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29 Mar 19:05

What is computational neuroscience? (XXVIII)The Bayesian brain

by romain

Our sensors give us an incomplete, noisy, and indirect information about the world. For example, estimating the location of a sound source is difficult because in natural contexts, the sound of interest is corrupted by other sound sources, reflections, etc. Thus it is not possible to know the position of the source with certainty. The ‘Bayesian coding hypothesis’ (Knill & Pouget, 2014) postulates that the brain represents not the most likely position, but the entire probability distribution of the position. It then uses those distributions to do Bayesian inference, for example, when combining different sources of information (say, auditory and visual). This would allow the brain to optimally infer the most likely position. There is indeed some evidence for optimal inference in psychophysical experiments – although there is also some contradicting evidence (Rahnev & Denison, 2018).

The idea has some appeal. The problem is that, by framing perception as a statistical inference problem, it focuses on the most trivial type of uncertainty, statistical uncertainty. It is illustrated by the following quote: “The fundamental concept behind the Bayesian approach to perceptual computations is that the information provided by a set of sensory data about the world is represented by a conditional probability density function over the set of unknown variables”. Implicit in this representation is a particular model, for which variables are defined. Typically, one model describes a particular experimental situation. For example, the model would describe the distribution of auditory cues associated with the position of the sound source. Another situation would be described by a different model, for example one with two sound sources would require a model with two variables. Or if the listening environment is a room and the size of that room might vary, then we would need a model with the dimensions of the room as variables. In any of these cases where we have identified and fixed parametric sources of variation, then the Bayesian approach works fine, because we are indeed facing a problem of statistical inference. But that framework doesn’t fit any real life situation. In real life, perceptual scenes have variable structure, which corresponds to the model in statistical inference (there is one source, or two sources, we are in a room, the second source comes from the window, etc). The perceptual problem is therefore not just to infer the parameters of the model (dimensions of the room etc), but also the model itself, its structure. Thus, it is not possible in general to represent an auditory scene by a probability distribution on a set of parameters, because the very notion of a parameter already assumes that the structure of the scene is known and fixed.

Inferring parameters for a known statistical model is relatively easy. What is really difficult, and is still challenging for machine learning algorithms today, is to identify the structure of a perceptual scene, what constitutes an object (object formation), how objects are related to each other (scene analysis). These fundamental perceptual processes do not exist in the Bayesian brain. This touches on two very different types of uncertainty: statistical uncertainty, variations that can be interpreted and expected in the framework of a model; and epistemic uncertainty,  the model is unknown (the difference has been famously explained by Donald Rumsfeld).

Thus, the “Bayesian brain” idea addresses an interesting problem (statistical inference), but it trivializes the problem of perception, by missing the fact that the real challenge is epistemic uncertainty (building a perceptual model), not statistical uncertainty (tuning the parameters): the world is not noisy, it is complex.

28 Mar 17:03

Duality, Fundamentality, and Emergence. (arXiv:1803.09443v1 [physics.hist-ph])

by Elena Castellani, Sebastian De Haro

We argue that dualities offer new possibilities for relating fundamentality, levels, and emergence. Namely, dualities often relate two theories whose hierarchies of levels are inverted relative to each other, and so allow for new fundamentality relations, as well as for epistemic emergence. We find that the direction of emergence typically found in these cases is opposite to the direction of emergence followed in the standard accounts. Namely, the standard emergence direction is that of decreasing fundamentality: there is emergence of less fundamental, high-level entities, out of more fundamental, low-level entities. But in cases of duality, a more fundamental entity can emerge out of a less fundamental one. This possibility can be traced back to the existence of different classical limits in quantum field theories and string theories.

27 Mar 20:40

Oopsie

by noreply@blogger.com (Atrios)
Arizona rolled out the regulation-free welcome mat after California basically kicked Uber out because Uber didn't think minimal "regulations" or "safety measures" applied to them.

After a fairly seamless, high-profile launch in Pittsburgh, the rollout in San Francisco was bumpy right from the beginning. First, the DMV issued a warning to Uber that it had not obtained the proper testing permits for its pilot program. Then, a few hours after the trial began, The Verge reported that one of Uber’s cars ran a red light, nearly hitting a (human-driven) Lyft car.


Uber reviewed the case and determined it was actually the fault of the human driver sitting in the car—remember, Uber still has human drivers who can “take over” from the self-driving system as needed.

Then there was the bike lane problem. Uber’s vehicles had a nasty habit of driving into San Francisco’s bike lanes without warning. This was not the fault of humans but a software error, claimed Uber, noting that the problem had not come up in Pittsburgh, which also has a robust cycling network. Uber pledged to fix it.



Wasn't that long ago:


Arizona has since built upon the governor’s action to become a favored partner for the tech industry, turning itself into a live laboratory for self-driving vehicles. Over the past two years, Arizona deliberately cultivated a rules-free environment for driverless cars, unlike dozens of other states that have enacted autonomous vehicle regulations over safety, taxes and insurance.

...

Mr. Ducey, a native of Ohio who came to Arizona for college and then stayed, was elected governor in 2014 on a pro-business and innovation platform. He quickly lifted restrictions on medical testing for companies like Theranos, a Silicon Valley company that later faced scrutiny for its business practices. He also touted Apple’s decision to build a $2 billion data center in the state.

“We can beat California in every metric; lower taxes, less regulations, cost of living, quality of life,” he said several months after he became governor.


Oh well.

PHOENIX, Ariz., March 26 (Reuters) - The governor of Arizona on Monday suspended Uber’s ability to test self-driving cars on public roads in the state following a fatal crash last week that killed a 49-year-old woman pedestrian.

In a letter sent to Uber Chief Executive Dara Khosrowshahi and shared with the media, Governor Doug Ducey said he found a video released by police of the crash “disturbing and alarming, and it raises many questions about the ability of Uber to continue testing in Arizona.”


Good calls, bro. All of them.

...I wrote this last night, but the local fishwrap is on it, also, too.
27 Mar 20:18

Derivation of the Boltzmann Equation for Financial Brownian Motion: Direct Observation of the Collective Motion of High-Frequency Traders

by Kiyoshi Kanazawa, Takumi Sueshige, Hideki Takayasu, and Misako Takayasu

Author(s): Kiyoshi Kanazawa, Takumi Sueshige, Hideki Takayasu, and Misako Takayasu

Using data on the activity of individual financial traders, researchers have devised a microscopic financial model that can explain macroscopic market trends.


[Phys. Rev. Lett. 120, 138301] Published Tue Mar 27, 2018

25 Mar 12:38

Iranian “CyberAttack” Threatens Elsevier Not USA

by Alex Tabarrok

Here’s what Geoffrey Berman, U.S. attorney for the Southern District of New York, said when announcing charges against a group of Iranian “cyber attackers”:

“We have worked tirelessly to identify you,” Berman said. “You cannot hide behind a keyboard halfway around the world and expect not to be held to account. Together, along with our law enforcement partners, we will work relentlessly and creatively to apply the legal tools at our disposal to unmask and charge you. We will do all we can to bring you to justice. While the defendants remain at large, they are now fugitives from the American judicial system.

So what are these horrendous people being charged with? Stealing unreleased scripts of Game of Thrones and a bunch of academic articles. I am not making this up.

…members of the conspiracy used stolen account credentials to obtain unauthorized access to victim professor accounts, through which they then exfiltrated intellectual property, research, and other academic data and documents from the systems of compromised universities, including, among other things, academic journals, theses, dissertations, and electronic books.

(That is from the press release and here is the earlier press release on GOT, with which this has been combined in many news accounts. The full indictment is here).

In other words, the Iranians were running something like Sci-Hub, the website that some of you have probably used to bypass publisher paywalls to read articles linked to on MR that you haven’t paid for. I don’t defend such actions but neither do I want the federal attorney  working tirelessly to identify you. As crimes go this is a yawner.

Indeed, since Sci-Hub is already used in Iran, one wonders how useful the additional Iranian hacking was. A few companies are also listed as targets, although they turn out to be publishers, a stock image company, two online car companies etc. A few government agencies are thrown in for good measure although that appears to be window dressing.

