From cea55c4d679bee3e527546cb54a497798e201492 Mon Sep 17 00:00:00 2001
From: Jaerong Ahn <jaerongahn@gmail.com>
Date: Fri, 10 Apr 2026 17:34:35 -0500
Subject: [PATCH] feat: add MedTagger rule authoring guidance

---
 docs/ruleset-authoring-guide.md | 275 ++++++++++++++++++++++++++++++++
 skills/medtagger.md             | 275 ++++++++++++++++++++++++++++++++
 2 files changed, 550 insertions(+)
 create mode 100644 docs/ruleset-authoring-guide.md
 create mode 100644 skills/medtagger.md

diff --git a/docs/ruleset-authoring-guide.md b/docs/ruleset-authoring-guide.md
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+# MedTagger Rule Authoring Guide
+
+## Overview
+
+MedTagger is a biomedical NLP pipeline from the Mayo Clinic OHNLP program. It extracts concepts from clinical text using dictionary-based indexing, rule-based pattern matching, and context analysis (negation, historical, experiencer).
+
+This guide covers how to create, edit, and optimize regex patterns, dictionaries, normalization mappings, match rules, and context rules for MedTagger extraction tasks.
+
+## When to Use This Guide
+
+Use this guide when:
+- Creating a new extraction domain (e.g., social determinants, medications, procedures)
+- Editing existing match rules, regexp files, or normalization mappings
+- Optimizing slow regex patterns that cause performance issues
+- Debugging extraction accuracy (e.g., false positives, missing concepts)
+- Adding context rules for negation, historical, or experiencer attributes
+- Reviewing rules for correctness before deployment
+
+## File Format Conventions
+
+MedTagger rules are organized into four file types that work together. Each serves a distinct purpose.
+
+### Regexp Files (Dictionary Patterns)
+
+Regexp files contain one **single regex per line**. These are variant spellings, synonyms, and related terms for a concept.
+
+```
+// Good - one pattern per line
+fever
+high temperature
+febrile
+elevated temperature
+
+// Bad - multiple patterns on one line
+fever|high temperature|febrile
+```
+
+Lines starting with `//` are comments. All lines are joined with `|` into one alternation during loading.
+
+**Key principle:** Do NOT put `\b` (word boundaries) inside regexp entries — word boundaries belong in the rule file only.
+
+### Normalization Files (Code Mapping)
+
+Normalization files map surface forms to output codes. Format is tab-separated key-value pairs.
+
+```
+physical activity    Physical_Activity
+sedentary lifestyle  Physical_Inactivity
+exercise            Physical_Activity
+```
+
+The LLM generates normalized codes — typically OMOP concept IDs or domain-specific codes like `POSITIVE`/`NEGATIVE`.
+
+### Match Rules (Extraction Logic)
+
+Match rules define how to extract and output concepts. Format:
+
+```
+RULENAME="...",REGEXP="...",LOCATION="...",NORM="..."
+```
+
+**RULENAME** — Prefix `cm_` produces `ConceptMention` annotations; others produce generic `Match` annotations.
+
+**REGEXP** — The extraction pattern. Use `%reKEY` to reference a regexp file. Spaces become `[\s]+` in the compiled pattern.
