Principal ML Scientist II - Biotherapeutics and Genetic Medicine

Company Description

About AbbVie

AbbVie's mission is to discover and deliver innovative medicines and solutions that solve serious health issues today and address the medical challenges of tomorrow. We strive to have a remarkable impact on people's lives across several key therapeutic areas including immunology, oncology and neuroscience - and products and services in our Allergan Aesthetics portfolio. For more information about AbbVie, please visit us at www.abbvie.com. Follow @abbvie on LinkedIn, Facebook, Instagram, X and YouTube.

Job Description

Position Overview: 

The Principal Machine Learning Scientist II will advance deep learning methods for biologics discovery at AbbVie.  

This individual contributor role focuses on advancing sequence- and structure-based deep learning models for protein and antibody design with emphasis on adapting them to the constraints of designing therapeutic antibodies. The work centers on building models that improve early decision-making in molecule prioritization and guide molecule optimization, while balancing multiple properties, in order to reduce drug discovery timelines and increase the probability of success in patients. 

A major focus of the role is extending protein modeling to support the complexities of biotherapeutics, including complex multispecific formats, sequence diversity, conformational flexibility, and induced-fit behavior, which present important modeling challenges and opportunities for innovation. 

The role requires close collaboration with antibody engineers, computational physicists, and biologists to translate domain concepts into modeling decisions that will drive therapeutic impact. 

Responsibilities:

• Advance sequence- and structure-conditioned generative modeling for biologics using protein language models, diffusion-based generative models, and graph- and geometry-based deep learning methods. 
• Develop modeling strategies that improve therapeutic relevance, support multi-objective optimization, and surface liabilities earlier in the discovery process. 
• Develop predictive modeling approaches for multispecific biologics that optimize chain-complexation states, linker architecture, and higher-order molecular geometry to identify designs with favorable efficacy and developability. 
• Adapt protein models to CDR H3 loop behavior, including high diversity, conformational flexibility, and induced-fit effects. 
• Build rigorous internal benchmarking frameworks, establish evaluation standards for external AI/ML platforms, and lead technical due diligence on partner capabilities. 
• Use interpretability methods to uncover missing biological concepts, guide targeted model improvements. 
• Partner with deployment engineers to deliver scalable, stable production models and model monitoring workflows.  

Qualifications

• MS with 14+ years’ or PhD with 8+ years’ in machine learning, computer science, applied mathematics, data science, computational biology, or a closely related field,  
• 2+ years of experience building models with biological data. 
• Deep expertise in modern deep learning methods, including transformers, graph neural networks, protein language models, diffusion models, or related architectures. 
• Experience applying ML to sequence-based and structure-based biological problems. 
• Strong track record of adapting models to complex, real-world scientific constraints. 
• Ability to reason about open-ended technical problems and define a path forward in ambiguous settings. 
• Strong python programming skills and familiarity with modern ML tools and frameworks, including distributed training workflows. 
• Ability to collaborate effectively with experimental and computational scientists. 
• Ability to communicate technical tradeoffs clearly across disciplines. 

Work Environment 

• Hybrid role based in Worcester, MA. 
• On-site presence required 3 days per week. Relocation is available for those not currently located in MA. 
• This is an individual contributor role. 

Additional Information

Applicable only to applicants applying to a position in any location with pay disclosure requirements under state or local law: ​

• The compensation range described below is the range of possible base pay compensation that th