Protocol Labs Network

Protocol Labs
Protocol Labs

Machine Learning Scientist

Software Engineering
Alameda, CA, USA
Posted on Tuesday, April 25, 2023
E11 Bio is a neuroscience moonshot building next-generation brain mapping technology to understand the brain, treat brain disorders and advance artificial intelligence research. We are building an interdisciplinary team of mission-driven scientists as a non-profit Focused Research Organization prioritizing open science and public benefit. Read our whitepaper and learn more.E11 Bio is seeking an experienced and motivated machine learning scientist to develop cutting edge models for image segmentation and proofreading of synaptic-level mammalian brain circuits, at unprecedented speed and scale. Responsibilities
  • Develop machine learning models to automate the segmentation of neuronal and synaptic morphology in large microscopy volumes
  • Deploy developed models in large cluster or cloud environments to apply them to imaging volumes of hundreds of TBs
  • Implement or develop human proofreading tools that minimize user interactions for fast and accurate neuronal segmentation
  • Work closely with wet lab and microscopy scientists to optimize data analysis and acquisition processes
  • Follow best practices for version control and sharing software with the scientific community
  • Engage in a culture of excellent laboratory science practices, prepare reports and manuscripts, and present results internally and externally

Required Qualifications
  • PhD in computer science, machine learning, applied math, computational biology or a related field in science and/or engineering or PhD-equivalent publication history
  • 3-5 years of relevant work or research experience, with strong history of independent and autonomous execution on hard machine learning problems
  • Strong background in computer vision and applying machine learning tools to the analysis of large (light) microscopy data
  • Experience with software engineering best practices (e.g. version control, code reviews, etc)
  • Excellent communication and collaboration skills, record keeping ability, and attention to detail

Preferred Qualifications
  • Experience with processing big data in the cloud (e.g. AWS or GCP) and familiarity with
  • Experience with large scale connectomics data and tools (e.g. Neuroglancer, CATMAID, Knossos, CAVE, or equivalent)
  • Strong record of publications in peer reviewed scientific journals a plus

In your first six months, you will have...
  • Worked together with experts at E11 and partners in academia and industry to extend existing ML segmentation methods to utilize barcoded imaging data
  • Built a data analysis pipeline to track relevant error scores and improvements in morphology segmentation

Within two years, you will have...
  • Collaborated with academic and industry experts on scaling up ML segmentations solutions to work on datasets of hundreds of TBs
  • Developed new algorithms to identify synaptic contacts and analyze their protein content based on antibody labeling data
  • Designed and implemented databases to store and track segmentation versions from human proofreaders
  • Improve or develop human proofreading tools, potentially in collaboration with academia or industry

You'll love this job if...
  • You are passionate about moonshot neuroscience, and want to broadly accelerate science through long-term commitment to a high-impact project with a tight-knit team.
  • You have a strong desire and intrinsic motivation to work collaboratively and inclusively as part of an interdisciplinary team science effort
  • You are committed to the ethos of open science, and want to see your work transparently disseminated
  • You’re mission-driven, and are seeking an environment where you can take long-term risks on moonshot science, shielded from academic or for-profit incentives
  • You’re seeking a high-leverage, non-traditional opportunity to maximize the impact of your science, establishing relationships with key stakeholders in the neuroscience community

We offer
  • An opportunity to help change the world and work with some of the most talented and collaborative experts across scientific fields
  • Competitive salary: $150,000 - $220,000
  • Excellent medical, dental, and vision insurance through a PPO plan; parental leave
  • Generous time off + paid holidays
  • Wellness allowance for fitness and wellness activities

Convergent Research aims to help fill a structural gap in today's R&D system. We enable fundamental research that requires unusual levels of scale and coordination yet is not rapidly monetizable by industry. We’re bringing together top talent from academia, industry, and startups to build a new model for innovative R&D. As an incubator within the Schmidt Futures Network, we identify high-impact scientific or technical research and development opportunities, ultimately defining and launching these projects as Focused Research Organizations.Convergent Research, LLC is an Equal Employment Opportunity employer that proudly pursues and hires a diverse workforce. We do not make hiring or employment decisions on the basis of race, color, religion or religious belief, ethnic or national origin, nationality, sex, gender, gender-identity, sexual orientation, disability, age, military or veteran status, or any other characteristic protected by applicable local, state, or federal law or Company policy. We strive for a healthy and safe workplace and strictly prohibit harassment of any kind.