Experience

Ardigen

• Poland
• Biotechnology Research
• 100 - 200 Employee

• Lead Data Scientist (Immunology R&D)

  • Nov 2022 - Present

  - Applying AlphaFold2 to predict protein structures- Deploying models to huggingface

• Senior Data Scientist (Immunology R&D)

  • Oct 2021 - Nov 2022

  - Predicting biological properties of short proteins with attention-based NLP models (transformers, huggingface)- Designing and implementing a package wrapping deep learning models (incl. CI, unit tests, documentation, docker images, dvc, lightning, mlflow)- Through model verification with tailored CV- Identifying immunogenic peptides with Bayesian models (MCMC, variational inference, jax, numpyro)

• Technical Lead (Microbiome R&D)

  • May 2021 - Oct 2021

  - Leading the development of a pipeline mixing bioinformatic tools and machine learning. The pipeline encompasses complex flow of large-scale metagenomic data, feature generation, training multiple models and generating reports.- Proposing and evaluating new directions for the development of our microbiome analysis platform.- Designing an ecosystem of modules for analyzing multi-omic data.

• Senior Data Scientist (Microbiome R&D)

  • Oct 2019 - Oct 2021

  - Analyzing challenging clinical data (<100 samples, high-dimensional, multimodal data)- Using classical, Bayesian and deep learning models, implementing & deploying customized algorithms.- ML stack: jupyter, pandas, sklearn, seaborn, git, kubernetes, docker, pytorch, tensorboard.- Bayesian modeling stack: numpyro, arviz, JAX- Authored a general-purpose machine-learning package (used company-wide) with CI, tests & documentation- Knowledge sharing: mentoring colleagues, giving talks at the company seminar, writing blog posts & papers- Leading interdisciplinary teams of data scientists and bioinformaticians- Working directly with clients, working hands-on and as a lead, creating proposals for new projects- Writing grants to The National Centre for Research and Development. Show less



Comma Soft AG

• Germany
• Business Consulting and Services
• 1 - 100 Employee

• Machine Learning Expert

  • Nov 2018 - Sep 2019

  - Working on FASTGenomics, a jupyter-based platform for analyzing and sharing of genomic data. - Creating and maintaining an ecosystem of python & R modules (github, docker hub, travis-ci, readthedocs, etc.). - Designing and implementing R- & python-based REST clients. - Wrapping machine-learning algorithms into production-quality docker images, including tests and contiguous integration. - Worked with sklearn, pandas, numpy, jupyter & more - Working on FASTGenomics, a jupyter-based platform for analyzing and sharing of genomic data. - Creating and maintaining an ecosystem of python & R modules (github, docker hub, travis-ci, readthedocs, etc.). - Designing and implementing R- & python-based REST clients. - Wrapping machine-learning algorithms into production-quality docker images, including tests and contiguous integration. - Worked with sklearn, pandas, numpy, jupyter & more



Bonn University

• Research Services
• 100 - 200 Employee

• Senior Postdoctoral Researcher

  • Nov 2016 - Oct 2018

  - Developing Bayesian models for single-cell data and fitting them with variational inference.- Developing and testing novel machine-learning methods for bioinformatics.- Implementing and maintaining pipelines for terabyte-scale genomic data.- Advising the research group on statistical methods.- Giving lectures & seminars on machine-learning for bioinformatics, organizing workshops on Julia & pipeline design.- Worked in Julia & Python.

• Postdoctoral Researcher

  • Nov 2014 - Oct 2016

  - Implementing high-performance numerical methods for differential equations in Julia.- Developing computer-assisted proofs in Mathematica.- Proving rigorous results in differential equations.



Motorola

• 1 - 100 Employee

• Summer Internship

  • Jul 2007 - Aug 2007

  Quality assurance Quality assurance