About Tomasz
Staff-level ML Engineer with 12+ years of experience across Knowledge Graphs, Proteomics, and Generative Biology. Proven track record of architecting end-to-end discovery platforms that translate high-dimensional biological data into actionable research hypotheses. Expert in scaling Agentic RAG systems and Foundation Models (scGPT, Geneformer etc.) within GCP/AWS environments. High-autonomy contributor with an extensive background in open-source development and remote-first leadership.
Polish
Native or bilingual
English
Fluent
French
Conversational
Italian
Conversational
German
Basic
Remote only
Primarily works remotely
Experience
- ArdigenLead Data Scientist (Machine Learning Engineer)July 2021 - Today (5 years)
- Discovery Architecture: Technical Lead for the development of an automated discovery portal, transitioning R&D prototypes to production-ready systems on GCP and AWS (Kubernetes/SageMaker)
- Knowledge Graph Reasoning: Architected a relational inference engine using ComplEx-N3 to predict drug-target interactions, providing technical validation that led to confirmed experimental hits
- Foundation Models: Engineered a unified benchmarking framework for single-cell models (scGPT, Cell2Sentence), enabling standardized evaluation of high-dimensional embeddings
- Agentic RAG Systems: Designed and implemented LLM-based agentic workflows (LangChain, Gemini/GPT-4) for automated knowledge extraction from clinical trials and single-cell protocols
- Population-Scale Proteomics: Optimized Multi-Task Learning (MTL) pipelines for the UK Biobank (UKB-PPP) dataset to identify latent biological signals at scale
- MojoRankData Scientist / ML Engineer (Project Lead)September 2019 - June 2021 (1 year and 9 months)
- Technical Ownership: Directed the full-cycle development of NLP-based search and recommendation systems, from initial prototyping to production deployment
- Multilingual NLP: Applied Transformer-based architectures (BERT) to improve retrieval and parsing performance across English and French datasets
- ML Pipelines: Built and maintained scalable ML workflows using AzureML and Kubernetes to support production-level inference requirements
- Lekta AIMachine Learning Engineer (R&D)December 2018 - July 2019 (7 months)
- NLU Research: Developed and optimized deep learning NLP models for intent recognition and entity extraction in Polish
- SOTA Prototyping: Applied early Transformer and RNN research to develop proof-of-concept NLU applications for specialized, low-resource environments
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Education
- MSc in Computer ScienceAGH University of Krakow2018MSc in Computer Science
- Technical Student (Backend)CERN (European Organization for Nuclear Research)2016Technical Student (Backend)
Certifications
- Google Cloud Professional Machine Learning EngineerGoogle Cloud2025