Machine Learning Research Scientist, Generative Biology

Department: Engineering

Location: New York HQ 🗽

Compensation: $120K – $250K • Offers Equity

Employment Type: FullTime

Join our team and help build the world's first biological reasoning model. Work with us to build generative foundational models that decode biological systems across scales — from molecules to organisms — enabling us to predict, understand, and program living systems in ways never before possible.

Output Biosciences is currently in stealth, operated by a team of repeat founders and biotech veterans with multiple exits in AI and biology, and backed by top VCs including Y Combinator.

As a Generative AI Research Scientist, you'll work alongside our founders and team members to develop advanced generative models that can synthesize and design biological systems at multiple scales. Building upon our biological reasoning model, you'll focus on creating the generative capabilities that turn insights into innovations.

• ⁠You will design and develop cutting-edge generative models specifically for biological data, creating AI systems that can generate novel molecular structures, protein designs, cellular components, and biological pathways.

• You will design and implement state-of-the-art generative algorithms including diffusion models, language diffusion models, diffusion transformers, and flow matching approaches and tailor them to biological constraints and properties

• You will train and scale innovative AI models using large, diverse biological multi-modal datasets across distributed GPU clusters.

• You will solve challenging AI research problems at scale, tackling key aspects such as model architecture and scaling, pre-training and fine-tuning strategies, and rigorous evaluation methods.

• Your work will span various advanced generative AI architectures, including transformers, diffusion models, and autoencoders, exploring and implementing these techniques to push the boundaries of biological AI.
  

Who We're Looking For:

• You have a Bachelor's degree in Computer Science, Computer Engineering, Mathematics, Physics, or a relevant technical field.

• You have a PhD with 2 years of research experience, or a Bachelor's degree with 4+ years of research or industry experience in Deep Learning, Artificial Intelligence, or other relevant fields.

• You have a strong publication record in top-tier AI conferences or journals (e.g., NeurIPS, ICML, ICLR).

• You have extensive hands-on experience building and training generative models, such as diffusion models, GANs, VAEs, normalizing flows, or autoregressive models.

• You are proficient in Python and have expertise in at least one major deep learning framework (PyTorch, TensorFlow, or JAX).
  

Who You Are:

• You have excellent problem-solving skills and the ability to quickly adapt to new challenges.

• You exhibit a proactive approach to problem-solving, thinking beyond the specific task, taking ownership of challenges, and taking pride in solving them.

• You have a mature mindset in ambiguous situations, helping to frame questions and seek clarity while making decisions in the face of uncertainty.

• You have excellent communication skills and can clearly articulate complex technical concepts.

• You are motivated by making a real impact and are committed to tackling problems of significant consequence with determination and creativity.

Bonus points:

• You have experience applying machine learning to biological or chemical problems.

• You have knowledge of physics, molecular biology, chemistry, computational biology, bioinformatics, cheminformatics or related fields.

• You have experience with multi-modal learning.

• You have contributed to open-source machine learning projects.

• You have experience in developing efficient code in C/C++.

Our Values

❤️ Heart: We foster a culture of ownership. We are assembling a team of individuals who are passionate and take pride in their contributions.

🏆 Excellence: We have an unwavering commitment to excellence and continuously challenge ourselves to reach the highest standards.

🚀 Practicality: We value practicality and results-oriented thinking. We are committed to making a tangible impact on the lives of patients and the broader community.

📣 Honesty: We place a high value on honesty and directness. We firmly believe in addressing issues as they arise, in an open and transparent manner.

🎮 Fun: We believe that life is too short to not have fun. Our goal is to create a workplace that is fun, engaging, rewarding and fulfilling.

What We Offer

• We encourage new and different ideas, creativity and contrarian thinking

• Healthy feedback focused environment to help you strive - leadership will have high expectations, regularly share constructive feedback, support you and help you grow, and welcome receiving feedback and ideas from you

• You own your day-to-day management. What we care about is that we all hit our milestones

• Competitive salary and equity in a growing, well-funded startup

• Excellent medical, dental, and vision coverage