Output Biosciences is pioneering Biologically-Aware Generative AI to finally understand complex biological systems. We are building Large Biological Models that can generate breakthrough medicines and transform the way we diagnose, treat and prevent disease. Output was founded by Adi Mashiach, MD and Mirella Mashiach. Adi is third time founder of AI-driven biotech startups (first was acquired, second is on Nasdaq), a former physician and researcher in computational systems biology focused on nonlinear dynamics; Mirella is a former big pharma exec and biotech investor.

The Role

Join us in creating biological reasoning and building foundational models for systems biology, harnessing generative AI to revolutionize our understanding and programming of biology from molecules to organisms. As a Machine Learning Engineer, you'll work alongside our founders and team members to develop and implement cutting-edge AI systems capable of complex biological reasoning across multiple scales.

• You will design and implement advanced machine learning algorithms to enhance model performance and biological understanding
• You will develop and fine-tune generative models for biological applications, exploring innovative architectures to capture the complexities of multi-scale biological systems
• You will work on distributed training systems to scale our models to billions of parameters, optimizing for performance and efficiency across multi-GPU and multi-node setups while handling large-scale biological datasets
• You will engineer efficient data pipelines to manage and process massive biological datasets, addressing challenges in data loading, splitting, and memory optimization
• You will develop and implement robust evaluation frameworks for complex biological models, ensuring data integrity and preventing leakage across dataset splits

Who We're Looking For:

• You have a Bachelor's in Computer Science, Machine Learning, or a related technical field
• You have 3+ years of experience in developing and implementing machine learning models
• You are proficient in Python and have expertise in at least one major deep learning framework (PyTorch, TensorFlow, or JAX)
• You have experience with deep learning and generative architectures such as transformers, diffusion models and autoencoders
• You are skilled in working with large-scale datasets and distributed computing environments
• You are skilled in scaling models and working with large-scale datasets and distributed computing environments, including experience with AWS for training, inference and deployment
• You have a strong understanding of machine learning fundamentals, including various model architectures, optimization techniques, and evaluation metrics
• You have experience in designing and implementing efficient data pipelines for processing and managing large datasets
• You are experienced in developing robust evaluation frameworks and ensuring data integrity in machine learning projects
• You are experienced in code organization, version control, and collaborative software development practices
• 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 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 biology or chemistry
• You have contributed to open-source machine learning projects or published research papers in the field of AI/ML
• You have experience optimizing machine learning models for high-performance computing environments
• You are familiar with ML-Ops practices and tools for managing ML experiments and deployments

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 our 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. That's why we're committed to creating an engaging and enjoyable work environment. Our goal is to create a workplace that is fun, rewarding and fulfilling.

What We Offer

• We encourage new and different ideas, creativity and contrarian thinking. We are looking forward to further shaping our culture with early team members. You'll have a chance to make your mark!
• You own your day-to-day management. We don't care when or where you work, we care if we all hit our milestones.
• Competitive salary and equity in a growing, well-funded startup
• Excellent medical, dental, and vision coverage
• 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