Senior AI Scientist, Foundation Models

Job Description

AI Research Scientist, Foundation Models

Our Artificial Intelligence Machine Learning (AI/ML) capabilities are critical accelerators to our mission of inventing new medicines that save and improve lives. Core to the Data, AI, and Genome Sciences (DAGS) function is an AI/ML-first approach to improving target and biomarker discovery, validation and selection, and elucidating complex disease mechanisms. As a senior AI scientist, you will be responsible for pre-training and fine-tuning biological foundation models on text, multi-omics, and imaging data, analyzing pre-trained models posthoc, building rigorous benchmarks for evaluating foundation models, and serving in-house trained foundation models. Your work will advance our understanding of complex diseases and support the development of innovative therapeutic strategies. You will be part of a cross-functional team of computational biologists, bioinformaticians, data scientists, software engineers, and machine learning researchers who strive to identify therapeutic targets and biomarkers.

Primary Responsibilities

• Collaborate with cross-functional teams to identify research questions and data requirements and develop appropriate solutions.
• Develop and train large foundation models for -omics data augmented with text and images.
• Interpret and critically post-hoc analyze pre-trained models.
• Rigorously benchmark and evaluate the performance of both in-house and publicly available models.
• Host and serve in-house state-of-the-art models and make them accessible to scientists across our company.
• Stay up to date with the latest advancements in machine learning and statistics and apply relevant advancements to improve existing methodologies and models.
• Publish research findings in relevant conferences and journals and actively contribute to the scientific community through knowledge sharing and collaborations.

Required Education, Experience, And Skills

• PhD, MS, or BS in Computer Science, Engineering, Data Science, AI/ML, Bioinformatics, Computational Biology, Genetics & Genomics, Mathematics, Statistics, Physics, Pharmaceutical Science, or related STEM field and 0+ years of full-time experience (with PhD), 4+ years of experience (with MS), or 7+ years of experience (with BS).
• Experience training large models on multi-node, multi-GPU environments.
• Experience designing novel architectures for multi-modal foundation models.
• Deep expertise in post-training foundation models, including some parameter efficient fine-tuning, post-hoc interpretability, and preference optimization.
• Demonstrated expertise in classical machine learning, statistical models, and in training, evaluating, and debugging models and data at scale.
• Excellent software design and development skills and strong proficiency in Python.
• Experience with standard deep learning frameworks like the PyTorch ecosystem for working with large foundation models.
• Excellent communication skills and ability to work collaboratively in a multi-disciplinary team.
• Interest in life sciences problems and disease biology, and willing to learn from and teach others.

Preferred Skills and Experience

• Experience with pre-training biological foundation models (transcriptomic, protein language models, DNA transformers, or structure-to-function models) is a strong plus.
• Familiarity with biological data and previous experience with protein language models and foundation models for omics is a strong plus.
• Experience training and working with large discrete diffusion models.
• Experience with reinforcement learning (RL) and using RL for training reasoning models.
• Relevant publications in scientific journals and experience contributing to research communities, including NeurIPS, ICML, ICLR, etc.

As an Equal Employment Opportunity Employer, we provide equal opportunities to all employees and applicants for employment and prohibit discrimination on the basis of race, color, age, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability status, or other applicable legally protected characteristics. As a federal contractor, we comply with all affirmative action requirements for protected veterans and individuals with disabilities. For more information about personal rights under the U.S. Equal Opportunity Employment laws, visit:

EEOC Know Your Rights

EEOC GINA Supplement

We are proud to be a company that embraces the value of bringing together, talented, and committed people with diverse experiences, perspectives, skills and backgrounds. The fastest way to breakthrough innovation is when people with diverse ideas, broad experiences, backgrounds, and skills come together in an inclusive environment. We encourage our colleagues to respectfully challenge one another's thinking and approach problems collectively.