The federal attorney claims the hacking (hacking not attacking) cost billions which they estimate because:

Through the course of the conspiracy, U.S.-based universities spent over approximately $3.4 billion to procure and access such data and intellectual property.

As Tim Worstall puts it:

That’s just DoJ making up some number to make them look good. The direct losses in this scheme almost certainly amount to zero, bupkiss, nada. Universities certainly haven’t lost anything – the data was copied, not taken. The publishers might have lost a bit, but even then it would only be the revenue they would have got from papers that would have been bought if they hadn’t been copied. A useful estimate of the size of that loss still being zero, bupkiss, nada.

Frankly, this is a joke of an indictment. But headlines like “US Charges 9 Iranians With Massive Cyberattack” are certainly fortuitously timed for new national security designate John Bolton and others who want to take a hardline on Iran.

The post Iranian “CyberAttack” Threatens Elsevier Not USA appeared first on Marginal REVOLUTION.

23 Mar 19:34

5 Things About John Bolton That Are Worse Than His Mustache

by Jacob Sullum

Donald Trump reportedly hesitated to appoint John Bolton as his national security adviser because he was put off by the former U.N. ambassador's walrus mustache. While this is one of the few areas where I see eye to eye with the president, there may be more substantive reasons to think twice about taking advice from Bolton, who never met a war he did not like and represents precisely the sort of reckless interventionism that Trump criticized during his campaign. Here are five things about John Bolton that are worse than his facial hair:

1. Bolton supported the 2002 invasion of Iraq and still thinks it was a dandy idea. As undersecretary of state for arms control and international security affairs, Bolton was largely responsible for the deception used to justify the invasion of Iraq, a stratagem that Trump has condemned in no uncertain terms. "They lied," Trump said during a presidential debate in February 2016. "They said there were weapons of mass destruction. There were none, and they knew there were none." Bolton is not only a liar, according to Trump, but a liar who does not learn from his big, fat mistakes. "I still think the decision to overthrow Saddam was correct," he told The Washington Examiner in 2015.

2. Bolton supported the U.S. intervention in the Libyan civil war. In 2011, while seeking the Republican presidential nomination, Bolton called for the assassination of Libyan strongman Moammar Gadhafi, saying he was "a legitimate military target." While Trump initially favored ousting Gadhafi, he later described it as a mistake that, like the Iraq war, created chaotic conditions conducive to terrorism. "Each of these actions [has] helped to throw the region into chaos and [given] ISIS the space it needs to grow and prosper," Trump said in an April 2016 speech. "It all began with the dangerous idea that we could make Western democracies out of countries that had no experience or interest in becoming a Western democracy."

3. Bolton thinks the U.S. should have intervened in the Syrian civil war sooner and more aggressively. "Whatever slim chance there was of empowering a 'moderate' anti-Assad opposition when the civil war began four years ago disappeared while Mr. Obama dithered," he wrote in 2015. As a presidential candidate, Trump counted U.S. meddling in Syria as one of the actions that "helped to throw the region into chaos," although since taking office he has taken a somewhat different view.

4. Bolton agitated for war with Iran. "Iran will not negotiate away its nuclear program," he wrote in 2015. "Nor will sanctions block its building a broad and deep weapons infrastructure. The inconvenient truth is that only military action...can accomplish what is required. Time is terribly short, but a strike can still succeed."

5. Bolton favors attacking North Korea. While Trump recently agreed to a meeting with North Korean leader Kim Jong-un in the hope of negotiating denuclearization, Bolton (as always) favors a more aggressive approach. In a Wall Street Journal op-ed piece last year, he laid out three "military options," including a pre-emptive strike on "Pyongyang's known nuclear facilities, ballistic-missile factories and launch sites, and submarine bases."

Trump has never been a consistent skeptic of unnecessary wars. Since taking office, he has warmed to war in Syria and Afghanistan. And even when he was highlighting the unintended effects of past interventions, he bragged that he was "a very militaristic person" and promised more money for armed forces he said were already doing too much. The omnibus spending bill that Congress approved this week delivers on that promise with $700 billion in military spending for the current fiscal year, including what the Senate Appropriations Subcommittee on Defense touts as "the biggest year-to-year increase in defense funding in 15 years."

Even before that increase, the U.S. had a larger military budget than the next eight biggest spenders combined. Throwing even more money at the Pentagon hardly seems consistent with Trump's complaint that "we're all over the place, fighting in areas that we just shouldn't be fighting in." An outsized military budget invites outsized thinking about how to use it, and an adviser like Bolton will have plenty of ideas.

22 Mar 04:41

Mark Jason Dominus: The 1943 Bengal famine

by mjd@plover.com (Mark Dominus)

A couple of years ago I was reading Wikipedia's article about the the 1943 Bengal famine, and I was startled by the following claim:

"If food is so scarce, why hasn’t Gandhi died yet?"

Winston Churchill's response to an urgent request to release food stocks for India.

It was cited, but also marked with the “not in citation” tag, which is supposed to mean that someone checked the reference and found that it did not actually support the claim.

It sounded like it might be the sort of scurrilous lie that is widely repeated but not actually supportable, so I went to follow it up. It turned out that although the quotation was not quite exact, it was not misleadingly altered, and not a scurrilous lie at all. The attributed source (Tharoor, Shashi "The Ugly Briton". Time, (29 November 2010).) claimed:

Churchill's only response to a telegram from the government in Delhi about people perishing in the famine was to ask why Gandhi hadn't died yet.

I removed the “not in citation” tag, which I felt was very misleading.

Still, I felt that anything this shocking should be as well-supported as possible. It cited Tharoor, but Tharoor could have been mistaken. So I put in some effort and dug up the original source. It is from the journal entry of Archibald Wavell, then Viceroy of India, of 5 July 1944:

Winston sent me a peevish telegram to ask why Gandhi hadn't died yet! He has never answered my telegram about food.

This appears in the published version of Lord Wavell's journals. (Wavell, Archibald Percival. Wavell: The Viceroy's journal, p. 78. Moon, Penderel, ed. Oxford University Press, 1973.) This is the most reliable testimony one could hope for. The 1973 edition is available from the Internet Archive.

A few months later, the entire article was massively overhauled by a group of anglophiles and Churchill-rehabilitators. Having failed to remove the quotation for being uncited, and then having failed to mendaciously discredit the cited source, they removed the quotation in a typical episode of Wikipedia chicanery. In a 5,000-word article, one sentence quoting the views of the then-current British Prime Minister was deemed “undue weight”, and a failure to “fairly represent all significant viewpoints that have been published by reliable sources”.

Further reading: In Winston Churchill, Hollywood rewards a mass murderer. (Tharoor again, in last week's Washington Post.)

21 Mar 15:02

Stabilizing Embedology: Geometry-Preserving Delay-Coordinate Maps

by Igor
Nosimpler

Haven't read this yet, but I think it's huge. Seeing the statement of Takens' embedding theorem is one of those WTF-how-did-they-do-that moments to begin with. Any progress on making it work as a practical tool is good news for us.

Chris just sent me the following:
Hi Igor-
I hope you are well. I wanted to alert you that our paper on delay-coordinate maps and Takens' embeddings has finally appeared.
Eftekhari, Armin, Han Lun Yap, Michael B. Wakin, and Christopher J. Rozell. "Stabilizing embedology: Geometry-preserving delay-coordinate maps." Physical Review E 97, no. 2 (2018): 022222.
http://dx.doi.org/10.1103/PhysRevE.97.022222
preprint:
http://arxiv.org/pdf/1609.06347
You had mentioned a much earlier preliminary result on your blog but this is the full and final result. It uses the tools familiar to this community (random measurements, stable embeddings) to address a fundamental observability result about nonlinear (perhaps even chaotic) dynamical systems from the physics community. The key question is "how much information is there in a time series measurement about the dynamical system that created it?". I think this result is a unique convergence of different fields, and our previous results analyzing recurrent neural networks were a distinct outgrowth of working on this problem.
regards,
chris
Thanks Chris for the update !


