Planning a BioMedCEP project proposal

[rainer93138]

Dear Carel and Erwin,

thank you very much for your very good input. This helps to shape our discussion, and your questions are exactly the main points which have to be answered.

- Your profile and specialisation on diabetes, elderly with multimorbidity and stroke patients fits perfectly with what we will address. Although it's actually up to the consortium to define the goals and what they want to investigate in their workpackages; so far it's only a first suggestion to speed up the discussion.

- Your idea of "... mobility, i.e. human movement in daily life and under ecological conditions (can be measured with e.g. accelerometers) as the parameter of environmental interaction and the human brain as the initiator and controller of movement..." and what you outline then, fits perfectly with our principal BioMedCEP idea and the approach of the TCNL/U Wisconsin. We would like to invite you to become co-authors of our final paper http://www.citt-online.de/downloads/3-D ... Etzion.pdf, what we can discuss within the next weeks.

Best regards,

Rainer

[rainer93138]

... I would like to thank you once again for considering us as potential partners in the very challenging BioMedCEP project proposal. I am sending this email in order to make clearer where we had contributed in the past and what could be our role in such a project.

Our research group specializes on

- Signal/image analysis, annotation and synthesis
- Intelligent systems based on neural and cognitive networks, evolutionary algorithms and generalized fuzzy logic approaches
- Feature fusion for multimodal/temporal data mining

with applications in biomedicine.

We are currently working on modeling infection progress from medical images and other clinical data, as well as on intuitionistic fuzzy cognitive models for decision making, in the framework of the IP EU project DebugIT. However, this describes only our current activities. An full online profile of our research group can be found here:

http://www.ctr.teilam.gr/ivibis/

Since the potential partners are a lot and their experience spans a wide range of research fields I would propose that BioMedCEP become an IP project, and if the ideas on the table are so novel to go for a FET action.

Ideas for possible contributions of our group include (but are not limited to):

a) Invoking visual information that could be associated with brain signals, in a way that reversibility is feasible. Here is a very interesting work http://www.sciencedirect.com/science/ar ... 2211009377

b) Novel cognitive and evolutionary models

c) Distributed collection and processing of knowledge from multiple modalities.

Of course I am willing to contribute in the writing of the proposal as well.

Kind regards,

Dimitris
--
Dimitris Iakovidis, MSc, PhD
Assistant Professor

Head of Dept Informatics and Computer Technology,
Vice-Director, School of Applied Technologies,
Technological Educational Institute of Lamia.
Vice-Director,
Center for Technological Research of Central Greece &
Head of the Information Technology Institute
3rd km Old National Road Lamias Athinas
GR 35100 Lamia,
Greece
Tel: +30 22310 60159 (office), +30 6932 252591 (mobile)
Email: iakovidis@ctr.teilam.gr
http://ivibis.ctr.teilam.gr/user_pages_en/iakovidis.htm
http://ivibis.ctr.teilam.gr
http://www.debugit.eu/

[rainer93138]

This was sent today; we will join with BioMedCEP:

Future and Emerging Technologies (FET): Join us at the Information day FP7 ICT Call 9 on 18 January 2012 in Brussels

Dear researcher,

We would like to draw your attention to the coming Information Day for the FP7 ICT Call 9 related to Future and Emerging Technologies (FET).

The event will take place on 18 January 2012 in Brussels. The day will provide first-hand information on the FET Call 9 objectives, as well as contractual, legal and administrative modalities. The formation of consortia will be facilitated through an open exchange "Proposers' Forum" where participants will have the opportunity to present research ideas and/or expertise.

Registration is free of charge but obligatory!
Once the capacity of the rooms (150) is reached the registration will be closed.

