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Luís F. Simões

Our approach to replication in computational science - 2 views

  • So what did we do to make this paper extra super replicable? If you go to the paper Web site, you'll find:
  • p.s. I think I have to refer to this cancer results not reproducible paper somewhere. Done.
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    good discussion on the replicability/reproducibility of scientific results (also a nice example of how to do it right... in bioinformatics at least)
LeopoldS

From Sci-Mate to Mendeley - a brief history of reference managers - Trading knowledge B... - 1 views

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    very nice comparison of reference managers ...
LeopoldS

Does the Feigel effect violate the first law? - 2 views

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    interestingly also with a reference to the ariadna study of Andreas ...
Luís F. Simões

Inferring individual rules from collective behavior - 2 views

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    "We fit data to zonal interaction models and characterize which individual interaction forces suffice to explain observed spatial patterns." You can get the paper from the first author's website: http://people.stfx.ca/rlukeman/research.htm
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    PNAS? Didnt strike me as sth very new though... We should refer to it in the roots study though: "Social organisms form striking aggregation patterns, displaying cohesion, polarization, and collective intelligence. Determining how they do so in nature is challenging; a plethora of simulation studies displaying life-like swarm behavior lack rigorous comparison with actual data because collecting field data of sufficient quality has been a bottleneck." For roots it is NO bottleneck :) Tobias was right :)
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    Here they assume all relevant variables influencing behaviour are being observed. Namely, the relative positions and orientations of all ducks in the swarm. So, they make movies of the swarm's movements, process them, and them fit the models to that data. In the roots, though we can observe the complete final structure, or even obtain time-lapse movies showing how that structure came out to be, getting the measurements of all relevant soil variables (nitrogen, phosphorus, ...) throughout the soil, and over time, would be extremely difficult. So I guess a replication of the kind of work they did, but for the roots, would be hard. Nice reference though.
nikolas smyrlakis

BBC News - European space missions given cost warning - 1 views

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    Cosmic Vision missions, some of which to be selected before the end of 2011.. Favorite phrase: "Mindful of the recent criticism the agency has received from member states on the issue of cost overruns, Professor David Southwood, Esa's director of science and robotics, told the teams: "Industry and the science community need to get to work on this; it's a collective responsibility."" :-> reference class forecasting!
Luís F. Simões

Seminar: You and Your Research, Dr. Richard W. Hamming (March 7, 1986) - 10 views

  • This talk centered on Hamming's observations and research on the question "Why do so few scientists make significant contributions and so many are forgotten in the long run?" From his more than forty years of experience, thirty of which were at Bell Laboratories, he has made a number of direct observations, asked very pointed questions of scientists about what, how, and why they did things, studied the lives of great scientists and great contributions, and has done introspection and studied theories of creativity. The talk is about what he has learned in terms of the properties of the individual scientists, their abilities, traits, working habits, attitudes, and philosophy.
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    Here's the link related to one of the lunch time discussions. I recommend it to every single one of you. I promise it will be worth your time. If you're lazy, you have a summary here (good stuff also in the references, have a look at them):      Erren TC, Cullen P, Erren M, Bourne PE (2007) Ten Simple Rules for Doing Your Best Research, According to Hamming. PLoS Comput Biol 3(10): e213.
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    I'm also pretty sure that the ones who are remembered are not the ones who tried to be... so why all these rules !? I think it's bullshit...
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    The seminar is not a manual on how to achieve fame, but rather an analysis on how others were able to perform very significant work. The two things are in some cases related, but the seminar's focus is on the second.
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    Then read a good book on the life of Copernic, it's the anti-manual of Hamming... he breaks all the rules !
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    honestly I think that some of these rules actually make sense indeed ... but I am always curious to get a good book recommendation (which book of Copernic would you recommend?) btw Pacome: we are in Paris ... in case you have some time ...
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    I warmly recommend this book, a bit old but fascinating: The sleepwalkers from Arthur Koestler. It shows that progress in science is not straight and do not obey any rule... It is not as rational as most of people seem to believe today. http://www.amazon.com/Sleepwalkers-History-Changing-Universe-Compass/dp/0140192468/ref=sr_1_1?ie=UTF8&qid=1294835558&sr=8-1 Otherwise yes I have some time ! my phone number: 0699428926 We live around Denfert-Rochereau and Montparnasse. We could go for a beer this evening ?
Loretta Latronico Poulain

