Scientist I - ML/AI algorithms for Multimodal Foundational Models

The Allen Institute is dedicated to understanding the principles of life and advancing health through innovative research. They are seeking a Scientist I to develop machine learning algorithms for multimodal data integration aimed at understanding Alzheimer’s disease pathology. The successful candidate will work in a collaborative environment, focusing on cutting-edge computational methodologies in bioscience. Responsibilities Develop modern machine learning algorithms to model multimodal omics data (transcriptional, chromatin accessibility, genetic, spatial, and protein information) Evaluate ML architectures able to characterize regulators of cell identity and neurodegenerative progression Implement sequence-based models to predict genetic contributions to disease Train large-scale models in multi-GPU environments efficiently Stay at the forefront of advances in AI for multimodal molecular biology Participate in a highly interactive and multidisciplinary environment Publish/present findings in peer-reviewed journals/scientific conferences Skills Ph.D. in Computer Science, Applied Math, Engineering, Computational Neuroscience, Computational Biology, or related field, or equivalent combination of degree and experience Experience working with recent Deep Learning Architectures/Foundational Models Experience with building, deploying and maintaining machine learning and foundational models Proficiency with cloud computing (AWS, GCP or Azure) and with on-prem clusters Proven ability to work independently and manage multiple projects simultaneously while meeting deadlines Experience with modeling gene regulatory networks, chromatin accessibility information, or related computational biology studies Experience building transformer-based foundational models of cell identity Working knowledge of AI/ML custom libraries, AI/ML execution platforms Strong publication track record Proven ability to work independently and manage multiple projects simultaneously while meeting deadlines in a highly collaborative environment Excellent written and verbal communication skills, with the ability to collaborate effectively in a multidisciplinary team environment Excellent written and verbal communication skills, with the ability to collaborate effectively in a multidisciplinary team environment Benefits Medical Dental Vision Basic life insurance 401k plan Paid time off Company Overview The Allen Institute is dedicated to answering some of the biggest questions in bioscience and accelerating research worldwide. It was founded in 2003, and is headquartered in Seattle, Washington, USA, with a workforce of 501-1000 employees. Its website is Company H1B Sponsorship Allen Institute has a track record of offering H1B sponsorships, with 41 in 2025, 33 in 2024, 25 in 2023, 26 in 2022, 17 in 2021, 7 in 2020. Please note that this does not guarantee sponsorship for this specific role.