Mathematics posts
- February 4, 2011
- 01:24 PM
- 1,196 views
Early Complex Societies & Early Organized Religions
by Cris Campbell in Genealogy of Religion
Historians have long known that the shelf life of complex societies throughout human history has been rather limited. Archaeologists are aware of this also. But how to explain it?
In a recent (open access) paper, “Cycling in the Complexity of Early Societies,” Sergey Gavrilets and colleagues mathematically modeled early complex societies using a number of variables [...]... Read more »
Gavrilets, Sergey, Anderson, David G., & Turchin, Peter. (2010) Cycling in the Complexity of Early Societies. Cliodynamics: The Journal of Theoretical and Mathematical History, 1(1), 59-80. info:/http://escholarship.org/uc/item/5536t55r
- February 3, 2011
- 11:40 AM
- 1,180 views
CoalHMM analysis of the human/chimpanzee ancestor, based on the orangutan genome
by Thomas Mailund in Mailund on the Internet
I’ve been wanting to write about our paper on the orangutan genome for a while, but I’ve just been too busy so far, so a little late I finally get to it. Besides the Nature paper, where we contributed to the analysis of the two sub-species of orangutans, we have two companion papers. One is [...]... Read more »
Hobolth, A., Dutheil, J., Hawks, J., Schierup, M., & Mailund, T. (2011) Incomplete lineage sorting patterns among human, chimpanzee and orangutan suggest recent orangutan speciation and widespread selection. Genome Research. DOI: 10.1101/gr.114751.110
- January 30, 2011
- 11:44 PM
- 1,250 views
Egypt Week – Corruption and Cooperation
by Jon Wilkins in Lost in Transcription
So, our next Egypt Week feature is a theoretical paper on a topic closely related to the last post. Once again, we are interested in understanding the mechanisms that are responsible for encouraging or enforcing cooperation, thereby facilitating collective action. Last time, we talked about a paper that found that "altruistic" or "third-party" punishment is common in large-scale, complex societies, but is rare in small-scale societies, while "spiteful" punishment is universal.
Many empirical and theoretical studies of cooperation focus on punishment as a mechanism for enforcing societal norms. Basically, you set up a situation where the group benefits if people cooperate, but each individual benefits by not cooperating. If mechanisms exist to punish people for not cooperating, you get cooperation. Which is to say that the existence of punishment changes the individuals' incentives. The benefits of not cooperating are outweighed by the cost of being punished. No big mystery there.
But what if punishment itself is costly? Punishment can stabilize cooperation, but what stabilizes punishment? Some models rely on an infinite succession of punishments, where people punish people who fail to punish people who fail to cooperate, and people punish people who fail to punish people who fail to punish people who fail to cooperate, and people punish ... well, you get the idea.
Today's paper asks if cooperation can be enforced by corrupt punishment. That is, while punishment is still treated as costly, punishers are not necessarily cooperators themselves, as is commonly assumed in models of this sort. Furthermore, the corrupt punishers ("policers") suffer a lower cost when punished than do non-punishers ("civilians").
A corrupt policer looks forward to a cushy retirement, thanks to his hypocritical enforcement of others' cooperation. Little does he suspect how a new, young partner, who colors outside the lines, but has a heart of gold, will turn his whole life upside-down, with hilarious consequences.
The model shows that in the presence of a modest power imbalance, cooperating civilians and corrupt policers can coexist. That is, a moderate level of corruption is consistent with, and can even stabilize cooperation. However, when the power imbalance becomes large, corrupt policers overrun the population, the system breaks down, and cooperation is lost.
The first part of the result is nice because it provides a degree of robustness to the "cooperation through punishment" paradigm, as it does not require the punishers to be acting altruistically themselves.
The second part of the result is perhaps more directly relevant to Egypt Week. Societies can function in the presence of a degree of inequality, and they can tolerate a certain amount of hypocrisy from their leaders. But too much hypocrisy and inequality is inconsistent with the type of collective action that governments are meant to facilitate.
It is heartening to see that when a less corrupt alternative presents itself, people are still capable of collective action on a massive scale.
Peace be upon you.
Úbeda, F., & Duéñez-Guzmán, E. (2010). POWER AND CORRUPTION Evolution DOI: 10.1111/j.1558-5646.2010.01194.x [1] [2]
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[1] This is an online, ahead-of-print publication, which is why there are no page numbers, but it should be findable through the DOI.