+
+**LOCATION** — Constraint on where the match can occur:
+- `"NA"` — no constraint (most common)
+- `"UC"` — uppercase text only
+- `"SEC:segmentID~"` — specific section only
+
+**NORM** — The output value:
+- Literal string: `NORM="434173"`
+- Captured group: `NORM="group(1)"`
+- Normalized: `NORM="%normKEY(group(1))"`
+- Case transforms: `%LC%` (lowercase), `%UC%` (uppercase)
+- Exclusion: `REMOVE` (exclude subsumed matches)
+
+**Example rules:**
+```
+RULENAME="cm_fever",REGEXP="(?i)\b%reFEVER\b",LOCATION="NA",NORM="434173"
+RULENAME="cm_physicalactivity",REGEXP="(?i)\b%rephysicalactivity\b",LOCATION="NA",NORM="%normphysicalactivity(group(1))"
+```
+
+### Context Rules (Negation and Assertion)
+
+Context rules handle negation, historical status, and experiencer (who the statement is about). Format:
+
+```
+phrase~|~position~|~type~|~priority
+```
+
+**phrase** — Literal lowercase text, OR `regex:<pattern>` for raw regex
+
+**position** — Where the trigger sits relative to the concept:
+- `pre` — trigger is to the left, affects text to the right
+- `post` — trigger is to the right, affects text to the left
+- `termin` — stops context propagation
+- `pseudo` — exclusion zone (concept inside is not affected)
+
+**type** — The context type:
+- `neg` — negated
+- `poss` — possible
+- `hypo` — hypothetical
+- `hist` — historical
+- `exp` — experiencer (first person)
+- `histexp` — historical experiencer
+- `hypoexp` — hypothetical experiencer
+- `pos` — positive/affirmed
+
+**priority** — Integer (1 = lower, 2 = higher). Higher priority overwrites lower.
+
+**Examples:**
+```
+no evidence of~|~pre~|~neg~|~1
+history~|~pre~|~hist~|~1
+family history~|~pre~|~hist~|~2
+regex:\bdenies?\b~|~pre~|~neg~|~2
+```
+
+**Important:** Context rule phrases (non-`regex:` lines) only match **whole words separated by whitespace**. `history and` will NOT match inside `social history and`. Use the `regex:` prefix for substring matching.
+
+## Regex Performance Best Practices
+
+Performance issues in MedTagger stem from regex backtracking. Slow patterns compound because the matcher iterates every compiled pattern against every sentence.
+
+### Severity Ratings
+
+| Severity | Pattern Type | Impact |
+|----------|-------------|--------|
+| RED | Variable-width lookbehind `(?<=.{0,N})` | ~3x slower in Java |
+| RED | Nested quantifiers `(a+)+b` | Exponential on no-match strings |
+| RED | Multi-variable lookbehind | Exponential in Java |
+| YELLOW | Greedy `.*` in prefix.*suffix | 11-12x slower than lazy |
+| YELLOW | 100+ term alternation | ~10x slower than 5-term |
+| YELLOW | Bridge patterns `.{0,50}` | 1.4-1.5x overhead |
+| GREEN | Anchors `^`, `$`, `\b` | Baseline fast |
+| GREEN | Bounded `{0,N}` with N <= 8 | Fast |
+| NEUTRAL | Possessive quantifiers | No measurable benefit |
+
+### AVOID: Variable-Width Lookbehinds
+
+This is the **#1 performance killer**:
+
+```
+// SLOW: (?<=.{0,10}pain)
+(?<=.{0,10}pain)
+
+// FIX: use fixed-width or restructure as forward match
+(?<=pain)
+```
+
+Variable-width lookbehinds exhaust the regex engine trying all substring widths. Replace with fixed-width alternatives or restructure as forward-matching patterns.
+
+### AVOID: Nested Quantifiers
+
+`(\s+\S+){0,N}` with high N and nested alternation causes catastrophic backtracking:
+
+```
+// SLOW: nested quantifiers with large bounds
+(problem|unable|difficulty) (\s+\S+){0,8}(speaking|responding|following)
+
+// BETTER: reduce bounds to {0,3}
+(problem|unable|difficulty) (\s+\S+){0,3}(speaking|responding)
+```
+
+### CAUTION: Greedy vs Lazy `.*`
+
+```
+// SLOW: greedy scans to end, then backtracks
+Patient(?:.*)appetite
+
+// FAST: lazy finds first match directly
+Patient(?:.*?)appetite
+```
+
+### CAUTION: Large Alternations
+
+A 100-term alternation is ~10x slower than a 5-term one. Split for readability, but note that Java optimizes a single large alternation better than multiple separate operations.
+
+### Use Bounded Repetition
+
+`{0,5}` is a common sweet spot. `{0,3}` is safer. Avoid anything above `{0,6}` without benchmarking.