Behavioural Economics? Try Biological Economics - 2 views

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    The "Biological Economics" thing is a hyping (or misunderstanding) of the BBC article. The work it refers to seems to be an application of Complex Networks theory to financial networks. I found what appear to be some of the related publications: Andrew G. Haldane (April 2009) Rethinking the financial network (further references in the footnote to page 10) Erlend Nier, Jing Yang, Tanju Yorulmazer and Amadeo Alentorn (April 2008) Network models and financial stability Funny how these issues have been repeatedly popping up at the ACT in recent weeks. This connects both with the discussions on information spreading in networks, and with roadmaps' robustness.
Luís F. Simões

Shell energy scenarios to 2050 - 6 views

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    just in case you were feeling happy and optimistic
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    An energy scenario published by an oil company? Allow me to be sceptical...
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    Indeed, Shell is an energy company, not just oil, for some time now ... The two scenarii are, in their approach, dependant of economic and political situation, which is right now impossible to forecast. Reference to Kyoto is surprising, almost out-dated! But overall, I find it rather optimistic at some stages, and probably the timeline (p37-39) is unlikely with recent events.
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    the report was published in 2008, which explains the reference to Kyoto, as the follow-up to it was much more uncertain at that point. The Blueprint scenario is indeed optimistic, but also quite unlikely I'd say. I don't see humanity suddenly becoming so wise and coordinated. Sadly, I see something closer to the Scramble scenario as much more likely to occur.
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    not an oil company??? please have a look at the percentage of their revenues coming from oil and gas and then compare this with all their other energy activities together and you will see very quickly that it is only window dressing ... they are an oil and gas company ... and nothing more
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    not JUST oil. From a description: "Shell is a global group of energy and petrochemical companies." Of course revenues coming from oil are the biggest, the investment turnover on other energy sources is small for now. Knowing that most of their revenues is from an expendable source, to guarantee their future, they invest elsewhere. They have invested >1b$ in renewable energy, including biofuels. They had the largest wind power business among so-called "oil" companies. Oil only defines what they do "best". As a comparison, some time ago, Apple were selling only computers and now they sell phones. But I would not say Apple is just a phone company.
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    window dressing only ... e.g. Net cash from operating activities (pre-tax) in 2008: 70 Billion$ net income in 2008: 26 Billion revenues in 2008: 88 Billion Their investments and revenues in renewables don't even show up in their annual financial reports since probably they are under the heading of "marketing" which is already 1.7 Billion $ ... this is what they report on their investments: Capital investment, portfolio actions and business development Capital investment in 2009 was $24 billion. This represents a 26% decrease from 2008, which included over $8 billion in acquisitions, primarily relating to Duvernay Oil Corp. Capital investment included exploration expenditure of $4.5 billion (2008: $11.0 billion). In Abu Dhabi, Shell signed an agreement with Abu Dhabi National Oil Company to extend the GASCO joint venture for a further 20 years. In Australia, Shell and its partners took the final investment decision (FID) for the Gorgon LNG project (Shell share 25%). Gorgon will supply global gas markets to at least 2050, with a capacity of 15 million tonnes (100% basis) of LNG per year and a major carbon capture and storage scheme. Shell has announced a front-end engineering and design study for a floating LNG (FLNG) project, with the potential to deploy these facilities at the Prelude offshore gas discovery in Australia (Shell share 100%). In Australia, Shell confirmed that it has accepted Woodside Petroleum Ltd.'s entitlement offer of new shares at a total cost of $0.8 billion, maintaining its 34.27% share in the company; $0.4 billion was paid in 2009 with the remainder paid in 2010. In Bolivia and Brazil, Shell sold its share in a gas pipeline and in a thermoelectric power plant and its related assets for a total of around $100 million. In Canada, the Government of Alberta and the national government jointly announced their intent to contribute $0.8 billion of funding towards the Quest carbon capture and sequestration project. Quest, which is at the f
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    thanks for the info :) They still have their 50% share in the wind farm in Noordzee (you can see it from ESTEC on a clear day). Look for Shell International Renewables, other subsidiaries and joint-ventures. I guess, the report is about the oil branch. http://sustainabilityreport.shell.com/2009/servicepages/downloads/files/all_shell_sr09.pdf http://www.noordzeewind.nl/
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    no - its about Shell globally - all Shell .. these participations are just peanuts please read the intro of the CEO in the pdf you linked to: he does not even mention renewables! their entire sustainability strategy is about oil and gas - just making it (look) nicer and environmentally friendlier
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    Fair enough, for me even peanuts are worthy and I am not able to judge. Not all big-profit companies, like Shell, are evil :( Look in the pdf what is in the upstream and downstream you mentionned above. Non-shell sources for examples and more objectivity: http://www.nuon.com/company/Innovative-projects/noordzeewind.jsp http://www.e-energymarket.com/news/single-news/article/ferrari-tops-bahrain-gp-using-shell-biofuel.html thanks.
santecarloni