[2] Disclosure: The first author on this paper is a long-time friend and colleague, and we have worked together on issues of intragenomic conflict. Here is photographic evidence of our friendship, from when we were traveling around Lyon, France like Thelmo and Louis following the 2010 SMBE meeting:
On our way to the Palais de Justice, we accidentally activated our Wonder-Twin Powers. Francisco took the shape of an evolutionary biologist, and I took the form of a French trash can. Photo by Gleek.
... Read more »
Úbeda, F., & Duéñez-Guzmán, E. (2010) POWER AND CORRUPTION. Evolution. DOI: 10.1111/j.1558-5646.2010.01194.x
- January 28, 2011
- 12:07 PM
- 1,087 views
Mathematicians and Mongeese: Peeing to Defend Territory? or Mates?
by Jon Wilkins in Lost in Transcription
So, you may have heard about Tihomir Petrov, the math professor at Cal State, Northridge who was arrested for urinating on his colleague's office door. Campus security got video footage of Petrov in the act when they set up video cameras following the discovery of "puddles of what they thought was urine."
You may be asking yourself, what the heck was this dude thinking? How should we interpret the behavior of this Homo mathematicus (not that there's anything wrong with it) specimen?
Fortunately, once again, Science!™ has an answer for you. Urine is commonly used as a scent marker to deter competitors. But deter them from what? Traditionally, it has been assumed that scent marking is primarily used to defend territory against intruders, thereby safeguarding resources such as food and space. However, some recent studies have suggested that scent marking may be used to defend mates and mating opportunities. One of the difficulties in studying such a question, however, is that in many systems, competitors for territory and competitors for mates are the same individuals.
A recent study by a group of researchers in the UK, Uganda, and Switzerland have attempted to separate out these two forms of competition in a study of the wild banded mongoose. This species lives in large social groups that share a territory. Thus territorial competition occurs primarily between different social groups, whereas competition over mates occurs primarily within groups.
"Anal gland secretion (AGS) and urine samples were collected under anaesthesia during routine trapping events" Image licensed under creative commons from Mike Rohde's Flickr photostream.
The researchers found that the mongoose populations marked uniformly throughout their territory, and did not appear to increase the frequency of marking in those regions where two territories overlapped. This suggests that, in this species at least, defense of mates and mating opportunities represents a major contribution to scent-marking behavior, perhaps more so than territorial defense.
So, can we extrapolate from the behavior of the wild banded mongoose to the behavior of wild banded mathematician Tihomir Petrov? Of course we can! Should we extrapolate? Absolutely not! But, here at Lost in Transcription, we're all about the possible, so here is the take-home message. Castle and Beckett should look beyond professional disputes between the two mathematicians. They need to be looking at the love-triangle angle (Love angle4?) for motive.
Alternate theory: As Northridge is, like, the pr0n capital of the country, Petrov might not have been the original urinator. When he saw that the cameras had been set up, he might have assumed that he had been cast in a movie, and that peeing on the floor was what was expected of him. Just sayin'.
Jordan, N., Mwanguhya, F., Kyabulima, S., Rüedi, P., & Cant, M. (2010). Scent marking within and between groups of wild banded mongooses Journal of Zoology, 280 (1), 72-83 DOI: 10.1111/j.1469-7998.2009.00646.x
... Read more »
Jordan, N., Mwanguhya, F., Kyabulima, S., Rüedi, P., & Cant, M. (2010) Scent marking within and between groups of wild banded mongooses. Journal of Zoology, 280(1), 72-83. DOI: 10.1111/j.1469-7998.2009.00646.x
- January 27, 2011
- 07:33 AM
- 650 views
the linguistics of heaven and hell
by Chris in The Lousy Linguist
The value of pop culture data for legitimate research is being put to the test. Exactly what, if anything, can the reality show Big Brother tell us about language change over time?Voice Onset Time is a measure of how long you wait to begin vibrating your vocal folds after you release a stop consonant. Voiced stop consonants like /b/ and /d/ require two things: 1) stop all airflow from escaping the airway by closing the glottis and 2) after the air is released, begin vibrating the glottis (by using the rushing air). For non-linguists, think of a garden hose. Imagine you use your thumb to stop the water for a second and you let the pressure build, then you let go and water rushes out, but then you use you thumb to clamp down just a bit on the water to spray it. This is kinda like the speech production of voiced stop consonants in human language.