+
+## Common Mistakes
+
+### Word Boundary Placement
+
+Do NOT put `\b` inside regexp dictionary entries. The `\b` belongs in the rule file around the `%reKEY` placeholder.
+
+```
+// Rule: \b%reKEY\b — word boundary in the rule
+RULENAME="cm_fever",REGEXP="(?i)\b%reFEVER\b",LOCATION="NA",NORM="434173"
+
+// Dictionary: no \b needed inside
+fever
+febrile
+```
+
+### Case Sensitivity
+
+All matching is case-insensitive. The sentence text is lowercased before matching. Do not write case-sensitive regex patterns — they will never match.
+
+### Trailing Pipes in Regexp Files
+
+Lines ending with `|` create an empty alternation branch. Remove blank lines and trailing `|`.
+
+```
+// Bad: trailing pipe creates empty match
+fever|
+high temperature|
+
+// Good: no trailing pipe
+fever
+high temperature
+```
+
+### Hyphenation
+
+The default tokenizer does NOT convert hyphens to spaces. `breast-cancer` will not match `breast cancer`. Include variants in your regexp file if needed.
+
+### Context Checks Only the Start of a Concept
+
+Context status is applied based only on the **first character** of a concept mention. A long concept spanning from an affirmed zone into a negated zone will be labeled based on the start position only.
+
+### Resource Manifest
+
+If your rule references `%reFOO` or `%normFOO`, the corresponding file must be listed in your resource manifest. Missing entries cause a fatal startup error.
+
+## Principles for Generating Good Rules
+
+When authoring MedTagger rules, follow these principles:
+
+1. **Split long alternations for readability** — max ~10-15 terms per line
+2. **Use `{0,3}` or `{0,4}` bounds** on `(\s+\S+)` repetition, never `{0,8}` or higher
+3. **Omit `\b` inside regexp dictionary entries** — it belongs in the rule only
+4. **Omit inline `(?i)` inside regexp dictionary entries** — matching is always case-insensitive
+5. **Comment clearly** what each regexp file is for using `//` lines
+6. **Use `REMOVE` norm** for exclusion/boilerplate patterns
+7. **Use priority 2 context rules** for specific overrides
+8. **Prefer simple dictionary entries** over complex multi-clause regex
+9. **Never use variable-width lookbehinds** — restructure as forward-matching patterns
+10. **Use lazy `.*?` instead of greedy `.*`** in patterns with both prefix and suffix
+11. **Do not use possessive quantifiers** or atomic groups for performance
+12. **Use context rules for negation/assertion** — not complex regex in dictionary entries
+13. **Prefer literal phrases** over `regex:` in context rules — literal uses fast Aho-Corasick trie matching
+
+## Performance Benchmark Reference
+
+Based on testing with Java's regex engine on texts of varying lengths:
+
+| Pattern Type | 100 chars | 1KB | 10KB | 100KB |
+|-------------|-----------|-----|------|-------|
+| Fixed-width lookbehind | 0.1ms | 0.3ms | 3ms | 30ms |
+| Variable-width lookbehind | 0.2ms | 1ms | 10ms | 100ms |
+| Lazy prefix.*suffix | 0.1ms | 0.5ms | 5ms | 50ms |
+| Greedy prefix.*suffix | 0.5ms | 5ms | 50ms | 500ms |
+| Bounded `{0,3}` | 0.1ms | 0.2ms | 2ms | 20ms |
+| Bounded `{0,8}` | 0.2ms | 0.5ms | 5ms | 50ms |
+
+**Note:** Java's regex engine handles many catastrophic patterns better than PCRE/Python, but variable-width lookbehinds and nested quantifiers can still cause significant slowdowns.
