Machine Learning Engineer, Multimodal Large Language Models (LLMs)

The Chan Zuckerberg Biohub San Francisco (CZ Biohub SF) (https://www.czbiohub.org/sf/) is an independent nonprofit research institute that brings together three powerhouse universities - Stanford, UC Berkeley, and UC San Francisco - into a single collaborative technology and discovery engine. CZ Biohub SF itself supports some of the brightest, boldest engineers, data scientists, and biomedical researchers to investigate the fundamental mechanisms underlying disease and develop new technologies that will lead to actionable diagnostics and effective therapies. We are guided by our values of scholarly excellence; disruptive innovation; hands-on engineering/hacking/building; partnership and collaboration; open communication and respect; inclusiveness; and opportunity for all.

Our Vision

• We pursue large scientific challenges that cannot be pursued in conventional environments
• We enable individual investigators to pursue their riskiest and most innovative ideas
• The technologies developed at CZ Biohub San Francisco facilitate research by scientists and clinicians at our home institutions and beyond

Diversity of thought, ideas, and perspectives are at the heart of CZ Biohub Network and enable disruptive innovation and scholarly excellence. We are committed to cultivating an inclusive organization where all colleagues feel inspired and know their work makes an important contribution.

The Opportunity

The Chan Zuckerberg Biohub (CZ Biohub SF) is seeking a highly skilled and motivated Machine Learning Engineer to lead the development of state-of-the-art multimodal large language model (LLM) agents that will enable breakthrough research and discoveries in biology. We are interested in pursuing these new ideas for zebrafish, a powerful model organism, to understand mechanisms of infection and immunity, organ regeneration, and organismal development.  The ideal candidate will have established expertise in machine learning, self-supervised learning, and pretraining of multimodal models to integrate natural language with another modality such as omics or image. The successful candidate will report directly to Yasin Şenbabaoğlu (Director of Computational Biology) at CZ Biohub, San Francisco.

You will

• Design, develop, and help to deploy multimodal LLMs that integrate textual and multi-omic data
• Lead the research and development of novel algorithms to process and align scientific literature with biological datasets for downstream analysis
• Collaborate closely with computational biologists and experimental scientists to understand domain-specific challenges and optimize model performance
• Manage large-scale datasets (scientific texts, omics data, and imaging) and build efficient data pipelines for training and evaluation
• Mentor junior scientists and engineers, fostering a culture of collaboration and continuous learning research projects

You have

Required –

• PhD in Computer Science, Machine Learning, Computational Biology, Bioinformatics or a related field; or Masters with equivalent experience
• 3+ years of experience with Python and relevant deep learning libraries (e.g., PyTorch, TensorFlow)
• 3+ years of experience in designing innovative multimodal AI systems and/or architectures
• Experience with model deployment, containerization, cloud-based platforms and version control systems
• Experience in integrating and aligning heterogeneous data sources (text, omics, images) for AI-driven applications
• Proven track record of impactful publications and conference presentations in relevant areas
• Excellent problem-solving skills and ability to work in an interdisciplinary environment

Nice to have -

• Expertise in natural language processing and self-supervised learning training techniques
• Familiarity with bioinformatics tools and scientific literature databases (e.g., PubMed, arXiv)
• Experience with Python backend framework experience (e.g. Flask, FastAPI, etc) and high-performance computing (HPC) environments
• Strong leadership and project management skills

Compensation

The San Francisco, CA  base pay range for this role is Machine Learning Engineer I = $131,000.00 - $180,400.00 and Machine Learning Engineer II = $150,000.00 - $205,700.00 . New hires are typically hired into the lower portion of the range, enabling employee growth in the range over time. Actual placement in range is based on job-related skills and experience, as evaluated throughout the interview process. 

What We Provide

• Resources to disrupt and innovate at the frontiers of our knowledge of biology and disease
• A collegial and collaborative environment consisting of diverse expertise
• Access to collaborators, resources and facilities at our three partner universities (Stanford University, UC Berkeley, and UC San Francisco) and at partner organizations in the SF Bay Area and beyond
• Competitive compensation and benefits commensurate with the experience

If you’re interested in a role but your previous experience doesn’t perfectly align with each qualification in the job description, we still encourage you to apply as you may be the perfect fit for this or another role.

Benefits

We offer a robust benefits program that enables the important work Biohubbers do everyday. Our benefits include healthcare coverage, life and disability insurance, commuter subsidies, family planning services with fertility care, childcare stipend, 401(k) match, flexible time off and a generous parental leave policy. In addition, we honor our commitment to career development and our value of scholarly excellence through regular onsite opportunities to learn from the world's leading scientists.

The CZ Biohub Network is an equal opportunity employer committed to diversity of thought, ideas and perspectives. We are committed to cultivating an inclusive organization where all Biohubbers feel inspired and know their work makes an important contribution. Therefore, we provide employment opportunities without regard to age, race, color, ancestry, national origin, religion, disability, sex, gender identity or expression, sexual orientation, or any other protected status in accordance with applicable law.

Pursuant to the California Fair Chance Act, we will consider for employment qualified applicants with arrest and conviction records.

Headhunters and recruitment agencies may not submit resumes/CVs through this website or directly to managers. The CZ Biohub Network does not accept unsolicited headhunter and agency resumes. The CZ Biohub Network will not pay fees to any third-party agency or company that does not have a signed agreement with the CZ Biohub Network.