Sharpening the Nanofocus: Berkeley Lab Researchers Use Nanoantenna to Enhance... - 0 views

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    See Also: Matter & Energy Nanotechnology Optics Physics Materials Science Graphene Organic Chemistry Reference White gold Electromagnetic radiation Nanomedicine Nanoparticle Any use for the smell project? "We have demonstrated resonant antenna-enhanced single-particle hydrogen sensing in the visible region and presented a fabrication approach to the positioning of a single palladium nanoparticle in the nanofocus of a gold nanoantenna,"
LeopoldS

[0812.2633] Ghost imaging with a single detector - 2 views

shared by LeopoldS on 20 Sep 11 - No Cached
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    anything happening on this since 3 years?
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    yes it seems like. most of it seems however directed toward understanding this effect, and not toward applications. But i'm still convinced that we could find many very interesting applications !!! a few references from ADS: 1 2011PhRvA..83f3807B 1.000 06/2011 A E X R C U Brida, G.; Chekhova, M. V.; Fornaro, G. A.; Genovese, M.; Lopaeva, E. D.; Berchera, I. Ruo Systematic analysis of signal-to-noise ratio in bipartite ghost imaging with classical and quantum light 2 2011PhRvA..83e3808L 1.000 05/2011 A E R U Liu, Ying-Chuan; Kuang, Le-Man Theoretical scheme of thermal-light many-ghost imaging by Nth-order intensity correlation 3 2011PhRvA..83e1803D 1.000 05/2011 A E R C U Dixon, P. Ben; Howland, Gregory A.; Chan, Kam Wai Clifford; O'Sullivan-Hale, Colin; Rodenburg, Brandon; Hardy, Nicholas D.; Shapiro, Jeffrey H.; Simon, D. S.; Sergienko, A. V.; Boyd, R. W.; Howell, John C. Quantum ghost imaging through turbulence 4 2011SPIE.7961E.160O 1.000 03/2011 A E T Ohuchi, H.; Kondo, Y. Complete erasing of ghost images caused by deeply trapped electrons on computed radiography plates 5 2011ApPhL..98k1115M 1.000 03/2011 A E R U Meyers, Ronald E.; Deacon, Keith S.; Shih, Yanhua Turbulence-free ghost imaging 6 2011ApPhL..98k1102G 1.000 03/2011 A E R C U Gan, Shu; Zhang, Su-Heng; Zhao, Ting; Xiong, Jun; Zhang, Xiangdong; Wang, Kaige Cloaking of a phase object in ghost imaging 7 2011RScI...82b3110Y 1.000 02/2011 A E R U Yang, Hao; Zhao, Baosheng; Qiu
nikolas smyrlakis

