Research Scientist, AI/ML Agentic Systems (BOSTON)

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Job Description

Title: Research Scientist, AI/ML – Agentic Systems

Position Overview

We are seeking a Research Scientist to develop agentic AI systems that transform how drug discovery research is conducted. As part of the AI/ML Foundation team, you will build autonomous AI agents capable of reasoning, planning, and executing complex scientific workflows—from literature synthesis and target identification to experimental design and data analysis. This role requires a unique combination of expertise in large language models, agentic frameworks, and understanding of drug discovery processes. You will translate standard research workflows into agentic frameworks, develop new agent skills, and deploy systems that augment scientist productivity across Computational Sciences and Global Research.

Key Responsibilities

• Develop agentic AI systems for drug discovery applications including target-disease association, automated literature search and synthesis, hypothesis generation, and intelligent design of experiments.
• Translate standard research workflows into agentic frameworks—decomposing complex scientific processes into autonomous agent tasks that can reason, plan, execute tools, and iterate based on results.
• Design and implement new agent skills (tools, functions, APIs) that extend agentic capabilities to specialized scientific domains including molecular design, property prediction, assay planning, and data analysis.
• Build agentic systems that integrate with foundation models and external knowledge sources for autonomous hypothesis generation, evidence retrieval, and scientific reasoning.
• Develop retrieval-augmented generation (RAG) pipelines connecting agents to internal and external scientific literature, databases, and experimental results.
• Partner with research scientists to understand workflow needs, validate agent outputs, and iterate on system design to ensure scientific rigor and utility.
• Stay current with advances in agentic AI, LLM applications, and scientific automation; contribute to internal knowledge sharing and external publications.

Qualifications

Required:

• PhD in Computer Science, Computational Biology, Bioinformatics, or related field
• Experience with large language models (GPT, Claude, Llama) and their application to complex reasoning tasks.
• Proficiency in Python and experience with agentic AI frameworks (LangChain, AutoGen, CrewAI, or similar).
• Experience building RAG systems including vector databases, embedding models, and retrieval pipelines.
• Understanding of drug discovery processes and scientific research workflows.
• Strong problem-solving skills and ability to translate complex scientific processes into computational workflows.

Preferred:

• Experience in pharmaceutical or biotech R&D environments.
• Background in biology, chemistry, or disease biology.
• Experience with reinforcement learning or planning algorithms for agent decision-making.
• Familiarity with scientific databases (PubMed, UniProt, ChEMBL) and APIs.
• Experience deploying AI systems in production environments.
• Track record of publications or presentations on LLM ap

ADDITIONAL INFORMATION

• The position will be based in Cambridge, MA. This position is currently classified as “hybrid” by Takeda’s Hybrid Work policy

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:

$116,000.00 - $182,270.00

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 employees may be eligible for short-term and/ or long-term incentives. 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 calen