Principal Scientist (m/f/d) Biomedical Machine Learning

The position

As for now, we are seeking a Principal Machine Learning Scientist to join our newly established Applied AI & Analytics team within Boehringer Ingelheim’s Global Computational Innovation Unit in Vienna (@computationalinnovation), a growing international team with colleagues in Vienna (Austria), Biberach (Germany), and Ridgefield (USA). As one of the first members of this growing international team, you will develop and fine-tune state-of-the-art Machine Learning and Deep Learning models using real-world biomedical, imaging, molecular, and multimodal data. Working closely with our oncology and biology partners, you will translate cutting-edge AI into practical solutions that accelerate drug discovery and advance human health. This is a hands-on, delivery-focused role where your success will be measured by the impact and adoption of the robust, scientifically validated models you deliver.

Tasks & responsibilities

• Build, fine-tune, and benchmark Machine Learning and Deep Learning models on biomedical data, with an initial focus on adapting pathology foundation models (e.g., Prov-GigaPath, Virchow, and H-Optimus-0) as well as multimodal imaging and omics models for downstream predictive tasks.
• Collaborate closely with computational biologists, oncologists, and pathologists to translate complex biological questions into well-defined machine learning problems and convert model outputs into biologically and clinically meaningful insights.
• Embed rigorous evaluation, validation, and interpretability throughout the model development lifecycle, leveraging approaches such as attention- and gradient-based methods, explainability techniques, and counterfactual analyses.
• Develop reusable and well-documented modeling frameworks, components, and best practices that accelerate future projects and promote scalability across the organization.
• Stay at the forefront of advances in computational pathology, multimodal AI, and machine learning, identifying and applying the most relevant innovations to deliver scientific impact.

Requirements

• PhD in Computer Science, Data Science, Bioinformatics, Computational Biology, or another relevant scientific discipline, combined with hands-on industry experience in Machine Learning and Deep Learning at a senior level.
• Deep and demonstrable expertise in Machine Learning and Deep Learning, supported by strong proficiency in Python and modern deep learning frameworks (e.g., PyTorch), as well as proven experience in fine-tuning, transfer learning, and adapting large pre-trained models.
• Strong hands-on experience working with biological and biomedical data, such as transcriptomics/RNA-seq, digital pathology, medical imaging, or other omics data, including a solid understanding of domain-specific challenges such as normalization, batch effects, label generation, and data quality considerations.
• Strong scientific rigor and critical thinking skills, with the ability to assess whether models are learning meaningful biological signals and to design robust evaluation strategies that withstand biological and clinical scrutiny.
• Proven experience leading ML projects end-to-end, collaborating effectively with both technical and domain experts, and applying software engineering best practices, including version control, reproducibility, and development on modern cloud-based ML platforms.

Your Benefits

• Flexible working time models: home office and flexible working hours, depending on department and position – many things are possible with us.
• Additional days off (“bridge-days”): more free time through additional days off to bridge single working days between bank holidays and the weekend – without having to use vacation days.
• Canteen & Cafeteria: whether it's coffee and croissant for breakfast, various lunch menus or snacks in between – our subsidized staff restaurant & cafeteria has something for every taste including vegetarian and vegan options.
• Learning & development: diverse training and development opportunities for your personal and professional growth. Because: you never stop learning.
• Health promotion: health is important to us – that's why we offer different programs to promote physical and mental health.
• Public transport ticket: we encourage our employees to use public transport on their daily way to work. Costs for public transport? We cover them!

The minimum gross annual salary for this position is € 90.900 per year (full-time) according to the classification in the collective bargaining agreement for the chemical industry. Depending on professional experience and qualifications, we offer an overpayment.

We are looking forward to receiving your application online!

By uploading your application documents via our application portal, we can treat your data confidentially and in compliance with the GDPR.

Do you have any additional questions about the position? Your HR Recruiting Manager for this position is Magdalena Dzieweczyńska.

On our career site you will find further information about Boehringer Ingelheim as an employer as well as information about the application process and our different departments.