The evolving face of networks |Technology |The Guardian - 3 views

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    really really interesting article also referring to a Nature paper called Evolutionary dynamics on graphs
LeopoldS

DESERTEC Foundation: Concept - 0 views

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    this is the project I was referring to in my topic post ...
ESA ACT

Slashdot | Cutting-Edge AI Projects? - 0 views

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    Read the first entries, are really funny. The ones tagged as "Informative" contain references that might be useful for us.
ESA ACT

PlagiarismDetect.com | Free Online Plagiarism Detection System - 0 views

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    If you get suspicious text you can have an automated check. However, I suggest to remove any references chapter since they boost the amount of hits. My last Ariadna report has a plagiarism rate of 8.7%. Anyone higher?
ESA ACT

2collab - 0 views

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    2collab is a new type of research tool launched in 2007- a collaboration platform designed specifically for researchers in the science, technical and medical communities. 1.Online bookmarking and reference management 2.Groups - for sharing with existing n
ESA ACT

Google Doctype - Google Code - 0 views

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    Google Doctype is an open encyclopedia and reference library. Written by web developers, for web developers.
LeopoldS

Operation Socialist: How GCHQ Spies Hacked Belgium's Largest Telco - 4 views

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    interesting story with many juicy details on how they proceed ... (similarly interesting nickname for the "operation" chosen by our british friends) "The spies used the IP addresses they had associated with the engineers as search terms to sift through their surveillance troves, and were quickly able to find what they needed to confirm the employees' identities and target them individually with malware. The confirmation came in the form of Google, Yahoo, and LinkedIn "cookies," tiny unique files that are automatically placed on computers to identify and sometimes track people browsing the Internet, often for advertising purposes. GCHQ maintains a huge repository named MUTANT BROTH that stores billions of these intercepted cookies, which it uses to correlate with IP addresses to determine the identity of a person. GCHQ refers to cookies internally as "target detection identifiers." Top-secret GCHQ documents name three male Belgacom engineers who were identified as targets to attack. The Intercept has confirmed the identities of the men, and contacted each of them prior to the publication of this story; all three declined comment and requested that their identities not be disclosed. GCHQ monitored the browsing habits of the engineers, and geared up to enter the most important and sensitive phase of the secret operation. The agency planned to perform a so-called "Quantum Insert" attack, which involves redirecting people targeted for surveillance to a malicious website that infects their computers with malware at a lightning pace. In this case, the documents indicate that GCHQ set up a malicious page that looked like LinkedIn to trick the Belgacom engineers. (The NSA also uses Quantum Inserts to target people, as The Intercept has previously reported.) A GCHQ document reviewing operations conducted between January and March 2011 noted that the hack on Belgacom was successful, and stated that the agency had obtained access to the company's
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    I knew I wasn't using TOR often enough...
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    Cool! It seems that after all it is best to restrict employees' internet access only to work-critical areas... @Paul TOR works on network level, so it would not help here much as cookies (application level) were exploited.
Dario Izzo

Miguel Nicolelis Says the Brain Is Not Computable, Bashes Kurzweil's Singularity | MIT ... - 9 views

