Inside Bioptimus: Training (and Tracking) Foundation Models for Biology

Discover how we at Bioptimus track and refine our foundation models for biology, to make them learn the language of life so they can help you accelerate drug discovery and compress development timelines.

At Bioptimus, we are pioneering the development of multi-scale foundation models for biology to help researchers and pharmaceutical teams accelerate drug discovery. By training our AI on protein sequences, DNA, and biopsy images, we are moving beyond fragmented approaches to model biology holistically—from molecules and cells up to tissues and patients. Our mission is to partner with you to compress drug development timelines from years to months and significantly improve the 90% clinical trial failure rate.

Building these massive, state-of-the-art models is an immense technical challenge. To ensure we deliver the most reliable and powerful AI tools to our customers, we utilize Neptune.ai as our essential experiment tracker. Because training foundation models requires extremely costly and complex experimentation, we rely on Neptune to seamlessly track intricate model dependencies, benchmark performance, and optimize our computational resources.

In this behind-the-scenes video, our team shares how this robust infrastructure directly benefits the tools we build for you. You'll learn:

  • Why we are building holistic foundation models to help you better predict how different patients will react to treatments.
  • How our partnership with Neptune ensures the absolute reliability of our data. By tracking an immense amount of metrics and hardware usage, we guarantee that the models we deploy for your research are thoroughly tested and optimized.
  • How a lightning-fast experimentation workflow allows our researchers to debug and iterate in real-time.

Because Neptune gives us the peace of mind to completely trust our experiment results, we can move faster and safely scale our AI. This rapid iteration means we can continuously deliver better, more reliable models to empower your medical research and ultimately help you save lives.

Read the full written Neptune AI case study here: https://neptune.ai/customers/bioptimus

More videos like this:

Rewriting Rare Disease R&D with Foundation Models
Video Thumbnail for: Rewriting Rare Disease R&D with Foundation Models
Join our CEO Jean-Philippe Vert on the RARECast podcast to discover how we are using foundation models to rewrite rare disease R&D and repurpose existing drugs .
Bridging the Gap: Bioptimus CEO Jean-Philippe Vert on Building the Foundational AI for Biology
Video Thumbnail for: Bridging the Gap: Bioptimus CEO Jean-Philippe Vert on Building the Foundational AI for Biology
In this deep-dive episode of the Empowered Paient Podcast, Jean-Philippe explains why understanding biology across all scales—from molecules to organs—is the key to unlocking the next generation of precision medicine.
Mathilda Strom, Founding COO @Bioptimus | Slush 2024
Video Thumbnail for: Mathilda Strom, Founding COO @Bioptimus | Slush 2024
At Slush 2024, our Founding COO Mathilda Strom took the stage to unveil how we at Bioptimus are building the world's first multiscale, multimodal foundation model for biology.
AI in Healthcare: Scaling Drug Discovery & Clinical Trials
Video Thumbnail for: AI in Healthcare: Scaling Drug Discovery & Clinical Trials
Join our Founding COO Mathilda Strom on the Startup Scaleup People podcast to explore how we are using AI to fix the 90% clinical trial failure rate. In this episode, Mathilda shares insights from her 20-year career in scaling high-impact ventures and explains why Bioptimus is a different kind of deep-tech challenge.
Bioptimus COO Mathilda Strom on AI, Compute, and the Future of Biological Foundation Models
Video Thumbnail for: Bioptimus COO Mathilda Strom on AI, Compute, and the Future of Biological Foundation Models
Mathilda Strom, the Founding COO at Bioptimus, shares her journey from building startups across Africa, Asia, and Latin America to helping shape one of the most ambitious AI and biology projects on the planet.
Foundation Models for Biology, Across Scales
Video Thumbnail for: Foundation Models for Biology, Across Scales
Discover how AI foundation models are revolutionising biology and drug discovery. Jean-Philippe Vert explores the future of multiscale virtual cells.
Mathilda Strom, Founding COO @Bioptimus | Slush 2024
Video Thumbnail for: Mathilda Strom, Founding COO @Bioptimus | Slush 2024
Slush is a founder-focused annual event delivering actionable company-building advice while bringing together the who’s who in startups and tech.
Building an AI model for Biology
Video Thumbnail for: Building an AI model for Biology
Could AI unlock the secrets of biology? In this WIRED Health 2025 Startup Pitch, Zelda Mariet, Principal Research Scientist and Co-Founder of Bioptimus, introduces their groundbreaking universal AI foundation model that connects biology at every scale - from molecules to cells, tissues, and organisms.
AI Is About to Simulate Human Biology
Video Thumbnail for: AI Is About to Simulate Human Biology
Can AI become a universal simulator of biology, helping predict disease, improve drug success rates, and reshape how medicine is developed? A thoughtful conversation on AI, biology, and the future of medicine. From lessons learned in big tech to what it takes to build enduring platforms in TechBio, this is a considered discussion for anyone interested in where scientific discovery is heading.