Senior Staff Software Engineer, Machine Learning

  Job Title:Senior Staff Software Engineer, Machine LearningLocation:San Diego, CA Position type:FLSA:Full time ExemptDepartment:Finance ID:AI Innovation7100-2025-7Strive to Bring a Profound Difference to our PatientsAt Avidity Biosciences, we are passionate about the impact of every employee in realizing our vision of improving people’s lives by delivering a new class of RNA therapeutics. Avidity is revolutionizing the field of RNA with its proprietary AOCs, which are designed to combine the specificity of monoclonal antibodies with the precision of oligonucleotide therapies to address targets and diseases previously unreachable with existing RNA therapies. If you are a committed, solution-oriented thinker, join us in making a difference and become part of our growing culture that is integrated, collaborative, agile and focused on the needs of patients. Avidity Biosciences, Inc.'s mission is to profoundly improve people's lives by delivering a new class of RNA therapeutics - Antibody Oligonucleotide Conjugates (AOCs™). Utilizing its proprietary AOC platform, Avidity demonstrated the first-ever successful targeted delivery of RNA into muscle and is leading the field with clinical development programs for three rare muscle diseases: myotonic dystrophy type 1 (DM1), Duchenne muscular dystrophy (DMD) and facioscapulohumeral muscular dystrophy (FSHD). Avidity is broadening the reach of AOCs with its advancing and expanding pipeline, including programs in cardiology and immunology through internal discovery efforts and key partnerships. Avidity is headquartered in San Diego, CA. For more information about our AOC platform, clinical development pipeline, and people, please visit www.aviditybiosciences.com and engage with us on LinkedIn and Twitter.The OpportunityAs a Senior Staff Software Engineer, Machine Learning, you will be a hands-on technical contributor to Avidity’s AI & Machine Learning team, reporting directly to the VP of AI/ML. This role offers the unique opportunity to drive innovation by building, deploying, and scaling machine learning systems that support a wide range of functions, from research and development to clinical and commercial teams, to operational improvements. In this role, you will be a key contributor from day one, working closely with teams across research, technical development & operations, clinical, commercial, and IT. At Avidity, we lead by doing, and even senior leaders are hands-on contributors. You’ll be a critical part of developing and executing Avidity’s AI and machine learning roadmap, helping to drive forward solutions that profoundly improve patient outcomes. What You Will Contribute

• Serve as our trusted software engineering lead, professionalizing and deploying tools that our team builds for the rest of our end-user community.
• Collaborate with cross-functional teams to identify engineering opportunities across clinical, research, and commercial domains.
• Build scalable, production-grade machine learning pipelines and integrate them into existing systems.
• Maintain and deploy interpreters, servers, code repos, and other similar processes needed by the AI Innovation Team.
• Stay current on advancements in AI/ML to evaluate and incorporate new techniques relevant to Avidity’s mission.
• Work hands-on with Python, TensorFlow, PyTorch, and modern data science frameworks to build and optimize models.
• Help to automate processes, including data manipulation at scale, posting and retrieving datasets, and through custom GUI deployments
• Contribute to building a culture of innovation, collaboration, and technical excellence within the AI/ML team.

What We Seek

• Bachelor’s degree in Computer Science, Biomedical Engineering, Machine Learning, or a related field; Advanced Degree (MS/PhD) preferred.
• 12+ years of experience in developing and deploying machine learning models as a software engineer, ideally in the biotech, healthcare, or pharmaceutical industries.
• Proficiency in Python and machine learning frameworks such as TensorFlow, PyTorch, and Scikit-learn.
• Strong foundation in data structures, algorithms, and software development best practices.
• Experience with cloud platforms (e.g., AWS, Azure, or GCP) and distributed computing.
• Familiarity with biological or clinical data, such as genomics or proteomics, is a plus.
• Demonstrated ability to work in a cross-functional matrix environment and adapt to rapidly changing priorities.
• A collaborative mindset with strong communication, problem-solving, and organizational skills.

What We Will Provide to You 

• The base salary range for this role is $185,250 - $204,750. The final compensation will be commensurate with relevant experience, skillset, internal equity, and market factors.
• Avidity offers competitive compensation and benefits, including the opportunity for annual and spot bonuses, stock options, and RSUs, as well as a 401(k) with an employer match. In addition, the comprehensive wellness program includes coverage for medical, dental, vision, and LTD and four weeks of time off.
• A commitment to learning and development, including a variety of internal programming developed by and for Avidity employees, opportunities for job-specific training offered by industry, and an education reimbursement program.

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