Delay-coordinate mapping is an effective and widely used technique for reconstructing and analyzing the dynamics of a nonlinear system based on time-series outputs. The efficacy of delay-coordinate mapping has long been supported by Takens' embedding theorem, which guarantees that delay-coordinate maps use the time-series output to provide a reconstruction of the hidden state space that is a one-to-one embedding of the system's attractor. While this topological guarantee ensures that distinct points in the reconstruction correspond to distinct points in the original state space, it does not characterize the quality of this embedding or illuminate how the specific parameters affect the reconstruction. In this paper, we extend Takens' result by establishing conditions under which delay-coordinate mapping is guaranteed to provide a stable embedding of a system's attractor. Beyond only preserving the attractor topology, a stable embedding preserves the attractor geometry by ensuring that distances between points in the state space are approximately preserved. In particular, we find that delay-coordinate mapping stably embeds an attractor of a dynamical system if the stable rank of the system is large enough to be proportional to the dimension of the attractor. The stable rank reflects the relation between the sampling interval and the number of delays in delay-coordinate mapping. Our theoretical findings give guidance to choosing system parameters, echoing the trade-off between irrelevancy and redundancy that has been heuristically investigated in the literature. Our initial result is stated for attractors that are smooth submanifolds of Euclidean space, with extensions provided for the case of strange attractors.


Join the CompressiveSensing subreddit or the Google+ Community or the Facebook page and post there !
20 Mar 19:32

Abel Prize to Langlands

by woit

The 2018 Abel Prize has been awarded to Robert Langlands, an excellent choice. The so-called “Langlands program” has been a huge influence on modern mathematics, providing deep insight into the structure of number theory while linking together disparate fields of mathematics, as well as quantum field theories and physics.

The Abel Prize site provides a wealth of information about Langlands and his work. Davide Castelvecchi at Nature appropriately describes the Langlands program as a “grand unified theory of mathematics” (Edward Frenkel’s Love and Math popularized this description).

Many blog posts here have discussed the Langlands program and ideas that have developed out of it. For a good example of how wide the impact of these ideas has been, this week the Perimeter Institute will be hosting a conference discussing the latest work on the geometric version of the Langlands program, as well as connections to gauge theory and conformal field theory.

For the original work of Langlands himself, besides the material at the Abel site, the AMS Bulletin has recently published a long article by Julia Mueller. For the original sources and a wealth of other material written by Langlands himself, see the IAS site that collects his writings.

20 Mar 14:49

Heckuva Job

by noreply@blogger.com (Atrios)
There were the evil bastards, and then there were the Model UN debate team crowd, young boy blunders putting on their first big boy suits writing for big boy magazines and being on big boy teevee shows, being patted on the head for punching hippies. War was very serious, they intoned, and only the Very Serious People could be trusted with it. It must have been so exciting!


No one knows for certain how many Iraqis have died as a result of the invasion 15 years ago. Some credible estimates put the number at more than one million. You can read that sentence again. The invasion of Iraq is often spoken of in the United States as a “blunder,” or even a “colossal mistake.” It was a crime. Those who perpetrated it are still at large. Some of them have even been rehabilitated thanks to the horrors of Trumpism and a mostly amnesiac citizenry. (A year ago, I watched Mr. Bush on “The Ellen DeGeneres Show,” dancing and talking about his paintings.) The pundits and “experts” who sold us the war still go on doing what they do. I never thought that Iraq could ever be worse than it was during Saddam’s reign, but that is what America’s war achieved and bequeathed to Iraqis.
20 Mar 14:47

Magnitude Homology Reading Seminar, I

by willerton
Nosimpler

I like this magnitude thing because it formalizes coarse-graining in a nice way. I still have no idea what homology really is, though.

MathML-enabled post (click for more details).

In Sheffield we have started a reading seminar on the recent paper of Tom Leinster and Mike Shulman Magnitude homology of enriched categories and metric spaces. The plan was to write the talks up as blog posts. Various things, including the massive strike that has been going on in universities in the UK, have meant that I’m somewhat behind with putting the first talk up. The strike also means that we haven’t had many seminars yet!

I gave the first talk which is the one here. It is an introductory talk which just describes the idea of categorification and the paper I wrote with Richard Hepworth on categorifying the magnitude of finite graphs, this is the idea which was generalized by Tom and Mike.

MathML-enabled post (click for more details).

Categorification

Categorification means many things. In this context it is supposed to be the idea of lifting an invariant from taking values in a set to values in a category. Let’s look at two examples.

[This is possibly a caricature of what actually happened. It would be nice to have some references!] In the eighteenth century, mathematicians such as Riemann knew about the Euler characteristic of surfaces (and possibly manifolds). This is a fundamental invariant which seems to crop up in all sorts of places. Towards the end of the century Poincar'e introduced homology groups H ⋆(M)\text{H}_\star(M) of a manifold MM and was aware

χ(M)=rank(H ⋆(M))=∑ i(−1) irank(H i(M)). \chi(M)=rank(\text{H}_\star(M))= \sum_i (-1)^i rank (\text{H}_i(M)).

I get the impression the functorial nature of homology was not appreciated until later, but this adds another layer of structure.

Around 1985 Jones introduced his eponymous polynomial J(L)∈ℤ[q ±1]\text{J}(L)\in \mathbb{Z}[q^{\pm 1}] for a knot or link LL in 33-space. This gives a polynomial invariant of links. In around 1999, Khovanov introduced Khovanov homology Kh ⋆,⋆(L)Kh_{\star, \star}(L) for a link LL, this is bigraded group. The Jones polynomial is obtained from it by taking the dimension (or Euler characteristic!) in an appropriate graded sense:

J(L)=∑ i,j(−1) iq jrank(Kh i,j(L)). \text{J}(L)= \sum_{i,j} (-1)^i q^j rank( Kh_{i,j}(L)).

In both these cases we lift an invariant which takes values in a set (either ℤ\mathbb{Z} or ℤ[q ±1] \mathbb{Z}[q^{\pm 1}]) to an invariant which takes values in a category (either graded groups or bigraded groups). This lifted invariant has a richer structure and functorial properties, but is probably harder to calculate! This is what we mean by categorifying an invariant.

Magnitude of enriched categories

There was a classical notion of Euler characteristic for finite groups and also one for finite posets. We know that finite groups and finite posets are both examples of finite categories (at one extreme with only one object and at the other extreme with at most one morphism between each pair of objects). Tom found a common generalization of these Euler characteristics which is the idea of an Euler characteristic for finite categories (we will see the definition next week). He further generalized that to the notion of an Euler characteristic for enriched categories (with a additional bit of structure, wait for next week). Finite metric spaces are examples of enriched categories and so have a notion of Euler characteristic. We decided the name was too confusing so after consulting a thesaurus we decided on “magnitude” (having toyed with the name “cardinality”). Tom later noticed something nice about the magnitude of the metric spaces that you get from finite graphs (partly because these have integer-valued metrics).

The journey from the Euler characteristics of finite posets and finite groups to the magnitude of finite graphs via a sequence of generalizations and specializations can be viewed as a trip up and then down the following picture.

hierarchy of some category enrichments

Magnitude of metric spaces (more next week)

For X={x 1,…x n}X=\{x_1,\dots x_n\} a finite metric space with the metric we can define a matrix ZZ by Z i,j=e −d(x i,x j)Z_{i,j}=e^{-\text{d}(x_i,x_j)}. The magnitude |X||X| is defined to be the sum of the entries of the inverse matrix (if it exists): |X|:=∑ i,j(Z −1) i,j|X|:=\sum_{i,j}(Z^{-1})_{i,j}. It is actually more interesting if we look at what happens as we scale XX (or perhaps if we introduce an indeterminate into the metric). For t>0t> 0, we define t⋅Xt\cdot X to have the same underlying set, but with the metric scaled by a factor of tt. This gives us the magnitude function |t⋅X|\left|t\cdot X\right| which is a function of tt.

