Postdoctoral Fellow - Natural Language Processing, Machine Learning, Bioinformatics & Systems Biology

UC San Diego Center for Microbiome Innovation & IBM
United States California La Jolla


The automatic knowledge base construction group in the UC San Diego-IBM Artificial Intelligence for Healthy Living (AIHL) program, led by Dr. Chun-Nan Hsu and Dr. Rob Knight , is seeking applications of a Postdoctoral Fellow in deep learning for natural language processing to extract microbiome knowledge from the scientific literature. The positions are available immediately. The project will be funded on a contract for three years.

The research group is part of the Center for Microbiome Innovation (CMI), one of the top research centers in the world in human microbiome research, developing AI, deep learning, and cutting edge data sciences to advance the understanding of the impact of microbiome to health. The knowledge base group has developed one of the most efficient and accurate algorithms in automated understanding of disease mentions in the scientific literature, winning the Best Application Award in the 2019 conference of Automated Knowledge Base Construction (AKBC). Our former master student was admitted to prestigious PhD programs with fellowships.

The group resides in the Qualcomm Institute (UC San Diego division of the California Institute for Telecommunications and Information Technology (Calit2)), the home of multidisciplinary research programs and startups at UCSD. The group has access to powerful GPU computer clouds at CMI and IBM. The group strives to deliver useful knowledge base systems and develop original, innovative, top-tier conference acceptable algorithms simultaneously. Group members work closely with CMI faculties and students and top-notch researchers from IBM in the Bay Area and around the world through frequent virtual and face-to-face meetings.

The postdoctoral fellow will be encouraged to take initiation to explore new ideas to accomplish fully automatic knowledge base construction for human microbiome and work on grant proposals to develop into an independent leader of scientific research.

Host faculty include Rob Knight (Pediatrics and Computer Science & Engineering) and Chun-Nan Hsu (Neurosciences).

Scope of research:
Learning from structured ontologies
Unsupervised, weakly supervised machine learning and active learning for NLP
Biomedical concept understanding
Event and relation extraction and inference


Ph.D. in a relevant discipline, including in the areas of natural language processing, machine learning, or bioinformatics and systems biology

Strong record in publications in top-tier AI conferences and Bioinformatics journals

Undergraduate or graduate coursework or degree in Biology or a related field is a plus

Start date

As soon as possible

How to Apply

Please email a completed application form ( and support documents to to apply.

Note: If you have relatives employed at UC San Diego, you must include the name, relationship and department where employed in your resume or cover letter. This information is used only for the purpose of complying with the University’s nepotism policy.


Daniel Freed