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    As I said ten years ago and psychoanalysts 100 years ago. Luis I am so sorry :) Also ... now that the commission funded the project blue brain is a rather big hit Btw Nicolelis is a rather credited neuro-scientist
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    nice article; Luzi would agree as well I assume; one aspect not clear to me is the causal relationship it seems to imply between consciousness and randomness ... anybody?
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    This is the same thing Penrose has been saying for ages (and yes, I read the book). IF the human brain proves to be the only conceivable system capable of consciousness/intelligence AND IF we'll forever be limited to the Turing machine type of computation (which is what the "Not Computable" in the article refers to) AND IF the brain indeed is not computable, THEN AI people might need to worry... Because I seriously doubt the first condition will prove to be true, same with the second one, and because I don't really care about the third (brains is not my thing).. I'm not worried.
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    In any case, all AI research is going in the wrong direction: the mainstream is not on how to go beyond Turing machines, rather how to program them well enough ...... and thats not bringing anywhere near the singularity
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    It has not been shown that intelligence is not computable (only some people saying the human brain isn't, which is something different), so I wouldn't go so far as saying the mainstream is going in the wrong direction. But even if that indeed was the case, would it be a problem? If so, well, then someone should quickly go and tell all the people trading in financial markets that they should stop using computers... after all, they're dealing with uncomputable undecidable problems. :) (and research on how to go beyond Turing computation does exist, but how much would you want to devote your research to a non existent machine?)
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    [warning: troll] If you are happy with developing algorithms that serve the financial market ... good for you :) After all they have been proved to be useful for humankind beyond any reasonable doubt.
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    Two comments from me: 1) an apparently credible scientist takes Kurzweil seriously enough to engage with him in polemics... oops 2) what worries me most, I didn't get the retail store pun at the end of article...
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    True, but after Google hired Kurzweil he is de facto being taken seriously ... so I guess Nicolelis reacted to this.
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    Crazy scientist in residence... interesting marketing move, I suppose.
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    Unfortunately, I can't upload my two kids to the cloud to make them sleep, that's why I comment only now :-). But, of course, I MUST add my comment to this discussion. I don't really get what Nicolelis point is, the article is just too short and at a too popular level. But please realize that the question is not just "computable" vs. "non-computable". A system may be computable (we have a collection of rules called "theory" that we can put on a computer and run in a finite time) and still it need not be predictable. Since the lack of predictability pretty obviously applies to the human brain (as it does to any sufficiently complex and nonlinear system) the question whether it is computable or not becomes rather academic. Markram and his fellows may come up with a incredible simulation program of the human brain, this will be rather useless since they cannot solve the initial value problem and even if they could they will be lost in randomness after a short simulation time due to horrible non-linearities... Btw: this is not my idea, it was pointed out by Bohr more than 100 years ago...
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    I guess chaos is what you are referring to. Stuff like the Lorentz attractor. In which case I would say that the point is not to predict one particular brain (in which case you would be right): any initial conditions would be fine as far as any brain gets started :) that is the goal :)
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    Kurzweil talks about downloading your brain to a computer, so he has a specific brain in mind; Markram talks about identifying neural basis of mental diseases, so he has at least pretty specific situations in mind. Chaos is not the only problem, even a perfectly linear brain (which is not a biological brain) is not predictable, since one cannot determine a complete set of initial conditions of a working (viz. living) brain (after having determined about 10% the brain is dead and the data useless). But the situation is even worse: from all we know a brain will only work with a suitable interaction with its environment. So these boundary conditions one has to determine as well. This is already twice impossible. But the situation is worse again: from all we know, the way the brain interacts with its environment at a neural level depends on his history (how this brain learned). So your boundary conditions (that are impossible to determine) depend on your initial conditions (that are impossible to determine). Thus the situation is rather impossible squared than twice impossible. I'm sure Markram will simulate something, but this will rather be the famous Boltzmann brain than a biological one. Boltzman brains work with any initial conditions and any boundary conditions... and are pretty dead!
