Scientist, Machine Learning; Principal Scientist - Associate Director Boston, MA

About Superluminal Medicines

Superluminal Medicines is a generative biology and chemistry company revolutionizing the speed and accuracy of how small molecule medicines are created. The Company’s platform aims to create candidate‑ready compounds with unprecedented speed using a combination of deep biology, computational and medicinal chemistry, machine learning, and proprietary big data infrastructure. We are expanding the team of talented scientists who seek to build the future of small molecule drug discovery with creativity and innovation.

We are seeking a Machine Learning Scientist to join our integrated discovery team and help advance small molecule drug discovery programs through applied ML. In this role, leading from the bench, you will enable the development, validation and deployment of state‑of‑the‑art ML models to generate the quantitative predictions necessary to drive drug discovery. Beyond technical mastery, you will serve as a core strategic partner to medicinal chemists, computational chemists, and biologists, building models that move programs efficiently toward program decision points and candidate nomination.

• Lead the application of Large Language Models (LLMs), co‑folding algorithms, and generative chemistry techniques to design novel chemical matter aimed at hitting key program milestones, such as establishing selectivity windows and optimizing drug‑like properties
• Serve as the machine learning POC on cross‑functional projects partnering with medicinal chemists and structural biologists to refine SAR and structure‑informed modeling efforts
• Synthesize complex ML outputs into clear, actionable design hypotheses that cross‑functional scientific stakeholders can use to make high‑stakes program decisions
• May be responsible for management and development of internal team members

• Ph.D. in Computational Chemistry, Computer Science, Machine Learning, or a related field
• 2+ years applying ML methods in a small molecule drug discovery program in biotech or pharma environments
• Demonstrated expertise in statistics, probability theory, data modeling, machine learning algorithms, and the languages used to implement analytics solutions
• Demonstrated success in a cross‑functional environment, including biologists, structural biologists, medicinal and computational chemists, with specific examples of computational designs/algorithms/models that directly influence achievement of program milestones
• Strong practical proficiency in Python and deep learning libraries (e.g., PyTorch, Tensor Flow) is required. Demonstrated ability to build and maintain robust, production‑quality ML code and data workflows

• Proven experience with protein‑ligand co‑folding models (e.g., Boltz, Open Fold, Alpha Fold, etc.) and the ability to integrate these structural insights into broader ML discovery pipelines
• Expertise fine‑tuning existing models with internally generated structural biology and biology data
• Strong knowledge of deep learning frameworks, specifically for affinity prediction, ADMET modeling, and the application of LLMs in a biological or chemical context
• Experience mentoring and developing teams
• A demonstrated track record of innovation in the ML/AI space, including developing and validating new architectures or novel applications of existing models to solve complex drug discovery problems
• Demonstrated expertise using small molecule drug discovery ML/AI tools e.g. Alpha Fold, Boltz, Open Fold, Chem Prop, Deep Chem, Reinvent, etc.
• Strong level coding for ML tasks including knowledge of key packages (RDKit, scikit‑learn, numpy, pandas, pytorch, Deep Chem, polars, PyG/DGL).
• Strong interpersonal and communication skills in the "why" behind a design to a diverse scientific audience

Superluminal offers a comprehensive benefits package that fully covers employees’ annual deductibles and monthly premiums for medical, dental, and vision insurance. The package also includes a 401(k) match program, a Massachusetts transportation subsidy, equity, unlimited paid time off, and both disability and life insurance.

Superluminal Medicines is an Equal Opportunity Employer committed to a culturally diverse workforce. All qualified applicants will receive consideration for employment without regard to race; color; creed; religion; national origin; age; ancestry; nationality; marital, domestic partnership or civil union status; sex, gender, gender identity or expression; affectional or sexual orientation; disability; veteran or military status or liability for military status.