AI for Synthetic Biology @ IJCAI 2016

Hello World
Gradient detection

Workshop Description

Our primary goal in this workshop is to draw the attention of the AI community to a novel and rich application domain, namely Synthetic Biology. Synthetic biology is the systematic design and engineering of biological systems. Synthetic organisms are currently designed at the DNA level, which limits the complexity of the systems. In this workshop we will have invited speakers introducing the domain, and describing the current workflow used by synthetic biologists. We will identify open problems and challenges in the Synthetic Biology and AI intersection through discussions and demonstrate the feasibility of progress through contributed talks.

Synthetic Biology holds the potential for revolutionary advances in medicine, environmental remediation, and many more. For example, some synthetic biologists are trying to develop cellular programs that will identify and kill cancer cells, while others are trying to design plants that will extract harmful pollutants like arsenic from the ground. However, the field has reached a complexity barrier that AI researchers can help it overcome. The state-of-the-art techniques in synthetic biology require practitioners to design organisms at the DNA level. This low-level, manual process becomes unmanageable as the size of design grows. This is analogous to writing a computer program in assembly language, which also becomes difficult quickly as the size of the program grows.

We believe that the time is ripe to gather researchers from synthetic biology and AI communities to cultivate a multi-disciplinary research community that can benefit both areas. For AI researchers it will be a never before explored novel domain with unique challenges, whereas for the synthetic biology community it will be an opportunity to break the complexity barrier it is facing.


The workshop is generously sponsored by BBN Technologies and the Bio-Design Automation Consortium. This has allowed us to sponsor some student travel to the workshop.

BBN Technologies
Bio-Design Automation Consortium

Invited Speaker

Dr. Natasa Miskov-Zivanov is a Professor in the Electrical and Computer Engineering, Bioengineering Department at the University of Pittsburgh. She earned a B.Sc. in Electrical and Computer Engineering from the University of Novi Sad. She earned a M.Sc. and Ph.D. in Electrical and Computer Engineering at Carnegie Mellon Univeristy in 2005 and 2009, respectively.


1:30 –Welcome
1:40 –Introduction to Synthetic Biology Slides(PDF)
A. Adler and F. Yaman
BBN Technologies, USA
2:00 –AI for Synthetic Biology Slides(PDF)
F. Yaman and A. Adler
BBN Technologies, USA
2:25 –Automated Reading, Assembly, and Explanation to Guide Biological Design
N. Miskov-Zivanov
University of Pittsburgh, USA
2:50 –Paper presentation: Debugging Genetic Programs with Bayesian Networks
G. Karlebach, L. Woodruff, C. Voigt and B. Gordon
MIT Broad Foundry, USA
3:10 –Paper presentation: Molecular Robots Obeying Asimov’s Three Laws of Robotics
G. Kaminka, R. Spokoini-Stern, Y. Amir, N. Agmon and I. Bachelet
Bar Ilan University & Augmanity, Israel
3:30 –Coffee Break
4:00 –Paper presentation: A Combinatorial Design Workflow for Search and Prioritization in Large-Scale Synthetic Biology Construct Assembly
J. Ng, A. Berliner, J. Lachoff, F. Mazzoldi, E. Groban
Autodesk Research, USA
4:20 –Paper presentation: MDP-based Planning for Design of Gene-Repression of Circuits
T. Amimeur and E. Klavins
University of Washington, USA
4:40 –Paper presentation: Using Machine Learning to Interpret Untargeted Metabolomics in the Context of Biological Samples
A. Tong, N. Alden, V. Porokhin, N. Hassanpour, K. Lee and S. Hassoun
Tufts University, USA
5:00 –Discussion & Closing remarks
5:30 –End of workshop

Important Dates

  • Paper submission deadline: April 18, 2016 May 1, 2016
  • Scholarship Applications: April 25, 2016 May 1, 2016
  • Paper Notifications: May 23, 2016
  • Scholorship Notifications: June 2, 2016
  • Workshop: July 9, 2016

Call for Papers

The field of synthetic biology, still in its early stages, has largely been driven by experimental expertise, and much of its success can be attributed to the skill of the researchers in specific domains of biology. There has been a concerted effort to assemble repositories of standardized components; however, creating and integrating synthetic components remains an ad hoc process.

AI techniques can help address the challenges that synthetic biology faces including:

  • representation of knowledge (e.g., semantic networks, frame representations, domain specific languages, data exchange),
  • acquisition of knowledge (e.g., machine learning, hypothesis generation),
  • planning and decision making (e.g., expert systems, constraint-based reasoning, planning under uncertainty), and
  • automated action (e.g., robotics).

We seek both position papers (up to 2 pages) and short papers (up to 6 pages) that address current or future research problems and/or approaches at the intersection of synthetic biology and AI.


Submission will be through Easy Chair, here.


We plan to provide scholarship funds to support travel to the workshop. To apply please send the following information to: and

  • Name, email, affiliation
  • Year (e.g., 2nd year undergraduate, 3rd year grad student, postdoc, professor)
  • Are you planning to submit an abstract?
  • One paragraph description of your research interests


Registration will be through the IJCAI website.

Workshop Organizers

Dr. Aaron Adler, BBN Technologies

Dr. June Medford, Colorado State University

Dr. Fusun Yaman, BBN Technologies