Head of Machine Learning Research

Bayer; Cambridge (MA); On-site; USD 177,000 - 266,000; Full time

Benefits offered by this job

Health care

Vision care

Dental care

Retirement plan

Paid time off

Job summary

Bayer is seeking a hands-on strategic leader to advance ML-enabled molecular design across our drug discovery portfolio in Cambridge, MA. You will co-own the multi-year technical roadmap, build and lead a ~25-person team, and ensure ML capabilities translate into better project decisions and faster nomination progress.

Required are a PhD in a molecular science/ML field and deep expertise in modern ML for molecules (GNNs, transformers, generative models, Bayesian optimization, and active

Qualifications

• PhD in computational chemistry or related field with depth in molecular science and ML
• Deep, current expertise across ML for molecules: GNNs, transformers, generative approaches, Bayesian optimization and active learning, transfer learning on sparse data, uncertainty quantification

Responsibilities

• Co-own the vision, roadmap, and investment case for ML-driven molecule design across small molecules and emerging modalities.
• Make build/buy/partner decisions for generative design, property prediction, structure-based ML, and synthesis planning; evaluate foundation models and external platforms with rigor.
• Set the standard for model validation, benchmarking, and reporting of failure modes.
• Partner with Drug Discovery Sciences to embed ML into live programs from hit identification through nomination.
• Co-own program-level design goals with chemistry leads: potency, selectivity, ADMET, developability, and IP position.
• Drive active learning and closed-loop DMTA cycles, including integration with high-throughput and automated synthesis where available.
• Ensure models are delivered as reliable, supported products that chemists actually use.
• Direct development of core capabilities: ADMET and property predictors, generative and de-novo design, retrosynthesis and synthetic accessibility, and structure-based ML.
• Work with data engineering to secure assay, structural, and DMTA data foundation; curation, provenance, harmonization across assays and sites; feedback capture.
• Establish MLOps practice: versioning, reproducibility, monitoring, and documentation.
• Build, lead, and develop a team of approximately 25 spanning ML research, computational chemistry, and ML engineering.
• Own budget, vendor relationships, and external collaborations with academic groups and biotech partners.
• Represent the function to R&D leadership and translate technical capability into portfolio impact.
• Contribute to the scientific community through publications and pre-competitive collaboration.

Skills

ML for molecules

Graph neural networks

Transformers

Generative models

Bayesian optimization

Active learning

Uncertainty quantification

Education

PhD in computational chemistry / cheminformatics / structural biology / biophysics / computer science

MSc with equivalent depth of experience

Job description

At Bayer we’re visionaries, driven to solve the world’s toughest challenges and striving for a world where 'Health for all Hunger for none’ is no longer a dream, but a real possibility. We’re doing it with energy, curiosity and sheer dedication, always learning from unique perspectives of those around us, expanding our thinking, growing our capabilities and redefining ‘impossible’. There are so many reasons to join us. If you’re hungry to build a varied and meaningful career in a community of brilliant and diverse minds to make a real difference, there’s only one choice.

Head of Machine Learning Research

We are seeking a scientific and technical leader to advance machine learning–enabled molecular design across our drug discovery portfolio. As a member of the Data Science & AI leadership team, you will define and deliver the models, platforms, and ways of working that shorten design–make–test–analyze cycles and improve the quality of molecules progressing toward nomination.

This is a hands‑on strategic leadership role —neither research-only nor delivery-only. You will set a multi-year technical roadmap, build and lead a team of approximately 25 scientists and engineers, and ensure that machine learning capabilities translate into better project decisions and faster progression to candidate selection.

You will lead the development and application of modern machine learning methods—including deep learning, neural networks, ensemble methods, natural language processing, and machine perception—to complex, high-dimensional scientific data. Your team will develop predictive and generative models that help discovery scientists understand biological and chemical patterns, prioritize experiments, optimize molecular properties, and design novel molecules.

Success in this role requires deep fluency in contemporary machine learning, combined with a practical understanding of the realities of medicinal chemistry, structural biology, and drug discovery. You will spend as much time engaging in project-team reviews and scientific decision‑making as you do shaping model architectures, platform strategy, and technical standards

YOUR TASKS AND RESPONSIBILITIES

The primary responsibilities of this role, Head of Machine Learning Research, are to:

Strategy and Technical Direction

• Co-own the vision, roadmap, and investment case for ML-driven molecule design and multi‑parameter optimization across small molecules and emerging modalities.
• Make build/buy/partner decisions across generative design, property prediction, structure‑based ML, and synthesis planning; evaluate foundation models and external platforms with rigor rather than hype.
• Set the standard for how models are validated, benchmarked prospectively, and retired — including uncertainty quantification, applicability domain, and honest reporting of failure modes.