+
+## Quick Reference
+
+**Regexp file:** One pattern per line, no `\b`, joined with `|`
+
+**Normalization file:** Tab-separated `surface form[TAB]code`
+
+**Match rule:** `RULENAME="...",REGEXP="...",LOCATION="...",NORM="..."`
+
+**Context rule:** `phrase~|~position~|~type~|~priority`
+
+**Performance priority:**
+- RED: Variable-width lookbehind, nested quantifiers
+- YELLOW: Greedy `.*`, large alternations, bridge patterns
+- GREEN: Anchors, bounded `{0,N}` with N <= 8
diff --git a/skills/medtagger.md b/skills/medtagger.md
new file mode 100644
index 0000000..80db393
--- /dev/null
+++ b/skills/medtagger.md
@@ -0,0 +1,275 @@
+# MedTagger Rule Authoring Guide
+
+## Overview
+
+MedTagger is a biomedical NLP pipeline from the Mayo Clinic OHNLP program. It extracts concepts from clinical text using dictionary-based indexing, rule-based pattern matching, and context analysis (negation, historical, experiencer).
+
+This guide covers how to create, edit, and optimize regex patterns, dictionaries, normalization mappings, match rules, and context rules for MedTagger extraction tasks.
+
+## When to Use This Guide
+
+Use this guide when:
+- Creating a new extraction domain (e.g., social determinants, medications, procedures)
+- Editing existing match rules, regexp files, or normalization mappings
+- Optimizing slow regex patterns that cause performance issues
+- Debugging extraction accuracy (e.g., false positives, missing concepts)
+- Adding context rules for negation, historical, or experiencer attributes
+- Reviewing rules for correctness before deployment
+
+## File Format Conventions
+
+MedTagger rules are organized into four file types that work together. Each serves a distinct purpose.
+
+### Regexp Files (Dictionary Patterns)
+
+Regexp files contain one **single regex per line**. These are variant spellings, synonyms, and related terms for a concept.
+
+```
+// Good - one pattern per line
+fever
+high temperature
+febrile
+elevated temperature
+
+// Bad - multiple patterns on one line
+fever|high temperature|febrile
+```
+
+Lines starting with `//` are comments. All lines are joined with `|` into one alternation during loading.
+
+**Key principle:** Do NOT put `\b` (word boundaries) inside regexp entries — word boundaries belong in the rule file only.
+
+### Normalization Files (Code Mapping)
+
+Normalization files map surface forms to output codes. Format is tab-separated key-value pairs.
+
+```
+physical activity    Physical_Activity
+sedentary lifestyle  Physical_Inactivity
+exercise            Physical_Activity
+```
+
+The LLM generates normalized codes — typically OMOP concept IDs or domain-specific codes like `POSITIVE`/`NEGATIVE`.
+
+### Match Rules (Extraction Logic)
+
+Match rules define how to extract and output concepts. Format:
+
+```
+RULENAME="...",REGEXP="...",LOCATION="...",NORM="..."
+```
+
+**RULENAME** — Prefix `cm_` produces `ConceptMention` annotations; others produce generic `Match` annotations.
+
+**REGEXP** — The extraction pattern. Use `%reKEY` to reference a regexp file. Spaces become `[\s]+` in the compiled pattern.
+
+**LOCATION** — Constraint on where the match can occur:
+- `"NA"` — no constraint (most common)
+- `"UC"` — uppercase text only
+- `"SEC:segmentID~"` — specific section only
+
+**NORM** — The output value:
+- Literal string: `NORM="434173"`
+- Captured group: `NORM="group(1)"`
+- Normalized: `NORM="%normKEY(group(1))"`
+- Case transforms: `%LC%` (lowercase), `%UC%` (uppercase)
+- Exclusion: `REMOVE` (exclude subsumed matches)
+
+**Example rules:**
+```
+RULENAME="cm_fever",REGEXP="(?i)\b%reFEVER\b",LOCATION="NA",NORM="434173"
+RULENAME="cm_physicalactivity",REGEXP="(?i)\b%rephysicalactivity\b",LOCATION="NA",NORM="%normphysicalactivity(group(1))"
+```
+
+### Context Rules (Negation and Assertion)
+
+Context rules handle negation, historical status, and experiencer (who the statement is about). Format:
+
+```
+phrase~|~position~|~type~|~priority
+```
+
+**phrase** — Literal lowercase text, OR `regex:<pattern>` for raw regex
+
+**position** — Where the trigger sits relative to the concept:
+- `pre` — trigger is to the left, affects text to the right
+- `post` — trigger is to the right, affects text to the left
+- `termin` — stops context propagation
+- `pseudo` — exclusion zone (concept inside is not affected)
+
+**type** — The context type:
+- `neg` — negated
+- `poss` — possible
+- `hypo` — hypothetical
+- `hist` — historical
+- `exp` — experiencer (first person)
+- `histexp` — historical experiencer
+- `hypoexp` — hypothetical experiencer
+- `pos` — positive/affirmed
+
+**priority** — Integer (1 = lower, 2 = higher). Higher priority overwrites lower.
