Paul Kalnins

Clinician, researcher, and writer exploring integrative and systems-based medicine.

Paul Kalnins, ND, MS

Naturopathic Physician
Bioinformaticist | Biomedical Data Scientist | Computational Biologist

About Me

Postdoctoral researcher with two years of experience in biomedical data analysis, clinical informatics, and predictive modeling.

Completed a master’s degree in bioinformatics and computational biomedicine, with a focus on developing and validating machine learning models for digital health and disease risk prediction. Contributed to clinical data extraction, transformation, and pipeline design for multimodal datasets.

Passionate about building interpretable, real-time AI systems that leverage physiological signals and biosensor data (e.g., HRV, retinal imaging, voice) to monitor organ health and anticipate disease risk.

Skilled in wearable analytics, digital biomarker discovery, and user-centered data visualization. Deeply interested in applying systems science and network physiology to develop scalable, clinically meaningful tools for precision health.

Committed to advancing human-centered AI in healthcare by bridging biosensing technologies, machine learning, and clinical utility.

Skills

Core Competencies

  • Machine learning, deep learning, preditive modeling, multimodal AI, digital health, precision medicine
  • Time-series analysis, signal processing
  • EHR and clinical data, data visualization, physiological computing, personal informatics, responsible AI

Programming & Tools

  • Python, R, SQL, Git, Bash, Jupyter, Google Colab, RStudio, VSCode
  • Scikit-learn, XGBoost, PyTorch, TensorFlow, Keras
  • Model interpretability (SHAP, LIME) cross-validation, hyperparameter tuning
  • Familiarity with HTML5, CSS3, JavaScript (Node.js/Express.js), Django
  • Hands-on experience with Arduino and Raspberry Pi Pico for creating interactive projects and biomedical applications

Data Science

  • Data wrangling, feature engineering, EDA, statistical modeling, clustering, classification, regression
  • Wearable signal analysis (HRV, ECG, PPG), biosensor data pipelines
  • Digital biomarkers, real-time physiology tracking

Clinical Informatics & Research

  • EHR data analysis, FHIR, OMOP, CDM, clinical decision support systems, patient dashboards
  • Clinical experience in chronic disease management
  • Extensive teaching experience
  • Scientific/technical writing

🎓 Education

Master of Science (MS)
Bioinformatics & Computational Biomedicine
Oregon Health & Science University (OHSU) | Portland, Oregon
July 2023 – July 2025

Naturopathic Doctor (ND)
Naturopathic Medicine
National University of Natural Medicine (NUNM) | Portland, Oregon
Sept 1993 – June 1998

Master of Science (MSOM)
East Asian Herbal Medicine & Acupuncture
National University of Natural Medicine (NUNM) | Portland, Oregon
Sept 1996 – June 1998

Bachelor of Science (BS)
Physics & Mathematics
The Ohio State University | Columbus, Ohio
Sept 1987 – June 1992

💼 Professional Experience

Research Data Analyst 1
Oregon Health & Science University (OHSU), Casey Eye Institute
Sept 2024 – July 2025

  • Transformed and merged large-scale NIH AI-READI datasets through rigorous ETL processes, ensuring robust data quality and integrity for subsequent deep learning analyses in healthcare

NLM Postdoctoral Fellow (Bioinformatics & Computational Biomedicine)
Oregon Health Sciences University (OHSU)
July 2023 - July 2025

  • Engineered machine learning pipelines using Python to predict chronic disease risk from multimodal biomedical data, including wearable signals, clinical labs, and survey data, thereby enhancing patient risk stratification.
  • Applied advanced signal processing and feature engineering techniques (FFT, SDNN, RMSSD) to time-series data from wearable biosensors, leading to the discovery of novel digital biomarkers for early disease detection.
  • Utilized interpretable machine learning methodologies (SHAP, ROC-AUC, precision/recall analysis) to rigorously evaluate model performance, thereby enhancing model explainability and informing clinical decision-making.
  • Established reproducible and scalable workflows integrating Python, SQL, and Git to streamline biomedical data analysis, fostering efficient collaboration and reliability in research outcomes.

