@inproceedings{rovai-2026-recovering,
title = "Recovering Method Parameters from Protocol Prose: Task Definition, Audited Extraction, and the Comparability It Licenses",
author = "Rovai, Fabio",
editor = "Accomazzi, Alberto and
Ghosal, Tirthankar and
Grezes, Felix and
Lockhart, Kelly and
Alkan, Atilla Kaan",
booktitle = "Proceedings of the 4th Workshop on Artificial Intelligence for Scientific Publications",
month = nov,
year = "2026",
address = "Hengqin, Zhuhai, China",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/2026.wasp-1.26/",
pages = "247--261",
ISBN = "979-8-89176-456-9",
abstract = "Repositories usually report metadata quality as completeness, the share of fields filled. We measure instead whether two deposited analyses record enough to be compared. Over all 167,331 pairs of gas chromatography analyses in Metabolomics Workbench, 120 pairs meet the necessary conditions for comparing retention indices and two meet those for comparing retention values; one field, the retention index reference series, recorded for 19 of 579 analyses, removes 99.9{\%} of the pairs that share a stationary phase. The oven temperature programme is usually written in the protocol prose instead, and the series sometimes is, so we define their recovery as an extraction task with ordered output and explicit abstention. Audited by two blind LLM raters whose error detection we measure on planted errors, the programme extractor is 65{\%} precise on 40 random MetaboLights recoveries with no fabricated value, recovers in full 49{\%} of the programmes stated in a separate random sample of 40 protocols, and the series extractor is correct on 57 of 66. On the census corpus itself, recovered series raise the pairs that can compare indices from 120 to 171, or from 78 to 92 when the two series must be identical. Of 239 populated Workbench programme fields, 130 hold only a range, a single temperature or a pointer to a paper, yet a completeness audit counts all of them as filled. Every released value carries its source sentence and is attributed to the extracting pipeline, not to the depositor."
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<abstract>Repositories usually report metadata quality as completeness, the share of fields filled. We measure instead whether two deposited analyses record enough to be compared. Over all 167,331 pairs of gas chromatography analyses in Metabolomics Workbench, 120 pairs meet the necessary conditions for comparing retention indices and two meet those for comparing retention values; one field, the retention index reference series, recorded for 19 of 579 analyses, removes 99.9% of the pairs that share a stationary phase. The oven temperature programme is usually written in the protocol prose instead, and the series sometimes is, so we define their recovery as an extraction task with ordered output and explicit abstention. Audited by two blind LLM raters whose error detection we measure on planted errors, the programme extractor is 65% precise on 40 random MetaboLights recoveries with no fabricated value, recovers in full 49% of the programmes stated in a separate random sample of 40 protocols, and the series extractor is correct on 57 of 66. On the census corpus itself, recovered series raise the pairs that can compare indices from 120 to 171, or from 78 to 92 when the two series must be identical. Of 239 populated Workbench programme fields, 130 hold only a range, a single temperature or a pointer to a paper, yet a completeness audit counts all of them as filled. Every released value carries its source sentence and is attributed to the extracting pipeline, not to the depositor.</abstract>
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%0 Conference Proceedings
%T Recovering Method Parameters from Protocol Prose: Task Definition, Audited Extraction, and the Comparability It Licenses
%A Rovai, Fabio
%Y Accomazzi, Alberto
%Y Ghosal, Tirthankar
%Y Grezes, Felix
%Y Lockhart, Kelly
%Y Alkan, Atilla Kaan
%S Proceedings of the 4th Workshop on Artificial Intelligence for Scientific Publications
%D 2026
%8 November
%I Association for Computational Linguistics
%C Hengqin, Zhuhai, China
%@ 979-8-89176-456-9
%F rovai-2026-recovering
%X Repositories usually report metadata quality as completeness, the share of fields filled. We measure instead whether two deposited analyses record enough to be compared. Over all 167,331 pairs of gas chromatography analyses in Metabolomics Workbench, 120 pairs meet the necessary conditions for comparing retention indices and two meet those for comparing retention values; one field, the retention index reference series, recorded for 19 of 579 analyses, removes 99.9% of the pairs that share a stationary phase. The oven temperature programme is usually written in the protocol prose instead, and the series sometimes is, so we define their recovery as an extraction task with ordered output and explicit abstention. Audited by two blind LLM raters whose error detection we measure on planted errors, the programme extractor is 65% precise on 40 random MetaboLights recoveries with no fabricated value, recovers in full 49% of the programmes stated in a separate random sample of 40 protocols, and the series extractor is correct on 57 of 66. On the census corpus itself, recovered series raise the pairs that can compare indices from 120 to 171, or from 78 to 92 when the two series must be identical. Of 239 populated Workbench programme fields, 130 hold only a range, a single temperature or a pointer to a paper, yet a completeness audit counts all of them as filled. Every released value carries its source sentence and is attributed to the extracting pipeline, not to the depositor.
%U https://aclanthology.org/2026.wasp-1.26/
%P 247-261
Markdown (Informal)
[Recovering Method Parameters from Protocol Prose: Task Definition, Audited Extraction, and the Comparability It Licenses](https://aclanthology.org/2026.wasp-1.26/) (Rovai, WASP 2026)
ACL