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GENIA

Introduced in GENIA corpus - a semantically annotated corpus for bio-textmining1 Jan 2003 archive 2025-07-28

The GENIA corpus is the primary collection of biomedical literature compiled and annotated within the scope of the GENIA project. The corpus was created to support the development and evaluation of information extraction and text mining systems for the domain of molecular biology.

The corpus contains 1,999 Medline abstracts, selected using a PubMed query for the three MeSH terms “human”, “blood cells”, and “transcription factors”. The corpus has been annotated with various levels of linguistic and semantic information.

The primary categories of annotation in the GENIA corpus and the corresponding subcorpora are:

  • Part-of-Speech annotation
  • Constituency (phrase structure) syntactic annotation
  • Term annotation
  • Event annotation
  • Relation annotation
  • Coreference annotation

Source: http://www.geniaproject.org/genia-corpus Image Source: http://www.geniaproject.org/genia-corpus

HomepageBenchmarksPapers JSON

Benchmarks archive 2025-07-28

All 7 leaderboards whose dataset resolves to this page shown (sort by any header). "First row" is the archive's own first row at snapshot, in the archive's row order; nothing here re-ranks and metric direction is not asserted.

First row (archive order)PaperCode
Nested Named Entity Recognition GENIA PIQN F1 81.77 Parallel Instance Query Network for Named Entity Recognition tricktreat/piqn 26 Compare
Named Entity Recognition (NER) GENIA DeepStruct multi-task w/ finetune F1 80.8 DeepStruct: Pretraining of Language Models for Structure... cgraywang/deepstruct 14 Compare
Dependency Parsing GENIA - LAS BiLSTM-CRF F1 91.92 From POS tagging to dependency parsing for biomedical... datquocnguyen/BioNLP +1 3 Compare
Dependency Parsing GENIA - UAS BiLSTM-CRF F1 92.84 From POS tagging to dependency parsing for biomedical... datquocnguyen/BioNLP +1 3 Compare
Event Extraction GENIA DeepEventMine F1 63.96 DeepEventMine: end-to-end neural nested event extraction... aistairc/DeepEventMine 2 Compare
Event Extraction GENIA 2013 DeepEventMine F1 56.72 DeepEventMine: end-to-end neural nested event extraction... aistairc/DeepEventMine 1 Compare
UIE GENIA KnowCoder-7b-IE F1 score 76.7 KnowCoder: Coding Structured Knowledge into LLMs for... ICT-GoKnow/KnowCoder 1 Compare

Papers archive 2025-07-28

30 shown of 31 papers with a leaderboard row on this dataset's benchmarks, newest first. The archive's own "papers using this dataset" list was never published, so this is the benchmark-backed subset; the archive's count for this dataset is 121. The Syntology column is from Syntology's graph (read 2026-09-24), stated per sample; it is not part of any archive number.

DateSamples run Syntology
To be Continuous, or to be Discrete, Those are Bits of Questions 1 1 12 Jun 2024 not harvested
KnowCoder: Coding Structured Knowledge into LLMs for Universal Information Extraction 1 1 12 Mar 2024 not harvested
UniversalNER: Targeted Distillation from Large Language Models for Open Named Entity Recognition 2 1 7 Aug 2023 ran 5 of 12 samples (7 unverified)
Comparing and combining some popular NER approaches on Biomedical tasks 1 1 30 May 2023 not harvested
DiffusionNER: Boundary Diffusion for Named Entity Recognition 3 1 22 May 2023 not harvested
Optimizing Bi-Encoder for Named Entity Recognition via Contrastive Learning 1 1 30 Aug 2022 ran 4 of 4 samples (0 unverified)
An Embarrassingly Easy but Strong Baseline for Nested Named Entity Recognition 1 1 9 Aug 2022 not harvested
DeepStruct: Pretraining of Language Models for Structure Prediction 1 3 21 May 2022 ran 7 of 13 samples (6 unverified)
BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model 1 1 8 Apr 2022 not harvested
Parallel Instance Query Network for Named Entity Recognition 1 1 20 Mar 2022 not harvested
Unified Named Entity Recognition as Word-Word Relation Classification 1 1 19 Dec 2021 not harvested
Fusing Heterogeneous Factors with Triaffine Mechanism for Nested Named Entity Recognition 1 1 14 Oct 2021 not harvested
Nested Named Entity Recognition via Explicitly Excluding the Influence of the Best Path 1 1 1 Aug 2021 not harvested
A Unified Generative Framework for Various NER Subtasks 1 1 2 Jun 2021 not harvested
A Sequence-to-Set Network for Nested Named Entity Recognition 1 1 19 May 2021 ran 5 of 5 samples (0 unverified; 5 pointer-only for licence)
Locate and Label: A Two-stage Identifier for Nested Named Entity Recognition 1 1 14 May 2021 not harvested
Nested Named Entity Recognition with Partially-Observed TreeCRFs 1 1 15 Dec 2020 not harvested
Biomedical Event Extraction with Hierarchical Knowledge Graphs 1 1 20 Sep 2020 not harvested
Pyramid: A Layered Model for Nested Named Entity Recognition 2 2 1 Jul 2020 not harvested
DeepEventMine: end-to-end neural nested event extraction from biomedical texts 1 2 17 Jun 2020 not harvested
Named Entity Recognition as Dependency Parsing 1 1 14 May 2020 ran 3 of 10 samples (7 unverified)
Bipartite Flat-Graph Network for Nested Named Entity Recognition 1 2 1 May 2020 not harvested
A Boundary-aware Neural Model for Nested Named Entity Recognition 1 2 1 Nov 2019 not harvested
Nested Named Entity Recognition via Second-best Sequence Learning and Decoding 3 5 5 Sep 2019 not harvested
Neural Architectures for Nested NER through Linearization 1 2 19 Aug 2019 not harvested
Sequence-to-Nuggets: Nested Entity Mention Detection via Anchor-Region Networks 1 2 10 Jun 2019 not harvested
SciBERT: A Pretrained Language Model for Scientific Text 6 4 26 Mar 2019 not harvested
Neural Segmental Hypergraphs for Overlapping Mention Recognition 1 2 3 Oct 2018 not harvested
A Neural Transition-based Model for Nested Mention Recognition 1 2 3 Oct 2018 not harvested
From POS tagging to dependency parsing for biomedical event extraction 2 2 11 Aug 2018 not harvested

The full list of 31 is in the JSON twin.

Dataset loaders archive 2025-07-28

No loader listed in the archive.

Tasks archive 2025-07-28

Named Entity Recognition (NER)UIEDependency ParsingEvent ExtractionNested Named Entity Recognition

License archive 2025-07-28

Unknown

Modalities archive 2025-07-28

TextsMedical

Languages archive 2025-07-28

English

Variants archive 2025-07-28

  • GENIA
  • GENIA - LAS
  • GENIA - UAS
  • GENIA 2013

4 variant names, as the archive lists them.

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