Naturopathic Physician | Telehealth Provider
Self-employed
Jan 2021 - Present

  • Deliver personalized, integrative care through telehealth to clients with chronic health conditions, including chronic pain, autoimmune disorders, and cardio-metabolic dysfunction.
  • Utilizing a holistic approach combining evidence-based naturopathic treatments with lifestyle interventions to optimize health outcomes.
  • Developing customized wellness plans, integrating nutrition, herbal medicine, and stress management strategies for long-term health and resilience.
  • Leveraging telemedicine technologies to expand patient access to integrative care and facilitate ongoing health monitoring.

Assistant Professor | Attending Physician
National University of Natural Medicine (NUNM)
Sept 2004 - Sept 2020

  • Led the instruction of biomedical science courses (physiology, biochemistry, endocrinology, pharmacology) to medical students, fostering a deep understanding of integrative medicine.
  • Supervised students in the university’s outpatient teaching clinics, providing hands-on training in patient care and clinical decision-making.
  • Mentored students in clinical research trials, guiding them through study design, data collection, and analysis to publish peer-reviewed work.
  • Contributed to the leadership and strategic direction of the university by actively participating in curriculum redesign and administrative committees.
  • Collaborated with faculty members to develop innovative course materials and teaching methodologies that integrated evidence-based medicine with holistic treatment approaches.

Naturopathic Physician | Private Practice
New Health Horizons, LLC
Jan 1999 - Sept 2004

  • Provided comprehensive naturopathic primary care in a multidisciplinary clinical setting.

Publications

Capstone

  • Kalnins, P. (2025). Wearable-derived autonomic metrics for predicting metabolic and hepatic risk: Insights from AI-READI (Master’s capstone project). Department of Medical Informatics and Clinical Epidemiology, School of Medicine, Oregon Health & Science University. DOI: 10.6083/bpxhc44709

Theses

  • Kalnins, P. Toxemia and Terrain: The Evolution of Intestinal Dysbiosis and Hyperpermeability (1998)
  • Kalnins, P. Goethean Phenomenology: An Alternative to Phytochemical Reductionism (1998)

Journal Articles

  • Mist SD, Aickin M, Kalnins P, et al. Reliability of AcuGraph system for measuring skin conductance at acupoints. Acupunct Med. 2011; 29(3):221-6. DOI: 10.1136/aim.2010.003012
  • Shaw K, Wright K, Wang J, Kalnins P. Synergism of herbs in classical Chinese medicine: evidence from HPLC. BMC Complement Altern Med 2012; 12(Suppl 1):P39. DOI: 10.1186/1472-6882-12-S1-P39
  • Dombrowski A, Imre K, Yan M, Kalnins P, et al. Treatment of Osteoarthritis With Low-level Laser Therapy, Acupuncture, and Herbal Therapy: A Case Report. Integr Med (Encinitas). 2018; 17(2):48-53. PMID: 30962785
  • Kalnins P, Brucker M, Spears D. Prolonged Survival in a Patient with Idiopathic Pulmonary Fibrosis Receiving Acupuncture and DHEA-Promoting Herbs with Conventional Management: A Case Report. Perm J. 2019; 23:18-074. DOI: 10.7812/TPP/18-074

Recent Coursework

Oregon Health Sciences University (OHSU)

  • Introduction to Biomedical Informatics (BMI 510)
  • Introduction to Clinical Informatics (BMI 512)
  • Introduction to Biostatistics (BSTA 525)
  • Probability & Statistical Inference (BMI 531)
  • Bioinformatics Algorithms (BMI 550)
  • Bioinformatics Programming & Scripting (BMI 565)
  • Bioinformatics Statistical Methods (BMI 551)
  • Network Science and Biology (BMI 567)
  • Software Engineering (BMI 546)
  • Machine Learning (BMI 543)
  • Clinical Research Informatics (BMI 523)
  • Scientific Writing & Communication (BMI 570)

Online Certifications (Coursera/Udemy)

  • Google Data Analytics Career Certificate (Coursera, 2022)
  • Complete Web Developer Bootcamp (Udemy, 2022)
  • Complete Python Bootcamp (Udemy, 2022)
  • Data Science & Machine Learning with Python (Udemy, 2022)
  • Deep Learning with PyTorch (Udemy, 2025)

Targeted Domains & Interests

Digital Biomarkers • Biosensors • Multimodal AI • Real-Time Physiology • Remote Monitoring • Biological Rhythms • Clinical Decision Support • EHR Visualization • Human-Centered AI in Healthcare • Salutogenic Healthcare • Stress Resilience • Machine learning • Deep learning