(image from Kval.com)Though I’m no phoneticist, I really like VOT as a target of linguistic study for one crucial reason: it’s a clear example of a linguistic feature that varies according to your human language system but which you do NOT have conscious control over. What that means is that you cannot consciously change the length of your own personal VOT. Go ahead, try it. Make your VOT 20 milliseconds longer. Go ahead, I’ll wait…Of course you can’t. Well, not consciously, but what researchers have found is that your brain, quite independent of conscious will or knowledge, can! Lab studies have found that people will unknowingly alter their VOTs according to certain situations, and the results are predictable. For example, they found that when listening to a set of long VOT stimuli, subjects will begin to lengthen their own VOTS, in essence accommodating the longer VOTs. Over the longer term it has also been shown that people will lengthen their VOT over their lifetime to accommodate cultural shifts. It has been shown that The Queen Mother herself now has a longer VOT than during her younger days (few other people have been recorded consistently over a long period to provide such valuable data, so thanks mum).Here’s what Bane et al. did: They took recordings of confessional sequences from the UK reality TV show Big Brother (where groups of strangers are made to live with each other and occasionally speak to a camera alone like a video diary) and tested what happened to 4 crucial individuals (the ones that stayed on the show long enough to provide several months worth of data points). What they found was that their VOTs did in fact change, though no linear pattern was discovered (i.e., they did not simply get longer in a steady line). This paper is labeled as a progress report because they don't have a firm hypothesis about what actually is happening. Nice trick there boys, ;)They did find one interesting thing: During part of the show, the house mates were physically divided into basically a caste system where half the people were low caste and half were high (a heaven and a hell. And this seemed to have an effect on VOT as well (sociolinguists are slap happy about this, I'm sure).I haven’t looked at the actual number very closely, but in section 6, they say “Housemate trajectories seem to diverge when the divide is present…” However, just taking a glance at the Figure 3, it looks like the diverge at the beginning, then converge at the end, episode 65 (and remain somewhat similar until several episodes of non-DIVIDE have gone by). If my cursory glance is correct, I would assume it takes awhile for the convergence to manifest, and then it persists for awhile after DIVIDE is gone. But this is just me looking at the picture, not the actual data.Finally, and this is just a readability point, but I would order the names in Figure 3 in the same order as the end point of each trajectory, making it easier to follow who is doing what.Max Ban, Peter Graf, & Morgan Sonderegge (2011). Longitudinal phonetic variation in a closed system Linguistic Society of America 2011 Annual Meeting.... Read more »
Max Ban, Peter Graf, & Morgan Sonderegge. (2011) Longitudinal phonetic variation in a closed system. Linguistic Society of America. info:/
- January 25, 2011
- 04:38 PM
- 964 views
This Week in the Universe: January 18th – January 24th
by S.C. Kavassalis in The Language of Bad Physics
Phenomenally beautiful math was the main highlight of this week, I’d say, although none of it for the very faint of heart.
The CMS on SUSY, Bill Unruh on simulated Hawking radiation, Ed Witten on knots, and Schenkel and Van Oystaeyen on noncommutative space(times):
High Energy Physics and Particles:
The LHC Doesn’t Need Data-Collecting Mode To Have Fun
CMS Collaboration (2011). Search for Supersymmetry in pp Collisions at 7 TeV in Events with Jets and Missing Transverse Energy arXiv arXiv: 1101.1628v1
The CMS Collaboration released results this month ruling out supersymmetric particles with masses of less than ~ 0.5 TeV/c2. This is just one of a series of ongoing SUSY related papers analyzing last years data and spitting out constraints on models (which is hugely important). We’ll be seeing results papers for years to come, but it’s nice to see evidence of the LHC being exactly what we all hoped it would be already: the thing that tells us if we’re likely on the right track or not.
For more, see Reality check at the LHC.
General Relativity, Quantum Gravity, et al.:
Measurement of Stimulated Hawking Emission
Silke Weinfurtner, Edmund W. Tedford, Matthew C. J. Penrice, William G. Unruh, & Gregory A. Lawrence (2010). Measurement of stimulated Hawking emission in an analogue system Phys. Rev. Lett., 106 (2), 1302-1306 arXiv: 1008.1911v2
The abstract:
Hawking argued that black holes emit thermal radiation via a quantum spontaneous emission. To address this issue experimentally, we utilize the analogy between the propagation of fields around black holes and surface waves on moving water. By placing a streamlined obstacle into an open channel flow we create a region of high velocity over the obstacle that can include surface wave horizons. Long waves propagating upstream towards this region are blocked and converted into short (deep-water) waves. This is the analogue of the stimulated emission by a white hole (the time inverse of a black hole), and our measurements of the amplitudes of the converted waves demonstrate the thermal nature of the conversion process for this system. Given the close relationship between stimulated and spontaneous emission, our findings attest to the generality of the Hawking process.
