mlsanityData to 14 Oct 2026

PMOA-TTS: Introducing the PubMed Open Access Textual Times Series Corpus

arXiv 2505.20323 ↗First posted 23 May 2025cs.CL cs.AI cs.LGcited by 3

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Abstract (arXiv)

Clinical narratives encode temporal dynamics essential for modeling patient trajectories, yet large-scale temporally annotated resources are scarce. We introduce PMOA-TTS, a corpus of 124,699 single-patient PubMed Open Access case reports converted into structured textual timelines of (event, time) pairs using a scalable large-language-model pipeline (Llama 3.3 70B and DeepSeek-R1). The corpus comprises over 5.6 million timestamped events, alongside extracted demographics and diagnoses. Technical validation uses a clinician-curated gold set and three measures: semantic event matching, temporal concordance (c-index), and alignment error summarized with Area Under the Log-Time CDF (AULTC). We benchmark alternative prompting and model choices and provide documentation to support reproduction. PMOA-TTS enables research on timeline extraction, temporal reasoning, survival modeling and event forecasting from narrative text, and offers broad diagnostic and demographic coverage. Data and code are openly available in public repositories.

Key facts. Cited by 3 papers in the map (data through 14 Oct 2026). Builds on 17 of its 56 references that are in the map. First posted on arXiv 23 May 2025.

Builds on

17 of 56 references.

References · 17

  1. 2020Language Models are Few-Shot Learnerscited by 32,419
  2. 2023GPT-4 Technical Reportcited by 18,396
  3. 2024The Llama 3 Herd of Modelscited by 14,715
  4. 2023LLaMA: Open and Efficient Foundation Language Modelscited by 14,132
  5. 2019BioBERT: a pre-trained biomedical language representation model for biomedical text miningcited by 1,947
  6. 2020Domain-Specific Language Model Pretraining for Biomedical Natural Language Processingcited by 1,009
  7. 2022BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Miningcited by 538
  8. 2016DeepSurv: Personalized Treatment Recommender System Using A Cox Proportional Hazards Deep Neural Networkcited by 358
  9. 2017Multitask learning and benchmarking with clinical time series datacited by 290
  10. 2024BioMedLM: A 2.7B Parameter Language Model Trained On Biomedical Textcited by 86
  11. 2023TimeBench: A Comprehensive Evaluation of Temporal Reasoning Abilities in Large Language Modelscited by 39
  12. 2020An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Miningcited by 35
5 more
  1. 2025TIMER: Temporal Instruction Modeling and Evaluation for Longitudinal Clinical Recordscited by 34
  2. 2020Clinical Temporal Relation Extraction with Probabilistic Soft Logic Regularization and Global Inferencecited by 20
  3. 2023Temporal Supervised Contrastive Learning for Modeling Patient Risk Progressioncited by 10
  4. 2025A Large-Language Model Framework for Relative Timeline Extraction from PubMed Case Reportscited by 10
  5. 2025Reconstructing Sepsis Trajectories from Clinical Case Reports using LLMs: the Textual Time Series Corpus for Sepsiscited by 5

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Cited by year (2026 to 14 Oct)

Citing papers per year: 2026: 3.

3 papers.

  1. 2026Temporally Phenotyping GLP-1RA Case Reports with Large Language Models: A Textual Time Series Corpus and Risk Modelingcited by 2
  2. 2026Text Knows What, Tables Know When: Clinical Timeline Reconstruction via Retrieval-Augmented Multimodal Alignmentcited by 2
  3. 2026Grounded Adjudication of Variations across Extracted TimeLines (GAVEL): Comparing Clinical Timelines Against Their Case Reportscited by 0

Similar, not cited

Close in wording, no citation either way

  1. 2025Large Language Models with Temporal Reasoning for Longitudinal Clinical Summarization and Prediction
  2. 2025Temporal Relation Extraction in Clinical Texts: A Span-based Graph Transformer Approach
  3. 2025OpenTSLM: Time-Series Language Models for Reasoning over Multivariate Medical Text- and Time-Series Data
  4. 2026Hindsight Bias in Clinical Temporal Reasoning: How Future Data Exposure Affects Large Language Model Judgment
  5. 2025Evaluating Open-Weight Large Language Models for Structured Data Extraction from Narrative Medical Reports Across Multiple Use Cases and Languages
  6. 2026ViSTA: A Simple Bridge Extends Visual Alignment to Clinical Time-Series Understanding in Multimodal LLMs
  7. 2025Rethinking Tokenization for Clinical Time Series: When Less is More
  8. 2026CRAFT: LLM-Based Iterative Refinement for Temporal Reasoning over Clinical Narratives