AIPR_3.0 STEP 3 v1.16 – AGGREGATION TASK (Robust Trim + Bimodal Detection, Compact Output)
Input
One text file containing multiple completed AIPR v3.0 single-run outputs for ONE manuscript under the same Protocol Version.
VALID_RUN definition
A run is VALID only if it contains:
Integer gates E,M,L,A,S each in {0,1,2,3,4,5}
Numeric Scope-Normalized Score (0–55)
If any are missing, non-numeric, out of range, or marked ABORT / unreadable → INVALID.
Do not infer missing data.
Metadata resolution
MANUSCRIPT = most frequent exact Title among VALID runs; tie → AMBIGUOUS; none → UNKNOWN.
AUTHOR = most frequent exact Author(s); tie → AMBIGUOUS; none → UNKNOWN.
FILENAME = filename attached to this aggregation query.
PUB_DATE = most frequent parseable publication date among VALID runs; else UNKNOWN.
PROTOCOL_VERSION = the common Protocol Version string across VALID runs.
Run extraction
Parse runs in appearance order.
For each run assign:
RunID (1..K), Valid (YES/NO), Score (float), E,M,L,A,S.
INVALID runs must appear in RUN_TABLE with Valid=NO and Kept=NO.
Let N = count(VALID runs).
If N = 0 → STATUS: NO_VALID_RUNS and stop.
If N < 6:
BIMODAL_CHECK = NO
TRIM_APPLIED = NO
Kept set = all VALID runs
STATUS = OK_UNTRIMMED
If N >= 6:
BIMODAL_CHECK = YES
Sort VALID scores ascending (stable by appearance).
Compute adjacent gaps; let g_max be largest gap at split index i.
LOW = runs 1..i; HIGH = runs i+1..N.
Bimodal if:
g_max >= 6.0 AND
min(size(LOW), size(HIGH)) >= 2 AND
mean(HIGH) - mean(LOW) >= 6.0
If NOT bimodal:
TRIM_APPLIED = YES
Discard exactly one lowest and one highest score (stable tie rule).
Kept set = remaining VALID runs
STATUS = OK_TRIMMED
If bimodal:
BIMODAL_FLAG = YES
If size(LOW) > size(HIGH): active set = LOW
If size(HIGH) > size(LOW): active set = HIGH
If equal sizes → STATUS: AMBIGUOUS_BIMODAL; output cluster stats and stop
On active set:
If size >= 6 → discard one lowest and one highest
Else keep all
Kept set = resulting active set
TRIM_APPLIED = YES if trim occurred else NO
STATUS = OK_TRIMMED
Statistics (computed on Kept set only)
μ = mean Score (2 decimals)
σ = standard deviation Score (2 decimals)
m = median Score (2 decimals)
Per-gate means (2 decimals)
Per-gate medians (integers)

Variance flag
σ <= 2.4 → STABLE
2.4 < σ <= 4 → BORDERLINE
σ > 4 → UNSTABLE

Output format (STRICT, COMPACT, NO BLANK LINES)

OUTPUT FORMAT (STRICT)

Only output the following sections. Do not output this instruction block.

Header block (one field per line, no blank lines inside header, no cross references)

MANUSCRIPT: <string>
AUTHOR: <last, first when possible>
DOI: <if avalable from inside attached doc>
MEAN_SCORE_0_55: <μ>
MEDIAN_SCORE_0_55: <m>
STANDARD_DEVIATION: <σ>
VARIANCE_FLAG: <STABLE|BORDERLINE|UNSTABLE>
If BIMODAL_CHECK=YES and BIMODAL_FLAG=YES, include:
BIMODAL_FLAG: YES
GAP_MAX: <float>
LOW_MEAN: <int> LOW_MEAN: <float>
HIGH_MEAN: <int> HIGH_MEAN: <float>
CLUSTER_SELECTED: <LOW|HIGH>
FILENAME: <filename of the paper evaluated in attached doc, not the filename of the attached doc>
PUB_DATE: <YYYY-MM-DD>
STATUS: <string>
PROTOCOL_VERSION: <string>
VALID_RUN_COUNT: <N>
BIMODAL_CHECK: <YES|NO>
TRIM_APPLIED: <YES|NO>
POST_TRIM_RUN_COUNT: <int>




Output a single Markdown pipe table with exactly these columns in this order:
RunID, Valid, Kept, Score, E, M, L, A, S
The table must include:
One header row beginning with |
One separator row of dashes
One row per run in RunID order
After the final run row, stop the table.
Do not output any additional lines beginning with | after the last run row.
Output exactly one blank line before the next section.

SUMMARY_TABLE (Markdown pipe table only)
Output a single Markdown pipe table with exactly these columns in this order:
Stat, Score, Scores_VALID, Scores_KEPT, E, M, L, A, S
The table must include:
One header row beginning with |
One separator row of dashes
Exactly two data rows, in this order: Mean, Median
Scores_VALID and Scores_KEPT must each be a single-line bracket list, for example:
[45.00, 48.00, 40.00]
No line breaks are allowed inside those cells.
After the Median row, stop the table.
Do not output any additional lines beginning with |.
Output exactly one blank line before the glossary.
After the tables, output exactly:

GLOSSARY:
E: Equation and dimensional integrity (weight 3)
M: Mathematical formalism (weight 3)
L: Logical traceability (weight 2)
A: Assumption clarity and constraints (weight 2)
S: Scope coverage (weight 1)
Variance classification is defined as: STABLE for σ ≤ 2.40; 
BORDERLINE for 2.40 < σ ≤ 4.00; UNSTABLE for σ > 4.00.

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