Raphael Kirchgaessner

Portland, OR 97225 (503) 206-2762 exitare@exitare.de

Pioneering the future of AI-driven healthcare as a biomedical PhD researcher at OHSU. I transform complex biological challenges into breakthrough solutions through cutting-edge machine learning, spatial omics, and cloud computing technologies.

Ready to revolutionize your organization? I deliver next-generation consulting that bridges scientific innovation with practical implementation. From advanced neural networks to intelligent data pipelines, let's build the future of your industry together.


Consulting Services

Transforming your business with cutting-edge artificial intelligence solutions and machine learning expertise

Machine Learning Setup

End-to-End ML Pipeline Development

Get started with robust machine learning pipelines tailored to your needs. Advanced deep learning architectures, neural networks, and AI model optimization for maximum performance.

Custom Neural Architectures
Pipeline Automation
Performance Optimization

AI Model Training & Analytics

Advanced Model Optimization & Intelligent Data Insights

Receive guidance with data preprocessing, model tuning, and evaluation. Neural architecture search and hyperparameter optimization for peak performance and accuracy.

Predictive Modeling
Model Evaluation
Data Preprocessing

Cloud AI Infrastructure

Scalable Computing Solutions

Optimize your AI projects with cloud-based solutions. Scalable computing, distributed training, and MLOps pipeline automation for enterprise-grade deployment.

Distributed Training
MLOps Automation
Auto-scaling Solutions

Website Development

Web Design & Development

Website development services to create stunning, responsive, and user-friendly websites. From design to deployment, I ensure your online presence is impactful and effective.

Responsive Design
Custom Development
SEO Optimization

Professional Experience

Building the future through innovation and expertise

PhD Researcher in Computational Oncology

Pioneering the next generation of AI-driven cancer research through advanced machine learning architectures and computational biology innovations. Creating robust algorithms for data-driven insights in precision oncology.

Technical Expertise
Graph Neural Networks Variational Autoencoders Deep Learning Spatial Omics Predictive Analytics
Impact & Value

Expertise in creating machine learning models to uncover novel insights from complex datasets—ideal for clients advancing data-driven solutions in precision medicine, healthcare, and beyond.

September 2019 - Present
Active

AI Consultant & Technical Mentor

Accelerating client success through personalized AI and machine learning mentorship, delivering cutting-edge technical guidance across diverse industries and skill levels.

Teaching Expertise
Angular Development Python Programming Machine Learning Data Science Cloud Architecture
Client Success

Customized, one-on-one guidance to boost technical skills and confidence, helping clients meet specific project needs and accelerate learning goals.

August 2022 - Present
Active

Founder & Technical Architect

Co-founded innovative AI-powered platform revolutionizing music production through intelligent audio processing and machine learning solutions. Led end-to-end product development and cloud infrastructure management.

Technical Leadership
Full-Stack Development Azure Cloud API Architecture ML Audio Processing DevOps
Innovation Impact

Experience in scalable AI application and service delivery, aligning technical solutions with creative industry needs and user-centered design principles.

January 2021 - Present
Active

Founder & AI Strategy Director

Leading strategic AI consulting firm, transforming businesses through data science excellence and next-generation intelligent solutions. Delivering comprehensive strategies and training for organizational advancement.

Strategic Consulting
AI Strategy Data Science Custom Training Business Intelligence Digital Transformation
Business Value

Proven success in executing marketing strategies and delivering tailored training for improved client operations and data-driven business evolution.

May 2022 - Present
Active

Academic Excellence

Forging expertise through cutting-edge research and innovation

Doctor of Philosophy (PhD)

Oregon Health & Science University
Biomedical Engineering • Computational Oncology

Pioneering AI-driven cancer research through advanced computational models and machine learning architectures, transforming complex biological data into actionable medical insights. Developing breakthrough methodologies for precision medicine.