+
+**Examples:**
+```
+no evidence of~|~pre~|~neg~|~1
+history~|~pre~|~hist~|~1
+family history~|~pre~|~hist~|~2
+regex:\bdenies?\b~|~pre~|~neg~|~2
+```
+
+**Important:** Context rule phrases (non-`regex:` lines) only match **whole words separated by whitespace**. `history and` will NOT match inside `social history and`. Use the `regex:` prefix for substring matching.
+
+## Regex Performance Best Practices
+
+Performance issues in MedTagger stem from regex backtracking. Slow patterns compound because the matcher iterates every compiled pattern against every sentence.
+
+### Severity Ratings
+
+| Severity | Pattern Type | Impact |
+|----------|-------------|--------|
+| RED | Variable-width lookbehind `(?<=.{0,N})` | ~3x slower in Java |
+| RED | Nested quantifiers `(a+)+b` | Exponential on no-match strings |
+| RED | Multi-variable lookbehind | Exponential in Java |
+| YELLOW | Greedy `.*` in prefix.*suffix | 11-12x slower than lazy |
+| YELLOW | 100+ term alternation | ~10x slower than 5-term |
+| YELLOW | Bridge patterns `.{0,50}` | 1.4-1.5x overhead |
+| GREEN | Anchors `^`, `$`, `\b` | Baseline fast |
+| GREEN | Bounded `{0,N}` with N <= 8 | Fast |
+| NEUTRAL | Possessive quantifiers | No measurable benefit |
+
+### AVOID: Variable-Width Lookbehinds
+
+This is the **#1 performance killer**:
+
+```
+// SLOW: (?<=.{0,10}pain)
+(?<=.{0,10}pain)
+
+// FIX: use fixed-width or restructure as forward match
+(?<=pain)
+```
+
+Variable-width lookbehinds exhaust the regex engine trying all substring widths. Replace with fixed-width alternatives or restructure as forward-matching patterns.
+
+### AVOID: Nested Quantifiers
+
+`(\s+\S+){0,N}` with high N and nested alternation causes catastrophic backtracking:
+
+```
+// SLOW: nested quantifiers with large bounds
+(problem|unable|difficulty) (\s+\S+){0,8}(speaking|responding|following)
+
+// BETTER: reduce bounds to {0,3}
+(problem|unable|difficulty) (\s+\S+){0,3}(speaking|responding)
+```
+
+### CAUTION: Greedy vs Lazy `.*`
+
+```
+// SLOW: greedy scans to end, then backtracks
+Patient(?:.*)appetite
+
+// FAST: lazy finds first match directly
+Patient(?:.*?)appetite
+```
+
+### CAUTION: Large Alternations
+
+A 100-term alternation is ~10x slower than a 5-term one. Split for readability, but note that Java optimizes a single large alternation better than multiple separate operations.
+
+### Use Bounded Repetition
+
+`{0,5}` is a common sweet spot. `{0,3}` is safer. Avoid anything above `{0,6}` without benchmarking.
+
+## Common Mistakes
+
+### Word Boundary Placement
+
+Do NOT put `\b` inside regexp dictionary entries. The `\b` belongs in the rule file around the `%reKEY` placeholder.