Analogues often make me a little uncomfortable in physics, for what are probably obvious reasons, but Bill Unruh has had a lot of success and acceptance with his analogue black hole/white hole models in the past. The line between similar and the same, and if it is actually telling us anything to observe properties in these analogue systems (which have some major fundamental differences) always gets to me in these matters, so I’m going to have to come back to this one to give further comments.
For more, see Wave-Generated ‘White Hole’ Boosts Hawking Radiation Theory: UBC Research.
Ed Witten on Khovanov Homology of Knots.
Edward Witten (2011). Fivebranes and Knots arXiv arXiv: 1101.3216v1
The abstract:
We develop an approach to Khovanov homology of knots via gauge theory (previous physics-based approches involved other descriptions of the relevant spaces of BPS states). The starting point is a system of D3-branes ending on an NS5-brane with a nonzero theta-angle. On the one hand, this system can be related to a Chern-Simons gauge theory on the boundary of the D3-brane worldvolume; on the other hand, it can be studied by standard techniques of S-duality and T-duality. Combining the two approaches leads to a new and manifestly invariant description of the Jones polynomial of knots, and its generalizations, and to a manifestly invariant description of Khovanov homology, in terms of certain elliptic partial differential equations in four and five dimensions.
So Ed Witten is one of those few authors whose work I can feel safe about getting excited over before I’ve read it, and at 146 pages, well, it’s unlikely I’ll ever make it through all of this (although its length is only due to the fact that it very thorough, and thus imaginably very useful). I’m going to defer to the University of Toronto’s Daniel Moskovich from Low Dimensional Topology (which I can’t recommend enough) on this one, as he wrote:... Read more »
CMS Collaboration. (2011) Search for Supersymmetry in pp Collisions at 7 TeV in Events with Jets and Missing Transverse Energy. arXiv. arXiv: 1101.1628v1
Silke Weinfurtner, Edmund W. Tedford, Matthew C. J. Penrice, William G. Unruh, & Gregory A. Lawrence. (2010) Measurement of stimulated Hawking emission in an analogue system. Phys. Rev. Lett., 106(2), 1302-1306. arXiv: 1008.1911v2
Edward Witten. (2011) Fivebranes and Knots. arXiv. arXiv: 1101.3216v1
Alexander Schenkel. (2011) Quantum Field Theory on Curved Noncommutative Spacetimes. arXiv. arXiv: 1101.3492v2
- January 20, 2011
- 03:22 PM
- 645 views
Finite formula found for partition numbers
by S.C. Kavassalis in The Language of Bad Physics
Credit: Emory and Ken Ono
So this isn’t physics*, but if you squint hard enough, you can probably make a connection. The hot topic today is Ken Ono‘s latest work on the partition function:
Ken Ono, Amanda Folsom, & Zach Kent (2011). l-adic properties of the partition function American Institute of Mathematics.
Ken Ono & Jan Bruinier (2011). AN ALGEBRAIC FORMULA FOR THE PARTITION FUNCTION American Institute of Mathematics.
A EurekAlert press release appeared today, entitled: New math theories reveal the nature of numbers and people are already whispering “Fields Medal”. Now, I haven’t thoroughly read the paper yet, but, since I’m not a number theorist, my commentary probably won’t change very much anyway. Obviously, like most press releases, this one is full of hyperbole and ridiculous sentences like, “the team was determined go beyond mere theories”, but the actual work being discussed is fascinating.
Now, when we talk about a partition function in the context of Ono’s work, we don’t mean the partition function that is familiar to most physicists, we mean what number theorists call a partition function.
In this setting, a partition is a way of representing a natural number as the sum of natural numbers (ie. for , we have three partitions, , , and , independent of order). Thus, the partition function, , represents the number of possible partitions of . So, , (for , we have: , , , , ) , etc..
To be slightly more technical, from Ken Ono and Kathrin Bringman [1],
A partition of a non-negative integer n is a non-increasing sequence of positive integers whose sum is .
The concept is straight forward, but how to obtain these partition numbers, in general, is actually no trivial matter.
The master of series, Leonhard Euler, worked on solving this problem, to less than fully satisfying results. Using the reciprocal of what is now called Euler’s function, we get the generator for by this infinite product,
.
Here, counts the number of ways to write, , for , where each number appears times.
Obviously, for large , this can be unwieldy, and it doesn’t lead to an explicit formula, but as long as you didn’t need more than 200~ partition numbers, it was okay.
