AI Research Scientist — BioDesign & Open Science

Allen Institute; Allen (TX); Hybrid; USD 147,000 - 183,000; Full time

Benefits offered by this job

Relocation assistance

Benefits package

Job summary

The Allen Institute in Washington State seeks an AI Research Scientist to invent and advance machine learning methods for biological discovery at scale. You will design, test, and refine new AI/ML models that operate across diverse and large-scale biological data, translating questions into computational frameworks.

You will work with scientists and engineers to evaluate model performance, communicate findings, and contribute to publications, benchmarks, and reusable methods in an open science

Qualifications

• PhD in Computer Science, Applied Mathematics, Statistics, Computational Biology, or a related field; or equivalent combination of degree and experience
• Demonstrated experience developing and evaluating novel AI/ML approaches for complex, large-scale datasets
• Proficiency in Python and modern deep learning frameworks (e.g., PyTorch, JAX)
• Strong foundation in machine learning, deep learning, and scientific computing, including experimentation, benchmarking, and model analysis

Responsibilities

• Develop, train, and evaluate large-scale AI/ML models across diverse biological data types, with attention to scientific relevance and rigor
• Investigate new modeling paradigms – such as representation learning, generative models, foundation models, and multimodal learning – to address open biological research questions
• Translate complex scientific questions into well-posed computational frameworks, experiments, and benchmarks
• Assess model behavior, limitations, and interpretability in scientific contexts, and communicate findings clearly to scientific and technical collaborators
• Design and run experiments at scale, including benchmarking and model analysis, using modern training and evaluation environments
• Build reusable modeling frameworks and reference implementations that accelerate research across teams
• Document methods and support reproducibility and open science practices, including code, data, and benchmark release where appropriate
• Contribute to the broader scientific community through publications, collaborations, conference participation, and methodological work

Skills

Python

ML research

Deep learning

Scientific computing

Experimentation

Education

PhD in CS/Applied Math/Stats/Computational Biology

Equivalent degree + experience

Tools

PyTorch

JAX

Job description

The Allen Institute in Washington State seeks an AI Research Scientist to invent and advance machine learning methods for biological discovery at scale. You will design, test, and refine new AI/ML models that operate across diverse and large-scale biological data, translating questions into computational frameworks.

You will work with scientists and engineers to evaluate model performance, communicate findings, and contribute to publications, benchmarks, and reusable methods in an open science