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    Say one has an accurate model of a brain. It may be the case that the initial and boundary conditions do not matter that much in order for the brain to function an exhibit macro-characteristics useful to make science. Again, if it is not one particular brain you are targeting, but the 'brain' as a general entity this would make sense if one has an accurate model (also to identify the neural basis of mental diseases). But in my opinion, the construction of such a model of the brain is impossible using a reductionist approach (that is taking the naive approach of putting together some artificial neurons and connecting them in a huge net). That is why both Kurzweil and Markram are doomed to fail.
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    I think that in principle some kind of artificial brain should be feasible. But making a brain by just throwing together a myriad of neurons is probably as promising as throwing together some copper pipes and a heap of silica and expecting it to make calculations for you. Like in the biological system, I suspect, an artificial brain would have to grow from a small tiny functional unit by adding neurons and complexity slowly and in a way that in a stable way increases the "usefulness"/fitness. Apparently our brain's usefulness has to do with interpreting inputs of our sensors to the world and steering the body making sure that those sensors, the brain and the rest of the body are still alive 10 seconds from now (thereby changing the world -> sensor inputs -> ...). So the artificial brain might need sensors and a body to affect the "world" creating a much larger feedback loop than the brain itself. One might argue that the complexity of the sensor inputs is the reason why the brain needs to be so complex in the first place. I never quite see from these "artificial brain" proposals in how far they are trying to simulate the whole system and not just the brain. Anyone? Or are they trying to simulate the human brain after it has been removed from the body? That might be somewhat easier I guess...
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    Johannes: "I never quite see from these "artificial brain" proposals in how far they are trying to simulate the whole system and not just the brain." In Artificial Life the whole environment+bodies&brains is simulated. You have also the whole embodied cognition movement that basically advocates for just that: no true intelligence until you model the system in its entirety. And from that you then have people building robotic bodies, and getting their "brains" to learn from scratch how to control them, and through the bodies, the environment. Right now, this is obviously closer to the complexity of insect brains, than human ones. (my take on this is: yes, go ahead and build robots, if the intelligence you want to get in the end is to be displayed in interactions with the real physical world...) It's easy to dismiss Markram's Blue Brain for all their clever marketing pronouncements that they're building a human-level consciousness on a computer, but from what I read of the project, they seem to be developing a platfrom onto which any scientist can plug in their model of a detail of a detail of .... of the human brain, and get it to run together with everyone else's models of other tiny parts of the brain. This is not the same as getting the artificial brain to interact with the real world, but it's a big step in enabling scientists to study their own models on more realistic settings, in which the models' outputs get to effect many other systems, and throuh them feed back into its future inputs. So Blue Brain's biggest contribution might be in making model evaluation in neuroscience less wrong, and that doesn't seem like a bad thing. At some point the reductionist approach needs to start moving in the other direction.
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    @ Dario: absolutely agree, the reductionist approach is the main mistake. My point: if you take the reductionsit approach, then you will face the initial and boundary value problem. If one tries a non-reductionist approach, this problem may be much weaker. But off the record: there exists a non-reductionist theory of the brain, it's called psychology... @ Johannes: also agree, the only way the reductionist approach could eventually be successful is to actually grow the brain. Start with essentially one neuron and grow the whole complexity. But if you want to do this, bring up a kid! A brain without body might be easier? Why do you expect that a brain detached from its complete input/output system actually still works. I'm pretty sure it does not!
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    @Luzi: That was exactly my point :-)
johannessimon81

Nuclear isomer - 2 views

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    We had a short discussion yesterday about using nuclear isomers as batteries for spacecraft. The principle is that energy is stored as an excitation of the nucleus which can then release the energy as a gamma-photon. However angular momentum has to be conserved an this suppresses the decay strongly - making these states stable up to 10^35 longer than a typical decay.
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    The key is the triggering of the dacay wheras the triggering comsumes less energy than the decay provides. The x-ray based triggering of the gamma photon decay turned out to be quite controversial and needs significantly more scientific attention.
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    I think that there should be some references and traces of the discussions we had on this on the shared drive or wiki ... One other aspect: converting the omnidirectional gamma bursts into useful energy ....
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