Senior Machine Learning Scientist

What if you could join an organization that creates, resources, and builds life sciences companies that invent breakthrough technologies in order to transform health care and sustainability?

FL94 Inc., is a privately held, early-stage biotechnology company pioneering the emerging field of Protein Editing. At FL94 we create small molecules that edit protein structure and function to unlock presently undruggable targets and a broad array of therapeutic modalities. Our platform integrates novel small molecule chemistry and chemoproteomic discovery technologies with Machine Learning (ML) to enable generative design. FL94 is backed by Flagship Pioneering, bringing their courage, vision, and resources to guide FL94 from platform validation to patient impact. We are seeking collaborative, relentless problem solvers that share our passion for impact to join us!

Position Summary:

FL94 is searching for a senior machine learning research scientist to develop predictive and generative AI to radically accelerate small molecule lead optimization.

Reporting directly to the CTO, you will collaborate with other ML scientists, engineers and medicinal chemists to design, develop and benchmark machine learning T models from public and in-house assay data. Youll design and implement active learning MPO strategies to reduce the number of compound optimization cycles in DMTA.

This role will require deep experience in state-of-the-art machine learning model development, pharmacology, and software engineering.

What You'll Do

• Develop predictive ADMET/QSAR models: Design, build and/or fine-tune cutting-edge global and local models for potency, selectivity, and key ADMET properties using state-of-the-art architectures.
• Leverage publicly available foundation models (e.g., TxGemma) and data to augment sparse functional data. Fine tune internal state-of-the-art models and design objective functions for Multi-Property Optimization (MPO).
• Enable synthesis-aware design: Integrate retrosynthesis prediction and reaction modeling into the design process to ensure that generated molecules are readily synthesizable.
• Build robust ML infrastructure: Establish and maintain data pipelines, stringent benchmarks and validation frameworks for rigorous, prospective model evaluation. You'll be responsible for deploying models that directly impact project decisions in our drug discovery programs.

Requirements:

• Ph.D. in CS, computational chemistry, applied mathematics, statistics, physics, or related discipline
• 5+ years of ML drug discovery experience: Proven track record of applying machine learning to solve problems in lead optimization, such as QSAR/ADMET modeling, hit-to-lead, or active learning within a design-make-test-analyze (DMTA) cycle.
• Core ML & Python expertise: Strong proficiency in Python and modern deep learning frameworks like PyTorch/TF, with experience building and deploying production-level ML systems in a fast-paced drug discovery startup environment.
• Expertise in generative AI & Geometric Deep Learning: Demonstrated experience in developing and applying generative models (e.g., conditional flow matching, diffusion, VAEs) and graph-based or 3D (multi-task) neural networks for molecular applications.
• Proficiency with Multi-Modal Models: Experience applying multi-modal architectures to fuse molecular structures and assay data with biological context from text and other modalities, enhancing the predictive power for QSAR/ADMET properties.
• Deep domain knowledge: A solid understanding of medicinal chemistry principles (e.g., SAR, MPO) and cheminformatics toolkits (e.g., RDKit). You should be comfortable translating drug discovery challenges into precise machine learning problems.
• Driven and a bias-to-action mindset: A proactive and detail-oriented approach, with excellent cross-functional communication skills for working closely with an interdisciplinary team of chemists, biologists, and engineers.

Bonus Points If You Have...

• A strong publication record: A track record of first-author publications in premier machine learning or computational chemistry venues (e.g., NeurIPS, ICML, J. Med. Chem., JCIM) or relevant patents.
• Open-source contributions: Meaningful contributions to major open-source projects in cheminformatics or machine learning (e.g., RDKit, DeepChem, PyG, Hugging Face).
• Quantum-informed modeling: Experience leveraging quantum chemistry (e.g., DFT) to generate physics-based descriptors for building accurate and robust QSAR/ADMET models.
• MLOps & scalability: Practical experience with MLOps tools (e.g., MLflow, W&B, Flyte) and training models at scale on cloud infrastructure (GCP/AWS/Azure) or HPC clusters.
• Leadership and mentoring: A history of mentoring junior scientists or engineers, or experience leading technical projects and influencing scientific strategy.

Location:Cambridge, MA

About Flagship

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanitys most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture. Flagship has been recognized twice on FORTUNEs Change the World list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Companys annual list of the Worlds Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com

Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

Recruitment & Staffing Agencies*: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, FSP) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneerings internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect there to.*

The salary range for this role is $168,000 - $258,500. Compensation for the role will depend on a number of factors, including a candidates qualifications, skills, competencies, and experience. FL94 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL94s good faith estimate as of the date of publication and may be modified in the future.