Mathematics had to wait until the early 1900s before anyone was to expand on Euler’s partition number generator, when Srinivasa Ramanujan made contact with G.H. Hardy. Ken Ono actually has a beautiful historical, and mathematical, account of the Ramanujan and Hardy story, called “The Last Words of a Genius” [pdf].
Ramanujan famously proved an unusual and surprising result that [2],
,
,
.
He was also responsible for the first attempt at an explicit, although not exact, formula for with Hardy,
as .
... Read more »
Ken Ono, Amanda Folsom, & Zach Kent. (2011) l-adic properties of the partition function. American Institute of Mathematics. info:/
Folsom A, & Ono K. (2008) The spt-function of Andrews. Proceedings of the National Academy of Sciences of the United States of America, 105(51), 20152-6. PMID: 19091951
- January 15, 2011
- 10:31 PM
- 1,346 views
Does mathematical training increase our risk tolerance?
by Jason Collins in Evolving Economics
Humans are inherently risk averse. When offered a coin toss with a reward of $10,000 for heads but a loss of $10,000 for tails, most people would decline. They would likely agree to pay a significant sum to avoid the gamble, despite the expected value of the gamble being zero. When economists describe the preferences [...]... Read more »
Dehaene, S., Izard, V., Spelke, E., & Pica, P. (2008) Log or Linear? Distinct Intuitions of the Number Scale in Western and Amazonian Indigene Cultures. Science, 320(5880), 1217-1220. DOI: 10.1126/science.1156540
- January 13, 2011
- 08:45 PM
- 1,077 views
Google Violates Benford's Law, Arrest Warrant Issued
by Jon Wilkins in Lost in Transcription
So, Google has already had it's Twitter account subpoenaed, and can look forward to months of molestation enhanced screening at the airport, all thanks to its brazen violation of Benford's Law.
What is this Benford's Law thing?
It is a statement that if you look at lists of numbers in empirical data, the first non-zero digit is distributed in a very specific way. At least for certain kinds of data. Specifically, if the logarithms of the numbers you are looking at are uniformly distributed, then the first digits of those numbers will be Benfordly distributed.
Here's what the relative probabilities of different first digits look like:
Here's a graphic that shows the frequencies of different letters and numbers in Google searches. The numbers are way down at the bottom.
Image via Gizmodo
The thing that you'll notice about this is that 6 is by far the most common digit (and that J/j is sad). Here's a plot of these relative frequencies on the same scale as the Benford's Law plot above.
Roughly speaking, this plot has the same shape as the one above, except for the fact that it includes 0, and that 6 is crazy. But, look at where the 0 value is: pretty much even with where you might expect the 6 to be. What happens if we assume that this was actually a transcription error that happened somewhere along the way? If we switch the 6 and 0 values, and then look at the relative probabilities of all of the non-zero digits, we get this:
The dark blue dots are the Benford's Law points that we showed before. The reddish squares are the new empirical distribution.
Now that we've switched the 6 and the 0, we get something that looks to me like a mixture of the Benford's Law distribution and a uniform distribution. But remember, Benford's Law applies to first digits. This is data from all google searches. So, that's going to be a mixture of first digits and non-first digits.
If we assume that 35% of the non-zero digits in searches are first digits, and that the other 65% are uniformly distributed between 1 and 9, we can back out the relative frequencies of the digits specifically in the first digit context.
The blue circles are the Benford's Law expectations, and the red squares are the inferred empirical distribution of first digits. The choice of 35% was established through manual trial and error, and the fit was done by visual inspection. So, you know, don't go and make any medical decisions based on this.
This is actually a reasonably good fit for this sort of thing, and constitutes fairly compelling evidence in support of the "sumbudy dun messed up" theory to my mind. Either that, or you have to invoke roughly 6 billion instances of people googling '666'.