Learn more about your rights, including under California, Colorado and other US State Acts

#EligibleforERP

Required Skills:
Artificial Intelligence (AI), Computer Science, Data Analysis, Data Engineering, Data Modeling, Data Science, Data Visualization, Foundation Models, Graphics Processing Units (GPUs), Life Science, Machine Learning (ML), Machine Learning Algorithms, Python (Programming Language), PyTorch, Reinforcement Learning, Software Development

Preferred Skills:
Diffusion Models, Multimodal Analysis

Current Employees apply HERE

Current Contingent Workers apply HERE

US and Puerto Rico Residents Only:

Our company is committed to inclusion, ensuring that candidates can engage in a hiring process that exhibits their true capabilities. Please click here if you need an accommodation during the application or hiring process.

As an Equal Employment Opportunity Employer, we provide equal opportunities to all employees and applicants for employment and prohibit discrimination on the basis of race, color, age, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability status, or other applicable legally protected characteristics. As a federal contractor, we comply with all affirmative action requirements for protected veterans and individuals with disabilities. For more information about personal rights under the U.S. Equal Opportunity Employment laws, visit:

EEOC Know Your Rights

EEOC GINA Supplement

We are proud to be a company that embraces the value of bringing together, talented, and committed people with diverse experiences, perspectives, skills and backgrounds. The fastest way to breakthrough innovation is when people with diverse ideas, broad experiences, backgrounds, and skills come together in an inclusive environment. We encourage our colleagues to respectfully challenge one another's thinking and approach problems collectively.

Learn more about your rights, including under California, Colorado and other US State Acts

U.S. Hybrid Work Model

Effective September 5, 2023, employees in office-based positions in the U.S. will be working a Hybrid work consisting of three total days on-site per week, Monday - Thursday, although the specific days may vary by site or organization, with Friday designated as a remote-working day, unless business critical tasks require an on-site presence.This Hybrid work model does not apply to, and daily in-person attendance is required for, field-based positions; facility-based, manufacturing-based, or research-based positions where the work to be performed is located at a Company site; positions covered by a collective-bargaining agreement (unless the agreement provides for hybrid work); or any other position for which the Company has determined the job requirements cannot be reasonably met working remotely. Please note, this Hybrid work model guidance also does not apply to roles that have been designated as remote".

The salary range for this role is
$141,900.00 - $223,300.00

This is the lowest to highest salary we in good faith believe we would pay for this role at the time of this posting. An employee's position within the salary range will be based on several factors including, but not limited to relevant education, qualifications, certifications, experience, skills, geographic location, government requirements, and business or organizational needs.

The successful candidate will be eligible for annual bonus and long-term incentive, if applicable.

We offer a comprehensive package of benefits. Available benefits include medical, dental, vision healthcare and other insurance benefits (for employee and family), retirement benefits, including 401(k), paid holidays, vacation, and compassionate and sick days. More information about benefits is available at https://jobs.merck.com/us/en/compensation-and-benefits .

You can apply for this role through https://jobs.merck.com/us/en (or via the Workday Jobs Hub if you are a current employee). The application deadline for this position is stated on this posting.

San Francisco Residents Only: We will consider qualified applicants with arrest and conviction records for employment in compliance with the San Francisco Fair Chance Ordinance

Los Angeles Residents Only: We will consider for employment all qualified applicants, including those with criminal histories, in a manner consistent with the requirements of applicable state and local laws, including the City of Los Angeles' Fair Chance Initiative for Hiring Ordinance

Search Firm Representatives Please Read Carefully
Merck & Co., Inc., Rahway, NJ, USA, also known as Merck Sharp & Dohme LLC, Rahway, NJ, USA, does not accept unsolicited assistance from search firms for employment opportunities. All CVs / resumes submitted by search firms to any employee at our company without a valid written search agreement in place for this position will be deemed the sole property of our company. No fee will be paid in the event a candidate is hired by our company as a result of an agency referral where no pre-existing agreement is in place. Where agency agreements are in place, introductions are position specific. Please, no phone calls or emails.

Employee Status:
Regular

Relocation:
Domestic

VISA Sponsorship:
Yes

Travel Requirements:
10%

Flexible Work Arrangements:
Hybrid

Shift:
Not Indicated

Valid Driving License:
No

Hazardous Material(s):
n/a

Job Posting End Date:
12/13/2025
*A job posting is effective until 11:59:59PM on the day BEFORE the listed job posting end date. Please ensure you apply to a job posting no later than the day BEFORE the job posting end date.

Requisition ID:R372774