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A Joint Neural Baseline for Concept, Assertion, and Relation Extraction from Clinical Text

Fei Cheng, Ribeka Tanaka, Sadao Kurohashi · Mar 8, 2026 · Citations: 0

Automatic Metrics
Open arXiv Find Implementation RSS feed Shortlist (0)

How to use this page

Low trust

Use this as background context only. Do not make protocol decisions from this page alone.

Best use

Background context only

What to verify

Validate the evaluation procedure and quality controls in the full paper before operational use.

Evidence quality

Low

Derived from extracted protocol signals and abstract evidence.

Abstract

Clinical information extraction (e.g., 2010 i2b2/VA challenge) usually presents tasks of concept recognition, assertion classification, and relation extraction. Jointly modeling the multi-stage tasks in the clinical domain is an underexplored topic. The existing independent task setting (reference inputs given in each stage) makes the joint models not directly comparable to the existing pipeline work. To address these issues, we define a joint task setting and propose a novel end-to-end system to jointly optimize three-stage tasks. We empirically investigate the joint evaluation of our proposal and the pipeline baseline with various embedding techniques: word, contextual, and in-domain contextual embeddings. The proposed joint system substantially outperforms the pipeline baseline by +0.3, +1.4, +3.1 for the concept, assertion, and relation F1. This work bridges joint approaches and clinical information extraction. The proposed approach could serve as a strong joint baseline for future research. The code is publicly available.

Abstract-only analysis — low confidence

All signals on this page are inferred from the abstract only and may be inaccurate. Do not use this page as a primary protocol reference.

  • This paper looks adjacent to evaluation work, but not like a strong protocol reference.
  • The available metadata is too thin to trust this as a primary source.
Human Eval Hub LLM-as-Judge Hub Pairwise Preference Hub

Should You Rely On This Paper?

This paper is adjacent to HFEPX scope and is best used for background context, not as a primary protocol reference.

Best use

Background context only

Use if you need

A secondary eval reference to pair with stronger protocol papers.

Main weakness

This paper looks adjacent to evaluation work, but not like a strong protocol reference.

Trust level

Low

Usefulness score

0/100 • Low

Treat as adjacent context, not a core eval-method reference.

Human Feedback Signal

Not explicit in abstract metadata

Evaluation Signal

Detected

Usefulness for eval research

Adjacent candidate

Extraction confidence 35%

If you are doing eval pipeline work, start here:

Human Eval Hub LLM-as-Judge Hub Pairwise Preference Hub Tool-Use Eval Hub

What We Could Verify

These are the protocol signals we could actually recover from the available paper metadata. Use them to decide whether this paper is worth deeper reading.

Human Feedback Types

missing

None explicit

No explicit feedback protocol extracted.

"Clinical information extraction (e.g., 2010 i2b2/VA challenge) usually presents tasks of concept recognition, assertion classification, and relation extraction."

Evaluation Modes

partial

Automatic Metrics

Includes extracted eval setup.

"Clinical information extraction (e.g., 2010 i2b2/VA challenge) usually presents tasks of concept recognition, assertion classification, and relation extraction."

Quality Controls

missing

Not reported

No explicit QC controls found.

"Clinical information extraction (e.g., 2010 i2b2/VA challenge) usually presents tasks of concept recognition, assertion classification, and relation extraction."

Benchmarks / Datasets

missing

Not extracted

No benchmark anchors detected.

"Clinical information extraction (e.g., 2010 i2b2/VA challenge) usually presents tasks of concept recognition, assertion classification, and relation extraction."

Reported Metrics

partial

F1

Useful for evaluation criteria comparison.

"Clinical information extraction (e.g., 2010 i2b2/VA challenge) usually presents tasks of concept recognition, assertion classification, and relation extraction."

Human Feedback Details

  • Uses human feedback: No
  • Feedback types: None
  • Rater population: Not reported
  • Expertise required: Medicine, Coding

Evaluation Details

  • Evaluation modes: Automatic Metrics
  • Agentic eval: None
  • Quality controls: Not reported
  • Evidence quality: Low
  • Use this page as: Background context only

Protocol And Measurement Signals

Benchmarks / Datasets

No benchmark or dataset names were extracted from the available abstract.

Reported Metrics

f1

Research Brief

Metadata summary

Clinical information extraction (e.g., 2010 i2b2/VA challenge) usually presents tasks of concept recognition, assertion classification, and relation extraction.

Based on abstract + metadata only. Check the source paper before making high-confidence protocol decisions.

Key Takeaways

  • Clinical information extraction (e.g., 2010 i2b2/VA challenge) usually presents tasks of concept recognition, assertion classification, and relation extraction.
  • Jointly modeling the multi-stage tasks in the clinical domain is an underexplored topic.
  • The existing independent task setting (reference inputs given in each stage) makes the joint models not directly comparable to the existing pipeline work.

Researcher Actions

  • Compare this paper against nearby papers in the same arXiv category before using it for protocol decisions.
  • Validate inferred eval signals (Automatic metrics) against the full paper.
  • Use related-paper links to find stronger protocol-specific references.

Caveats

  • Generated from abstract + metadata only; no PDF parsing.
  • Signals below are heuristic and may miss details reported outside the abstract.

Recommended Queries

F1

Research Summary

Contribution Summary

  • We empirically investigate the joint evaluation of our proposal and the pipeline baseline with various embedding techniques: word, contextual, and in-domain contextual embeddings.
  • The proposed joint system substantially outperforms the pipeline baseline by +0.3, +1.4, +3.1 for the concept, assertion, and relation F1.

Why It Matters For Eval

  • We empirically investigate the joint evaluation of our proposal and the pipeline baseline with various embedding techniques: word, contextual, and in-domain contextual embeddings.

Researcher Checklist

  • Gap: Human feedback protocol is explicit

    No explicit human feedback protocol detected.

  • Pass: Evaluation mode is explicit

    Detected: Automatic Metrics

  • Gap: Quality control reporting appears

    No calibration/adjudication/IAA control explicitly detected.

  • Gap: Benchmark or dataset anchors are present

    No benchmark/dataset anchor extracted from abstract.

  • Pass: Metric reporting is present

    Detected: f1

Related Papers

Papers are ranked by protocol overlap, extraction signal alignment, and semantic proximity.

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