We can have a look at a simple example where we take XX to be a three-point metric space in which two points are much, much closer to each other than they are to the third point. Here is a picture of t⋅Xt\cdot X.

mh_sem_1_three_points.png

Here is the graph of the magnitude function of the metric space XX.

graph of the magnitude function

This shows in some sense how the magnitude can be viewed as an “effective number of points”. At small scales there is effectively one point, at middling scales there is effectively two points and at very large scales there are effectively three points.

Although the definition looks rather ad hoc, it turns out that it has various connections to thinks like measurements of biodiversity, Hausdorff dimension, volumes, potential theory and several other fun things.

Magnitude of graphs

Suppose that GG is a finite graph, then it gives rise to a finite metric space (which we will also write as GG) which has the vertices of GG as its points and the shortest path distance as its metric, where all edges have length one.

For example we have the five-cycle graph below with d(g 0,g 3)=2\text{d}(g_0, g_3)=2.

mh_sem_1_five_cycle_graph.png

Tom noticed that we can use the magnitude function of the associated metric space to get an integral power series from the graph. Firstly, we can write q=e −tq=e^{-t} then the entries of the matrix ZZ are just integer powers of qq as all of the distances in GG are integral. This means that the entries of Z −1Z^{-1} are just rational functions of qq (with integer coefficients) and hence so is their sum, the magnitude function. Moreover the denominator of this rational function is the determinant of ZZ which, as the diagonal entries of ZZ are all e 0e^{0}, i.e., 11, is of the form 1+powers of q1+\text{powers of }q. So we can take a power series expansion of |t⋅G||t\cdot G| to get an integer power series in q=e −tq=e^{-t}. We denote this power series by #G\# G.

For example, for the five-cycle graph C 5C_5 pictured above we have

#C 5=5−10q+10q 2−20q 4+40q 5−40q 6+⋯. \# C_5 = 5-10q+10q^2-20q^4+40q^5-40q^6+\cdots.

In general we can identify the first two coefficients as the number of vertices and −2-2 times the number of edges, respectively.

Categorifying the magnitude of graphs

As Richard Hepworth noticed, we can categorify this! In other words, we can find a homology theory which has the magnitude power series #G∈Z[q]\# G\in \Z[q] as its graded Euler characteristic.

For a finite graph GG define the magnitude chain groups as follows.

MC k,l(G)=⟨(x 0,…,x k)|x i−1≠x i,∑dd(x i−1,x i)=l⟩. MC_{k,l}(G)=\left\langle (x_0,\dots, x_k) \big | x_{i-1}\ne x_{i},\quad \sum \dd(x_{i-1}, x_i)=l\right\rangle.

For example a chain group generator for the five-cycle graph from above is (g 0,g 1,g 2,g 4,g 2)∈MC 4,6(C 5)(g_0, g_1, g_2, g_4, g_2)\in MC_{4,6}(C_5).

We define maps ∂ i:MC k,l(G)→MC k−1,l(G)\partial_i\colon MC_{k,l}(G)\to MC_{k-1,l}(G) for i=1,…,k−1i=1,\dots, k-1:

∂ i(x 0,…,x k)={(x 0,…,x i^,…,x k) ifx i−1<x i<x i+1, 0 otherwise. \partial_{i}(x_0,\ldots,x_k) = \begin{cases} (x_0,\ldots,\widehat{x_i},\ldots,x_k) & \text{if}\,\, x_{i-1}&lt;x_{i}&lt;x_{i+1}, \\ 0 & \text{otherwise}. \end{cases}

where x i−1<x i<x i+1x_{i-1}&lt;x_{i}&lt;x_{i+1} means that x ix_i lies on a shortest path between x i−1x_{i-1} and x i+1x_{i+1}, i.e., d(x i−1,x i)+d(x i,x i+1)=d(x i−1,x i+1)\text{d}(x_{i-1},x_i)+\text{d}(x_i,x_{i+1})=\text{d}(x_{i-1},x_{i+1}).

So for our example chain generator in C 5C_5 you can check that we have

∂ i(g 0,g 1,g 2,g 4,g 2)={(g 0,g 2,g 4,g 2) ifi=1, 0 otherwise. \partial_{i}(g_0, g_1, g_2, g_4, g_2) = \begin{cases} (g_0, g_2, g_4, g_2) & \text{if}\,\, i=1, \\ 0 & {otherwise}. \end{cases}

In the usual way, the differential ∂:MC k,l(G)→MC k−1,l(G)\partial\colon MC_{k,l}(G)\to MC_{k-1,l}(G) is defined as the alternating sum

∂=∂ 1−∂ 2+⋯+(−1) k−1∂ k−1. \partial=\partial_1-\partial_2+\cdots+(-1)^{k-1}\partial_{k-1}.

One can show that this is a differential, so that ∂∘∂=0\partial\circ\partial =0. Then taking homology gives what is defined to be magnitude homology groups of the graph:

MH k,l(G)=H k(MC *,l(G),∂). \MH_{k,l}(G)= \text{H}_k(\MC_{\ast,l}(G), \partial).

By direct computation you can calculate the ranks of the magnitude homology groups of the five-cycle graph. The following table shows the ranks rank(MH k,l(C 5))rank(MH_{k,l}(C_5)) for small kk and ll.

k 0 1 2 3 4 5 6 χ(MH *,l(C 5)) 0 5 5 1 10 −10 2 10 10 l 3 10 10 0 4 30 10 −20 5 50 10 40 6 20 70 10 −40 \begin{array}{rrrrrrrrrrc} &&&&&k\\ &&0&1&2&3&4&5&6&&\chi(MH_{\ast,l}(C_5))\\ &0 & 5&&&&&&&\qquad&5\\ & 1 & & 10 &&&&&&&-10 \\ &2 & && 10 &&&&&&10\\ l& 3 &&& 10 & 10 &&&&&0 \\ & 4 &&&& 30 & 10 &&&&-20\\ & 5 &&&&& 50 & 10 &&&40 \\ & 6 &&&&& 20 & 70 & 10 &&-40 \end{array}

The final column shows the Euler characteristics, which are just the alternating sums of entries in the rows. You can check that these are precisely the coefficients in the power series #C 5\# C_5 given above: this illustrates the fact that graph magnitude homology does indeed categorify graph magnitude in the sense of the following theorem.

Theorem #G=∑ k,l≥0(−1) kq lrank(MH k,l(G))∈ℤ[[q]]. \#G = \sum_{k,l\geq 0} (-1)^k q^l \,rank \bigl(MH_{k,l}(G)\bigr)\in \mathbb{Z}[[q]].

Thus we have MH *,*MH_{\ast,\ast} which a bigraded group valued invariant of graphs which is functorial with respect to certain maps of graphs and has properties like Kunneth Theorem and long exact sequences: richer but harder to calculate than the graph magnitude.

In the following weeks we will hopefully see how Mike and Tom have generalized this construction up to the top of the picture above, namely to certain enriched categories with extra structure.

20 Mar 14:29

Exploiting symmetry in network analysis. (arXiv:1803.06915v5 [math.CO] UPDATED)

by Ruben J Sanchez-Garcia
Nosimpler

Yet another paper on graph symmetries. Apparently quotients preserve lots of standard graph measures.

Virtually all network analyses involve structural measures between pairs of vertices, or of the vertices themselves, and the large amount of symmetry present in real-world complex networks is inherited by such measures. This has practical consequences which have not yet been explored in full generality, nor systematically exploited by network practitioners. Here we study the effect of network symmetry on arbitrary network measures, and show how this can be exploited in practice in a number of ways, from redundancy compression, to computational reduction. We also uncover the spectral signatures of symmetry for an arbitrary network measure such as the graph Laplacian. Computing network symmetries is very efficient in practice, and we test real-world examples up to several million nodes. Since network models are ubiquitous in the Applied Sciences, and typically contain a large degree of structural redundancy, our results are not only significant, but widely applicable.

