Green Brain - Computational Modelling of the Honeybee Brain

Lead Research Organisation: University of Sussex
Department Name: Sch of Engineering and Informatics

Abstract

Building intelligent machines that can perform complex cognitive tasks as well as or better than the human brain is a long-standing challenge of modern science. This quest has seen one of its highlights when IBM's Deep Blue chess computer beat the world champion Kasparov in 1997. Despite its superior performance in chess, this system was however in no way similar to or as powerful and versatile as a brain. More recently the Blue Brain initiative, also partially funded by IBM, set out to build a real-scale model of a cortical column of the human brain, moving us closer to the goal of eventually building an artificial brain that works like its biological counterpart.

In the Green Brain project we propose to build such an artificial brain, but of the smaller brain of the honeybee. We will work with the world-leading research group of Prof. Martin Giurfa in Toulouse, who are experts in all aspects of bee brain anatomy, physiology and bee cognition and behavior. Bees have a surprisingly large cognitive capacity including transfer of learned associations across sensory modalities, e.g. from smells to colors, and learning abstract concepts such as the categories of "the same" and "different". At the same time their brains are much smaller, structured and (proportionally) much better researched than the complex human brain. It is also much easier to perform invasive manipulations to dissect how different parts of the bee brain function.

In the Green Brain project we will build detailed computer models of the two most important sensory systems of the bee, the senses of smell (olfactory system) and of sight (visual system). In doing so, we will incorporate existing data, models and principles and identify further how they give rise to the observed impressive cognitive abilities. We will then combine the sensory systems with learning models and models of sensory integration in close collaboration with the experts in the Giurfa lab to eventually build a full-scale model of the bee brain. This model will be implemented on state-of-the-art massively parallel graphical processing unit (GPU) based super-computers, a new technology spearheaded by NVIDIA Corporation who is supporting this project with GPU hardware donations. Using GPU computing will allow us to simulate our Green Brain model in real time, which will be essential for the final phase of the project when we will put the Green Brain to work as the brain of an autonomous flying robot. This is an important further advance over current work on brain models because it is becoming more and more clear that an essential aspect of brain function is that the brain is not acting in isolation but in constant interaction with the body and the environment. This concept of "embodiment" and its consequences for cognition are important insights of modern cognitive science and will become equally important for modern neuroscience.

The outputs from the Green Brain project will have impacts in several academic areas. In the neurosciences it will advance the field of large scale brain models and our understanding of how information is processed in the sensory systems of bees. We will also contribute new tools for the use of modern GPU technology for artificial brains and employing them in bio-mimetic robotics. For the cognitive sciences we will contribute to the understanding of embodiment in biologically realistic model systems.

Beyond academia, the development of autonomous flying robots may have applications in environmental exploration, search and rescue and artificial pollination. Developing a better understanding of the mechanisms underlying cognition may ultimately translate into greater insights into human cognition and cognitive disorders. Finally, developing a better understanding of the honeybee may prove to be important in its own right as bees are a key pollinator in most ecologies and hence a 'keystone species' and vital for food security.
 
Description We have developed the code generation based GeNN framework for accelerated neuronal network simulations on GPUs. In brief, the GeNN framework allows scientists and engineers to describe a neuronal network model in a comparatively simple C++ API and GeNN transforms this description into optimised GPU accelerated code. This is an important step forward as the intricacies of effective GPU acceleration have been a roadblock to all but the most expert GPU users. The GeNN framework has enabled our partners in Sheffield to build an autonomous robot that is performing obstacle avoidance based on a bio-mimetic neuronal network controller simulated on an embedded GPU accelerator.
Exploitation Route The GeNN framework is freely available under the open source GPL v2 license. It can be used for research in computational neuroscience and artificial intelligence. It can also be used as a basis for developing further software for GPU acceleration.
Since the research has been completed we have won additional funding from the EPSRC in the Brains on Board program grant (EP/P006094/1). The GeNN software is one of the main pillars underpinning a large program of research with strong emerging impacts in this new initiative.
Sectors Digital/Communication/Information Technologies (including Software),Education,Other

URL https://github.com/genn-team/genn
 
Description We are working with a large IT company to generate research software products based on the GeNN framework.
First Year Of Impact 2019
Sector Digital/Communication/Information Technologies (including Software)
Impact Types Economic

 
Description EPSRC Programme Grant
Amount £4,816,675 (GBP)
Funding ID EP/P006094/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 12/2016 
End 11/2021
 
Description EfuturesXD staff award
Amount £46,346 (GBP)
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 03/2014 
End 09/2014
 
Description HFSP Program Grant
Amount $337,500 (USD)
Funding ID RGP0053/2015 
Organisation Human Frontier Science Program (HFSP) 
Sector Charity/Non Profit
Country France
Start 07/2015 
End 06/2018
 
Description Marie Sklodowska Curie Fellow Dr. Michael Schmuker
Amount € 231,283 (EUR)
Organisation European Commission 
Department Seventh Framework Programme (FP7)
Sector Public
Country European Union (EU)
Start 09/2014 
End 08/2016
 
