mlsanityData to 7 Oct 2026

An Extensive Data Processing Pipeline for MIMIC-IV

arXiv 2204.13841 ↗First posted 29 Apr 2022cs.LGcited by 39

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Abstract (arXiv)

An increasing amount of research is being devoted to applying machine learning methods to electronic health record (EHR) data for various clinical purposes. This growing area of research has exposed the challenges of the accessibility of EHRs. MIMIC is a popular, public, and free EHR dataset in a raw format that has been used in numerous studies. The absence of standardized pre-processing steps can be, however, a significant barrier to the wider adoption of this rare resource. Additionally, this absence can reduce the reproducibility of the developed tools and limit the ability to compare the results among similar studies. In this work, we provide a greatly customizable pipeline to extract, clean, and pre-process the data available in the fourth version of the MIMIC dataset (MIMIC-IV). The pipeline also presents an end-to-end wizard-like package supporting predictive model creations and evaluations. The pipeline covers a range of clinical prediction tasks which can be broadly classified into four categories - readmission, length of stay, mortality, and phenotype prediction. The tool is publicly available at https://github.com/healthylaife/MIMIC-IV-Data-Pipeline.

Key facts. Cited by 39 papers in the map (data through 7 Oct 2026). Builds on 8 of its 34 references that are in the map. First posted on arXiv 29 Apr 2022.

Builds on

8 of 34 references.

References · 8

  1. 2016Temporal Convolutional Networks for Action Segmentation and Detectioncited by 504
  2. 2015Attention-Based Models for Speech Recognitioncited by 400
  3. 2017Multitask learning and benchmarking with clinical time series datacited by 287
  4. 2019BEHRT: Transformer for Electronic Health Recordscited by 258
  5. 2019MIMIC-Extract: A Data Extraction, Preprocessing, and Representation Pipeline for MIMIC-IIIcited by 121
  6. 2021HiRID-ICU-Benchmark -- A Comprehensive Machine Learning Benchmark on High-resolution ICU Datacited by 38
  7. 2019Reproducibility in Machine Learning for Healthcited by 24
  8. 2019Obesity Prediction with EHR Data: A deep learning approach with interpretable elementscited by 15

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Cited by year (2026 to 7 Oct)

Citing papers per year: 2023: 4; 2024: 7; 2025: 16; 2026: 12.

39 papers.

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  1. 2023EHRSHOT: An EHR Benchmark for Few-Shot Evaluation of Foundation Modelscited by 101
  2. 2023Multimodal Clinical Benchmark for Emergency Care (MC-BEC): A Comprehensive Benchmark for Evaluating Foundation Models in Emergency Medicinecited by 24
  3. 2023Mimic-IV-ICD: A new benchmark for eXtreme MultiLabel Classificationcited by 19
  4. 2025EHR-R1: A Reasoning-Enhanced Foundational Language Model for Electronic Health Record Analysiscited by 17
  5. 2024Confidence on the Focal: Conformal Prediction with Selection-Conditional Coveragecited by 14
  6. 2023Unmasking the Chameleons: A Benchmark for Out-of-Distribution Detection in Medical Tabular Datacited by 8
  7. 2024Vertical Federated Learning with Missing Features During Training and Inferencecited by 6
  8. 2024Benchmarking with MIMIC-IV, an irregular, spare clinical time series datasetcited by 5
  9. 2025Enforcing Fundamental Relations via Adversarial Attacks on Input Parameter Correlationscited by 5
  10. 2025Revisiting the MIMIC-IV Benchmark: Experiments Using Language Models for Electronic Health Recordscited by 5
  11. 2024meds_reader: A fast and efficient EHR processing librarycited by 4
  12. 2025Bridging Data Gaps of Rare Conditions in ICU: A Multi-Disease Adaptation Approach for Clinical Predictioncited by 4
27 more
  1. 2025Cross-Representation Benchmarking in Time-Series Electronic Health Records for Clinical Outcome Predictioncited by 4
  2. 2024HealthGAT: Node Classifications in Electronic Health Records using Graph Attention Networkscited by 3
  3. 2024MENSA: A Multi-Event Network for Survival Analysis with Trajectory-based Likelihood Estimationcited by 3
  4. 2026A Multimodal Data Processing Pipeline for MIMIC-IV Datasetcited by 3
  5. 2025Leveraging MIMIC Datasets for Better Digital Health: A Review on Open Problems, Progress Highlights, and Future Promisescited by 2
  6. 2026Retrieval-aligned Tabular Foundation Models Enable Robust Clinical Risk Prediction in Electronic Health Records Under Real-world Constraintscited by 2
  7. 2024Mitigating Overconfidence in Out-of-Distribution Detection by Capturing Extreme Activationscited by 1
  8. 2025Med-gte-hybrid: A contextual embedding transformer model for extracting actionable information from clinical textscited by 1
  9. 2025Unmasking Societal Biases in Respiratory Support for ICU Patients through Social Determinants of Healthcited by 1
  10. 2025The CRITICAL Records Integrated Standardization Pipeline (CRISP): End-to-End Processing of Large-scale Multi-institutional OMOP CDM Datacited by 1
  11. 2025SurvBench: A Standardised Preprocessing Pipeline for Multi-Modal Electronic Health Record Survival Analysiscited by 1
  12. 2026A Multimodal Deep Learning Framework for Predicting ICU Deterioration: Integrating ECG Waveforms with Clinical Data and Clinician Benchmarkingcited by 1
  13. 2025Challenges and recommendations for Electronic Health Records data extraction and preparation for dynamic prediction modelling in hospitalized patients -- a practical guidecited by 0
  14. 2025Towards Unified Approaches in Self-Supervised Event Stream Modeling: Progress and Prospectscited by 0
  15. 2025Censoring-Aware Tree-Based Reinforcement Learning for Estimating Dynamic Treatment Regimes with Censored Outcomescited by 0
  16. 2025Validating Emergency Department Admission Predictions Based on Local Data Through MIMIC-IVcited by 0
  17. 2025Partial VOROS: A Cost-aware Performance Metric for Binary Classifiers with Precision and Capacity Constraintscited by 0
  18. 2025Towards symbolic regression for interpretable clinical decision scorescited by 0
  19. 2026DT-ICU: Towards Explainable Digital Twins for ICU Patient Monitoring via Multi-Modal and Multi-Task Iterative Inferencecited by 0
  20. 2026Learning temporal embeddings from electronic health records of chronic kidney disease patientscited by 0
  21. 2026On Safer Reinforcement Learning for Sedation and Analgesia in Intensive Carecited by 0
  22. 2026An exponential mechanism based on quadratic approximations for fine-tuning machine learning models with privacy guaranteescited by 0
  23. 2026Improving Patient Subtyping on Longitudinal Data using Representations from Mamba-based Architecturecited by 0
  24. 2026CoMedBench: A Multi-Source Benchmark of Synthetic Medical Data Fidelity and Downstream Utilitycited by 0
  25. 2026How Compliant is Sepsis Treatment? An Expert-Guided Neuro-symbolic Pipeline for Generating Clinical Compliance Insightscited by 0
  26. 2026A Deep Latent Variable Framework for Jointly Modeling Missingness, Measurement Error, and Heterogeneitycited by 0
  27. 2026Beyond Demographic Balance: Multi-Metric and Intersectional Evaluation of Fairness in MIMIC-IV Mortality Predictioncited by 0