Aaron D. Adler

Aaron D. Adler

Aaron Adler

Scientist
BBN Technologies

Address:
10 Moulton Street
Cambridge, MA 02138

Phone:
617.873.3517

Email:
aadler at bbn dot com

This page is mirrored at BBN and MIT CSAIL.
Last updated: July 15, 2012

Projects:

I am currently working on these projects at BBN:

TASBE (A Tool-chain to Accelerate Synthetic Biology) IRAD: A short-term BBN-funded continuation of the TASBE project described below but with a focus on creating web service versions of the tools developed in TASBE. See synbiotools.bbn.com. My work includes using Octave, Drupal, PHP, and Python to create the online versions of the tools.
MADV: Morphogenetically Assisted Design Variation. MADV is a joint project with iRobot funded by DARPA DSO. MADV seeks to simplify robot redesign using morphogenesis. I am a co-PI on this project.
BBAC (Behavior-Based Access Control): BBAC is a security project with Drexel University funded by AFRL. I am currently designing and implementing a URL classified to help identify possible malicious behavior.
TORQUE: TORQUE is a Quantum Computer project sponsored by IARPA. My work in this project involves helping to refine QuaFL, a quantum computing programming language, and converting quantum algorithm specifications into QuaFL.

My previous projects at BBN include:

TASBE: A Tool-chain to Accelerate Synthetic Biology. TASBE was a joint project with MIT and BU, funded by DARPA. My work on the project included: compiler optizations, robotic automation, and DNA characterization.
Advanced Protective Services (APS). APS is an AFRL funded project to develop a protection and containment system for web services which we call a Crumple Zone. I helped design and develop components for the Crumple Zone.
Plan Order Induction by Reasoning from One Trial (POIROT). I worked on the XPLAIN and IODA components of the POIROT integrated learning project. The goal of the POIROT project is to learn how to execute a sequence of web service calls from a single demonstration trace by combining various machine learning algorithms. The IODA component analyses the data dependencies in the trace and the XPLAIN component uses generic rules to form groups of related steps and identify user actions such as saving or submitting data.

My Ph.D. thesis centered on constructing multimodal interactive dialogues: combining speech recognition and sketch recognition for user input and generating speech and sketching for multimodal computer output. MIDOS (Multimodal Interactive DialOgue System) helps the user describe simple mechanical (Rube-Goldberg-like) devices by asking questions. A qualitative physics simulator is used to generate possible questions to ask the user. At MIT CSAIL I was part of the design rationale group (now the Multimodal Understanding Group) led by Professor Randy Davis. Prior to that I did research with the aire group, whose focus is pervasive computing applications for intelligent spaces.

Here is a link to my Curriculum Vitae.

Refereed Publications:

Beal, Jacob; Weiss, Ron; Densmore, Douglas; Adler, Aaron; Appleton, Evan; Babb, Jonathan; Bhatia, Swapnil; Davidsohn, Noah; Haddock, Traci; Loyall, Joseph; Schantz, Richard; Vasilev, Viktor; and Yaman, Fusun. An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications. ACS Synthetic Biology, online publication. July 2012. [pdf] [bib]

Yaman, Fusun; Bhatia, Swapnil; Adler, Aaron; Densmore, Douglas; and Beal, Jacob. Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks. ACS Synthetic Biology, online publication. July 2012. [pdf] [bib]

Beal, Jacob; Mostafa, Hala; Axelrod, Benjamin; Mozeika, Annan; Adler, Aaron; Markiewicz, Gretchen; and Usbeck, Kyle. A Manifold Operator Representation for Adaptive Design. In Proceedings of the Fourteenth International Conference on Genetic and Evolutionary Computation Conference (GECCO). July 2012, pp. 529-536. [pdf] [bib]

Beal, Jacob; Weiss, Ron; Densmore, Douglas; Adler, Aaron; Appleton, Evan; Babb, Jonathan; Bhatia, Swapnil; Davidsohn, Noah; Haddock, Traci; Loyall, Joseph; Schantz, Richard; Vasilev, Viktor; and Yaman, Fusun. Results from TASBE. In 4th International Workshop on Bio-Design Automation (IWBDA). June 2012, pp. 13-15. [pdf] [bib]

Adler, Aaron; Yaman, Fusun; Cleveland, Jeffrey; and Beal, Jacob. Morphogenetically Assisted Design Variation. In 2nd International Conference on Morphological Computation (ICMC). Venice, Italy, September 2011, pp. 106-108. [pdf] [bib]

