Staff Data Scientist / Protein Design

This is a (minimum four days/week in office) full-time position based in our Menlo Park, CA office. This position reports to the Director of Data Science of the Company.

Aether Biomachines is on a mission to build the post-scarcity future using peptide-based nanotechnology as the driving force for the next industrial revolution. By creating the world's most advanced high-throughput robotic laboratory, we are generating data at unprecedented scales to fuel deep learning algorithms. We're assembling a diverse and dynamic team of self-starters, engineers, sci-fi enthusiasts, and visionaries, and we invite you to join us on this journey.

We're breaking barriers in laboratory automation to power world-class machine learning models with faster, broader, and more robust robotic sample processing systems. We aim to transform peptides from niche catalysts into general-purpose molecular assemblers using our platform, enabling a future of abundance for the human race.

Aether's Machine Learning (“ML”) team is spearheading innovation in enzyme engineering by capitalizing on advanced computational methodologies. Faced with the intricate and multidimensional challenges of enzyme engineering, the ML team employs refined data-cleaning algorithms to curate and preprocess extensive volumes of experimental data meticulously. By deploying state-of-the-art predictive models, the team can accurately predict enzyme-substrate interactions, uncover novel enzymatic activities, and optimize enzyme performance across diverse experimental conditions. Furthermore, by utilizing cutting-edge multi-objective search and optimization algorithms, the ML team can concurrently navigate multiple solution spaces, adeptly navigating trade-offs between conflicting objectives to engineer optimal enzyme designs. Aether's innovative fusion of data science and biotechnology facilitates the creation of pioneering solutions that address pressing challenges within the biotech industry and unleash the boundless potential of enzymes for a wide array of applications.

What we are looking for in you

We seek an experienced and highly motivated Staff Data Scientist to join our ML team and contribute to the cutting-edge protein and enzyme design field. In this role, you will be responsible for developing novel machine learning models, particularly Physics-Informed GNNs, diffusion models, and large language models (LLMs), to advance the design and engineering of proteins and enzymes. Your work will play a pivotal role in driving the innovation and success of our enzyme engineering projects.

What you will be doing

• Development Maintenance and use of  Physics-Informed GNNs
• Development Maintenance and use of LLM-based machine learning models for enzyme design.
• Hybridization of LLM and Diffusion models. 
• Collaboration with cross-functional teams, including chemists, biochemists, and data scientists.
• Analysis and interpretation of experimental data to validate and refine machine learning models.
• Presentation of research findings, model performance, and insights to internal teams and external collaborators.
• Staying current with advances in machine learning, computational biology, and protein engineering to inform model development and improvement.
• Contributing to the preparation of scientific publications, technical reports, and patent applications.
• Building internal tools for research teams to interpret and categorize data generated by protein and enzyme engineering experiments.

What you should have

• Strong understanding of the mathematical foundation of diffusion models.
• Ability to develop efficient GPU accelerated models using the available AI frameworks.
• Strong ability to recreate models from literature and improve them with novel Ideas.    
• Understanding of protein structure, function, and biochemistry.
• Proven experience developing and applying machine learning models, in a biological or biochemical context.
• Proficiency in Python and experience with machine learning frameworks such as TensorFlow, jax, or PyTorch and MD frameworks such as openmm. 
• Strong problem-solving and critical-thinking skills, with a high level of attention to detail.

What you must have

• Ph.D. in Mathematics, Computer Science, Computational Biology or a related field or demonstrated exceptional ability outside of the context of a Ph.D.
• Experience in developing and validating Diffusion Models (optimally applied in a biological context) 
• 5 years experience 

Not sure you meet 100% of our qualifications? 

We encourage anyone who thinks they would excel at Aether to apply, no matter their background or how they identify.

Benefits and Perks

• Full suite of health benefits (medical, dental, vision)
  • Aether pays 100% of the premiums for employees and 90% of the premiums for dependents.
  • HSA Option w/ company contribution
• Basic Life, AD&D, and Long Term Disability Insurance at no cost.
• Flexible Spending Accounts
  • Health Care FSA
  • Dependent Care FSA
  • Commuter FSA w/ up to $100 Aether match per month
• 401(k) Retirement Plan
• Flexible & generous Time Off policy plus 12 Paid Holidays
• Free meals during working hours + Stocked kitchen with snacks and drinks
• On-Site Amenities include free EV charging, shuttle services to public transportation and free on-site fitness center.
• Learning & Development: You may purchase up to $50/month in books or other learning materials on any topic without any prior approval

EEO

Our company values diversity and believes diverse teams make innovation possible. We work on complex, difficult problems with no linear or clear solutions. We believe that a diverse team can bring different perspectives and approaches, and whose experiences reflect the full set of clients we seek to serve. As such, Aether Biomachines, Inc. is committed to a diverse representation among our employees. Legal authorization to work in the U.S. is required.  Aether may agree to sponsor an individual for an employment visa now or in the future if there is a shortage of individuals with particular skills for this job.  In compliance with federal law, all persons hired will be required to verify identity and eligibility to work in the United States and to complete the required employment eligibility verification form upon hire. This position is based in our California location.