More information, including registration and draft program of the event can be found at http://cordis.europa.eu/fp7/ict/fet-pro ... 12_en.html

The following FET themes will be addressed:

FP7-ICT-2011.9.9:
Quantum ICT (QICT) including ERA-NET-Plus

FP7-ICT-2011.9.10:
Fundamentals of Collective Adaptive Systems (FOCAS)

FP7-ICT-2011.9.11:
Neuro-Bio-Inspired Systems (NBIS)

FP7-ICT-2011.9.12:
Coordinating Communities, Identifying new research topics for FET Proactive initiatives and Fostering Networking of National and Regional Research Programmes

We would appreciate if you could forward this information to potentially interested parties.

On behalf of
Wolfgang Boch - Head of Unit FET Proactive
Information Society and Media Directorate General
European Commission

ICT FET Proactive info desk: infso-ictfet@ec.europa.eu

[rainer93138]

Minutes of the conference call, 5 Dec 2011

We discussed the minutes of the last telco 21 Nov 2011 viewtopic.php?f=13&t=316&start=30 and its following postings.

0) The next concal
will take place on Monday next week, 12 Dec 2011, 4-6 pm. invitation within the next days.

1) Full papers / Extended abstracts
1.1 University Medical Center Leiden and TU Delft (Carel, Erwin) join the first paper http://www.citt-online.de/downloads/3-D ... Etzion.pdf. They insert their ideas as sketched viewtopic.php?f=13&t=316&start=30#p129 until next telco 12 Dec. This paper should become the positioning basis regarding the FET-Proactive Call-9, NBIS outcomes http://cordis.europa.eu/fp7/ict/fet-pro ... .html#what and can have 20 or more pages.

1.2 Andree and Paul will extend the paper http://www.citt-online.de/downloads/EV-Poznan2011.pdf up to 20 or more pages and insert what Andree has additionally sketched with "... Strategies to cope with mental deficits, neuro-degenerative diseases and learning deficiencies. More efficient methods in education...". Colleagues who have already praised her ideas about "Ageing..." are asked to contribute to this paper, shape it according to the first paper (see above) and the NBIS outcomes. Carel, Erwin and some more will contact her and team up with Andree within this week. We shall discuss the outline at the next telco 12 Dec.

1.3 Pietro as the attending "proxy" of Filippo, Vanessa and the team of the paper http://www.citt-online.de/downloads/4-C ... -et-al.pdf will shape the outline according to the first paper and the NBIS outcomes. We discuss the outline at the next telco 12 Dec.

1.4 Björn as the attending "proxy" of Gabor, Andreas and the team of the paper http://www.citt-online.com/downloads/5- ... -Meyer.pdf will shape the outline according to the first paper and the NBIS outcomes. We discuss the outline at the next telco 12 Dec.

2) Open and future calls for BioMedCEP
In connection with the overview of open and future calls which we discussed at the last telco http://www.citt-online.com/downloads/Op ... -Calls.doc, we decided now to focus on FET Proactive Call-9, NBIS as IP.

3) Potential coordinator
In the case of an IP, CITT cannot make the official coordinator, because if the coordinator is not a university or an industrial Big Dog, one has to provide a bank guarantee about 10 Mio or more according to the project budget.
As the most of you know, the CITT is a microSME (with a PIC for FP7) and was founded 2005 according to the idea "From student to entrepreneur" as a network platform to evangelize edBPM and since 2009 also the enhancement to the U-CEP concept as well as to initiate projects between academia and industry (see also http://ec.europa.eu/research/innovation ... ssion_id=9, they are looking for young innovative SMEs).
CITT / U Appl.Sc Regensburg "generated" diploma theses on the basis of our courses and curricula and around 10 doctoral candidates and some of them are doctors in the meantime, we are still working on the entrepreneurs. Such founding ideas fit very well with the FET-Flagship Initiative 2020 and Beyond, also to develop new curricula for innovative courses.

To show such (SME) foundations and that your communities (VPH + U-CEP) have not started just yesterday or right now but work systematically together as proven teams since years as well as that these approaches will be continued by start-ups or in new clinical applications in the next years as a folllow-up of a BioMedCEP project - such points also have to be emphasized in our proposal.