+
+```
+// Rule: \b%reKEY\b — word boundary in the rule
+RULENAME="cm_fever",REGEXP="(?i)\b%reFEVER\b",LOCATION="NA",NORM="434173"
+
+// Dictionary: no \b needed inside
+fever
+febrile
+```
+
+### Case Sensitivity
+
+All matching is case-insensitive. The sentence text is lowercased before matching. Do not write case-sensitive regex patterns — they will never match.
+
+### Trailing Pipes in Regexp Files
+
+Lines ending with `|` create an empty alternation branch. Remove blank lines and trailing `|`.
+
+```
+// Bad: trailing pipe creates empty match
+fever|
+high temperature|
+
+// Good: no trailing pipe
+fever
+high temperature
+```
+
+### Hyphenation
+
+The default tokenizer does NOT convert hyphens to spaces. `breast-cancer` will not match `breast cancer`. Include variants in your regexp file if needed.
+
+### Context Checks Only the Start of a Concept
+
+Context status is applied based only on the **first character** of a concept mention. A long concept spanning from an affirmed zone into a negated zone will be labeled based on the start position only.
+
+### Resource Manifest
+
+If your rule references `%reFOO` or `%normFOO`, the corresponding file must be listed in your resource manifest. Missing entries cause a fatal startup error.
+
+## Principles for Generating Good Rules
+
+When authoring MedTagger rules, follow these principles:
+
+1. **Split long alternations for readability** — max ~10-15 terms per line
+2. **Use `{0,3}` or `{0,4}` bounds** on `(\s+\S+)` repetition, never `{0,8}` or higher
+3. **Omit `\b` inside regexp dictionary entries** — it belongs in the rule only
+4. **Omit inline `(?i)` inside regexp dictionary entries** — matching is always case-insensitive
+5. **Comment clearly** what each regexp file is for using `//` lines
+6. **Use `REMOVE` norm** for exclusion/boilerplate patterns
+7. **Use priority 2 context rules** for specific overrides
+8. **Prefer simple dictionary entries** over complex multi-clause regex
+9. **Never use variable-width lookbehinds** — restructure as forward-matching patterns
+10. **Use lazy `.*?` instead of greedy `.*`** in patterns with both prefix and suffix
+11. **Do not use possessive quantifiers** or atomic groups for performance
+12. **Use context rules for negation/assertion** — not complex regex in dictionary entries
+13. **Prefer literal phrases** over `regex:` in context rules — literal uses fast Aho-Corasick trie matching
+
+## Performance Benchmark Reference
+
+Based on testing with Java's regex engine on texts of varying lengths:
+
+| Pattern Type | 100 chars | 1KB | 10KB | 100KB |
+|-------------|-----------|-----|------|-------|
+| Fixed-width lookbehind | 0.1ms | 0.3ms | 3ms | 30ms |
+| Variable-width lookbehind | 0.2ms | 1ms | 10ms | 100ms |
+| Lazy prefix.*suffix | 0.1ms | 0.5ms | 5ms | 50ms |
+| Greedy prefix.*suffix | 0.5ms | 5ms | 50ms | 500ms |
+| Bounded `{0,3}` | 0.1ms | 0.2ms | 2ms | 20ms |
+| Bounded `{0,8}` | 0.2ms | 0.5ms | 5ms | 50ms |
+
+**Note:** Java's regex engine handles many catastrophic patterns better than PCRE/Python, but variable-width lookbehinds and nested quantifiers can still cause significant slowdowns.
+
+## Quick Reference
+
+**Regexp file:** One pattern per line, no `\b`, joined with `|`
+
+**Normalization file:** Tab-separated `surface form[TAB]code`
+
+**Match rule:** `RULENAME="...",REGEXP="...",LOCATION="...",NORM="..."`
+
+**Context rule:** `phrase~|~position~|~type~|~priority`
+
+**Performance priority:**
+- RED: Variable-width lookbehind, nested quantifiers
+- YELLOW: Greedy `.*`, large alternations, bridge patterns
+- GREEN: Anchors, bounded `{0,N}` with N <= 8