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kirilklein/README.md

Kiril Klein, PhD

Machine Learning Engineer

LinkedIn Google Scholar Email

Some professional work appears under my work GitHub account: @kvk-cmd


Machine Learning Engineer with a PhD in Machine Learning and Causal Inference. I work on ML systems, clinical NLP, and causal inference using longitudinal electronic health records.


πŸ› οΈ What I work on πŸ› οΈ

πŸ₯ At Aiomic (Copenhagen), I work on ML pipelines that combine transformers and classical ML for clinical data
πŸ” Data preparation, model training and validation, Docker-based services, and CI/CD
🧠 Transformers and NLP on clinical data, including pre-training on structured longitudinal EHR and fine-tuning for predictive tasks
πŸŽ“ PhD in Machine Learning and Causal Inference, University of Copenhagen. Dissertation: Scalable Causal Inference on Electronic Health Records Using Transformers
🌍 Contributor to MEDS, the community standard and ecosystem for ML on structured medical data


βš™οΈ Languages & Tools βš™οΈ


PyTorch Lightning Hydra XGBoost LightGBM TF-IDF CI/CD


πŸ”¬ Selected work πŸ”¬

BONSAI
Current collaborative codebase for transformer-based modeling of Electronic Health Records

Stars Forks
CORE-BEHRT (paper)
A Carefully Optimized and Rigorously Evaluated BEHRT. PMLR vol. 252, 2024 (joint first authorship)

PMLR
PHAIR-EHR
Research extension of CORE-BEHRT for causal analyses on EHR data

Stars Forks
CORE-BEHRT (original)
Original CORE-BEHRT implementation. Contributor.

Stars Forks
MEDS β€” An Emerging Data Standard and Ecosystem for Health AI Research
NEJM AI, 2026, co-author. Community standard for ML on structured medical data (website Β· GitHub org)

NEJM AI

πŸ”Ž Show More πŸ”

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  1. FGA-DIKU/BONSAI FGA-DIKU/BONSAI Public

    A BERT-based framework for processing and analyzing Electronic Health Records (EHR) data. It provides an end-to-end pipeline for data preprocessing, model training, and clinical outcome prediction.

    Python 11 6

  2. mikkelfo/CORE-BEHRT mikkelfo/CORE-BEHRT Public

    Jupyter Notebook 19 5

  3. CausalEstimate CausalEstimate Public

    Lightweight causal inference from precomputed propensity scores and outcome predictions: IPW, AIPW, TMLE, matching, bootstrap CIs. Pandas-native.

    Python 2 2

  4. PHAIR_EHR PHAIR_EHR Public

    A fork of the EHR corebehrt repo for causal inference.

    Python 2 2

  5. FGA-DIKU/ehr2meds FGA-DIKU/ehr2meds Public

    Scripts for transforming raw EHR data into the structured MEDS format

    Python 4 2