17 Mar 16:30

But What If Programs Help Rich People Too?

by noreply@blogger.com (Atrios)
This justification for lack of universal coverage of [insert appropriate government function here] is just a mirror image of the "what if your tax moneys go to blah people????" that conservatives use to fight the same things. People making the argument are stupid or lying (always the question). Benefits can be universal and taxes can be progressive. The top 1% doesn't care about receiving these benefits, anyway, they just don't want to pay the taxes.
15 Mar 19:53

Non-Hermitian dynamics of slowly-varying Hamiltonians. (arXiv:1803.04411v2 [quant-ph] UPDATED)

by Hailong Wang, Li-Jun Lang, Y. D. Chong

We develop a theoretical description of non-Hermitian time evolution that accounts for the break- down of the adiabatic theorem. We obtain closed-form expressions for the time-dependent state amplitudes, involving the complex eigen-energies as well as inter-band Berry connections calculated using basis sets from appropriately-chosen Schur decompositions. Using a two-level system as an example, we show that our theory accurately captures the phenomenon of "sudden transitions", where the system state abruptly jumps from one eigenstate to another.

15 Mar 19:42

The sensorimotor loop as a dynamical system: How regular motion primitives may emerge from self-organized limit cycles. (arXiv:1511.04338v2 [q-bio.NC] UPDATED)

by Bulcsú Sándor, Tim Jahn, Laura Martin, Claudius Gros

We investigate the sensorimotor loop of simple robots simulated within the LPZRobots environment from the point of view of dynamical systems theory. For a robot with a cylindrical shaped body and an actuator controlled by a single proprioceptual neuron we find various types of periodic motions in terms of stable limit cycles. These are self-organized in the sense, that the dynamics of the actuator kicks in only, for a certain range of parameters, when the barrel is already rolling, stopping otherwise. The stability of the resulting rolling motions terminates generally, as a function of the control parameters, at points where fold bifurcations of limit cycles occur. We find that several branches of motion types exist for the same parameters, in terms of the relative frequencies of the barrel and of the actuator, having each their respective basins of attractions in terms of initial conditions. For low drivings stable limit cycles describing periodic and drifting back-and-forth motions are found additionally. These modes allow to generate symmetry breaking explorative behavior purely by the timing of an otherwise neutral signal with respect to the cyclic back-and-forth motion of the robot.

13 Mar 06:56

Quantum information in the Posner model of quantum cognition. (arXiv:1711.04801v3 [quant-ph] UPDATED)

by Nicole Yunger Halpern, Elizabeth Crosson

Matthew Fisher recently postulated a mechanism by which quantum phenomena could influence cognition: Phosphorus nuclear spins may resist decoherence for long times, especially when in Posner molecules. The spins would serve as biological qubits. We imagine that Fisher postulates correctly. How adroitly could biological systems process quantum information (QI)? We establish a framework for answering. Additionally, we construct applications of biological qubits to quantum error correction, quantum communication, and quantum computation. First, we posit how the QI encoded by the spins transforms as Posner molecules form. The transformation points to a natural computational basis for qubits in Posner molecules. From the basis, we construct a quantum code that detects arbitrary single-qubit errors. Each molecule encodes one qutrit. Shifting from information storage to computation, we define the model of Posner quantum computation. To illustrate the model's quantum-communication ability, we show how it can teleport information incoherently: A state's weights are teleported. Dephasing results from the entangling operation's simulation of a coarse-grained Bell measurement. Whether Posner quantum computation is universal remains an open question. However, the model's operations can efficiently prepare a Posner state usable as a resource in universal measurement-based quantum computation. The state results from deforming the Affleck-Kennedy-Lieb-Tasaki (AKLT) state and is a projected entangled-pair state (PEPS). Finally, we show that entanglement can affect molecular-binding rates, boosting a binding probability from 33.6% to 100% in an example. This work opens the door for the QI-theoretic analysis of biological qubits and Posner molecules.

13 Mar 06:07

Cognition, Convexity, and Category Theory

by john
Nosimpler

I finally commented on the n-category cafe. God help me.

MathML-enabled post (click for more details).

guest post by Tai-Danae Bradley and Brad Theilman

Recently in the Applied Category Theory Seminar our discussions have returned to modeling natural language, this time via Interacting Conceptual Spaces I by Joe Bolt, Bob Coecke, Fabrizio Genovese, Martha Lewis, Dan Marsden, and Robin Piedeleu. In this paper, convex algebras lie at the heart of a compositional model of cognition based on Peter Gärdenfors’ theory of conceptual spaces. We summarize the ideas in today’s post.

Sincere thanks go to Brendan Fong, Nina Otter, Fabrizio Genovese, Joseph Hirsh, and other participants of the seminar for helpful discussions and feedback.

MathML-enabled post (click for more details).

Introduction

A few weeks ago here at the Café, Cory and Jade summarized the main ideas behind the DisCoCat model, i.e. the categorical compositional distributional model of meaning developed in a 2010 paper by Coecke, Sadrzadeh, and Clark. Within the comments section of that blog entry, Coecke noted that the DisCoCat model is essentially a grammatical quantum field theory — a functor (morally) from a pregroup to finite dimensional real vector spaces. In this model, the meaning of a sentence is determined by the meanings of its constituent parts, which are themselves represented as vectors with meanings determined statistically. But as he also noted,

Vector spaces are extremely bad at representing meanings in a fundamental way, for example, lexical entailment, like tiger < big cat < mammal < animal can’t be represented in a vector space. At Oxford we are now mainly playing around with alternative models of meaning drawn from cognitive science, psychology and neuroscience. Our Interacting Conceptual Spaces I is an example of this….

This (ICS I) is the paper that we discuss in today’s blog post. It presents a new model in which words are no longer represented as vectors. Instead, they are regions within a conceptual space, a term coined by cognitive scientist Peter Gärdenfors in Conceptual Spaces: The Geometry of Thought. A conceptual space is a combination of geometric domains where convexity plays a key role. Intuitively, if we have a space representing the concept of fruit, and if two points in this space represent banana, then one expects that every point “in between” should also represent banana. The goal of ICS I is to put Gärdenfors’ idea on a more formal categorical footing, all the while adhering to the main principles of the DisCoCat model. That is, we still consider a functor out of a grammar category, namely the pregroup Preg(n,s)\mathsf{Preg}(n,s), freely generated by noun type nn and sentence type ss. (But in light of Preller’s argument as mentioned previously, we use the word functor with caution.) The semantics category, however, is no longer vector spaces but rather ConvexRel,\mathsf{ConvexRel}, the category of convex algebras and convex relations. We make these ideas and definitions precise below.

Preliminaries

A convex algebra is, loosely speaking, a set equipped with a way of taking formal finite convex combinations of its elements. More formally, let AA be a set and let D(A)D(A) denote the set of formal finite sums ∑ ip ia i\sum_i p_i a_i of elements of A,A, where p i∈ℝ ≥0p_i\in\mathbb{R}_{\geq 0} and ∑ ip i=1.\sum_i p_i=1. (We emphasize that this sum is formal. In particular, AA need not be equipped with a notion of addition or scaling.) A convex algebra is a set AA together with a function α:D(A)→A\alpha\colon D(A)\to A, called a “mixing operation,” that is well-behaved in the following sense:

  • the convex combination of a single element is itself, and
  • the two ways of evaluating a convex combination of a convex combination are equal.

For example, every convex subspace of ℝ n\mathbb{R}^n is naturally a convex algebra. (And we can’t resist mentioning that convex subspaces of ℝ n\mathbb{R}^n are also examples of algebras over the operad of topological simplices. But as we learned through a footnote in Tobias Fritz’s Convex Spaces I, it’s best to stick with monads rather than operads. Indeed, a convex algebra is an Eilenberg-Moore algebra of the finite distribution monad.) Join semilattices also provide an example of convex algebras. A finite convex combination of elements a ia_i in the lattice is defined to be the join of those elements having non-zero coefficients: ∑ ip ia i:=∨ i{a i:p i≠0}\sum_i p_i a_i:=\vee_i \{a_i:p_i\neq 0\}. (In particular, the coefficients play no role on the right-hand side.)

