Job Description

The AI/ML organization at Takeda is building a team to transform how medicines are discovered. Our goal is to apply AI and machine learning across the entire drug discovery process, not just isolated steps, but as an integrated approach from target identification through development. This requires discernment: knowing which models and methods fit each problem, and the creativity to adapt when they don't. We work with foundational models, generative approaches, and autonomous systems, but the tools only matter when paired with people who understand the science deeply enough to use them well. Our team brings together computational scientists, biologists, engineers, and drug hunters. If you want to contribute your expertise to hard problems alongside colleagues with different perspectives, and help shape how AI delivers real impact in drug discovery, we'd like to hear from you.

Position Overview

We are seeking an innovative and dynamic AI/ML Associate Director with a passion for leveraging AI/ML across large molecule drug discovery and development - including antibody design, bispecifics, ADCs, fusion proteins, and other biologics modalities to join our Large Molecule AI/ML team. This role will be part of a multidisciplinary team focused on integrating advanced computational methods with cutting-edge experimental strategies to drive breakthrough discoveries in large molecule therapeutics and deepen our understanding of disease biology. The ideal candidate will have a strong background in computational biology, machine learning, and structural modeling and specifically with the application of AI/ML in diverse biologics modalities, with a demonstrated ability to embed AI/ML capabilities directly within drug programs to address a broad range of discovery and development needs. Beyond technical execution, this Associate Director is expected to operate with a high degree of strategic autonomy: shaping the team's methodological roadmap, mentoring scientists across functions, and serving as a primary AI/ML voice to senior cross-functional stakeholders in Program teams.

Key Responsibilities

• Develop and implement state-of-the-art AI/ML methodologies for de novo biologics design and optimization across modalities including antibodies, bispecifics, VHH/nanobodies including fine-tuning protein language models and generative protein design.
• Develop, implement, and deploy advanced machine learning algorithms for the multi-objective optimization of antibodies, antigens, ADCs, and other biologics.
• Build tools to incorporate data from integrated Design-Predict-Make-Confirm cycles with automated experimental platforms generating quality data at scale needed for project-specific and foundational models.
• Innovate, develop, and apply predictive models for protein design and developability engineering, utilizing large-scale NGS, in vitro, in vivo and other proprietary in-house and external data sources.
• Manage and process large-scale biological datasets for model training and evaluation
• Stay abreast of advancements in NLP, ML, and generative AI to build novel tools that enhance therapeutic discovery and development.
• Communicate complex scientific ideas effectively to both technical and non-technical audiences, fostering collaboration across multidisciplinary teams.
• Proactively identify and champion opportunities to apply AI/ML across the drug program portfolio, engaging program teams early to scope computational contributions and translate scientific questions into tractable ML problems.
• Represent the AI/ML function as a scientific and strategic partner to senior cross-functional stakeholders, including Discovery Biology, CMC, and Program Leadership, contributing to portfolio-level decision-making.

Qualifications

• PhD degree in a scientific discipline (or equivalent) with 6+ years relevant experience, or MS with 12+ years relevant experience, or BS with 14+ years relevant experience Proven track record in developing machine learning models for chemical and biological data, including AI/ML-enabled molecular generation and affinity prediction.
• Demonstrated experience in modeling antibody/ antigen sequence, structure and interaction.
• Proficiency in programming languages such as Python and experience with cloud computing capabilities.
• Strong analytical and problem-solving skills, with demonstrated creativity and the ability to contribute individually and collaboratively.
• Versatile communicator who can elucidate complex ideas to non-specialists and commitment to continuous improvement and innovation.
• Demonstrated learning agility, and scientific curiosity while maintaining focus on driving greater impact in the face of uncertainty and change.
• Strong problem-solving aptitude and strategic thinking with an entrepreneurial mindset.

Preferred Qualifications & Skills:

• Experience developing or applying modern ML architectures for antibody design models (LLMs, diffusion models, flow-matching, Bayesian Optimization, GNNs, etc.)
• Experience designing de novo binders for specified targets and epitopes
• Experience analyzing NGS-derived antibody repertoires for sequence- and structure-based design
• Experience with molecular simulation and conformational analysis techniques

ADDITIONAL INFORMATION

• The position will be based in Cambridge, MA

Takeda Compensation and Benefits Summary

We understand compensation is an important factor as you consider the next step in your career. We are committed to equitable pay for all employees, and we strive to be more transparent with our pay practices.

For Location:
Boston, MA

U.S. Base Salary Range:
$154,400.00 - $242,550.00

The estimated salary range reflects an anticipated range for this position. The actual base salary offered may depend on a variety of factors, including the qualifications of the individual applicant for the position, years of relevant experience, specific and unique skills, level of education attained, certifications or other professional licenses held, and the location in which the applicant lives and/or from which they will be performing the job. The actual base salary offered will be in accordance with state or local minimum wage requirements for the job location.

For information about our benefits, please click here.

Locations
Boston, MA

Worker Type
Employee

Worker Sub-Type
Regular

Time Type
Full time

Job Exempt
Yes

It is unlawful in Massachusetts to require or administer a lie detector test as a condition of employment or continued employment. An employer who violates this law shall be subject to criminal penalties and civil liability.