Beal, Jacob; Weiss, Ron; Densmore, Douglas; Adler, Aaron; Babb, Jonathan; Bhatia, Swapnil; Davidsohn, Noah; Haddock, Traci; Yaman, Fusun; Schantz, Richard; and Loyall, Joseph. TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering. In 3rd International Workshop on Bio-Design Automation (IWBDA). June 2011, pp. 19-21. [pdf] [bib]

Yaman, Fusun; Bhatia, Swapnil; Adler, Aaron; Densmore, Douglas; Beal, Jacob; Weiss, Ron; and Davidsohn, Noah. Toward Automated Selection of Parts for Genetic Regulatory Networks. In 3rd International Workshop on Bio-Design Automation (IWBDA). June 2011, pp. 22-23. [pdf] [bib]

Vasilev, Viktor; Liu, Chenkai; Haddock, Traci; Bhatia, Swapnil; Adler, Aaron; Yaman, Fusun; Beal, Jacob; Babb, Jonathan; Weiss, Ron; and Densmore, Douglas. A Software Stack for Specification and Robotic Execution of Protocols for Synthetic Biological Engineering. In 3rd International Workshop on Bio-Design Automation (IWBDA). June 2011. [pdf] [bib]

Atighetchi, Michael; Pal, Partha; Adler, Aaron; Gronosky, Andrew; Yaman, Fusun; Webb, Jonathan; Loyall, Joseph; Sinclair, Asher; and Payne, Charles. Crumple Zones: Absorbing Attack Effects Before They Become a Problem. In CrossTalk - The Journal Of Defense Software Engineering, Special Issue on Rugged Software. March/April 2011, pp. 4-11. [pdf] [bib]

Adler, Aaron. Reasoning About Sketches Using Context, Domain Knowledge, and Interaction with the User. In Visual Representations and Reasoning: A Workshop of the 24th AAAI Conference on Artificial Intelligence (AAAI-10). Atlanta, Georgia, July 11, 2010. [pdf] [bib]

Adler, Aaron. Symmetric Multimodal Dialogues. In SkCHI: Designing Sketch Recognition Interfaces: A CHI 2010 Workshop. Atlanta, Georgia, April 10, 2010. [pdf] [bib]

Hammond, Tracy; Lank, Edward; and Adler, Aaron. SkCHI: Designing Sketch Recognition Interfaces. In Proceedings of CHI 2010 (Extended Abstracts). Atlanta, Georgia, April 10-15, 2010. [pdf] [bib]

Bischel, David; Stahovich, Thomas; Peterson, Eric; Davis, Randall; and Adler, Aaron. Combining Speech and Sketch to Interpret Unconstrained Descriptions of Mechanical Devices. In Proceedings of the 2009 International Joint Conference on Artificial Intelligence (IJCAI). Pasadena, California, July 2009, pp. 1401-1406. [pdf] [bib]

Adler, Aaron and Davis, Randall. Symmetric Multimodal Interaction in a Dynamic Dialogue. In 2009 Intelligent User Interfaces Workshop on Sketch Recognition. February 2009. [pdf] [bib]

Adler, Aaron and Davis, Randall. Speech and Sketching: An Empirical Study of Multimodal Interaction. In Proceedings of Fourth Eurographics Conference on Sketch Based Interfaces and Modeling. Riverside, California, August 2-3 2007. [bib] [pdf] [talk slides - pps]

Adler, Aaron; Eisenstein, Jacob; Oltmans Michael; Guttentag, Lisa; and Davis, Randall. Building the Design Studio of the Future. In Proceedings of AAAI Fall Symposium: Making Pen-Based Interaction Intelligent and Natural, pp. 1-7. Menlo Park, California, October 21-24 2004. [bib] [pdf]

Adler, Aaron and Davis, Randall. Speech and Sketching for Multimodal Design. In Proceedings of the 9th International Conference on Intelligent User Interfaces, pp. 214--216. ACM Press, 2004. [ps] [pdf] [bib]

Oh, Alice; Fox, Harold; Van Kleek, Max; Adler, Aaron; Gajos, Krzysztof; Morency, Louis-Philippe, Morency; and Darrell, Trevor. Evaluating Look-to-Talk: A Gaze-Aware Interface in a Collaborative Environment. ACM SIGCHI 2002. [ps] [pdf] [bib]

Other Publications:

Beal, Jacob; Weiss, Ron; Yaman, Fusun; Davidsohn, Noah; and Adler, Aaron. A Method for Fast, High-Precision Characterization of Synthetic Biology Devices. MIT CSAIL Tech Report 2012-008. April 2012. [pdf] [bib]