Given two convex algebras (A,α)(A,\alpha) and (B,β)(B,\beta), a convex relation is a binary relation R⊆A×BR\subseteq A\times B that respects convexity. That is, if R(a i,b i)R(a_i,b_i) for all i=1,…,ni=1,\ldots,n then R(α(∑ i=1 np ia i),β(∑ i=1 np ib i))R\left(\alpha(\sum_{i=1}^n p_i a_i),\beta(\sum_{i=1}^n p_i b_i)\right). We then define ConvexRel\mathsf{ConvexRel} to be the category with convex algebras as objects and convex relations as morphisms. Composition and identities are as for usual binary relations.

Now since in this model, the category of vector spaces is being replaced by ConvexRel\mathsf{ConvexRel}, one hopes that (in keeping with the spirit of the DisCoCat model), the latter admits a symmetric monoidal compact closed structure. Indeed it does.

  • ConvexRel\mathsf{ConvexRel} has a symmetric monoidal structure given by the Cartesian product: We use (A,α)⊗(B,β)(A,\alpha)\otimes(B,\beta) to denote the set A×BA\times B equipped with mixing operation given by D(A×B) ⟶A×B ∑p i(a i,b i) ↦(α(∑p ia i),β(∑p ib i)). \begin{aligned} D(A\times B)&\longrightarrow A\times B\\ \sum p_i(a_i,b_i)&\mapsto \left(\alpha(\sum p_i a_i),\beta(\sum p_i b_i)\right). \end{aligned} The monoidal unit is the one-point set ⋆\star which has a unique convex algebra structure. We’ll denote this convex algebra by I.I.
  • Each object in ConvexRel\mathsf{ConvexRel} is self-dual, and cups and caps are given as follows: η A:I→(A,α)⊗(A,α) is the relation{(⋆,(a,a)):a∈A)} ϵ A:(A,α)⊗(A,α)→I is the relation{((a,a),⋆):a∈A}\begin{aligned} \eta_A\colon I \to(A,\alpha)\otimes(A,\alpha) \quad &\text{ is the relation} \quad \{(\star,(a,a)):a\in A)\}\\ \epsilon_A\colon (A,\alpha)\otimes(A,\alpha)\to I \quad &\text{ is the relation} \quad \{((a,a),\star):a\in A\} \end{aligned}

The compact closed structure guarantees that ConvexRel\mathsf{ConvexRel} fits nicely into the DisCoCat framework: words in a sentence are assigned types according to a chosen pregroup grammar, and a sentence is deemed grammatical if it reduces to type ss. Moreover, these type reductions in Preg(n,s)\mathsf{Preg}(n,s) give rise to corresponding morphisms in ConvexRel\mathsf{ConvexRel} where the meaning of the sentence can be determined. We’ll illustrate this below by computing the meaning of the sentence

bananastastesweet. b a n a n a s\; t a s t e\; s w e e t.

To start, note that this sentence is comprised of three grammar types:

and each corresponds to a different conceptual space noun, n⇝Nsentence, s⇝Sverb, n rsn l⇝N⊗S⊗N\text{noun, }\; n \rightsquigarrow N \qquad\qquad \text{sentence, }\; s \rightsquigarrow S \qquad\qquad \text{verb, }\; n^r s n^l \rightsquigarrow N\otimes S \otimes N which we describe next.

Computing Meaning

The Noun Space NN

A noun is a state I→NI\to N, i.e. a convex subset of the noun space NN. Restricting our attention to food nouns, the space NN is a product of color, taste, and texture domains: N=N color⊗N taste⊗N texture⊂ℝ 8N=N_{\text{color}}\otimes N_{\text{taste}}\otimes N_{\text{texture}} \subset \mathbb{R}^8 where

  • N colorN_{\text{color}} is the RGB color cube, i.e. the set of all triples (R,G,B)∈[0,1] 3(R,G,B)\in [0,1]^3.
  • N tasteN_{\text{taste}} is the taste tetrahedron, i.e. the convex hull of four basic tastes: sweet, sour, bitter, and salty.
  • N textureN_{\text{texture}} is the unit interval [0,1][0,1] where 0 represents liquid and 1 represents solid.

The noun banana is then a product of three convex subregions of NN:

That is, banana is the product of a yellow/green region, the convex hull of three points in the taste tetrahedron, and a subinterval of the texture interval. Other foods and beverages, avocados, chocolate, beer, etc. can be expressed similarly.

The Sentence Space SS

The meaning of a sentence is a convex subset of a sentence space SS. Here, SS is chosen as a simple-yet-sensible space to capture one’s experience when eating and drinking. It is the join semilattice on four points

where in the first component, 0 = negative and 1 = positive, while in the second component, 0 = not surprising and 1 = surprising. For instance, (0,1)(0,1) represents negative and surprising while the convex subset {(1,1),(1,0)}\{(1,1),(1,0)\} represents positive.

The Verb Space N⊗S⊗NN\otimes S\otimes N

A transitive verb is a convex subset of N⊗S⊗NN\otimes S\otimes N. For instance, if we suppose momentarily that we live in a world in which one can survive on bananas and beer alone, then the verb taste can be represented by taste =Conv({greenbanana⊗{(0,0)}⊗bitter} ∪{greenbanana⊗{(1,1)}⊗sweet} ∪{yellowbanana⊗{(1,0)}⊗sweet} ∪{beer⊗{(0,1)}⊗sweet} ∪{beer⊗{(1,0)}⊗bitter}) \begin{aligned} t a s t e &= \text{Conv}( \{g r e e n\; b a n a n a \otimes\{(0,0)\}\otimes b i t t e r\}\\ &\,\cup \{g r e e n\; b a n a n a\otimes\{(1,1)\}\otimes s w e e t\}\\ &\,\cup \{y e l l o w\; b a n a n a\otimes\{(1,0)\}\otimes s w e e t\}\\ &\,\cup \{b e e r \otimes\{(0,1)\}\otimes s w e e t\}\\ &\,\cup \{b e e r\otimes\{(1,0)\}\otimes b i t t e r\}) \end{aligned} where Conv denotes the convex hull of the argument. Here, green is an intersective adjective, so green banana is computed by taking the intersection of the banana space with the green region of the color cube. Likewise for yellow banana.

Tying it all together

Finally, we compute the meaning of bananas taste sweet, which has grammar type reduction n(n rsn l)n≤(nn r)s≤s.n(n^r s n^l)n\leq (nn^r )s\leq s. In ConvexRel\mathsf{ConvexRel}, this corresponds to the following morphism: Nbananas⊗N⊗S⊗Ntaste⊗Nsweet⟶ϵ N⊗1 S⊗ϵ NS\overset{\text{bananas}}{N}\otimes\;\; \overset{\text{taste}}{N\;\; \otimes \;\; S\;\; \otimes \;\;N}\;\; \otimes \overset{\text{sweet}}{N}\;\;\;\overset{\epsilon_N\otimes 1_S\otimes\epsilon_N}{\longrightarrow}\;\;\; S bananastastesweet =(ϵ N⊗1 S⊗ϵ N)(bananas⊗taste⊗sweet) =(ϵ N⊗1 S)(banana⊗(greenbanana⊗{(1,1)} ∪yellowbanana⊗{(1,0)} ∪beer⊗{(0,1)})) ={(1,1),(1,0)} =positive \begin{aligned} b a n a n a s\; t a s t e\; s w e e t &= (\epsilon_N\otimes 1_S\otimes \epsilon_N)(b a n a n a s \otimes t a s t e \otimes s w e e t)\\ &=(\epsilon_N\otimes 1_S)(b a n a n a\otimes (g r e e n\; b a n a n a \otimes \{(1,1)\} \\ &\qquad\qquad\qquad\qquad\quad \cup y e l l o w\; b a n a n a \otimes\{(1,0)\} \\ &\qquad\qquad\qquad\qquad\quad \cup b e e r\otimes\{(0,1)\}))\\ &=\{(1,1),(1,0)\}\\ &= p o s i t i v e \end{aligned} Note that the rightmost ϵ N\epsilon_N selects subsets of the taste space that include sweet things and then deletes “sweet.” The leftmost ϵ N\epsilon_N selects subsets of the taste space that include banana and then deletes “banana.” We are left with a convex subset of SS, i.e. the meaning of the sentence.