Description Task 11.3.6 of the Human Brain Project FET Flagship
Amount € 113,276 (EUR)
Organisation European Commission 
Department Seventh Framework Programme (FP7)
Sector Public
Country European Union (EU)
Start 04/2014 
End 03/2016
 
Description The Leverhulme Trust Senior Research Fellowship
Amount £44,522 (GBP)
Organisation Royal Academy of Engineering 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2014 
End 08/2015
 
Description Collaboration with University of Sheffield 
Organisation University of Sheffield
Country United Kingdom 
Sector Academic/University 
PI Contribution We work together on the Green Brain project. Our team at Sussex contributes the GPU computing expertise and in particular the GeNN framework. We also provide models of olfaction.
Collaborator Contribution The Sheffield partners provide robotics and visual system modelling.
Impact The outputs are recorded as outputs of our joint EPSCR grant.
Start Year 2013
 
Title GPU enhanced Neuronal Networks (GeNN) 
Description Software package to simulate neuronal networks on GPU accelerators using a domain specific language/ code-generation approach. (latest release 1.2, 2014) 
Type Of Technology Software 
Year Produced 2013 
Open Source License? Yes  
Impact The tool is still in alpha. Notable impacts are expected somewhat later. 
URL https://github.com/genn-team/genn
 
Title SpineCreator 
Description The SpineCreator graphical tool is a cross platform (OSX with retina support, Linux and (potentially) Windows) graphical drag and drop tool for SpineML model editing and simulation. It features OpenGL visualisation of networks, simulator integration and graphical analysis tools. See http://bimpa.group.shef.ac.uk/SpineML/index.php/Gui for details. 
Type Of Technology Software 
Year Produced 2014 
Open Source License? Yes  
Impact The software is being used in the European seventh framework project NoTremor (http://notremor.eu/notremor/) 
URL https://github.com/SpineML/SpineCreator
 
Title SpineML_2_GeNN 
Description SpineML_2_GeNN converts neural models described in the SpineML description format into the GeNN GPU simulation framework 
Type Of Technology Software 
Year Produced 2014 
Open Source License? Yes  
Impact This software allows computational neuroscience models to be easily simulated on the embarrassingly parallel hardware of modern NVidia graphics cards, vastly decreasing the cost required to improve simulation performance. 
URL https://github.com/genn-team/genn
 
Title brian2genn 
Description This software provides an interface from the popular "Brian" simulator (version 2) to our GPU enhanced neuronal networks (GeNN) framework that allows users to define computational neuroscience models in Brian 2 and with a single command run them on a GPU accelerator. Depending on the type of model and accelerator, considerable speedups are possible without any additional effort by the users. The software is in pre-alpha stage and will be released in beta together with the first full release of Brian 2. 
Type Of Technology Software 
Year Produced 2015 
Open Source License? Yes  
Impact We are waiting on measurable impacts which we expect upon the first public release. 
URL https://github.com/brian-team/brian2genn
 
Description Big Bang Observatory Science Centre 2014 - outreach activity about bee vision 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Schools
Results and Impact Large interest of school children to see and try our virtual reality simulation of bee vision. We had some very positive feedback from individual visitors afterwards.

We do not have access to data.
Year(s) Of Engagement Activity 2014
 
Description Big Bang Solent 2014 - outreach activity about bee vision 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Schools
Results and Impact We had long queues of school children who wanted to try our virtual reality simulation of bee vision. This was one of the most popular activities in the entire event.

We do not have access to this data.
Year(s) Of Engagement Activity 2014
 
Description Big Bang SouthEast 2014 - outreach activity about bee vision 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Schools
Results and Impact Lots of interest in the activity; we brought 2 separate setups to accommodate large numbers of visitors and yet still incurred waiting lines.

We do not have access to this data.
Year(s) Of Engagement Activity 2014
 
Description Cafe Scientifique Brighton 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Presentation of research including the Green Brain Project and Human Frontiers Odor Objects project to the general public, including detailed Q&A.
Year(s) Of Engagement Activity 2016
 
Description Closed Loop Electrophysiology - AIMS workshop on closed loop interaction, Madrid 2014 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Lively discussion after the talk which was very well received.

no measurable data available.
Year(s) Of Engagement Activity 2014
 
Description Green Brain: Modeling the honeybee brain 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact There were several questions after the talk and lively informal discussions.

no measureable data available.
Year(s) Of Engagement Activity 2014
 
Description Invited scientific talk at Keele Univeristy 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact I presented recent research at Keele University to an audience of researchers and students. Much of the work reported was based on the Green Brain Project.
Year(s) Of Engagement Activity 2014
 
Description Invited talk at the Neural Codign workshop in Koeln, Germany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Scientific talk covering work from the Green Brain project and the HFSP funded "Odor Objects" project.
Year(s) Of Engagement Activity 2016
 
Description Invited talk at the Neuromorphic Computing workshop (NICE) in Berkeley, California 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Invited talk in which I presented our benchmarking work of neural network algorithms, comparing neuromorphic platforms against our GPU accelerator framework (developed within the Green Brain project)
Year(s) Of Engagement Activity 2016
 
Description Media coverage including New Scientist and Sunday Times 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact -

Coverage included (among others)

"Summon the bee bots: Can flying robots save our crops?", November 18th November 2013, New Scientist (on the cover).
"Flight of the robo-bee to save fruit crops", 7th October 2012, The Sunday Times.
Year(s) Of Engagement Activity 2012,2013
 
Description Oral presentation in Bernstein Conference, Green Brain workshop in Goettingen (2-5 September 2014) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact The talk helped better understanding of our goal and achievements by colleagues and it was followed by a discussion.