Frank Benford (1938). The law of anomalous numbers Proceedings of the American Philosophical Society, 78 (4), 551-572
... Read more »
Frank Benford. (1938) The law of anomalous numbers. Proceedings of the American Philosophical Society, 78(4), 551-572. info:other/
- December 29, 2010
- 04:44 AM
- 1,761 views
What’s the actual size of your personal social network? Some numbers
by ---a in Bodyspacesociety.eu
In 1992 Robin Dunbar proposed a rough estimate of 150. But the "Dunbar's number" pretty much doubled in 1998, when Peter Killworth suggested a mean personal network size of 290. And in 2010 that number doubled again, as Matthew Salganik came up with 610 personal. So who says 1,200?... Read more »
Bickart, K., Wright, C., Dautoff, R., Dickerson, B., & Barrett, L. (2010) Amygdala volume and social network size in humans. Nature Neuroscience. DOI: 10.1038/nn.2724
Dunbar, R. (1992) Neocortex size as a constraint on group size in primates. Journal of Human Evolution, 22(6), 469-493. DOI: 10.1016/0047-2484(92)90081-J
Killworth, P., Johnsen, E., Bernard, H. R., Shelley, G., & McCarty, C. (1990) Estimating the size of personal networks. Social Networks, 12(4), 289-312. DOI: 10.1016/0378-8733(90)90012-X
McCormick, T., Salganik, M., & Zheng, T. (2010) How Many People Do You Know?: Efficiently Estimating Personal Network Size. Journal of the American Statistical Association, 105(489), 59-70. DOI: 10.1198/jasa.2009.ap08518
- December 26, 2010
- 10:37 AM
- 815 views
Oscar: training data, models, etc
by egonw in Chem-bla-ics
Oscar uses a Maximum Entropy Markov Model (MEMM) based on n-grams. Peter Corbett has written this up (doi:10.1186/1471-2105-9-S11-S4). So, it basically is statistics once more. If you really want a proper bioinformatics education, so do your PhD at a (proteo)chemometrics department.
N-grams are word parts of n characters. For example, the trigrams of acetic acid include ace, cid, tic, eti, and aci. N-grams of length four include acid, etic, and acet. The MEMM assigns weights to these n-grams, and based on that decided if something is in deed a named entity (in Oscar terminology). For example, consider the acet n-gram: acetone should be matched, but facet not.
Put this in perspective in the ongoing refactoring of the Oscar software. We are changing normalization (e.g. converting all unicode hyphen alternatives into one specific hyphen), updating the tokenizer (e.g. changing the list of non-sentence-endings like Prof.). It is clear this changes the n-grams typical for chemical-like things. Worse, the weights are tuned towards to know n-grams, and statistical models are generally a bit overtrained for the data, or, at least, specific for it.
Now, if the distribution of n-grams changes, the weights in the model need to be updated too, to not degrade the model performance. So, Oscar is useless if we cannot retrain its MEMM component after a refactoring. If that would be impossible, we would have effectively created an intellectual monopoly.
Thus, what the Oscar project needs, is one or more free sets of annotated literature, which can be used to train new MEMM models. The SciBorg corpus was used to train the current Oscar3 and Oscar4 models. This data (copyright RSC) will very likely be available under a Creative Commons license (RSC++), but may have the NC clause, which would not be good for developing a business model around the opensource Oscar (such as providing a high-performance web service via a subscription service). I have recently written up the problems the NC clause introduces, and some examples of commercial Open Source cheminformatics projects.
We need not focus only on this SciBorg data, however. In fact, we will need multiple models anyway. For example, the SciBorg papers (42 if not mistaken) are around a particular kind of literature. So, it introduces the risk of using it to analyse papers out of the application domain. Furthermore, I am very interested (and others indicated so too) to use Oscar for other languages. Surely, English is the major language, but there are many use cases for Oscar when useful for other languages.
Therefore, for what we need in the Oscar project, is a registry of training (/test) data, annotated itself with metadata around how that data was created (what quality assurance, what kind of named entity types, how many domain experts were involved, etc), test results for those data sets, etc. My time on the Oscar project is almost over, and I have no clue when I will be able to invest the same amount of time into the project as I did in the past three months. But the creation of this registry is clear step that must be taken in the Oscar4 development.