Closing Remarks

Although not shown in the example above, one can also account for relative pronouns using certain morphisms called multi-wires or spiders (these arise from commutative special dagger Frobenius structures). The authors also give a toy example from the non-food world by modeling movement of a person from one location to another, using time and space to define new noun, sentence, and verb spaces.

In short, the conceptual spaces framework seeks to capture meaning in a way that resembles human thought more closely than the vector space model. This leaves us to puzzle over a couple of questions: 1) Do all concepts exhibit a convex structure? and 2) How might the conceptual spaces framework be implemented experimentally?

09 Mar 14:10

A self-contained, brief and complete formulation of Voevodsky’s univalence axiom

by Martin Escardo

I have often seen competent mathematicians and logicians, outside our circle, making technically erroneous comments about the univalence axiom, in conversations, in talks, and even in public material, in journals or the web.

For some time I was a bit upset about this. But maybe this is our fault, by often trying to explain univalence only imprecisely, mixing the explanation of the models with the explanation of the underlying Martin-Löf type theory, with none of the two explained sufficiently precisely.

There are long, precise explanations such as the HoTT book, for example, or the various formalizations in Coq, Agda and Lean.

But perhaps we don’t have publicly available material with a self-contained, brief and complete formulation of univalence, so that interested mathematicians and logicians can try to contemplate the axiom in a fully defined form.

So here is an attempt of a  self-contained, brief and complete formulation of Voevodsky’s Univalence Axiom in the arxiv.

This has an Agda file with univalence defined from scratch as an ancillary file, without the use of any library at all, to try to show what the length of a self-contained definition of the univalence type is. Perhaps somebody should add a Coq “version from scratch” of this.

There is also a web version UnivalenceFromScratch to try to make this as accessible as possible, with the text and the Agda code together.

The above notes explain the univalence axiom only. Regarding its role, we recommend Dan Grayson’s introduction to univalent foundations for mathematicians.

05 Mar 15:35

Sparse Identification of Nonlinear Dynamics for Rapid Model Recovery. (arXiv:1803.00894v2 [physics.data-an] UPDATED)

by Markus Quade, Markus Abel, J. Nathan Kutz, Steven L. Brunton

Big data has become a critically enabling component of emerging mathematical methods aimed at the automated discovery of dynamical systems, where first principles modeling may be intractable. However, in many engineering systems, abrupt changes must be rapidly characterized based on limited, incomplete, and noisy data. Many leading automated learning techniques rely on unrealistically large data sets and it is unclear how to leverage prior knowledge effectively to re-identify a model after an abrupt change. In this work, we propose a conceptual framework to recover parsimonious models of a system in response to abrupt changes in the low-data limit. First, the abrupt change is detected by comparing the estimated Lyapunov time of the data with the model prediction. Next, we apply the sparse identification of nonlinear dynamics (SINDy) regression to update a previously identified model with the fewest changes, either by addition, deletion, or modification of existing model terms. We demonstrate this sparse model recovery on several examples for abrupt system change detection in periodic and chaotic dynamical systems. Our examples show that sparse updates to a previously identified model perform better with less data, have lower runtime complexity, and are less sensitive to noise than identifying an entirely new model. The proposed abrupt-SINDy architecture provides a new paradigm for the rapid and efficient recovery of a system model after abrupt changes.

03 Mar 19:51

Nonstandard Integers as Complex Numbers

by John Baez

 

I just read something cool:

• Joel David Hamkins, Nonstandard models of arithmetic arise in the complex numbers, 3 March 2018.

Let me try to explain it in a simplified way. I think all cool math should be known more widely than it is. Getting this to happen requires a lot of explanations at different levels.

Here goes:

The Peano axioms are a nice set of axioms describing the natural numbers. But thanks to Gödel’s incompleteness theorem, these axioms can’t completely nail down the structure of the natural numbers. So, there are lots of different ‘models’ of Peano arithmetic.

These are often called ‘nonstandard’ models. If you take a model of Peano arithmetic—say, your favorite ‘standard’ model —you can get other models by throwing in extra natural numbers, larger than all the standard ones. These nonstandard models can be countable or uncountable. For more, try this:

Nonstandard models of arithmetic, Wikipedia.

Starting with any of these models you can define integers in the usual way (as differences of natural numbers), and then rational numbers (as ratios of integers). So, there are lots of nonstandard versions of the rational numbers. Any one of these will be a field: you can add, subtract, multiply and divide your nonstandard rationals, in ways that obey all the usual basic rules.

Now for the cool part: if your nonstandard model of the natural numbers is small enough, your field of nonstandard rational numbers can be found somewhere in the standard field of complex numbers!

In other words, your nonstandard rationals are a subfield of the usual complex numbers: a subset that’s closed under addition, subtraction, multiplication and division by things that aren’t zero.

This is counterintuitive at first, because we tend to think of nonstandard models of Peano arithmetic as spooky and elusive things, while we tend to think of the complex numbers as well-understood.

However, the field of complex numbers is actually very large, and it has room for many spooky and elusive things inside it. This is well-known to experts, and we’re just seeing more evidence of that.

I said that all this works if your nonstandard model of the natural numbers is small enough. But what is “small enough”? Just the obvious thing: your nonstandard model needs to have a cardinality smaller than that of the complex numbers. So if it’s countable, that’s definitely small enough.

This fact was recently noticed by Alfred Dolich at a pub after a logic seminar at the City University of New York. The proof is very easy if you know this result: any field of characteristic zero whose cardinality is less than or equal to that of the continuum is isomorphic to some subfield of the complex numbers. So, unsurprisingly, it turned out to have been repeatedly discovered before.

And the result I just mentioned follows from this: any two algebraically closed fields of characteristic zero that have the same uncountable cardinality must be isomorphic. So, say someone hands you a field F of characteristic zero whose cardinality is smaller than that of the continuum. You can take its algebraic closure by throwing in roots to all polynomials, and its cardinality won’t get bigger. Then you can throw in even more elements, if necessary, to get a field whose cardinality is that of the continuum. The resulting field must be isomorphic to the complex numbers. So, F is isomorphic to a subfield of the complex numbers.

To round this off, I should say a bit about why nonstandard models of Peano arithmetic are considered spooky and elusive. Tennenbaum’s theorem says that for any countable non-standard model of Peano arithmetic there is no way to code the elements of the model as standard natural numbers such that either the addition or multiplication operation of the model is a computable function on the codes.

We can, however, say some things about what these countable nonstandard models are like as ordered sets. They can be linearly ordered in a way compatible with addition and multiplication. And then they consist of one copy of the standard natural numbers, followed by a lot of copies of the standard integers, which are packed together in a dense way: that is, for any two distinct copies, there’s another distinct copy between them. Furthermore, for any of these copies, there’s another copy before it, and another after it.

I should also say what’s good about algebraically closed fields of characteristic zero: they are uncountably categorical. In other words, any two models of the axioms for an algebraically closed field with the same cardinality must be isomorphic. (This is not true for the countable models: it’s easy to find different countable algebraically closed fields of characteristic zero. They are not spooky and elusive.)

So, any algebraically closed field whose cardinality is that of the continuum is isomorphic to the complex numbers!

For more on the logic of complex numbers, written at about the same level as this, try this post of mine:

The logic of real and complex numbers, Azimuth 8 September 2014.

