Spring 2018

   Patrice Lopez


ISTEX & bibliographical references

  • GROBID 2014-2015: references perfectly recognized, f-score 60-65%
  • Training completed for bib.ref. GROBID by ISTEX team based on 10k native publisher XML

      ➡ Perfectly recognized references: f-score up to 75%
      ➡ Estimated 90% for recent articles

      ➡ 1 millionPDF processed in 24h (Xeon 10 CPU, 10

GB RAM, 3GB used in average, 9 threads) - so 11,5 PDF/s

      ➡ very large Open citation dataset (at least ~10 times Open Citation corpus)

The legendary GROBID CRF cascade

Segmentation model

133 documents PMC/HAL

Addition of 91 documents ISTEX

Segmentation model


Evaluation on 19 ISTEX documents

Segmentation model


split 80-20% on 97 documents

Full text model


20 documents de PubMed Central et HAL

Addition of 59 ISTEX full texts

Full text model


evaluation on 18 ISTEX documents

Full text model

split 80-20% on 97 documents

Improvement on Pubmed Central API - Header model


Ratcliff/Obershelp Matching, similarity at 0.95)
===== Field-level results =====     end 2015

                       label                accuracy     precision    recall       f1      

all fields        95.2        78.03        71.45        74.59      (micro average)
                       95.2        77.98        70.86        74.17      (macro average)
===== Field-level results =====     version 0.4.1

all fields        95.69       80.31       74.71        77.41      (micro average)
                       95.69       80.57       74.32        77.24      (macro average)

===== Field-level results =====   with current with new CrossRef API - v0.5.1

all fields        96.56        87.39      82.98        85.13      (micro average)
                96.56       86.94       82.08        84.32      (macro average)


Support of CrossRef REST API

  • Solution for title/author look-up in particular header model, not supporting the usual journal name/volume/first page query so weak for bib. references
  • A "slow" consolidation based on old CrossRef OpenURL web API would still be necessary for bibliographical reference
  • ... but we might simply implement our own resolver service by acquiring the complete CrossRef repo, subscribing to the new CrossRef Metadata APIs Plus Service (proposed since January 2018, with a SLA)



TEI-based full-text benchmarking


  • We routinely evaluate GROBID with the PubMed Central sample, 1942 PDF + nlm files, in particular for each release to monitor accuracy, runtime, etc.
  • Following an evaluation exercice of ISTEX R&D on automatic full text structuring with GROBID, we extended the benchmarking to PDF + TEI files, with TEI generated by Pub2TEI from the native publisher XML file


Current work in progress


  • Better PDF parsing: pdfalto (composed and special characters, reading order, spacing, etc.)

  • Structuring ebook (pdf/ALTO): training based on embedded "outline" (project Opaline)

  • Long due new header model: regenerate and reformat training data, new features, etc. targeting 0.90 f1 instance-based

  • New DL models for sequence labelling, and for text classification (Keras, efficient java embeddings)

    • it is challenging to make it production ready (loading of resources, native integration, memory usage)


Thanks !

   Patrice Lopez


GROBID Camp 27.03.2018 - 2

By kermitt2

GROBID Camp 27.03.2018 - 2

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