Research Innovation
Variational Autoencoders Graph Neural Networks Data Embeddings Cancer Biology AI Protein Imputation Spatial Omics
Impact & Innovation
Revolutionary ML models advancing precision medicine and laying the groundwork for unified embedding patient databases.
Vector database innovations with applications in cancer treatment optimization
September 2019 - 2025
In Progress

Bachelor of Science

University of Applied Sciences Karlsruhe
Business Information Systems

Built foundational expertise in enterprise technology solutions, combining business strategy with technical implementation to drive organizational success. Developed comprehensive understanding of information systems architecture.

Thesis Project
Geolocation Intelligence Framework

Engineered intelligent customer acquisition system leveraging location analytics to optimize business growth strategies and streamline acquisition processes.

Business Analysis System Architecture Data Analytics Geolocation Systems Process Optimization
Academic Excellence (1.6)
Final Grade: 2.1 (Excellent)
September 2013 - September 2017
Completed

Technical Expertise

Cutting-edge technologies and professional capabilities

AI & Machine Learning

Advanced

Advanced expertise in cutting-edge machine learning frameworks and neural network architectures, specializing in biomedical applications and data-driven insights.

TensorFlow PyTorch Graph Neural Networks Variational Autoencoders MLFlow Deep Learning LLM

Programming Languages

Advanced

Proficiency in multiple programming paradigms with focus on scalable, production-ready code for data science, web development, and system architecture.

Python TypeScript C# Bash/Shell Others

Frameworks & Development Tools

Advanced

Comprehensive toolkit for full-stack development, data pipeline orchestration, and scalable application architecture across multiple platforms.

Angular Node.js React Ionic SnakeMake Docker Git/GitHub

Cloud & Database Systems

Advanced

Extensive experience in cloud architecture, database design, and scalable infrastructure management for high-performance computing and data-intensive applications.

Proficient in Azure cloud services and infrastructure as code
SQL, NoSQL and Vector database architectures
Advanced API design and microservices architecture
Microsoft Azure Redis Vactor Databases

Professional & Research Skills

PhD Level

Comprehensive professional capabilities combining technical expertise with research methodology, communication excellence, and strategic problem-solving approaches.

Scientific writing and technical communication
Complex problem solving and innovative solution design
Research methodology and data-driven insights
System architecture and scalable solution design
Team leadership and mentorship
Business strategy and technical consulting

Research & Publications

Computational biology research using machine learning to extract meaningful insights from complex biological data

Aggregating multimodal cancer data across unaligned embedding spaces maintains tumor of origin signal

Raphael Kirchgaessner, Kaya Keutler, Layaa Sivakumar, Xubo Song, Kyle Ellrott
Biorxiv, May 2025 Latest Publication

Machine Learning algorithms that preserve the underlying signal when aggregating multimodal cancer data, advancing computational approaches for comprehensive cancer analysis.

Multimodal Data Embedding Spaces Cancer Analysis Signal Preservation Vector Database Oncology Research

Imputing Single-Cell Protein Abundance in Multiplex Tissue Imaging

Raphael Kirchgaessner, Cameron Watson, Allison Creason, Kaya Keutler, Jeremy Goecks
Nature Communications, May 2025 Published

Innovative approach to impute protein abundance in tissue imaging, advancing the analysis of complex biological systems and enhancing data interpretation in biomedical research.

Single-Cell Analysis Protein Abundance Tissue Imaging Biomedical Research Deep Learning Oncology Research

SyntheVAEiser: augmenting traditional machine learning methods with VAE-based gene expression sample generation

Brian Karlberg, Raphael Kirchgaessner, Jordan Lee, Matthew Peterkort, Liam Beckman, Jeremy Goecks, Kyle Ellrott
Genome Biology, December 2024 Published

SyntheVAEiser, a variational autoencoder-based tool, synthesizes gene expression samples to augment datasets for machine learning tasks. Trained and tested on over 8,000 cancer samples, enhancing prediction accuracy for cancer subtypes.

8,000+ cancer samples analyzed
Improved prediction accuracy for underrepresented cohorts
Variational Autoencoders Gene Expression Cancer Subtypes Synthetic Data Oncology Research

Tumor model to tumor treatment: Applying deep learning approaches to map multimodal data

Brian Karlberg, Raphael Kirchgaessner, Jeremy R. Jacobson, Kyle Ellrott, Sara J. Gosline
Cancer Research, March 2024 Published

Novel VAE-based strategy for correcting platform effects in cancer drug response data, enhancing cross-model prediction accuracy and advancing translatability of proteogenomic studies.