Comment wrt. coordinator-role: I have taken sabbatical time since July 2011 to bring together people, to visit some of the key players like U Wisconsin/TCNL, etc.. I'll still organise the proposal until call 9 is open in January 2012 and perhaps submit the pre-check, but then we must find a solution for the IP (and the related follow-up actions like pre-assessment travels to Brussels, if so, f2f meetings, negotiation meetings, etc. ... until end of 2012. Perhaps I can do it as a coordinating subcontractor or working directly/remotely for one of our organisations to help the coordination, if needed. Everybody in the final consortium would have to commit to attend such meetings with the EC and not to withdraw when we have started the submission process in January. We discussed the well known problems with LOI's and especially with signing a memorandum.

4) WP structure
We discussed the WP-structure and how to shape it, explicitly wrt. NBIS topic of Call 9.

• The WP structure should be as simple as possible ( http://cordis.europa.eu/fp7/ict/fet-pro ... -04_en.pdf)
• We agreed in principle regarding the structure, but now we must make very explicit what is the relation to the targeted outcomes of NBIS.
• We agreed that WP 2 "Reference Models, Architectures, ..." where we bring together all the needed technologies as listed in our first paper, fits very well with NBIS obviously. This is a task of the project, nobody on this planet has ever done it so far, and the separate or single technological approaches are just emerging in these days, as we describe this in our papers as State of the Art and what is Beyond. This is also actually our suggestion for a radically new approach which is needed for FET Proactive , also as high risk, but imaginable and with a chance to get realized.
• The WP4 ff are then the use cases to exploit the technological approach as well as the basis to adjust the reference models and architectures as a loop process.

Björn/ETHZ, Pietro/U Cambridge, Erwin and Carel from TU Delft and University Medical Center Leiden and I send their concrete suggestions until the next telco. They have already relatively concrete ideas, also how to position disease modelling as an appropriate use case for NBIS what they discuss with the group of Andreas Schuppert/RWTH Aachen within the next days.

5) Consortium members
We discussed a first list of so far interested consortium members, how to balance a good consortium and how to summarize some colleagues under one umbrella (e.g. Erwin + Carel) in order to reduce the number to less than 15 organisations. This is important for the evaluation criterion "Quality of consortium as a whole".

[rainer93138]

Hi Björn,
thanks very much for your very worthwhile comments which must be discussed carefully when we shape BioMedCEP for NBIS. Some remarks to your points what is very helpful for writing already a good abstract or an one-pager for the pre-check:

Björn Menze/ETHZ wrote 7 Dec 2011:
(...) I understood you correctly that BrainPort and related Neuro-Rehabilitation/-Prosthetic Projects would be the driving technology you have in mind here? And remaining work packages would be centered around it? ...
... one should have a very good reason as of _why_ one wanted to leave the subject/organ level of standard BCI (and related technology) and go down through all the scales down to protein (?) level. As you know, every scale comes with different models even for the same disease. And if one chooses to go through multiple scales, it should be - on a very technical, experimental level - clear of how to inform the related models through data (...)

Some possible answers:

BrainPort and CN-NINM technology of the TCNL approach is used to show the State of the Art and that the Brain could be "rebooted" by stimulating and training it on the organ-level with events (patterns), a non-invasive approach, without any drugs, very effective and efficient, healing results after a very short time of treatment, as it seems. This can be explained by the TCNL colleagues Yuri Danilov, Mitch Tyler and Kurt Kaczmarek in more details (see viewtopic.php?f=13&t=261&start=10#p1215, and the following postings).

This existing approach should now be enhanced by U-CEP and exploited in other use cases like understanding Ageing, Inner Clock of the brain, etc. and diseases like depression, diabetes and obesity as some of the main diseases of our society.

