E11 Bio - Machine Learning Scientist
Alameda, California
E11 Bio – E11 Bio /
Full Time /
On-site
E11 Bio is a Focused Research Organization (FRO) with a long-term mission to make connectomics scalable and cost-effective for mammalian brains – first for mice, and eventually for humans.
We have recently developed PRISM, a platform technology for low cost optical connectomics. PRISM integrates advances in genetic cell barcoding, multiplexed expansion microscopy, and Machine Learning (ML)-based spatial reconstruction to solve key bottlenecks in data acquisition and analysis. We anticipate that PRISM will reduce the cost of connectomics 100-fold and thereby transform neuroscience, treatments for brain disorders, and neuro-inspired computing.
We are looking to scale PRISM to petascale data sets, and we are seeking a talented and driven ML scientist to join us in this effort. As an ML scientist at E11 Bio, you will develop innovative and scalable methods to realize the potential of optical barcode connectomics.
Responsibilities
- Develop machine learning models to automate the reconstruction and processing of large microscopy volumes
- Deploy developed models and algorithms in large cluster or cloud environments for distributed processing
- Act as a point-of-contact for external collaborators that want to access the generated segmentation data for analysis
- 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 in applying machine learning tools to the analysis of large (light) microscopy data sets
- 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 shape reasoning and point affinity transformer approaches
- Experience with processing big data in the cloud (e.g. AWS or GCP)
- 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…
- Developed innovative ML approaches for (automated) proofreading of segmentations in large optical connectomics volumes, leveraging shape and/or barcode information
- Aided the development of a robust data processing pipeline using innovative ML approaches to cross spatial discontinuities
Within three years, you will have played a critical role in…
- Scaling up the optical connectomics reconstruction pipeline to entire brain areas.
- Achieving greater than cubic-mm scale imaging and 100x lower cost reconstruction
- Collaborating with academic and industry experts on building and extending tools for integrating barcode information into annotation and visualization software (i.e. neuroglancer, CAVE)
- Engaging the broader ML and academic community
- Pioneering the Focused Research Organization approach to team science and spinning out the first FRO follow-on effort.
- Building the pipeline and analyzing the data necessary to catalyze a whole-brain optical mouse connectome project
You are:
- Passionate about working in a startup-inspired environment with minimal red tape and very high trust, autonomy and camaraderie
- Enthusiastic about working with high performers on hard problems in a moonshot, team science environment
- Mission-driven, and are fired up by an opportunity to work on a highly ambitious connectomics project that will transform neuroscience
- Committed to open science, and want to see your work lift all boats
- Collaborative and want to work in partnership with some of the best teams across the field
You value
- Impact & mission focus – you’re committed to the mission of unlocking low-cost mammalian connectomics
- High performance – you set ambitious goals and do whatever it takes to meet them.
- Winning as a team – you’re always open to working on projects which best support the team, even if it’s outside your comfort zone. You’re allergic to “sunk cost”.
- Mutual respect and support – you believe each team member has an important contribution to make to the success of the project and want to help others excel
- Candid & curious communication – you are open to giving and receiving clear and honest feedback in a spirit of mutual respect and curiosity.
- Initiative and resourcefulness – you are not afraid to take initiative and lead a new direction when it is needed for the success of the team. “Not my job” is not in your vocabulary.
- Finding joy in our work – You strive to bring a sense of enthusiasm and optimism to your day-to-day work, and recognize that “laughter is the best correlate of success”
We Offer
- An opportunity to help change the world and work with some of the most talented and collaborative experts across scientific fields.
- An opportunity to gain experience on a field-defining moonshot effort.
- Excellent medical, dental, and vision insurance through a PPO plan; parental leave.
- Generous time off + paid holidays.
- Ample healthy and energizing food including daily lunches.
- Wellness allowance for fitness and wellness activities.
$127,000 - $160,000 a year
Bonus: Performance-based, up to 20% of base salary
Total potential compensation: $152,400 - $192,000 annually
Offers are normally made at the lower portion of the range, enabling employee growth within the range over time. Final base pay for a given candidate may differ based on factors such as prior experience, education and training, market trends, and skillset, and additional qualifications. The listed range refers to salary only. The total compensation package also includes a health and wellness stipend, matched 401K contributions, corporate holidays, flexible employee vacation, and other benefits.
E11 Bio, 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 basis protected by applicable local, state, or federal laws or prohibited by Company policy. We strive for a healthy and safe workplace and strictly prohibit harassment of any kind.
