Associate Director, AI/ML (Biologics)

Takeda Pharmaceutical Co.; Boston (MA); On-site; USD 154,000 - 243,000; Full time

Job summary

Takeda’s AI/ML organization in the Boston area seeks an innovative AI/ML Associate Director to apply AI across large molecule drug discovery, including antibodies, bispecifics, ADCs, and other modalities. You will join a multidisciplinary team to embed computational methods within drug programs and shape methodological roadmaps.

The role emphasizes mentoring scientists, partnering with senior stakeholders, and advancing AI‑driven discovery with strategic autonomy in program teams.

Qualifications

• PhD with 6+ years of relevant experience (or MS 12+, BS 14+).
• Proven track record in ML models for chemical/biological data; AI/ML-enabled molecular generation and affinity prediction.
• Experience modeling antibody/ antigen sequence, structure and interaction.
• Proficiency in Python and cloud computing.
• Strong analytical and problem‑solving skills with creative, collaborative mindset.

Responsibilities

• Develop and implement AI/ML methods for de novo biologics design across modalities.
• Develop, implement, and deploy ML algorithms for multi‑objective optimization of antibodies and biologics.
• Build tools to integrate Design‑Predict‑Make‑Confirm cycles with scalable data generation.
• Innovate predictive models for protein design and developability using large‑scale data sources.
• Stay abreast of NLP, ML, and generative AI to create new discovery tools.
• Communicate complex ideas effectively to technical and non‑technical audiences.

Skills

Python

Cloud computing

Analytical skills

Communication

Learning agility

Entrepreneurial mindset

Problem-solving

ML architectures

Education

PhD degree (or equivalent)

MS degree

BS degree

Tools

LLMs

Diffusion models

Flow-matching

Bayesian optimization

GNNs

Job description

Job Description

At Takeda, we are a forward-looking, world-class R&D organization that unlocks innovation and delivers transformative therapies to patients. By focusing R&D efforts on three therapeutic areas and other targeted investments, we push the boundaries of what is possible to bring life-changing therapies to patients worldwide.

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.

EEO Statement

Takeda is proud in its commitment to creating a diverse workforce and providing equal employment opportunities to all employees and applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, gender expression, parental status, national origin, age, disability, citizenship status, genetic information or characteristics, marital status, status as a Vietnam era veteran, special disabled veteran, or other protected veteran in accordance with applicable federal, state and local laws, and any other characteristic protected by law.

Locations

Boston, MA

Worker Type

Employee

Worker Sub-Type

Regular

Time Type

Full time

Job Exempt

YesIt 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.