After the talk I could discuss with experts in my field about my and their methods and results.
Year(s) Of Engagement Activity 2014
URL http://www.nncn.de/en/bernstein-conference/2014/workshops/green-brain-how-models-of-invertebrate-bra...
 
Description Outreach event for school aged children 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact We organized two days of activities on "behavioral robotics" involving school aged children to work with simple controllers for autonomous robots in order to solve set challenges, e.g. following a light trace. The activities took place in teh framework of teh Brighton Science Festival "BrightSparks" event.
Year(s) Of Engagement Activity 2017
 
Description Panelist at the National Women in Engineering Day - Celebration Event 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact 20 female students and 10 faculty members attended talks by female scientists and a panel discussion about women in neuroscience. The audience reported that they learned a lot from the experience of the participants and that the event encouraged them to pursue their career as a woman in STEM.
Year(s) Of Engagement Activity 2016
URL http://www.sussex.ac.uk/informatics/about/newsandevents?id=35932
 
Description Parameter Estimation using GPU super-computing - Neural Coding Workshop Versailles 2014 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Several questions from the audience.

No measurable data.
Year(s) Of Engagement Activity 2014
 
Description Presentation at the "X Science Fair" 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Prof Thomas Nowotny presented the work in the Green Brain project at the X Science Fair at the X headquarters in Mountainview, California.
Year(s) Of Engagement Activity 2016
 
Description Presentation at the joint SP4/SP9 Human Brain Project workshop on at the European Institute for Theoretical Neuroscience in Paris 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Gave a presentation on models that tolerate diversity and engaged on a debate on the theory and practice of neuromorphic computing.
Year(s) Of Engagement Activity 2015
 
Description Presentation at the mini air show event in Brighton, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact I gave a presentation related to the Green Brain project to an audience of drone enthusiasts at the min air show event, related to International Drone Day.
Year(s) Of Engagement Activity 2016
URL http://www.miniatureairshow.com/
 
Description Presentation at the workshop on Code Generation at the Institute for Theoretical Neuroscience in Paris 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact In this workshop I reported on our work of building a GPU meta-compiler for efficient simulation of Neural Networks on GPU accelerators. The remainder of the event was a lively exchange among practitioners of research involving advanced software development/ code generation.
Year(s) Of Engagement Activity 2014
 
Description Presentation of Green Brain and Brains on Board projects 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact I presented our research portfolio at the "Digi Drop-in" of the Brighton Digital Catapult centre. Both, work from the Green Brain and the planned work for the Brains on Board project were presented.
Year(s) Of Engagement Activity 2017
 
Description Press release on our results of Drosophila Receptor responses to a large set of chemicals 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact The press release sparked large media attention including print and online news, radio interviews and a short report on the local TV station. overall there were about
- 58 items in print and online media
- Interviews/news items on BBC world service (Reach: 409000), BBC Radio Sussex (Reach 73000), BBC Radio Shropshire (Reach 29666), BBC Radio Wales (Reach 137000), and more.
- News item on BBC Southeast (TV)

I do not know how to measure impacts on thousands of listeners/viewers.
Year(s) Of Engagement Activity 2014
 
Description Public talk in the FabLab London, within the "Hacking the Senses" series 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Invited talk presenting our research on insect olfaction (related to the Green Brain poject). Also demonstrated our Bee Eye virtual reality simulator.
Year(s) Of Engagement Activity 2016
URL https://www.eventbrite.com/e/hack-the-senses-s01e04-animal-perception-tickets-22776381771#
 
Description Scientific talk at the "Brains and Roses" workshop in London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Gave a presentation partially based on the work in the Green Brain project.
Year(s) Of Engagement Activity 2015
 
Description Scientific talk at the Jubilee of Prof Ulrich Behn, University of Leipzig, Germany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Scientific talk drawing on results from the Green Brain Project among others.
Year(s) Of Engagement Activity 2015
 
Description Scientific talk at the University of Edinburgh 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Gave and invited talk in the Informatics Forum of the University of Edinburgh drawing partially on the work in the Green Brain project.
Year(s) Of Engagement Activity 2015
 
Description Speaker in the Lewes U3A Science Series 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Presentation of a research lecture involving work from the Green Brain project, Odor Objects project and the planned work in Brains on Board.
Year(s) Of Engagement Activity 2017
 
Description Visit and exhibition at the X Science fair in Mountain View California 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact I was invited and accepted to present our research (in particular Green Brain and Odor Objects projects) at the X science fair, organized at X headquarters in Mountain View, California.
Year(s) Of Engagement Activity 2016