---
language:
- en
license: cc-by-4.0
pretty_name: ProSearch
tags:
- scientific-information-retrieval
- experimental-protocols
- benchmark
- AI-for-science
task_categories:
- text-retrieval
---

# ProSearch: Benchmarking Multi-Constraint Protocol Retrieval in Experimental Science

ProSearch is a benchmark for retrieving scientific method paragraphs
that satisfy natural-language queries containing multiple experimental
constraints. A relevant paragraph should support the constraints within
one coherent experimental setup.

The benchmark covers six experimental-science domains, with **1,515
queries** and **358,178 method paragraphs**.

## Dataset structure

Each domain directory contains four JSON files:

``` text
prosearch/
├── cell_culture/
├── electrochemistry/
├── immunotechnology/
├── inorganic_materials/
├── organic_synthesis/
└── polymer_materials/
```

Each directory contains:

| File | Description |
|---|---|
| `paragraphs.json` | Method paragraph candidate corpus used in the main experiments reported in the paper. |
| `all_paragraphs.json` | Full paragraph candidate corpus used for full-text retrieval comparisons. |
| `queries_raw.json` | Raw queries for the domain. |
| `qrels_stage1.json` | Query–paragraph relevance judgments. The JSON object maps each query ID to paragraph IDs with relevance label 1. |

## Dataset statistics

| Domain | Queries | Method paragraph pool | Full paragraph pool |
|---|---:|---:|---:|
| Cell culture | 284 | 46,004 | 311,042 |
| Electrochemistry | 201 | 91,375 | 409,133 |
| Immunotechnology | 264 | 93,315 | 644,077 |
| Inorganic materials | 247 | 46,136 | 240,380 |
| Organic synthesis | 252 | 30,371 | 197,506 |
| Polymer materials | 267 | 50,977 | 283,907 |
| **Total** | **1,515** | **358,178** | **2,086,045** |

The method paragraph pool is stored in `paragraphs.json`, while the full
paragraph pool is stored in `all_paragraphs.json`. The method paragraph
pool is used for the main benchmark experiments. The full paragraph pool
is used for the full-text retrieval analysis and contains paragraphs from
all body sections of the paper. Only the candidate pool changes between
the two settings; the queries and relevance definition remain the same.

## Data construction

The data were derived from English-language open-access scientific
articles. The construction pipeline includes article parsing,
method-paragraph selection, structured protocol extraction and
normalization, query construction, candidate-pool construction, and
relevance judgment against the original paragraph text.

Candidate-pool membership alone does not determine relevance; relevance
labels are provided in the corresponding qrels files.

## License

This dataset is released under the **Creative Commons Attribution 4.0
International (CC BY 4.0)** license. See the [license
text](https://creativecommons.org/licenses/by/4.0/).

## Citation

If you use ProSearch, please cite:

*ProSearch: Benchmarking Multi-Constraint Protocol Retrieval in
Experimental Science.* NeurIPS 2026 Evaluations & Datasets Track.

## Limitations

While ProSearch provides a systematic evaluation of multi-constraint
protocol retrieval, several limitations remain. First, the field schemas
and constraint rules are designed by domain experts for selected
experimental protocol types across six domains, limiting coverage of other
experimental procedures and requiring additional expert effort for
extension. Second, ProSearch focuses on individual method paragraphs and
does not evaluate evidence integration across multiple paragraphs, tables,
or supplementary materials. Third, LLM-based protocol extraction and
relevance labeling, together with annotation pools constructed from
extracted records, may introduce errors or omit relevant evidence.
Although expert audits and robustness analyses support the stability of
the main retrieval findings, systematic biases cannot be fully ruled out.
Finally, while the queries are grounded in real experimental records, they
are generated using templates and may not fully reflect researchers' actual
information needs. Whether benchmark scores translate into retrieval
usefulness in real scientific workflows also remains to be established.
Future work will extend ProSearch to cross-paragraph protocol retrieval and
incorporate researcher-authored queries and human evaluations to assess its
practical applicability.