Tabulus-Runs

Tabulus-Runs contains recorded Atomic Layer Deposition (ALD) and Area-Selective Deposition (ASD) experiments accompanying the Tabulus study on reference-aware scientific table extraction.

Software: https://github.com/sciknoworg/tabulus
Documentation: https://tabulus.readthedocs.io/en/latest/
Gold-standard dataset: https://huggingface.co/datasets/SciKnowOrg/tabulus-gold

The release is organized around the objects a researcher is most likely to inspect:

domain → paper → pipeline Step → recorded artifacts

Tabulus-Runs contains recorded predictions and experimental outputs. The authoritative controlled gold-standard annotations and evaluator-facing expected outputs are published separately in Tabulus-Gold.

What is Tabulus?

Tabulus is a modular framework for digitizing scientific review tables into structured, citation-aware data. Its seven-Step workflow covers table localization and reconstruction, identification of reference-bearing tables, bibliography extraction, citation-to-bibliography matching, scholarly-reference resolution, and export of resolved structured tables.

Tabulus-Runs records artifacts produced while applying these Steps to review papers from the ALD and ASD literature.

Dataset structure

tabulus-runs/
├── README.md
├── ALD/
│   ├── README.md
│   ├── Cremers_2019/
│   ├── Miikkulainen_2013/
│   └── Puurunen_2005/
├── ASD/
│   ├── README.md
│   ├── Bent_2025/
│   ├── Bonvalot_Vallee_2021/
│   ├── Choi_2023/
│   ├── Mackus_2014/
│   ├── Park_2026/
│   ├── Parsons_2020/
│   └── Tonner-Zech_2025/
└── analysis/
    ├── README.md
    ├── all_runs.csv
    ├── step5_runs.csv
    ├── step5_ambiguous.csv
    ├── step5_skipped.csv
    └── step5_unmatched.csv

The release covers 10 source papers: 3 ALD papers and 7 ASD papers. Each paper directory contains the recorded artifacts retained for the seven pipeline Steps and, where applicable, machine-actionable examples.

The source publication PDFs are not distributed as part of the public dataset. Paper-level documentation identifies the corresponding source publication.

Recorded pipeline artifacts

Step	Recorded task	Public artifact role
Step 1 — Table localization	Locate and profile table regions in the source document	Recorded localization, crop, and related table-detection artifacts
Step 2 — Table reconstruction	Reconstruct detected tables as structured tabular data	Adapter-specific reconstructed table outputs
Step 3 — Reference-table classification	Identify reconstructed tables containing explicit literature-reference information	Recorded classification outputs exposed under step3/
Step 4 — Bibliography extraction	Extract the ordered bibliography of the source publication	Recorded bibliography artifacts
Step 5 — Reference matching	Match citations in table cells to bibliography positions	Recorded citation-to-bibliography matching outputs exposed under step5/
Step 6 — Scholarly reference resolution	Resolve linked bibliography entries to scholarly identities	Recorded paper-level resolution outputs
Step 7 — Resolved-table export	Join table content, bibliography links, and resolved scholarly identities	Deterministically generated resolved-table outputs

Step 3 and Step 5 artifacts were originally produced within adapter-specific reconstruction runs. They are exposed as explicit step3/ and step5/ directories in this public release for clarity.

Public directory and filename terminology uses Step, not Stage. Historical field names inside preserved machine-generated metadata are retained where changing them would alter the recorded artifact.

Release contents

The public release contains:

• 10 paper-level experiment directories
• 153 Step 3 classification artifacts
• 153 Step 5 reference-matching artifacts
• 10 Step 6 paper-level reference-resolution artifacts
• 153 Step 7 manifests
• 1,327 Step 7 resolved CSV outputs

The analysis/ directory additionally contains experiment-level summaries and Step 5 diagnostic tables retained for research inspection.

These counts describe recorded artifacts rather than independent gold-standard evaluation instances. Controlled quality targets are provided separately in Tabulus-Gold.

Recorded-run provenance

Operational cluster logs and _run_metadata/ directories are intentionally excluded from the public release. Research-relevant run summaries are retained under analysis/.

Legacy absolute filesystem paths embedded in retained artifacts were normalized to portable provenance identifiers such as original-run://.... These identifiers preserve the logical provenance relationship of the recorded artifact but are not expected to resolve on another machine.

The public release preserves scientific experiment outputs while excluding machine-specific operational information that is not required to inspect or reuse the recorded results.

Relationship to Tabulus-Gold

Tabulus-Gold contains the authoritative annotations and expected outputs used for controlled quality evaluation of the Tabulus pipeline.

Tabulus-Runs contains recorded experimental artifacts from the wider ALD and ASD study corpus.

Keeping the resources separate distinguishes the evaluation targets from the system outputs and recorded experiments being evaluated.

Citation

When using Tabulus-Runs, please cite the dataset repository. A DOI-based citation may be added if an archival DOI record is published in the future.

If you use the Tabulus software, please also cite the software repository:

@software{tabulus,
  author = {D'Souza, Jennifer and Rumleanschi, Vladimir},
  title = {Tabulus: End-to-End Scientific Review Table Digitization Pipeline},
  url = {https://github.com/sciknoworg/tabulus},
  year = {2026}
}

Tabulus was first developed in the following master's thesis:

@mastersthesis{rumleanschi2026tabulus,
  author = {Rumleanschi, Vladimir},
  title = {Tabulus: AI-Assisted Tabular Knowledge Extraction and Semantic Integration Framework for Scientific Literature},
  year = {2026},
  doi = {10.15488/21618},
  url = {https://doi.org/10.15488/21618}
}

License

The original experiment metadata, recorded Tabulus outputs, analysis files, and other original content created for Tabulus-Runs are licensed under the Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA 4.0).

You are free to share and adapt these materials for any purpose, provided that appropriate credit is given to the creators and that adapted material is distributed under the same or a compatible license.

Third-party material derived from the source publications is not covered by this license unless explicitly stated otherwise. Copyright and reuse rights for such material remain with the respective copyright holders.