Takeda
By clicking the “Apply” button, I understand that my employment application process with Takeda will commence and that
the information I provide in my application will be processed in line with
Takeda’s
Privacy Notice
and
Terms of Use .
I further attest that all information I submit in my employment application
is
true to the best of my knowledge. Job Description
Position Overview
At Takeda, we are building the next generation of intelligent R&D platforms by integrating
Generative AI
and
agentic AI systems
into drug discovery. We seek a
Senior Scientist with deep expertise in AI model development
to lead efforts in designing foundation models and autonomous agents that drive innovation across our therapeutic areas, including oncology, neuroscience, and inflammatory diseases. This execution-focused role centers on the development and deployment of
LLMs, generative protein models, and autonomous reasoning agents
within an AI-first computational biology group. The ideal candidate will be a builder — someone who can translate cutting-edge research in generative modeling into scalable, drug-discovery tools and autonomous pipelines. Key Responsibilities
Design and implement
next-generation generative AI models
for biologics discovery, including LLMs, protein language models, diffusion models, and multi-modal architectures. Build and refine
agentic AI frameworks
(e.g., tool-using agents, retrieval-augmented generation (RAG), memory-augmented LLMs) to autonomously plan and optimize design–make–test–analyze (DMTA) cycles. Collaborate with bioinformatics, automation, and wet-lab teams to build
lab-in-the-loop systems , enabling AI agents to initiate hypotheses, request experiments, and iterate based on outcomes. Develop reusable AI pipelines that integrate
multi-objective optimization
(e.g., binding affinity, immunogenicity, developability, manufacturability) from in vitro and in silico data sources. Lead or contribute to the
development of internal foundation models
for biological design, including fine-tuning of LLMs on proprietary sequence, omics, and experimental datasets. Prototype and deploy agentic AI solutions using industry-standard frameworks such as LangChain, OpenAI API, Hugging Face Transformers, or similar. Stay current with advancements in
transformer architectures, RLHF, memory systems, cognitive planning agents , and apply these innovations to real-world therapeutic discovery challenges. Clearly communicate ideas to cross-functional stakeholders and contribute to internal and external scientific knowledge-sharing. Required Qualifications
PhD degree in Computer Science, Computational Biology, Machine Learning, Bioinformatics, or related field (or equivalent) with 2+ years relevant experience, or MS with 8+ years relevant experience, or BS with 10+ years relevant experience Demonstrated expertise in
developing large-scale deep learning models , including LLMs, generative models (e.g., diffusion, VAEs, autoregressive transformers), or multi-modal architectures. Proficiency in Python and modern ML frameworks (e.g., PyTorch, Hugging Face, JAX, LangChain); strong software engineering and reproducibility skills. Experience applying machine learning to
biological sequences, experimental data, or computational biology pipelines
(e.g., protein or antibody engineering, `omics analysis, etc.). Experience working with
large datasets
(NGS, high-throughput screens, bioassays) for supervised or unsupervised model training and evaluation. Deep familiarity with
agentic AI design : planning agents, tool-using agents, memory-augmented LLMs, or lab automation interfaces (e.g., lab robots, simulation frameworks, or autonomous workflows). Proven ability to integrate AI models into production environments and iterative workflows, preferably within a pharmaceutical or biotech context. Excellent interpersonal and written communication skills; thrives in collaborative, interdisciplinary environments. Preferred Qualifications
Prior experience fine-tuning or training
foundation models
(e.g., ESM, ProGen, ProtGPT2, OpenFold, GPT-style LLMs) on biological or scientific data. Familiarity with
retrieval-augmented generation (RAG) , tool-use planning, graph-enhanced reasoning, or long-context transformers for scientific applications. Knowledge of
wet-lab feedback integration
for DMTA cycles or closed-loop experimental platforms. Experience with cloud-based model deployment, distributed training, and model evaluation pipelines. Understanding of key
drug-like properties
(e.g., immunogenicity, aggregation risk, developability) and how to model them computationally. Demonstrated thought leadership (e.g., peer-reviewed publications, open-source contributions, patents) in GenAI or AI for biology. 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: $137,000.00 - $215,270.00
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. U.S. based
e
mployee
s
may be eligible for
s
hort
-
t
erm and/
or
l
ong-
t
erm
incentive
s
.
U.S.
based employees
may be
eligible to
participate
in medical, dental, vision insurance, a 401(k) plan and company match, short-term and long-term disability coverage, basic life insurance, a tuition reimbursement program, paid volunteer time off, company holidays, and
well-being
benefits, among others. U.S.
based employees are also eligible to receive, per calendar year, up to
80 hours
of sick time, and new hires are eligible to
accrue
up to
120 hours of paid vacation. 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. #J-18808-Ljbffr
the information I provide in my application will be processed in line with
Takeda’s
Privacy Notice
and
Terms of Use .
