Machine Learning Engineer

Protocol Labs, Inc.; San Francisco (CA); On-site; USD 180,000 - 240,000; Full time

Job summary

Protocol Labs, Inc. is hiring a Senior Machine Learning Engineer to design and train foundational models across neural data and behavior. You will work on the core generative model, handle end-to-end training, and shape modeling direction with a small team in San Francisco.

Focus areas include architecture, scalable training, and representation learning across EEG/MEG/fMRI signals. Strong collaboration with data and research teams is expected to deliver production-ready, well-documented code.

Qualifications

• Trained large deep learning models end-to-end.
• Experience training transformer or large sequence models with distributed training.
• Proficiency in Python and PyTorch, with reproducible model code.
• Strong prototyping across research and engineering at scale.
• Comfort working with multimodal or time-series data.
• Ability to learn new domains quickly from literature.

Responsibilities

• Design, train, and iterate on large generative models over multimodal neural data.
• Own training at scale: data loading, distributed multi-node training, hyperparameter optimization.
• Develop representations that capture structure across species and modalities.
• Train models on neural and behavioral data, including EEG/MEG/fMRI related signals.
• Deliver modular components of the modeling stack as working, documented code.

Skills

Deep learning

Transformer

Distributed training

Python

PyTorch

Multimodal data

Time-series

Research & engineering

End-to-end ownership

Experiment design

Communication

Job description

Senior Machine Learning Engineer (Foundation Models)

Type: Full-time

Location: San Francisco, United States. In person.

At this time we are only able to hire candidates who are already based in the US and able to work in-person in San Francisco. We do not support relocation at this time.

PLEASE DO NOT USE AI IN YOUR APPLICATION.

The Role

We're building a foundation model of the brain and behavior across species, trained on large-scale multimodal neural and behavioral data (including EEG, MEG, and fMRI), and this role is central to designing and training it. You'll work on the core generative model: architecture, training at scale, and representation learning across neural signals and behavior, along with the research questions that come with modeling biological data as sequences. You'll join a small team and work alongside our existing ML engineer, with room to shape the modeling direction as we grow. This is early-stage scope in a much less explored space, so you'll train greenfield models, own parts of the stack, and see your work define the company's core asset.

Responsibilities

Model development and training

• Design, train, and iterate on large generative (recurrent or transformer-based) models over multimodal neural and behavioral data
• Own training at scale: data loading, distributed multi-node training, hyperparameter optimization, and evaluation
• Develop representations that capture structure across species and modalities
• Train models on animal and human behavioral data as well as direct neural data
• Take ownership of distinct components of the modeling stack and deliver them as working, well-documented modules

Research and evaluation

• Define and run experiments to test modeling choices, and build the evaluation that tells us whether the model is learning what we need
• Draw on the neuroscience and sequence-modeling literature to inform architecture and training, creatively adapting ideas from other modalities (e.g. vision, audio, language) to EEG and other neural signals
• Rapidly prototype new ideas and turn research findings into reproducible, production-quality model code

Collaboration

• Partner with the data engineering team on data readiness and with the research team on what the model needs to capture
• Contribute to the shared modeling roadmap alongside our existing ML engineer
• Communicate your process, results, and trade-offs clearly to technical and scientific colleagues

Requirements

Core (essential)

• You've trained large deep learning models end to end, in production or research settings
• Hands-on experience training transformer or other large sequence models, including distributed training and scaling
• Proficiency in Python and PyTorch, with clean, concise coding practices and the discipline to write reproducible model code
• Strong implementation and prototyping skills, and comfort working across both research and engineering at scale
• Comfort working with large, messy, multimodal or time-series data
• Ability to learn new domains quickly, orient yourself in the academic literature, and implement new ideas
• An organized, methodical approach to research, with excellent communication and collaboration skills
• Pragmatism for an early-stage environment where you own work from end to end

Valued

• Enthusiasm for the science of modeling biological data, the intersection of the brain and AI, and building foundation models for neural data such as EEG, MEG, and fMRI
• Experience with representation learning and self-supervised or generative modeling, such as VAEs, GANs, diffusion models, and contrastive learning
• Background or strong interest in neuroscience, biosignals, or computational cognitive science
• Familiarity with signal processing (especially for EEG) and time-series analysis
• Experience training on large-scale, multi-node GPU clusters, or with hyperparameter optimization, training infrastructure, or evaluation frameworks
• Experience contributing to large existing codebases and ramping up quickly
• Published machine learning research in well-respected venues, or open-source contributions in relevant areas