Postdoctoral Fellow

COMPANY:          ViQi, Inc.

POSITION:           Postdoctoral Fellow

JOB TYPE:            12 month assignment

REPORTS TO: Chief Science Officer

LOCATION:          Santa Barbara, CA or Remote

COMPANY DESCRIPTION

Come join a team excited to share knowledge and expertise in a highly technical field that is leveraging the market’s need for greater integration between computer science and life sciences. ViQi is made up of world class experts that are trailblazers in the AI/ML sector, with cutting edge understanding in large-scale image analysis, but our real strength is how we work together collaboratively and welcome diverse backgrounds and thoughts. Our cloud-based AI-driven platform is solving real problems for our customers, and our expertise in a niche industry combined with our core team’s in-depth knowledge has propelled ViQi into an exciting place in its evolution.

ViQi is creating innovative solutions by automating research workflows and expediting discovery processes and results. Most recently the ViQi team has focused its energy and talents to develop AIs for cell-based assays. AVIA™ (Automated Viral Infectivity Assay) is a quantitative viral infectivity assay using automated brightfield microscopy and machine learning to rapidly detect viral infection. We have a proclivity for collaboration and are passionate about being part of the solution to create positive change. At our core, we’re a tight-knit team who enjoys complex scientific data issues, solving problems, and learning new methods. We’re excited to meet you.

OPPORTUNITY

ViQi is seeking a postdoctoral candidate for the NSF SBIR Innovative Postdoctoral Entrepreneurial Research Fellowship (details below). In this role, you will lead efforts to develop analytical tools for the JUMP-Cell Painting Consortium principal dataset: a recently released open-source, high-content screen of over 100,000 compounds collected across 10 pharmaceutical companies. You will be responsible for writing, testing, and troubleshooting code to analyze this dataset including quantitative comparison between phenotypes, discovering linkage between phenotype similarities and biological pathways, training large neural network models to make predictions based on the phenotypes in this dataset, and developing tools for quantitative comparisons of phenotypes between customer-generated screens and JUMP. The role requires a high degree of autonomy during the research, planning and execution phases, therefore the candidate must be a self-starter with an entrepreneurial mind-set and have exceptional problem solving skills. This position can be in-person at ViQi Inc. or remote.

THE JUMP CONSORTIUM

The Joint Undertaking for Morphological Profiling (JUMP)-Cell Painting Consortium is a project initiated by Anne Carpenter's group at the Broad Institute to establish an open benchmark for tools used in phenotypic profiling for High Content Screens (HCS). The consortium is a collaboration between 10 pharmaceutical companies, 6 technology companies, and 2 non-profit partners. This dataset in its entirety includes: 

  • ~116,000 unique compounds

  • ~12,000 over-expressed genes

  • ~8,000 CRISPR-Cas9 knockouts

  1. Dataset GitHub

  2. JUMP Cell Painting gallery

  3. JUMP paper

THE JUMP PROJECT AT VIQI 

In an initial assessment of this dataset and ViQi's existing tooling (https://viqiai.com/autohcs), we've investigated subsets of the first-released image collection (CPG0012) and the JUMP pilot dataset (CPG 0000), training AIs to quantify phenotypic differences between compound and genetic manipulations. We have already found interesting phenotype clusters indicative of cellular function, and are investigating ways to do this systematically for all available data.

Following this first pass, we have designed a postdoctoral project that will require 1) optimizing AI performance to tackle the larger datasets in JUMP and 2) using your expertise in bioinformatics to validate our phenotypic clustering using biological pathway databases as well as cheminformatics databases of structure-activity relationships.

Qualifications:

  • Doctorate degree in Computer Science, Engineering, Mathematics, Statistics, Life Science, Physics or a related field

  • 3+ years of experience in Bioinformatics 

  • 1+ years of experience in Data Science

  • Expertise with Python and machine learning toolboxes like TensorFlow

  • Experience with cloud technologies, particularly AWS (Azure/Google Cloud a plus)

  • Experience in building AI models and deploying to production

  • Experience mentoring and managing others a plus

  • Ability to explain technical concepts (programming/databases/stats) to non-technical audiences

  • Ability to make recommendations when faced with imperfect information

  • Contributions to Open Source Projects a plus

  • Strong client service and proactive mindset

  • Strong oral and written communication skills, most importantly, must be a team player

  • Ability to build a sense of trust and rapport that creates a comfortable and effective workplace

  • Interested in expanding one’s horizons and solving some of the hardest problems in computing

THE INNOVATIVE POSTDOCTORAL ENTREPRENEURIAL RESEARCH FELLOWSHIP

About NSF I-PERF

This is your opportunity to use your skills at a high-tech start-up and gain experience in industry. Funded by the National Science Foundation (NSF), the Innovative Postdoctoral Entrepreneurial Research Fellowship (I-PERF) recruits, trains, and funds early-career Science and Engineering doctoral degree recipients to participate in innovative research at an NSF-funded start-up. 

Compensation & Benefits 

I-PERF fellows receive an annual stipend of $78,000 per year, optional individual health and life insurance benefits, relocation assistance, a professional conference travel allowance, and scripted professional development training funded by the NSF. Additional company stipends are negotiable based on experience. 

Applicant Eligibility 

Applicants must hold an earned doctoral degree in an NSF-supported STEM discipline from a recognized Ph.D. granting institution. They must have earned this degree within 7 years of application to I-PERF and be a U.S. citizen, national, or permanent resident at the time of application. Emphasis will be placed on members of socio-economic disadvantaged groups, members of underrepresented groups in science and engineering, persons with disabilities, veterans of the U.S. Armed Forces, and first generation college graduates. For more information, visit: https://iperf.asee.org/

TO APPLY 

Create an applicant account at this link: https://iperfapp.asee.org/

Once your application is complete (under Applicant Profile), select Research Opportunities,  search for ViQi, and connect with us!