02 Mar 15:30

Screening of Fungi for the Application of Self-Healing Concrete. (arXiv:1711.10386v6 [q-bio.OT] UPDATED)

by Rakenth R. Menon, Jing Luo, Xiaobo Chen, Preeth Sivakumar, Zhiyong Liu, Guangwen Zhou, Ning Zhang, Congrui Jin

Concrete is susceptible to cracking owing to drying shrinkage, freeze-thaw cycles, delayed ettringite formation, reinforcement corrosion, creep and fatigue, etc. Since maintenance and inspection of concrete infrastructure require onerous labor and high costs, self-healing of harmful cracks without human interference or intervention could be of great attraction. The goal of this study is to explore a new self-healing approach in which fungi are used as a self-healing agent to promote calcium carbonate precipitation to fill the cracks in concrete structures. Recent research results in the field of geomycology have shown that many species of fungi could play an important role in promoting calcium carbonate mineralization, but their application in self-healing concrete has not been reported. Therefore, a screening of different species of fungi has been conducted in this study. Our results showed that, despite the drastic pH increase owing to the leaching of calcium hydroxide from concrete, Aspergillus nidulans (MAD1445), a pH regulatory mutant, could grow on concrete plates and promote calcium carbonate precipitation.

27 Feb 21:30

Also, Pot

by noreply@blogger.com (Atrios)
Waaahhhh...young people don't vote, and they especially don't vote in midterms. Fucking young people.

Be the party that wants to legalize the weed while you can still get some electoral payoff out of it, idiots.
24 Feb 20:37

Communication Melting in Graphs and Complex Networks. (arXiv:1802.07809v1 [physics.soc-ph])

by Najlaa Alalwan, Alex Arenas, Ernesto Estrada

Complex networks are the representative graphs of interactions in many complex systems. Usually, these interactions are abstractions of the communication/diffusion channels between the units of the system. Real complex networks, e.g. traffic networks, reveal different operation phases governed by the dynamical stress of the system. Here we show how, communicability, a topological descriptor that reveals the efficiency of the network functionality in terms of these diffusive paths, could be used to reveal the transitions mentioned. By considering a vibrational model of nodes and edges in a graph/network at a given temperature (stress), we show that the communicability function plays the role of the thermal Green's function of a network of harmonic oscillators. After, we prove analytically the existence of a universal phase transition in the communicability structure of every simple graph. This transition resembles the melting process occurring in solids. For instance, regular-like graphs resembling crystals, melts at lower temperatures and display a sharper transition between connected to disconnected structures than the random spatial graphs, which resemble amorphous solids. Finally, we study computationally this graph melting process in some real-world networks and observe that the rate of melting of graphs changes either as an exponential or as a power-law with the inverse temperature. At the local level we discover that the main driver for node melting is the eigenvector centrality of the corresponding node, particularly when the critical value of the inverse temperature approaches zero. These universal results sheds light on many dynamical diffusive-like processes on networks that present transitions as traffic jams, communication lost or failure cascades.

24 Feb 01:24

An innate circuit for object craving

by Dayu Lin

An innate circuit for object craving

An innate circuit for object craving, Published online: 23 February 2018; doi:10.1038/s41593-018-0087-3

Using a series of functional manipulation and in vivo recording tools, Park et al. identify a pathway from medial preoptic CaMKIIα-expressing neurons to the ventral periaqueductal gray that mediates object craving and prey hunting.
20 Feb 20:34

Metastable state en route to traveling-wave synchronization state

by Jinha Park and B. Kahng

Author(s): Jinha Park and B. Kahng

The Kuramoto model with mixed signs of couplings is known to produce a traveling-wave synchronized state. Here, we consider an abrupt synchronization transition from the incoherent state to the traveling-wave state through a long-lasting metastable state with large fluctuations. Our explanation of t...


[Phys. Rev. E 97, 020203(R)] Published Tue Feb 20, 2018

19 Feb 23:20

Minimal Algorithmic Information Loss Methods for Dimension Reduction, Feature Selection and Network Sparsification. (arXiv:1802.05843v10 [cs.DS] UPDATED)

by Hector Zenil, Narsis A. Kiani, Jesper Tegnér

We introduce a family of unsupervised, domain-free, and asymptotically optimal model-independent algorithms based on the principles of algorithmic probability and information theory designed to minimize the loss of algorithmic information, and thereby avoiding certain deceiving phenomena and distortions known to occur in statistics and entropy-based approaches. Our methods include a lossless-compression-based lossy compression algorithm that can select and coarse-grain data in an algorithmic-complexity fashion (without the use of popular compression algorithms) by collapsing regions that may procedurally be regenerated from a computable candidate model. We show that the method can perform dimension reduction, denoising, feature selection, and network sparsification, while preserving the properties of the objects. As validation case, we demonstrate the methods on image segmentation against popular methods like PCA and random selection, and also demonstrate that the method preserves the graph-theoretic indices measured on a well-known set of synthetic and real-world networks of very different nature, ranging from degree distribution and clustering coefficient to edge betweenness and degree and eigenvector centralities, achieving equal or significantly better results than other data reduction and the leading network sparsification methods (Spectral, Transitive).

16 Feb 20:17

'CAMERA records cell action with new CRISPR tricks

by Cohen, J.
12 Feb 20:28

Viewpoint: Quantum Computer Simulates Excited States of Molecule

by Sukin Sim, Jonathan Romero, Peter D. Johnson, and Alán Aspuru-Guzik
Nosimpler

File with "Neural network used to understand brain".

Author(s): Sukin Sim, Jonathan Romero, Peter D. Johnson, and Alán Aspuru-Guzik

Excited-state energies of the hydrogen molecule have been calculated using a two-qubit quantum computer.


[Physics 11, 14] Published Mon Feb 12, 2018

10 Feb 16:50

Earth-like and Tardigrade survey of exoplanets. (arXiv:1802.02714v2 [physics.pop-ph] UPDATED)

by MadhuKashyap Jagadeesh, Milena Roszkowska, Lukasz Kaczmarek

Finding life on other worlds is a fascinating area of astrobiology and planetary sciences. Presently, over 3500 exoplanets, representing a very wide range of physical and chemical environments, are known. Tardigrades (water bears) are microscopic invertebrates that inhabit almost all terrestrial, freshwater and marine habitats, from the highest mountains to the deepest oceans. Thanks to their ability to live in a state of cryptobiosis, which is known to be an adaptation to unpredictably fluctuating environmental conditions, these organisms are able to survive when conditions are not suitable for active life; consequently, tardigrades are known as the toughest animals on Earth. In their cryptobiotic state, they can survive extreme conditions, such as temperatures below -250{\deg}C and up to 150{\deg}C, high doses of ultraviolet and ionising radiation, up to 30 years without liquid water, low and high atmospheric pressure, and exposure to many toxic chemicals. Active tardigrades are also resistant to a wide range of unfavourable environmental conditions, which makes them an excellent model organism for astrobiological studies. In our study, we have established a metric tool for distinguishing the potential survivability of active and cryptobiotic tardigrades on rocky-water and water-gas planets in our solar system and exoplanets, taking into consideration the geometrical means of surface temperature and surface pressure of the considered planets. The Active Tardigrade Index (ATI) and Cryobiotic Tardigrade Index (CTI) are two metric indices with minimum value 0 (= tardigrades cannot survive) and maximum 1 (= tardigrades will survive in their respective state). Values between 0 and 1 indicate a percentage chance of the active or cryptobiotic tardigrades surviving on a given exoplanet.

08 Feb 22:15

A Categorical Semantics for Causal Structure

by John Baez

 

The school for Applied Category Theory 2018 is up and running! Students are blogging about papers! The first blog article is about a diagrammatic method for studying causality:

• Joseph Moeller and Dmitry Vagner, A categorical semantics for causal structure, The n-Category Café, 22 January 2018.

Make sure to read the whole blog conversation, since it helps a lot. People were confused about some things at first.

Joseph Moeller is a grad student at U.C. Riverside working with me and a company called Metron Scientific Solutions on “network models”—a framework for designing networks, which the Coast Guard is already interested in using for their search and rescue missions:

• John C. Baez, John Foley, Joseph Moeller and Blake S. Pollard, Network Models. (Blog article here.)

Dmitry Vagner is a grad student at Duke who is very enthusiastic about category theory. Dmitry has worked with David Spivak and Eugene Lerman on open dynamical systems and the operad of wiring diagrams.

It’s great to see these students digging into the wonderful world of category theory and its applications.

To discuss this stuff, please go to The n-Category Café.