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 / Time | Activity / Title | Author (s) / Speaker(s) | |
|---|---|---|---|
| Thursday | |||
| 9:00am – 9:15am | Symposium introduction | ||
| 9:15am – 10:30am | Introduction to Synthetic Biology | Eric Young (WPI) | |
| 10:30am – 11:00am | Coffee Break | ||
| 11:00am – 12:30pm | Talk: Cell-free synthetic biology as a source for deep learning | Zachary Sun | |
| Talk: Using Synthetic Biology for bio-inspired computing? | Martín Gutiérrez, Javier Carrión and Yerko Ortiz | ||
| Talk: Formalizing Sample Transformation Plans | Daniel 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 Arrays | Adam Wang, Jongseok Park, Doohwan Jung, Gregory Junek and Hua Wang | ||
| 12:30pm – 2:00pm | Lunch | ||
| 2:00pm – 3:00pm | Introduction to AI | Hector Munoz-Avila (Lehigh University) | |
| 3:00pm – 3:30pm | Talk: Making AI Work for Synthetic Biology: Challenges and Opportunities | Rajmonda Caceres and Timothy Dasey | |
| 3:30pm – 4:00pm | Coffee Break | ||
| 4:00pm – 5:30pm | Discussion Session: What are the big/hard problems in Synthetic Biology? | ||
| 6:00pm – 7:00pm | Reception | ||
| 7:00pm – ? | Group outing (optional) | ||
| Friday | |||
| 9:00am – 10:00am | Keynote | Ron Weiss (MIT) | |
| 10:00am – 10:30am | Talk: Mixing metadata without mixing metaphors: Integration of Expert and Deep Learning for Detection of Engineered DNA | Misha Wolfson, Sandrine Boissel, Nancy Zhang, Michael Napolitano, Lucas Hartsough, Patrick Boyle, and Joshua Dunn | |
| 10:30am – 11:00am | Coffee Break | ||
| 11:00am – 11:30am | Talk: A Framework to Determine Number of Biological Replicates for Unsupervised Learning | Mohammed Eslami, Sahil Loomba, Diogo Camacho, James Collins and Narendra Maheshri | |
| 11:30am – 12:30pm | Brainstorming AI Solutions; AI lightning talks | ||
| 12:30pm – 2:00pm | Lunch | ||
| 2:00pm – 3:30pm | Government Funded Research in AI + SynBio | Jennifer Roberts (DARPA I2O); Matthew Hepburn (DARPA BTO); Mathew Lux (Edgewood Chemical Biological Center – Army); Mitra Basu (NSF); David Rampulla (NIH) | |
| 3:30pm – 4:00pm | Coffee Break | ||
| 4:00pm – 5:30pm | Talk: An Automated Scientist for Designing and Optimizing Microbial Strains for Production of Small Molecules | Amoolya Singh, Benjamin Kaufmann-Malaga and Joshua Lerman | |
| Talk: The Transcriptic cloud lab enables closed-loop biological optimization | Yang Choo, Donald Dalton and Peter L. Lee | ||
| Talk: Learning Composition Rules for Mammalian Circuits with Neural Attention | Jenhan Tao, Gregory Fonseca, Christopher Benner and Christopher Glass | ||
| Talk: Predictive Engineering in Synthetic Biology via Active Learning | Peter Tonner, Swarnavo Sarkar, A. Gilad Kusne, Daniel Samarov and David Ross | ||
| 6:00pm – 7:30pm | Plenary Session | ||
| Saturday | |||
| 9:00am – 9:50am | Synthetic Biology and AI ethics | ||
| 9:50am – 10:30am | Talk: Synthetic Gene Network Parameter Identification in Coupled Differential Systems via Finite Element Discretization and Neural Network Analysis | Harley Edwards and Peng Xu | |
| Talk: A Tool To Create Models of BioChemical Cascades | Chun Wai Liew and Robert Kurt | ||
| 10:30am – 11:00am | Coffee Break | ||
| 11:00am – 12:30pm | Brainstorming/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