I further attest that all information I submit in my employment application
is
true to the best of my knowledge. Job Description
Position Overview
At Takeda, we are building the next generation of intelligent R&D platforms by integrating
Generative AI
and
agentic AI systems
into drug discovery. We seek a
Senior Scientist with deep expertise in AI model development
to lead efforts in designing foundation models and autonomous agents that drive innovation across our therapeutic areas, including oncology, neuroscience, and inflammatory diseases. This execution-focused role centers on the development and deployment of
LLMs, generative protein models, and autonomous reasoning agents
within an AI-first computational biology group. The ideal candidate will be a builder — someone who can translate cutting-edge research in generative modeling into scalable, drug-discovery tools and autonomous pipelines. Key Responsibilities
Design and implement
next-generation generative AI models
for biologics discovery, including LLMs, protein language models, diffusion models, and multi-modal architectures. Build and refine
agentic AI frameworks
(e.g., tool-using agents, retrieval-augmented generation (RAG), memory-augmented LLMs) to autonomously plan and optimize design–make–test–analyze (DMTA) cycles. Collaborate with bioinformatics, automation, and wet-lab teams to build
lab-in-the-loop systems , enabling AI agents to initiate hypotheses, request experiments, and iterate based on outcomes. Develop reusable AI pipelines that integrate
multi-objective optimization
(e.g., binding affinity, immunogenicity, developability, manufacturability) from in vitro and in silico data sources. Lead or contribute to the
development of internal foundation models
for biological design, including fine-tuning of LLMs on proprietary sequence, omics, and experimental datasets. Prototype and deploy agentic AI solutions using industry-standard frameworks such as LangChain, OpenAI API, Hugging Face Transformers, or similar. Stay current with advancements in
transformer architectures, RLHF, memory systems, cognitive planning agents , and apply these innovations to real-world therapeutic discovery challenges. Clearly communicate ideas to cross-functional stakeholders and contribute to internal and external scientific knowledge-sharing. Required Qualifications
PhD degree in Computer Science, Computational Biology, Machine Learning, Bioinformatics, or related field (or equivalent) with 2+ years relevant experience, or MS with 8+ years relevant experience, or BS with 10+ years relevant experience Demonstrated expertise in
developing large-scale deep learning models , including LLMs, generative models (e.g., diffusion, VAEs, autoregressive transformers), or multi-modal architectures. Proficiency in Python and modern ML frameworks (e.g., PyTorch, Hugging Face, JAX, LangChain); strong software engineering and reproducibility skills. Experience applying machine learning to
biological sequences, experimental data, or computational biology pipelines
(e.g., protein or antibody engineering, `omics analysis, etc.). Experience working with
large datasets
(NGS, high-throughput screens, bioassays) for supervised or unsupervised model training and evaluation. Deep familiarity with
agentic AI design : planning agents, tool-using agents, memory-augmented LLMs, or lab automation interfaces (e.g., lab robots, simulation frameworks, or autonomous workflows). Proven ability to integrate AI models into production environments and iterative workflows, preferably within a pharmaceutical or biotech context. Excellent interpersonal and written communication skills; thrives in collaborative, interdisciplinary environments. Preferred Qualifications
Prior experience fine-tuning or training
foundation models
(e.g., ESM, ProGen, ProtGPT2, OpenFold, GPT-style LLMs) on biological or scientific data. Familiarity with
retrieval-augmented generation (RAG) , tool-use planning, graph-enhanced reasoning, or long-context transformers for scientific applications. Knowledge of
wet-lab feedback integration
for DMTA cycles or closed-loop experimental platforms. Experience with cloud-based model deployment, distributed training, and model evaluation pipelines. Understanding of key
drug-like properties
(e.g., immunogenicity, aggregation risk, developability) and how to model them computationally. Demonstrated thought leadership (e.g., peer-reviewed publications, open-source contributions, patents) in GenAI or AI for biology. 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: $137,000.00 - $215,270.00
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. U.S. based
e
mployee
s
may be eligible for
s
hort
-
t
erm and/
or
l
ong-
t
erm
incentive
s
.
U.S.
based employees
may be
eligible to
participate
in medical, dental, vision insurance, a 401(k) plan and company match, short-term and long-term disability coverage, basic life insurance, a tuition reimbursement program, paid volunteer time off, company holidays, and
well-being
benefits, among others. U.S.
based employees are also eligible to receive, per calendar year, up to
80 hours
of sick time, and new hires are eligible to
accrue
up to
120 hours of paid vacation. 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. #J-18808-Ljbffr