Corbett, P., & Copestake, A. (2008). Cascaded classifiers for confidence-based chemical named entity recognition BMC Bioinformatics, 9 (Suppl 11) DOI: 10.1186/1471-2105-9-S11-S4... Read more »
Corbett, P., & Copestake, A. (2008) Cascaded classifiers for confidence-based chemical named entity recognition. BMC Bioinformatics, 9(Suppl 11). DOI: 10.1186/1471-2105-9-S11-S4
- December 14, 2010
- 07:55 PM
- 598 views
Towards Preventing Alzheimer's Disease: A Mathematical Model
by Michael Long in Phased
A mathematical model suggests that inhibiting the immune response in the brain may be the most effective means of controlling Alzheimer's disease.... Read more »
Puri, I. K., & Li, L. (2010) Mathematical Modeling for the Pathogenesis of Alzheimer's Disease. PLoS ONE, 5(12). DOI: 10.1371/journal.pone.0015176
- December 5, 2010
- 02:00 PM
- 918 views
Acupuncture, some dodgy maths and a cracking review paper
by Lorimer Moseley in BodyInMind
I have a challenge for you. Imagine you’re in ancient China and you’ve had this idea that health and disease hang on the flow of energy through invisible energy pathways called meridians that can be manipulated by applying needles in certain specific points. How do you go about systematically validating this theory? How do you [...]... Read more »
Donald M. Marcus. (2010) Is Acupuncture for Pain a Placebo Treatment? An examination of the evidence. The Rheumatologist. info:/
- December 4, 2010
- 01:34 PM
- 773 views
Psi Skeptics: If Psychologists Find Signs of ESP, Maybe Psychologists Have a Problem
by David Berreby in Mind Matters
Daryl J. Bem's experiments on psi caught the world's attention, as I posted last month, because he used standard psychology-lab methods to gather and analyze his data. Imagine what astronomers might feel if NASA announced that the Hubble space telescope had found evidence for astrology: How do you ...Read More... Read more »
Daryl J. Bem. (2011) Feeling the future: Experimental evidence for anomalous retroactive influences on cognition and affect. Journal of Personality and Social Psychology. info:/10.1037/a0021524
- December 3, 2010
- 07:27 PM
- 1,216 views
Networks in the autistic brain: insights from graph theory
by Jon Brock in Cracking the Enigma
A couple of weeks ago I travelled from Sydney to a conference taking place in San Diego, California. There isn't a direct flight to San Diego so instead I had to fly via Los Angeles. Colleagues coming from Melbourne had an even more convoluted journey - they had to get a connecting flight to Sydney first before they could fly to LA. The point here is that airline routes are determined by economic pressures. There simply aren't enough people wanting to travel from Sydney or Melbourne to San Diego on a regular basis for a direct route to be commercially viable. Instead, travellers rely on a small number of long-distance routes with local connecting flights at either end. In this way, it's still possible to get between any two airports with only a couple of flight transfers along the way. Altogether now, "It's a small world after all..."But what has all this to do with autism?It turns out that the brain operates according to similar network economics. Neurons communicate via action potentials - electric pulses sent along their axons. Ordinarily, these are quite slow, so in order to send messages quickly over long distances in the brain, axons have to be insulated by a fatty sheath known as myelin. However, it's not feasible to have every axon heavily myelinated - for one thing, the myelinated axons would take up too much space in the brain. So, as with the airlines, there are lots of local connections within brain regions and a limited number of long-range super-fast myelinated connections. And as with the airlines, this actually allows messages to be sent across the brain relatively efficiently, with every neuron being only a few synapses (flight transfers) from every other neuron.This is more than just an extended metaphor. In fact, there is an entire branch of mathematics, known as 'graph theory', that can be applied to pretty much every imaginable kind of network - from airports around the world to co-stars in Hollywood movies, or friendship 'circles' on Facebook. Researchers have recently begun applying those same graph theory principles to human neuroimaging data. And now, in a new paper, currently in press at Neuropsychologia, Pablo Barttfeld and colleagues from Buenos Aires have applied graph theory to autism. In graph theory, networks range from completely orderly (left) to completely random (right). "Small world" networks lie between these two extremes. In Barttfeld et al.'s study, 10 adults with autism and 10 non-autistic adults were simply asked to look at a cross on a computer screen, while the electrical currents generated by their brains were measured via 128 EEG electrodes placed strategically in different locations on their scalps. The researchers then estimated the strength of the connection between each pair of electrodes. If two electrodes recorded similar changes in the EEG response across time, they were deemed to be strongly connected. Connections below a certain threshold were eliminated, leaving a network with only the stronger connections. The researchers then used graph theory to characterise the network of inter-electrode connections.The main findings were as follows:The brain networks for autistic adults were less interconnected than those for the control group. On average, each electrode had fewer neighbours to which it was connected. In our air travel