Workshop date:
Sunday, July 15, 2018 : Full day workshop. The workshop is part of the IJCAI / FAIM conferences : http://www.ijcai-18.org
UPDATES:
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: aaron.adler@raytheon.com & fusun.yaman@raytheon.com
Registration:
http://www.ijcai-18.org/register/
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.
Sponsors:
Workshop Schedule:
| Day / Time | Activity / Title | Author (s) / Speaker(s) |
|---|---|---|
| Thursday | ||
| 9:00am – 9:15am | Symposium Introduction | |
| 9:15am – 9:45am | Intro Talks for AI and SynBio | |
| 9:45am – 10:00am | Discussion of Community Resources | |
| 10:00am – 10:30am | Talk: Collaborative Development and Evaluation of Data-driven Biological Models | Mohammed Eslami, Hamed Eramian and Nicholas Leiby |
| 10:30am – 11:00am | Coffee Break | |
| 11:00am – 12:00pm | Panel to Discuss Challenges of AI in SynBio | |
| 12:00pm – 12:30pm | Talk: Using Machine Learning and Big Data to Select Smart Microbes for Generating Electricity from Wastewaters | Charles Zhou and Ying Zhao |
| 12:30pm – 2:00pm | Lunch | |
| 2:00pm – 2:30pm | Talk: The Case for A New AI+Cyber+Bio Security Paradigm | William Streilein and Catherine Cabrera |
| 2:30pm – 3:00pm | Talk: A Bayesian Model for Experiment Choice in Synthetic Biology | Robert P. Goldman, Puja Trivedi, Daniel Bryce, Matthew Dehaven and Alex Plotnick |
| 3:00pm – 3:30pm | Talk: AI Challenges and Applications in Detecting Engineering in Single Cells | Aaron 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 – 4:00pm | Coffee Break | |
| 4:00pm – 4:30pm | Talk: 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 – 5:30pm | Discussion Session (Breakout Groups for Data, Tools, Applications) | |
| 6:00pm – 7:00pm | Reception | |
| 7:00pm – ? | Group outing (optional) | |
| Friday | ||
| 9:00am – 10:00am | Keynote: Human vs Machine: Challenges for Applying AI in Biology | Josh Dunn, Ginkgo Bioworks |
| 10:00am – 10:30am | Talk: The DSGRN Database: Identifying Network Function with Network Topology | Konstantin Mischaikow, Chris Mischaikow, Breschine Cummins and Tomas Gedeon |
| 10:30am – 11:00am | Coffee Break | |
| 11:00am – 11:30am | Talk: Convolutional Neural Networks Guide Rationally Engineered Protein Stability | Raghav Shroff, Austin Cole, Andrew Ellington and Ross Thyer |
| 11:30am – 12:00pm | Talk: Convolutional Neural Net Learns Promoter Sequence Features Driving Transcription Strength | Nicholas Leiby, Ayaan Hossain and Howard M Salis |
| 12:00pm – 12:30pm | Talk: Sequence to Sequence Transfer Learning for DNA Phenotyping | Niall Dalton, Peter Morales, Rajmonda Caceres, Matt Walsh, Christina Zook, Catherine Van Praagh, Nicholas Guido and Todd Thorsen |
| 12:30pm – 2:00pm | Lunch | |
| 2:00pm – 2:30pm | Talk: Algorithmic Optimization for Pathway Engineering and Beyond | Eric Young |
| 2:30pm – 3:00pm | Talk: Computational Modeling of Cell Signaling and Mutations in Pancreatic Cancer | Cheryl Telmer, Khaled Sayed, Adam Butchy, Kara Bocan, Christof Kaltenmeier, Michael Lotze and Natasa Miskov-Zivanov |
| 3:00pm – 3:30pm | Talk: ART: A Machine Learning Automated Recommendation Tool for Guiding Synthetic Biology | Hector Garcia Martin |
| 3:30pm – 4:00pm | Coffee Break | |
| 4:00pm – 4:30pm | Talk: On Chemical Reaction Network Design by a Nested Evolution Algorithm | Elisabeth Degrand, Mathieu Hemery and François Fages |
| 4:30pm – 5:30pm | Breakout Group Discussions | |
| 6:00pm – 7:30pm | Plenary Session | |
| Saturday | ||
| 9:00am – 10:30am | Breakout Group Discussions | |
| 10:30am – 11:00am | Coffee Break | |
| 11:00am – 12:30pm | Breakout Groups Debrief and Next Steps Discussion |
Workshop location:
Stockholm, Sweden
Previous Workshop:
https://www.ai4synbio.org/events/ai-for-synthetic-biology-ijcai-2016/
Organizers:
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.