The connection between U-CEP and the U Wisconsin/TCNL or the Deep Brain Stimulation approaches is that we would be able to experiment with complex event patterns for stimulating the brain or the tongue very much better or more target-oriented, more fine-grained even on the basis of an EPL logic and of arbitrary event sources - from other senses, from the environment or from the global event cloud of the Internet of Things and Services. The event modelling can take place "on the fly" during the experiment or the treatment of the patient. Additionally, in the future such a device with the accelerometers will be miniaturized so much, that the "device" could be worn permanently or could be implanted e.g. in the tongue. Body Area Networks and Wearable Technologies viewtopic.php?f=13&t=299 would be a kind of an infrastructure for combining all the needed technological components of biosensing via event adapters on the organ- or the cell-level depending on the targets, the exocortex system based on IBM's cognitive computing chips or quantum- and bio-computing (e.g. see BrainScaleS or the comparison of artificial brain and neuroscience projects http://synapticlink.org/BrainProjectCom ... htm?mid=54), mapping technologies of the event-processing results of the exocortex to the brain and the human body.

We could experiment on both levels: on the organ-level as sketched in paper 1, and on the cell- and protein-machinery level. We use event adapters for living cells engineered to shuttle electrons across a cell’s membrane to an external acceptor along a well-defined path viewtopic.php?f=13&t=268 or the proton-based chips viewtopic.php?f=13&t=261&start=20#p1230 or IBM's cognitive computing chips viewtopic.php?f=13&t=261&start=20#p1230 or Princeton university's electronic skin viewtopic.php?f=13&t=261&start=10#p1217. Some of the questions are - what we have addressed viewtopic.php?f=13&t=261&start=10#p1222:

With our combined approach we distinguish between:

1) use another organ (or a robot) to substitute a (damaged) sense and what makes it with the brain or how is the brain recovered/reorganized/changed
2) enhance the sensitivity range of a sense and what would the brain do? adapt as well? or would we become crazy respectively could not (re-) act sensefully with an enhanced sensitivity range? Then would we need an exocortex to translate or map this additional "information" to our brain?
3) add new or additional senses, ditto, and would we recognize a new "reality"?

For instance, it is imaginable that we can enhance the sensitivity range of the sense of smell via an exocortex system according to today's specially trained dogs which can smell cancer cells in a human body in a very early stage, and we can trigger biological processes to influence the metabolism on the protein level to destroy or repair such cancer cells, or we can trigger nanobot-based processes which destroy or repair the cells.

We want to investigate reasons why and when to leave the subject/organ level of standard BCI (and related technology) and go down through all the scales down to protein level. Every scale comes with different models even for the same disease. To go through multiple scales, it will be - on a very technical, experimental level - investigated how to inform the related models through data respectively events.

We experiment with that on the mentioned basis of U-CEP and genetic cassettes or other (e.g. protonic or graphene-based) event adapters and influence a protein machinery based on changing complex event patterns and event processing at all. We try to heal some more diseases than the use cases addressed in the BioMedCEP proposal (e.g. schizophrenia, addiction, parkinson, etc.) - also non-invasively and without drugs - and the brain should stably or durably change after short time, as TCNL has proved this for their experiments and "use cases" (as we call it in the discipline of Software Engineering) already.

A human body can be seen as a collaboration of around 50 or more trillion cells (as an event processing network EPN) which do event processing and collaborating via the receptors of the cell membrane (event adapters) and the related effectors (event processing agents EPA) which “manage” or control the processes of a protein machinery. To model and control the event processing of specific biomarkers can be the basis to avoid and heal diseases.

Especially interesting are the dynamic aspects of a not strongly fixed and in advance defined collaboration of processes. The processes can be combined dynamically as it is perhaps also typical in the fields of biology and medicine. This also includes the aspects of Uncertainty modeling (as also mentioned in Ch. 5 of the VPH-FET roadmap). We experiment with modeling approaches from UAI (Uncertainty in Artificial Intelligence, http://www.auai.org/, http://citeseerx.ist.psu.edu/viewdoc/do ... 1&type=pdf, http://citeseerx.ist.psu.edu/viewdoc/do ... 1&type=pdf) as well as the suggestion of a reference model for non-deterministic U-CEP applications (see workshop paper Danilov/Tyler/Ammon/Etzion) and special aspects of uncertainty in the disciplin of CEP (Etzion/Niblett 2010).