analogy, this corresponds to there being fewer routes between different airports.The path length was also longer. Path length refers to the minimum number of steps it takes to get from A to B. My journey from Sydney to San Diego via LA had a path length of two because there were two separate flights involved. My colleagues from Melbourne had a path length of three.Finally, the autistic network was more modular - removing the weaker connections very quickly led to a sub-divided network where it was impossible to get from one region to another. The analogy would be a network where it was possible to fly around Australia or America but impossible to get between the two.To be perfectly honest, the study doesn't really tell us a whole lot we don't already know about autism. There's plenty of evidence from other studies that autistic brains are less well connected (or the connection patterns are different to typical brains). What it does achieve, however, is to introduce a new way of thinking about the autistic brain. And I think this is pretty exciting.In particular, thinking in terms of networks and graph theory might finally allow us to reconcile connectivity theories of autism with other theories that focus more on localised brain dysfunction. Over the years, it has been variously argued that autism is caused by dysfunction of the hippocampus, the cerebellum, the temporo-parietal junction, the medial prefrontal cortex, and the amygdala, to name just a few brain regions. What these regions have in common is that they are all highly connected with other brain regions - they are the Chicago O'Hares and London Heathrows of the brain. Dysfunction of any of these regions could have huge impacts on the whole of the brain (imagine the knock-on effects of closing Heathrow airport). On the other hand, changes in global connectivity would have greatest impact on the functioning of these hubs. ... Read more »
Pablo Barttfeld, Bruno Wicker, Sebastián Cukier, Silvana Navarta, Sergio Lew, & Mariano Sigman. (2010) A big-world network in ASD: Dynamical connectivity analysis reflects a deficit in long-range connections and an excess of short-range connections. Neuropsychologia. arXiv: 1007.5471v1
- November 22, 2010
- 01:35 PM
- 1,183 views
The Obesity Paradox Revisited
by Travis Saunders, MSc in Obesity Panacea
As Peter and I discuss frequently here at Obesity Panacea, the relationship between body weight and health is not always as neat and tidy as you might expect (For all the details, check out Peter’s 5-part series on metabolically healthy obesity). A recent paper published in the International Journal of Obesity by Drs DK Childers and David Allison examines a number of these issues, and suggests ways that they may be at least partially resolved.
In the intro to this new paper, the authors point out 3 confusing issues surrounding the relationship between body weight and health:
1. The relationship between body mass and mortality in epidemiological studies is “U-shaped” – high health risk for individuals with a body mass that is very high or very low, and low risk for individuals with intermediate body mass (e.g. 18-28 kg/m2 or so, ... Read more »
Childers, D., & Allison, D. (2010) The ‘obesity paradox’: a parsimonious explanation for relations among obesity, mortality rate and aging?. International Journal of Obesity, 34(8), 1231-1238. DOI: 10.1038/ijo.2010.71
- November 18, 2010
- 05:39 AM
- 988 views
Fractals in clouds – why clouds appear ‘cloudlike’
by Croor Singh in Learning to be Terse
Clouds have distinctive shapes. Or they seem to have distinctive shapes. It turns out that is likely due to the fractal nature of clouds. The fractal nature of clouds was first shown in this paper in Science, from 1982.... Read more »
LOVEJOY, S. (1982) Area-Perimeter Relation for Rain and Cloud Areas. Science, 216(4542), 185-187. DOI: 10.1126/science.216.4542.185
- November 18, 2010
- 05:35 AM
- 763 views
Fractals in clouds
by Croor Singh in Learning to be Terse
Clouds have distinctive shapes. Or they seem to have distinctive shapes. It turns out that is likely due to the fractal nature of clouds. The fractal nature of clouds was first shown in this paper in Science, from 1982.... Read more »
LOVEJOY, S. (1982) Area-Perimeter Relation for Rain and Cloud Areas. Science, 216(4542), 185-187. DOI: 10.1126/science.216.4542.185
- November 16, 2010
- 12:00 PM
- 1,646 views
The more colourful the lie, the more people believe it, man!
by Caspar Addyman in Your Brain on Drugs
The Splintered Mind has a great guest piece by G. Randolph Mayes reflecting on John Allen Paulos’s latest piece in the New York Times, entitled “Stories vs. Statistics” , which reflects on counter intuitve work of Nobel prize winning work of Tversky and Kahneman on conjunction fallacies.... Read more »
Tversky, A., & Kahneman, D. (1983) Extensional versus intuitive reasoning: The conjunction fallacy in probability judgment. Psychological Review, 90(4), 293-315. DOI: 10.1037/0033-295X.90.4.293
- November 14, 2010
- 06:31 PM
- 722 views
The limits of the immune system
by David Basanta in Cancerevo: Cancer evolution
After spending a good part of Wednesday talking with scientists at the department of immunology at Moffitt I am well aware of the importance of the immune system as an anticancer mechanism. The immune system is not perfect though...... Read more »
Martin, L., & Coon, C. (2010) Infection Protection and Natural Selection. Science, 330(6004), 602-603. DOI: 10.1126/science.1198303
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