mlsanityData to 7 Oct 2026

Literature-Augmented Clinical Outcome Prediction

arXiv 2111.08374 ↗First posted 16 Nov 2021cs.CL cs.AI cs.IRcited by 20

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Abstract (arXiv)

We present BEEP (Biomedical Evidence-Enhanced Predictions), a novel approach for clinical outcome prediction that retrieves patient-specific medical literature and incorporates it into predictive models. Based on each individual patient's clinical notes, we train language models (LMs) to find relevant papers and fuse them with information from notes to predict outcomes such as in-hospital mortality. We develop methods to retrieve literature based on noisy, information-dense patient notes, and to augment existing outcome prediction models with retrieved papers in a manner that maximizes predictive accuracy. Our approach boosts predictive performance on three important clinical tasks in comparison to strong recent LM baselines, increasing F1 by up to 5 points and precision@Top-K by a large margin of over 25%.

Key facts. Cited by 20 papers in the map (data through 7 Oct 2026). Builds on 18 of its 45 references that are in the map. First posted on arXiv 16 Nov 2021.

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18 of 45 references.

References · 18

  1. 2018BERT: Pre-training of Deep Bidirectional Transformers for Language Understandingcited by 40,204
  2. 2019BioBERT: a pre-trained biomedical language representation model for biomedical text miningcited by 1,935
  3. 2019Publicly Available Clinical BERT Embeddingscited by 995
  4. 2019Latent Retrieval for Weakly Supervised Open Domain Question Answeringcited by 691
  5. 2019Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasetscited by 298
  6. 2018Scalable and accurate deep learning for electronic health recordscited by 275
  7. 2019ScispaCy: Fast and Robust Models for Biomedical Natural Language Processingcited by 244
  8. 2021MS2: Multi-Document Summarization of Medical Studiescited by 80
  9. 2019Inferring Which Medical Treatments Work from Reports of Clinical Trialscited by 63
  10. 2020UmlsBERT: Clinical Domain Knowledge Augmentation of Contextual Embeddings Using the Unified Medical Language System Metathesauruscited by 53
  11. 2021Clinical Outcome Prediction from Admission Notes using Self-Supervised Knowledge Integrationcited by 43
  12. 2021Launching into clinical space with medspaCy: a new clinical text processing toolkit in Pythoncited by 40
6 more
  1. 2020Evidence Inference 2.0: More Data, Better Modelscited by 39
  2. 2019Clinical XLNet: Modeling Sequential Clinical Notes and Predicting Prolonged Mechanical Ventilationcited by 30
  3. 2018Improving Hospital Mortality Prediction with Medical Named Entities and Multimodal Learningcited by 14
  4. 2019Towards unstructured mortality prediction with free-text clinical notescited by 8
  5. 2021Domain-Specific Pretraining for Vertical Search: Case Study on Biomedical Literaturecited by 6
  6. 2019An Analysis of Attention over Clinical Notes for Predictive Taskscited by 4

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Cited by year (2026 to 7 Oct)

Citing papers per year: 2022: 3; 2023: 6; 2024: 2; 2025: 6; 2026: 3.

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  1. 2023Parameter-Efficient Fine-Tuning of LLaMA for the Clinical Domaincited by 38
  2. 2022A Computational Inflection for Scientific Discoverycited by 22
  3. 2022Retrieval augmentation of large language models for lay language generationcited by 21
  4. 2024RAM-EHR: Retrieval Augmentation Meets Clinical Predictions on Electronic Health Recordscited by 21
  5. 2022PMC-Patients: A Large-scale Dataset of Patient Summaries and Relations for Benchmarking Retrieval-based Clinical Decision Support Systemscited by 17
  6. 2023Pre-training Multi-task Contrastive Learning Models for Scientific Literature Understandingcited by 16
  7. 2025Towards Omni-RAG: Comprehensive Retrieval-Augmented Generation for Large Language Models in Medical Applicationscited by 13
  8. 2023General-Purpose Retrieval-Enhanced Medical Prediction Model Using Near-Infinite Historycited by 12
  9. 2023Jointly Extracting Interventions, Outcomes, and Findings from RCT Reports with LLMscited by 10
  10. 2025Explainable AI for Clinical Outcome Prediction: A Survey of Clinician Perceptions and Preferencescited by 4
  11. 2026MRAG: Benchmarking Retrieval-Augmented Generation for Bio-medicinecited by 4
  12. 2023BLIAM: Literature-based Data Synthesis for Synergistic Drug Combination Predictioncited by 3
8 more
  1. 2023Clinical Note Owns its Hierarchy: Multi-Level Hypergraph Neural Networks for Patient-Level Representation Learningcited by 2
  2. 2025Data-efficient Meta-models for Evaluation of Context-based Questions and Answers in LLMscited by 2
  3. 2025CliniBench: A Clinical Outcome Prediction Benchmark for Generative and Encoder-Based Language Modelscited by 1
  4. 2026Pursuing Best Industrial Practices for Retrieval-Augmented Generation in the Medical Domaincited by 1
  5. 2024Automatic Extraction of Disease Risk Factors from Medical Publicationscited by 0
  6. 2025CKD-EHR:Clinical Knowledge Distillation for Electronic Health Recordscited by 0
  7. 2025Integrating Text and Time-Series into (Large) Language Models to Predict Medical Outcomescited by 0
  8. 2026Enhancing Extubation Failure Prediction with LLM-Derived Features from Respiratory Therapy Clinical Notescited by 0