AI for Synthetic Biology 2 @ FAIM 2018 (Federated Artificial Intelligence Meeting)

Workshop date:
Sunday, July 15, 2018 : Full day workshop. The workshop is part of the IJCAI / FAIM conferences :


We have money to support student travel. If interested, please contact us.

We would like to give AI researchers a chance to talk about their expertise in their area of research. If you would be willing to give a lightning talk in the afternoon, please contact us.

Contact info: &


Travel support:
We have sponsorship funds from AI Journal. Details on receiving travel support will be forthcoming. Preference will be given to those with accepted papers.


AI Journal
Sponsored by AI Journal
BBN Technologies
Sponsored by Raytheon BBN Technologies
Bio-Design Automation Consortium, Inc.
Sponsored by Bio-Design Automation Consortium, Inc.

Workshop Schedule:

Day / TimeActivity / TitleAuthor (s) / Speaker(s)
9:00am – 9:15amSymposium Introduction
9:15am – 9:45amIntro Talks for AI and SynBio
9:45am – 10:00amDiscussion of Community Resources
10:00am – 10:30amTalk: Collaborative Development and Evaluation of Data-driven Biological ModelsMohammed Eslami, Hamed Eramian and Nicholas Leiby
10:30am – 11:00amCoffee Break
11:00am – 12:00pmPanel to Discuss Challenges of AI in SynBio
12:00pm – 12:30pmTalk: Using Machine Learning and Big Data to Select Smart Microbes for Generating Electricity from WastewatersCharles Zhou and Ying Zhao
12:30pm – 2:00pmLunch
2:00pm – 2:30pmTalk: The Case for A New AI+Cyber+Bio Security ParadigmWilliam Streilein and Catherine Cabrera
2:30pm – 3:00pmTalk: A Bayesian Model for Experiment Choice in Synthetic BiologyRobert P. Goldman, Puja Trivedi, Daniel Bryce, Matthew Dehaven and Alex Plotnick
3:00pm – 3:30pmTalk: AI Challenges and Applications in Detecting Engineering in Single CellsAaron Adler, Adam Abate, Joseph Collins, Benjamin Demaree, Kevin Keating, Xiangpeng Li, Thomas Mitchell, David Ruff, Allison Taggart, Shu Wang, Daniel Weisgerber, Daniel Wyschogrod, Fusun Yaman, Eric Young and Nicholas Roehner
3:30pm – 4:00pmCoffee Break
4:00pm – 4:30pmTalk: Design and Analysis of Toehold Switches via a Two-Headed Convolutional Hierarchy Model of Riboswitch Architecture (CHiMeRA)Jacqueline A. Valeri, Katherine M Collins, Bianca A. Lepe, Miguel A. Alcantar, Timothy K. Lu and Diogo M. Camacho
4:30pm – 5:30pmDiscussion Session (Breakout Groups for Data, Tools, Applications)
6:00pm – 7:00pmReception
7:00pm – ?Group outing (optional)
9:00am – 10:00amKeynote: Human vs Machine: Challenges for Applying AI in BiologyJosh Dunn, Ginkgo Bioworks
10:00am – 10:30amTalk: The DSGRN Database: Identifying Network Function with Network TopologyKonstantin Mischaikow, Chris Mischaikow, Breschine Cummins and Tomas Gedeon
10:30am – 11:00amCoffee Break
11:00am – 11:30amTalk: Convolutional Neural Networks Guide Rationally Engineered Protein StabilityRaghav Shroff, Austin Cole, Andrew Ellington and Ross Thyer
11:30am – 12:00pmTalk: Convolutional Neural Net Learns Promoter Sequence Features Driving Transcription StrengthNicholas Leiby, Ayaan Hossain and Howard M Salis
12:00pm – 12:30pmTalk: Sequence to Sequence Transfer Learning for DNA PhenotypingNiall Dalton, Peter Morales, Rajmonda Caceres, Matt Walsh, Christina Zook, Catherine Van Praagh, Nicholas Guido and Todd Thorsen
12:30pm – 2:00pmLunch
2:00pm – 2:30pmTalk: Algorithmic Optimization for Pathway Engineering and BeyondEric Young
2:30pm – 3:00pmTalk: Computational Modeling of Cell Signaling and Mutations in Pancreatic CancerCheryl Telmer, Khaled Sayed, Adam Butchy, Kara Bocan, Christof Kaltenmeier, Michael Lotze and Natasa Miskov-Zivanov
3:00pm – 3:30pmTalk: ART: A Machine Learning Automated Recommendation Tool for Guiding Synthetic BiologyHector Garcia Martin
3:30pm – 4:00pmCoffee Break
4:00pm – 4:30pmTalk: On Chemical Reaction Network Design by a Nested Evolution AlgorithmElisabeth Degrand, Mathieu Hemery and Fran├žois Fages
4:30pm – 5:30pmBreakout Group Discussions
6:00pm – 7:30pmPlenary Session
9:00am – 10:30amBreakout Group Discussions
10:30am – 11:00amCoffee Break
11:00am – 12:30pmBreakout Groups Debrief and Next Steps Discussion

Workshop location:
Stockholm, Sweden

Previous Workshop:

Dr. Aaron Adler, BBN Technologies
Dr. Fusun Yaman, BBN Technologies
Dr. Eric Klavins, University of Washington
Dr. Natasa Miskov-Zivanov, University of Pittsburgh

Our primary goals for this workshop are to draw the attention of the AI community to a novel and rich application domain, namely Synthetic Biology, and to build mutually beneficial collaborations between the two communities. 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, 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. We will also have a high level talk about different AI techniques targeted towards participants with a Synthetic Biology background.

This workshop at FAIM 2018 seeks to bring together the AI and Synthetic Biology communities. 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.

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),
  • prediction and modeling of complex and multi-cellular behavior (e.g., multi- agent systems),
  • 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.

Please note that this workshop is in addition to a possible AAAI fall symposium.