Sr. Machine Learning Scientist

Key Skills

Algorithms, CUDA/GPU programming, HTML, JavaScript, Machine learning techniques, PyTorch, UI design, UX design, Workfusion

Job Description

The Sr. Machine Learning Scientist serves a key role within Peptilogics’ Discovery Team, advancing Peptilogics’ peptide drug design programs and Nautilus™ generative AI platform for AI-driven design of peptide therapeutics. The Sr. Machine Learning Scientist will lead development and implementation of AI/ML algorithms and models and their application to drug design programs, working in close collaboration with teams in computational and structural biology, peptide science, and clinical development.

The candidate must demonstrate exceptional technical, collaborative, and communication skills to work across AI/ML, software implementation, and drug design. The role requires expertise in deep learning, machine learning, and reinforcement learning, coupled with domain knowledge of chemistry and proteins, high proficiency with Python, and experience using high-performance computing (HPC) systems and applications. Excellent communication skills are required for presenting and publishing results.

Core Responsibilities

• Develop, evaluate, implement, validate, and apply AI/ML algorithms for peptide drug design.
• Drive AI/ML strategy and execution for Peptilogics’ drug discovery programs.
• Deploy AI/ML tools as production workflows within Peptilogics’ Nautilus™ platform, supporting a high degree of reliability, reproducibility, reusability, and ease of use.
• Collaborate across the Discovery team to identify, acquire, preprocess, and curate relevant data and develop data pipelines.
• Communicate technical approaches, results, and impact to Peptilogics leadership in an effective, timely, concise manner.
• Perform other duties as assigned.
• Represent Peptilogics externally, including through partnerships, at conferences, and by publishing.
• Work in an interdisciplinary, multicultural, distributed team focused on collaboration, innovation, and quality. This includes working with external partners with the U.S. and globally.
• Consistently demonstrate exceptional communication, interpersonal, organizational, and management skills to collaborate effectively across functions and efficiently develop and execute programs in drug discovery and R&D.
• Stay abreast of advances in relevant areas by monitoring publications, conferences, and other sources.
• Ensure strong adherence to Peptilogics’ cybersecurity policies and best practices.
• Develop software consistently with Peptilogics’ software engineering guidelines, emphasizing on scalability, efficiency, reliability, and reproducibility.
• Thrive in a dynamic, rapidly evolving, results-focused environment.
• Travel as needed.

Required Skills

• PhD in machine learning, chemistry, biochemistry, chemical engineering, physics, or a related field, or MS in such a field plus 3 years of relevant experience developing AI/ML for chemistry-centered applications
• Excellent knowledge of deep learning including topics such as graph neural networks, diffusion, attention mechanisms, reinforcement learning, as well as traditional machine learning
• Domain knowledge of chemical physics, organic chemistry, biochemistry, molecular biology, and/or biophysics
• Proficiency and experience with PyTorch and PyG
• Strong understanding of software engineering in Python
• Experience working in HPC environments, including profiling and optimizing AI/ML workflows
• Excellent communication and organizational skills
• Passion for learning and the ability to work cross-functionally and in a dynamic, rapidly changing environment

Preferred Skills

• As for Required, plus chemistry coursework including organic chemistry and physical chemistry
• Experience in drug discovery and design
• Experience developing machine learning algorithms for accelerating physics-based simulations
• Proficiency in quantum chemistry methods applicable to peptide-protein systems
• Experience developing machine learning algorithms for optimizing force fields or scoring functions
• Understanding of AI accelerators and related hardware
• Understanding of pharmacology
• Proficiency in scientific and information visualization