Delivery into Discovery Projects

• Partner with Drug Discovery Sciences — medicinal chemistry, structural biology, biophysics, screening, DMPK, and safety — to embed ML into live programs from hit identification through candidate nomination.
• Co‑own program‑level design goals with chemistry leads: potency, selectivity, ADMET, developability, and IP position optimized together rather than sequentially.
• Drive active learning and closed‑loop DMTA cycles, including integration with high‑throughput and automated synthesis where available.
• Ensure models are delivered as reliable, supported products that chemists actually use, not one‑off analyses.

Platform and Data Foundation

• Direct development of core capabilities: ADMET and property predictors, generative and de‑novo design, retrosynthesis and synthetic accessibility, and structure‑based ML including co‑folding, pose prediction, docking rescoring, and ML‑accelerated free energy methods.
• Work with data engineering to secure the assay, structural, and DMTA data foundation these models depend on — curation, provenance, harmonization across assays and sites, and feedback capture from every make‑test cycle.
• Establish MLOps practice appropriate to a regulated R&D environment: versioning, reproducibility, monitoring, and documentation.

Leadership and Organization

• Build, lead, and develop a team of approximately 25 spanning ML research, computational chemistry, and ML engineering; grow leaders within the group.
• Own budget, vendor relationships, and external collaborations with academic groups, consortia, and biotech partners.
• Represent the function to R&D leadership, translating technical capability into portfolio impact and translating portfolio priorities into technical strategy.
• Contribute to the broader scientific community through publication, presentation, and pre‑competitive collaboration where appropriate.

WHO YOU ARE

Bayer seeks an incumbent who possesses the following:

Required Qualifications

• PhD in computational chemistry, cheminformatics, structural biology, biophysics, computer science, or a related field, with demonstrated depth in both a molecular science and machine learning. Exceptional candidates with an MSc and equivalent depth of experience will be considered;
• Deep, current expertise across modern ML for molecules: graph neural networks, transformers, generative approaches (diffusion, flow matching, autoregressive), Bayesian optimization and active learning, transfer learning on sparse assay data, and uncertainty quantification;
• Working command of the discovery domain: SAR interpretation, multi‑parameter optimization, ADMET and developability, protein structure and ligand binding, docking and free energy methods;
• Demonstrated impact on real programs — molecules advanced, cycles shortened, decisions changed. A publication record without program impact is not sufficient for this role;
• Proven ability to partner with medicinal chemists and structural biologists as scientific peers, including the credibility to challenge and be challenged on design decisions;
• Track record of delivering software or models into production use by scientists, not just prototypes.

Preferred Qualifications

• 12+ years of relevant experience, including 5+ years leading technical teams; experience leading leaders strongly preferred.
• Experience with modalities beyond conventional small molecules — PROTACs and molecular glues, macrocycles, peptides, covalent inhibitors, or oligonucleotides;
• Familiarity with lab automation, self‑driving lab concepts, or high‑throughput chemistry integration;
• Experience evaluating or deploying large‑scale pretrained models for chemistry or protein structure;
• Prior experience in a large matrixed pharma R&D organization, or scaling a capability from startup to enterprise;
• Strong external profile: publications, conference presence, or leadership in pre‑competitive consortia.

Employees can expect to be paid a salary between $177,400.00 - $266,200.00. Additional compensation may include a bonus or commission (if relevant). Additional benefits include health care, vision, dental, retirement, PTO, sick leave, etc.

This salary range is merely an estimate and may vary based on an applicant’s location, market data/ranges, an applicant’s skills and prior relevant experience, certain degrees and certifications, and other relevant factors.

This posting will be available for application until at least 09/29/2026.

Bayer is an Equal Opportunity Employer/Disabled/Veterans

Bayer is committed to providing access and reasonable accommodations in its application process for individuals with disabilities and encourages applicants with disabilities to request any needed accommodation(s) using the contact information below.

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Bayer is an E-Verify Employer.

Location

United States : Massachusetts : Cambridge || United States : New Jersey : Whippany

Division

Pharmaceuticals

Reference Code

885870

Contact Us

Email: [e-mail]