Galdzicki, Michal; Wilson, Mandy L.; Rodriguez, Cesar A.; Pocock, Matthew R.; Oberortner, Ernst; Adam, Laura; Adler, Aaron; Anderson, J. Christopher; Beal, Jacob; Chandran, Deepak; Densmore, Douglas; Drory, Omri A.; Endy, Drew; Gennari, John H.; Grünberg, Raik; Ham, Timothy S.; Hillson, Nathan J.; Johnson, Jeffrey D.; Kuchinsky, Allan; Lux, Matthew W.; Madsen, Curtis; Misirli, Goksel; Myers, Chris J.; Peccoud, Jean; Plahar, Hector; Platt, Darren; Roehner, Nicholas; Sirin, Evren; Smith, Trevor F.; Stan, Guy-Bart; Villalobos, Alan; Wipat, Anil; Sauro, Herbert M. Synthetic Biology Open Language (SBOL) Version 1.1.0. BioBricks Foundation Request for Comments (BBF RFC) #87. March 2012. [pdf] [bib]

Beal, Jacob; Weiss, Ron; Densmore, Douglas; Adler, Aaron; Babb, Jonathan; Bhatia, Swapnil; Davidsohn, Noah; Haddock, Traci; Yaman, Fusun; Schantz, Richard; and Loyall, Joseph. A Tool-Chain to Accelerate Synthetic Biological Engineering. Abstract in SB5.0: the Fifth International Meeting on Synthetic Biology. June 2011. [pdf] [bib]

Yaman, Fusun; Bhatia, Swapnil; Adler, Aaron; Babb, Jonathan; Beal, Jacob; Davidson, Noah; Densmore, Douglas; Haddock, Traci; Loyall, Joseph; Schantz, Richard; and Weiss, Ron. Toward Automated Selection of Parts for Genetic Regulatory Networks. Abstract in SB5.0: the Fifth International Meeting on Synthetic Biology. June 2011. [pdf] [bib]

Yaman, Fusun; Bhatia, Swapnil; Adler, Aaron; Densmore, Douglas; Beal, Jacob; Babb, Jonathan; Davidson, Noah; Haddock, Traci; Loyall, Joseph; Schantz, Richard; and Weiss, Ron. Toward Automated Selection of Parts for Genetic Regulatory Networks. Abstract in IBE 2011. March 2011. [pdf] [bib]

Aaron Daniel Adler. MIDOS: Multimodal Interactive DialOgue System. Ph.D. Thesis for Massachusetts Institute of Technology. June 2009. [pdf] [bib] [defense slides - PPS]

Adler, Aaron. Multimodal Interactive Digital Whiteboard. Ph.D. Thesis Proposal. MIT, Cambridge, MA. February 2007. [pdf]

Aaron Adler. Segmentation and Alignment of Speech and Sketching in a Design Environment. Master's Thesis for Massachusetts Institue of Technology. February 2003. [pdf] [zip of ps] [bib]

Eisenstein, Jacob; Adler, Aaron; Guttentag, Lisa. A Trimodal Dialogue Corpus: Speech, Gesture, and Sketching. Fourth Annual MIT CSAIL Student Oxygen Workshop, September 2004. [pdf] [bib]

Adler, Aaron. Creating a Multimodal Design Environment Using Speech and Sketching. MIT Student Oxygen Workshop, September 2003. [ps] [pdf] [bib] [talk slides - 1.6MB pps]

Adler, Aaron and Davis, Randall. Using Speech and Sketching in a Design Environment. MIT Computer Science and Artificial Intelligence Laboratory Annual Research Abstract, February 2004. [pdf] [bib]

Adler, Aaron; Davis, Randall; and Shrobe, Howard. Mutual Disambiguation of Verbal and Sketching Inputs in a Design Environment. MIT Artificial Intelligence Laboratory Annual Abstract, September 2002. [ps] [pdf] [bib]

Davis, Randall; Adler, Aaron; Alvarado, Christine; Hammond, Tracy; Hitchcock, Rebecca; Oltmans, Michael; Sezgin, Tevfik Metin; and Veselova, Olya. Designs for the Future. MIT Artificial Intelligence Laboratory Annual Abstract, September 2002. [ps] [pdf] [bib]

Talks:

A Tool-Chain Approach to Predictive Design of Biological Circuits. Biological Systems Design SIG at International Society for Computational Biology (ISCB). Long Beach, CA, July 13, 2012. [Slides - pdf]

Education:

PhD. in Computer Science and Electrical Engineering from Massachusetts Institute of Technology, Cambridge, MA, June 2009.

M.Eng. in Computer Science and Engineering from Massachusetts Institute of Technology, Cambridge, MA, January 2003.

S.B. in Computer Science from Massachusetts Institute of Technology, Cambridge, MA, June 2001.