Scientist/Sr. Scientist, Experimental Data Generation for AI/ML

Compass Consulting
Madison, WI

Our client is building the next generation of AI-driven structural biology, integrating cutting-edge in vivo data with machine learning to model protein conformations in disease.


About the Role:

We are seeking a highly motivated Scientist / Senior Scientist to lead experimental data generation for an AI/ML-driven structural biology platform. This role sits at the intersection of wet-lab science and machine learning, focused on generating high-quality, ML-ready datasets derived from complex biological systems.

You will play a critical role in designing and executing experiments that directly inform and improve machine learning models. This is a hands-on, cross-functional position working closely with computational teams to iterate rapidly and refine data quality and experimental approaches.


Key Responsibilities:

  • Own the wet-lab R&D pipeline for generating machine learning training data
  • Translate AI/ML model requirements into well-designed experimental plans
  • Design, execute, and analyze experiments end-to-end, including:
  • Sample preparation and reagent selection
  • Automation and liquid handling setup
  • LC/MS operation and peptide mapping
  • Data processing and interpretation
  • Generate high-quality, structured datasets for machine learning applications
  • Collaborate closely with computational teams to iterate experiments based on model feedback
  • Maintain thorough documentation, data formatting, and dataset curation standards
  • Source and manage biological reagents, inventory, and lab readiness
  • Support external and internal projects by generating and analyzing experimental data
  • Communicate findings and progress clearly to cross-functional stakeholder


Required Qualifications:

  • PhD (or MS with significant industry experience) in:
  • Biochemistry
  • Analytical Chemistry
  • Chemical Biology
  • Structural Biology
  • Or related field
  • Strong hands-on experience with LC/MS-based proteomics workflows
  • Proven ability to independently design and execute complex experiments
  • Experience working in fast-paced, evolving environments
  • Strong communication and collaboration skills across scientific disciplines
  • Excellent organizational and project management abilities


Preferred Qualifications:

  • Experience with structural mass spectrometry techniques, such as:
  • Hydroxyl Radical Footprinting (HRF)
  • HDX-MS, XL-MS, or related methods
  • Familiarity with laboratory automation and liquid handling systems
  • Proficiency in R or similar tools for data analysis and visualization
  • Understanding of protein structure, conformational dynamics, or antibody systems
  • Industry experience in drug discovery, biologics, or structural biology


What You’ll Bring:

  • A hands-on, problem-solving mindset with strong experimental rigor
  • Ability to bridge experimental science and computational needs
  • Curiosity and adaptability in a fast-moving, innovative environment
  • A collaborative approach and passion for advancing scientific discovery


Why Join:

  • Opportunity to work on cutting-edge applications at the intersection of structural biology and AI/ML
  • Direct impact on the development of novel therapeutic discovery platforms
  • High level of ownership and influence on experimental strategy
  • Collaborative, mission-driven environment focused on scientific innovation

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