2018 AAAI Fall Symposium: Artificial Intelligence for Synthetic Biology

October 18-20, 2018
Westin Arlington Gateway, Arlington, Virginia, USA

Our primary goal for this symposium is to begin to connect and build mutually beneficial collaborations between the AI and the synthetic biology communities. There are many problems and applications at the intersection of these two fields.

Synthetic biology is the systematic design and engineering of biological systems. It is a relatively new field and holds the potential for revolutionary advances in medicine, materials engineering, environmental remediation, and more. Synthetic biology can be used for a range of diverse goals, for example developing genetic programs to identify and kill cancer cells or designing plants that can extract pollutants from the ground. AI has the capacity to advance the progress of synthetic biology, and to help realize these goals.

Collaborative Documents

Artificial Intelligence Terms and Definitions, and Conferences

Synthetic Biology Terms and Definitions, and Conferences

Questions for Government Panel

Schedule

Group outing details coming soon. Government panel includes DARPA, SBME, NSF, and NIH. Hardcopy schedules (PDF) will be available at the symposium.

Day / TimeActivity / TitleAuthor (s) / Speaker(s) 
Thursday
9:00am - 9:15amSymposium introduction
9:15am - 10:30amIntroduction to Synthetic BiologyEric Young (WPI)
10:30am - 11:00amCoffee Break
11:00am - 12:30pmTalk: Cell-free synthetic biology as a source for deep learningZachary Sun
Talk: Using Synthetic Biology for bio-inspired computing?Martín Gutiérrez, Javier Carrión and Yerko Ortiz
Talk: Formalizing Sample Transformation PlansDaniel Bryce, Robert Goldman, Ugur Kuter, Alex Plotnick, Matt DeHaven, Chris Geib, Jake Beal, Nic Roehner and Bryan Bartley
Talk: Enabling AI-Assisted Drug Screening and Synthetic Biology Engineering: Multi-Parametric Data-Driven Cell Profiling by CMOS Multi-Modal Cellular Interfacing ArraysAdam Wang, Jongseok Park, Doohwan Jung, Gregory Junek and Hua Wang
12:30pm - 2:00pmLunch
2:00pm - 3:00pmIntroduction to AIHector Munoz-Avila (Lehigh University)
3:00pm - 3:30pmTalk: Making AI Work for Synthetic Biology: Challenges and OpportunitiesRajmonda Caceres and Timothy Dasey
3:30pm - 4:00pmCoffee Break
4:00pm - 5:30pmDiscussion Session: What are the big/hard problems in Synthetic Biology?
6:00pm - 7:00pmReception
7:00pm - ?Group outing (optional)
Friday
9:00am - 10:00amKeynoteRon Weiss (MIT)
10:00am - 10:30amTalk: Mixing metadata without mixing metaphors: Integration of Expert and Deep Learning for Detection of Engineered DNAMisha Wolfson, Sandrine Boissel, Nancy Zhang, Michael Napolitano, Lucas Hartsough, Patrick Boyle, and Joshua Dunn
10:30am - 11:00amCoffee Break
11:00am - 11:30amTalk: A Framework to Determine Number of Biological Replicates for Unsupervised LearningMohammed Eslami, Sahil Loomba, Diogo Camacho, James Collins and Narendra Maheshri
11:30am - 12:30pmBrainstorming AI Solutions; AI lightning talks
12:30pm - 2:00pmLunch
2:00pm - 3:30pmGovernment Funded Research in AI + SynBioJennifer Roberts (DARPA I2O); Matthew Hepburn (DARPA BTO); Mathew Lux (Edgewood Chemical Biological Center - Army); Mitra Basu (NSF); David Rampulla (NIH)
3:30pm - 4:00pmCoffee Break
4:00pm - 5:30pmTalk: An Automated Scientist for Designing and Optimizing Microbial Strains for Production of Small MoleculesAmoolya Singh, Benjamin Kaufmann-Malaga and Joshua Lerman
Talk: The Transcriptic cloud lab enables closed-loop biological optimizationYang Choo, Donald Dalton and Peter L. Lee
Talk: Learning Composition Rules for Mammalian Circuits with Neural AttentionJenhan Tao, Gregory Fonseca, Christopher Benner and Christopher Glass
Talk: Predictive Engineering in Synthetic Biology via Active LearningPeter Tonner, Swarnavo Sarkar, A. Gilad Kusne, Daniel Samarov and David Ross
6:00pm - 7:30pmPlenary Session
Saturday
9:00am - 9:50amSynthetic Biology and AI ethics
9:50am - 10:30amTalk: Synthetic Gene Network Parameter Identification in Coupled Differential Systems via Finite Element Discretization and Neural Network AnalysisHarley Edwards and Peng Xu
Talk: A Tool To Create Models of BioChemical CascadesChun Wai Liew and Robert Kurt
10:30am - 11:00amCoffee Break
11:00am - 12:30pmBrainstorming/Breakout session; Next steps discussion

Topics of interest include (but not limited to):

  • Managing design complexity, e.g., current design happens at a low level analogous to writing programs in assembly language
  • Emerging techniques and tools in synthetic biology produce large amounts of data; understanding and processing this data provides avenues for AI techniques to make a big impact
  • Data driven modeling of biological systems presents opportunities to apply AI techniques; work is needed to help predict the outcome of genetic modification, identify the root cause of failure in circuit, and predict the effect of circuit on host organism
  • Most organism engineering workflows have little automation and rely heavily on domain expertise, only some of which is shared in publications. Tools that support or carry out information integration and informed decision making can improve the efficiency and speed of organism engineering

The symposium will include: introduction to each domain to ensure it is accessible to attendees with both backgrounds; identification of open problems and challenges in the intersection of AI and synthetic biology; contributed talks; panel discussions; and small and large group discussions mixing synthetic biologists and AI researchers.

Submissions Due July 20 August 6

Full papers (7 pages) Presenting a problem in the synthetic biology space that AI techniques might address, and optionally a description of the technique that addresses it. Alternatively, presenting a technique from AI that is relevant for synthetic biology problems.

Short position paper(2 pages) outlining new or controversial views of the intersection of AI and Synthetic biology research or describing ongoing AI/Synthetic Biology research.

Submission site: http://easychair.org/conferences/?conf=fss18

Format: Please use AAAI format : 2018 AAAI Author Kit

Registration

September 21, 2018 deadline: https://www.regonline.com/builder/site/Default.aspx?EventID=2525570

Hotel

September 26, 2018 deadline: https://www.starwoodmeeting.com/events/start.action?id=1803274093&key=1ECBBF2E

Organizing Committee

Aaron Adler (BBN Technologies), Mohammed Ali Eslami (Netrias, LLC), Jesse Tordoff (MIT), and Fusun Yaman (BBN Technologies)

Contact

Please email:  ai4sb_fss18 <at> easychair.org