[:\-]"):
+    if _has(t, r"assistant\(s\):") or _has(t, r"\bassistant(s)?[:\-]"):  # generic assistant section → likely MD
         has_md_do = True
     if has_pa_np:
         modifiers.append({"modifier": "AS", "reason": "Non-physician assistant at surgery."})
@@ -315,7 +346,12 @@ def _detect_case_modifiers_and_complications(note: str) -> Tuple[List[Dict[str,
     if any(m["modifier"] == "53" for m in modifiers):
         modifiers = [m for m in modifiers if m["modifier"] != "52"]
 
-    # ——— Complications ———
+    # Corpectomy-specific rule: suppress -52 if “partial decompression” inside a corpectomy case
+    if any(m["modifier"] == "52" for m in modifiers):
+        if _has(t, r"\bcorpectomy\b") and _has(t, r"\bpartial\b.*\b(decompression|laminectomy|facetectomy)\b"):
+            modifiers = [m for m in modifiers if m["modifier"] != "52"]
+
+    # Complications
     comp_rules = [
         ("dural_tear_or_durotomy",           r"\b(dural tear|durotom(y|ies)|csf leak|cerebrospinal fluid leak)\b"),
         ("neuromonitoring_change",           r"(loss|significant (decrease|change)).*(ssep|mep|meps|tcem|neuromonitor)"),
@@ -329,7 +365,7 @@ def _detect_case_modifiers_and_complications(note: str) -> Tuple[List[Dict[str,
         ("positioning_injury",               r"\b(pressure (injury|ulcer)|brachial plexus|ulnar neuropathy|peroneal neuropathy)\b"),
         ("transfusion",                      r"\btransfus(ed|ion)|prbc\b|\bcell saver\b"),
         ("massive_blood_loss",               r"\bebl\b.*\b(> ?800\s?ml|>\s?1(\.|,)?0?00\s?ml|> ?1\s?l|> ?1000\s?cc)\b"),
-        ("unplanned_return_to_or",           r"\bunplanned return\b.*\b(operating|op)\s*room\b"),
+        ("unplanned_return_to_or",           r"\b(take[- ]?back|unplanned return)\b.*\b(operating|op)\s*room\b"),
         ("wound_dehiscence",                 r"\bwound dehiscence\b|\bdehisced\b"),
     ]
     for key, pat in comp_rules:
@@ -338,7 +374,7 @@ def _detect_case_modifiers_and_complications(note: str) -> Tuple[List[Dict[str,
         if hit:
             complications_list.append(key.replace("_", " ").title())
 
-    # Negation in IONM lines
+    # Negation in IONM (“no significant changes”) → clear flag
     if _has(t, r"no significant changes in (motor|sensory) evoked potentials|neuromonitoring.*no (significant )?changes"):
         complications_map["neuromonitoring_change"] = False
         complications_list = [c for c in complications_list if c != "Neuromonitoring Change"]
@@ -346,7 +382,7 @@ def _detect_case_modifiers_and_complications(note: str) -> Tuple[List[Dict[str,
     return modifiers, complications_map, complications_list
 
 # spine_coder_core_pro.py
-# Vertebro FINAL-v2.2-PRO   (Block 4/4)
+# Vertebro FINAL-v2.2-PRO  (Block 5/5)
 # Output builder & main entrypoint with top_k + backward-compat alias
 
 def vertebro_infer(note: str, payer: str = "Medicare", top_k: int = 10) -> Dict[str, Any]:
@@ -354,7 +390,7 @@ def vertebro_infer(note: str, payer: str = "Medicare", top_k: int = 10) -> Dict[
     t = _norm(note)
     levels = _extract_levels(t)
     region = _classify_region(levels)
-    inters = _count_interspaces(levels)
+    inters  = _count_interspaces(levels)
     laterality, mods_stub = _laterality_and_modifiers(t)
 
     # Inference
@@ -362,7 +398,7 @@ def vertebro_infer(note: str, payer: str = "Medicare", top_k: int = 10) -> Dict[
     extra_rows = _apply_specialty_packs(t, region, inters, levels)
     rows = base_rows + extra_rows
 
-    # Merge duplicates (max confidence, concat rationale)
+    # De-dup: keep max confidence, concat rationale
     merged: Dict[tuple, Dict[str, Any]] = {}
     for r in rows:
         key = (r["cpt"], r["category"])
@@ -383,7 +419,7 @@ def vertebro_infer(note: str, payer: str = "Medicare", top_k: int = 10) -> Dict[
     }
     tech_flags = [k for k, v in flags_map.items() if v]
 
-    # Attach tech info to primary rows
+    # Attach tech info to primary row(s)
     if tech_flags:
         tech_txt = f" (Tech: {', '.join(tech_flags)})"
         for r in rows:
@@ -406,7 +442,7 @@ def vertebro_infer(note: str, payer: str = "Medicare", top_k: int = 10) -> Dict[
                 if r.get("modifiers"):
                     r["modifiers"] = [m for m in r["modifiers"] if m != "53"]
 
-    # Top-K cap
+    # Top-K cap (HF UI)
     try:
         k = int(top_k)
         if k > 0:
@@ -436,12 +472,12 @@ suggest_with_cpt_billing = vertebro_infer
 # Quick CLI test
 if __name__ == "__main__":
     sample = """
-    Assistant(s): Dr. Amber Parker
+    Assistant(s): Dr. Amber Parker, PA-C
     Preop Dx: C3–C6 stenosis with myelopathy.
     Procedure:
       1. C3–C6 laminectomy and medial facetectomies.
       2. C2–T1 posterolateral arthrodesis; posterior instrumentation C2–T1.
       3. Navigation and fluoroscopy utilized; neuromonitoring with no significant changes.
-    EBL 1200 mL. Dural tear identified and repaired primarily.
+    EBL 1200 mL. Dural tear identified and repaired primarily. Unplanned return to operating room noted.
     """
     print(json.dumps(vertebro_infer(sample, top_k=12), indent=2))