The vision of the BioMedCEP project is to bring together a team of brain researchers, biologists, from epigenetics and from medicine regarding the understanding of the neurobiological processes and the definition of biomarkers with specialists of process or event modelling methodology to implement such neuro-bio-inspired systems for biosensing and biomarkers and with IT specialists of Ubiquitous Complex Event Processing of accordant real-time processing platforms for a tremendous vast amount of events or signals per second as an interaction between a human and the surrounding universe.

That would be some ideas on the way to write an abstract or one-pager so far. Must be better integrated of course, but could be a basis for our discussion on Monday.

I tried to change the workpackages structure according to the NBIS objectives, as you already got it with the invitation to the 3rd conference call 12 Dec 2011

(downloadable as ppt http://www.citt-online.com/downloads/WP ... MedCEP.ppt, please feel free to change and send back)

Best regards

Rainer

[rainer93138]

BioMedCEP / Minutes from 12 Dec / Next telco 19 Dec

On 19 Dec, we discuss further the agenda and the minutes of conference call 12 Dec 2012
viewtopic.php?f=13&t=316&start=40#p1304

I'll send the concal invitation.

In addition:

1) Submission of a 10 pager version of our papers to Turing Centenary Conference, Cambridge, deadline 20 January 2012
http://www.mathcomp.leeds.ac.uk/turing2012/WScie12/

2) Full papers / Extended journal version - State of preparation

3) Information day FP7 ICT Call 9 on 18 January 2012 - Presentation of BioMedCEP
viewtopic.php?f=13&t=316&start=40#p1303

4) Shaping BioMedCEP wrt. NBIS objectives
viewtopic.php?f=13&t=316&start=40#p1305
Please make sure that everybody has understood the objectives, outcomes, impacts of NBIS as summarized in the first slide
http://www.citt-online.com/downloads/WP ... MedCEP.ppt
We discuss further the WP-structure and the use cases depending on:
4.1 What are the reasons why the use cases of the diseases like depression, diabetes, obesity are needed? or should be changed (e.g. Parkinson's, stroke, schizophrenia...)?
4.2 Do we have the medical experts for modelling biomarkers etc. wrt. the use cases/diseases?
4.3 What are the discriminant challenges for each use case/disease and why do we need the use case for our research?

Some comments wrt. the use cases:

- We are already strong and have good expertise for Ageing and Mobility and other Ageing-related questions

- Depression
Different types of depression. Our U-CEP-based approach as non-invasive and without drugs means:
Electrical shock does mostly not change the brain durably. Must be repeated. Damages the brain more or less.
U-CEP based approach as a neuro-bio-inspired system on the organ-level (e.g. event adapters according to biomarkers implanted in the tongue, other TCNL approaches)
U-CEP based approach as a neuro-bio-inspired system on the cell-level/protein level, changing the metabolism because depression is a fault of the metabolism...

- Diabetes
What is additional / special? Do we need the use case (except that it is one of the main disease problems of the society)? What would we learn about neuro-bio-inspired systems and the brain functions in addition?

- Obesity
What is additional / special? Do we need the use case (except that it is one of the main disease problems of the society)? ditto...

[rainer93138]

If you don't know it yet, this is a great TEDTalk presented by Daniel Kraft, FutureMed Executive Director:

http://www.ted.com/talks/view/lang/en//id/1168

It should not be a problem to position the BioMedCEP project proposal and to prepare a similar presentation specialized on the specific aspects of BioMedCEP.