Deep Learning Drug Response Proteogenomics Cross-Model Prediction Oncology Research

Computational Pipeline to Identify Gene Signatures Defining Cancer Subtypes

Ekansh Mittal, Vatsal Parikh, Raphael Kirchgaessner
bioRxiv, November 2022

Developed a novel computational pipeline for identifying gene signatures in cancer subtypes, demonstrating the power of data-driven approaches in oncology research.

Computational Pipeline Gene Signatures Cancer Subtypes Oncology Research

Project Portfolio

Innovative products and projects showcasing expertise in machine learning, application development, and biomedical research

PhD by AnoBrain.ai

SaaS Platform Live Product

Academic success platform that streamlines research project management for students, postdocs, and researchers. AI-powered tools help organize publications, grants, experiments, writing, and deadlines in one smart dashboard.

AI-powered journal suggestions and milestone creation
Smart calendar integration and deadline tracking
Institutional licenses for labs and universities
AI/ML Academic Research Project Management SaaS Development Calendar Integration

Divey

Mobile Application Live Product

A dive buoyancy calculator app leveraging AI to enhance diving safety and convenience. Advanced algorithms provide precise buoyancy calculations for safer underwater experiences.

Available on iOS and Android platforms
AI-powered safety calculations for diving
AI/ML Mobile Development Safety Systems Cross-Platform

Story Time: Paramithi

Open Source Educational

A storytelling app for children and parents featuring multi-language story starters. Designed to foster creativity and language learning through interactive storytelling experiences.

Multi-language support for global accessibility
Family-friendly interactive storytelling platform
Mobile Development Multi-language UI/UX Design Educational Tech

Origin Audio

Web Service Live Service

Comprehensive audio processing platform offering AI-powered tools for musicians and audio professionals. Features multiple services including intelligent auto-slicing, batch normalization, stem isolation, and format conversion - all with no upload limits or account requirements.

AI Auto Slicer - Automatically organize instrument samples into folders
Stem Isolator - Extract vocals, drums, bass, and instruments
Batch Normalizer & File Converter with unlimited processing
Free tier up to 25MB - No signup required for basic features
AI Audio Processing Stem Separation Batch Operations File Conversion Audio Normalization Cloud Service

Vector Database Explorer

Research Platform Live Platform

Advanced exploration platform for multimodal cancer data through vector embeddings. Based on groundbreaking research demonstrating how embeddings from unaligned latent spaces can encode complex biological data while preserving relationships between entities and tumor origin signals.

Multimodal cancer data analysis through vector embeddings
High-performance similarity search across high-dimensional embeddings
Interactive UMAP visualizations of vector spaces
3D interactive exploration of embedding space to explore relationships between entities
ChromaDB integration with comprehensive metadata support
Research Foundation: Published findings show that unaligned embedded values conserve signals for tumor classification and data modality recognition
Vector Embeddings ChromaDB UMAP Visualization Multimodal Analysis Biomedical Research High-Dimensional Data

Schedule Genius

SaaS Platform Live Product

Intelligent recruitment event management platform designed for higher education admissions. Streamlines complex interview scheduling with smart matching algorithms, automated coordination, and optimization engines that reduce scheduling time by 85%.

Smart matching system with preference-based optimization
85% reduction in scheduling time, 99% fewer conflicts
Seamless Excel export with professional formatting
Trusted by leading graduate programs and universities
85% Time Reduction
99% Fewer Conflicts
4.9/5 Admin Satisfaction
Optimization Algorithms Smart Matching Form Builder Real-time Dashboard Excel Integration Academic Systems

Connect With Me

Ready to harness the power of AI for your next project? Let's collaborate and create something extraordinary together.

Launch Your AI Project

Ready to transform your ideas into intelligent solutions

Email

exitare@exitare.de

Location

Portland, OR

Response Time

Within 24 hours