More about:
FutureMed
http://futuremed2020.com/

Singularity University's mission at Stanford is to assemble, educate and inspire a cadre of leaders who strive to understand and facilitate the development of exponentially advancing technologies to address humanity’s challenges.

[rainer93138]

Last year I mentioned another project, HIVE viewtopic.php?f=13&t=268#p1072, which should be relevant for BioMedCEP. HIVE was started from 2008 to 2012 as a European FET-OPEN project.

We submit a presentation about our BioMedCEP approach to their 2nd workshop in Berlin, 27-28 April 2012 http://hive-eu.org/hive2012/home.

See also the presentations of the HIVE workshop 2009 at Rennes, France:
http://hive-eu.org/node/224

As it seems from the presentations, the HIVE members focus on TMS resp. TNS, tDCS, etc.. We shall discuss the connection with the U-CEP approach.

[rainer93138]

This is some of the context and of the future horizon of the BioMedCEP proposal:

The status of goals of the DARPA synapse brain emulation project. It appears on track for human scale brain emulation by 2019. It is funded at $30 million per year. Europe could kick off a $1.6 billion human brain emulation project with a target for 2024. It seems like there will be a human brain emulation race. China and other countries likely to join (...)

The vision of the Systems of Neuromorphic Adaptive Plastic Scalable Electronics (SyNAPSE) program is the development of biological-scale neuromorphic electronic systems for autonomous, unmanned, robotic systems where humans are currently the only viable option (...)

Assuming that both Synapse and Markram are funded through 2024, then the total funding would be over $2 billion for human brain emulation. If there is even the smallest belief in the possibility of success with these projects there will also be comparable scale projects in China, Japan, India, Russia and other countries. It seems that any failure of the Singularity and human level general intelligence will not be from lack of funding, desire or effort. However, it could be like nuclear fusion where large sums are spent on approaches that are flawed.
More: http://nextbigfuture.com/2011/07/darpa- ... rgets.html

And this challenge is one of which fit with our BioMedCEP for instance:
"Demonstrate a dynamic neural system simulation of approximately one million neurons (Ed: still in 2011) that shows plasticity, self-organization, and network stability in response to sensory stimulus and system level reinforcement."

We actually go the reverse approach with BioMedCEP and investigate what a human brain would do, how would it change or adapt if we enhance the sensitivity range of a sense or if we add new senses, and how to map the additional events (event types) to the brain, probably via an exocortex, bio-markers, bio-sensors, different technologies of event adapters on organ- or cell-level, body area networks, etc. as we have sketched this already.

[rainer93138]

Filippo Castiglione wrote today (and agreed to put it on the discussion forum. BTW: as already mentioned some months ago, everybody could comment on the discussion forum directly, but you must register):

Dear all, 10 people have express interest in collaborating in the writing of a spin-off paper from the chapter topic 5 of the VPH-FET roadmap that I will coordinate.

The plan is the following: as last time, since we are too many, there is no way we can proceed in a sequential manner; I suggest
Phase 1. We have a re-read to the document in attachment and use the Word track changes to annotate your additions. You'll send it to me and I will merge the whole stuff.
Phase 2. You will receive a modified version and have the chance to update the doc again. Again, track changes on, send back to me.

What's new with respect to the roadmap chapter? Well, first we should try to expand a bit the concepts we had in mind at that time. Possibly by updating a bit the references. Pictures are welcome. Secondly, we should try to integrate the thing with the U-CEP. This task will be mainly performed by myself and Rainer. You all will have the chance to read this aspect in the second round. Third, this is important, we should expand the modeling part by describing how VPH (or other) models can proficiently use the accumulated data from sensors. Possible keywords could be: pollution and environmental data, patient-specific data, cloud computing, live-modeling, health-forecast, ...

I am open to suggestions on all aspects.

As for a deadline I suggest before 31/12 so that we can start phase 2 at the beginning of the next year.
If someone can't make it, please let me know.

Thanks in advance and Happy Christmas
Filippo