Sunday, December 09, 2012

Sunday Morning Insight: Can L1 help Inpainting ?

In most cases of interest, the answer is no as shown in The Lost Honour of ℓ2-Based Regularization by Uri Ascher. Similar questions were answered negatively before in :


There seems to be some confusion: compressive sensing has never been an interpolation or inpainting issue. Even the type of sparse sampling used in compressive sensing covers and oversamples all the data. This reminds me of a question asked by Inspector Clouzeau "Does your dog bite ?"....





Thanks Laurent for the heads-up.



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Friday, December 07, 2012

Google+ and Reddit Experiments

Google+ decided to have communities so I started one on Compressive Sensing, Advanced Matrix Factorization and Randomized Linear Algebra, or any development susceptible to help deal with the current tsunami of data. The motto is " Defeating the Data Tsunami, one algorithm at a time".:The community is here and waiting for your Google+ items.
This is a community of people interested in Compressive Sensing, Advanced Matrix Factorization, Randomized Linear Algebra and any other means of defeating the curse of dimensionality. Theoreticians all the way to hardware hackers are welcome.
We are 14 now, bring your like minded friends along, who will be the first to post something there ? Leon started the Machine Learning community while Eric started the Signal Processing community.

Our Reddit Experiment started two months ago and we now have 60 readers (or subscribers of the subreddit). Still not much engagement as far as posting or commenting but some of the readers are beginning to provide some Karma points to some of the entries.

The subject area that are considered ok include compressive sensing in a broad sense as well as anything pertaining to advanced matrix factorization. We welcome your contributions. On a tablet, we like to watch it with scrolldit.

Plenoptic Function Sensing Hacks




After seeing what's in the animal world (Thanks Lauren and Arthropoda) or potentially humans, 


and reading Compressive Sensing of  High-Dimensional Visual Signals  by Aswin Sankaranarayanan, I could not stop thinking that there are several ways to sample the plenotpic function and that in some way, they are all ... hacks.
It's been a while since I have done this but let me list some other potential hacks.sensing mechanisms that cross my radar screen recently. Let us note that today's entry mixes hacks sensors and multiplexers at different levels of  Technology Readiness Levels.scale.

  • Flat Lenses that are nanodesigned. see [1]. some simple explanations are given here.


[1] Aberration-Free Ultrathin Flat Lenses and Axicons at Telecom Wavelengths Based on Plasmonic Metasurfaces by Francesco Aieta, Patrice Genevet, Mikhail A. Kats, Nanfang Yu, Romain Blanchard, Zeno Gaburro, and Federico Capasso (other relevant papers can be found  here)
[2] New Dark Matter Detectors using DNA for Nanometer Tracking by Andrzej Drukier, Katherine Freese, David Spergel, Charles Cantor, George Church, Takeshi Sano





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Thursday, December 06, 2012

NuMax: A Convex Approach for Learning Near-Isometric Linear Embeddings - implementation -

How we design measurement matrices (embeddings) that are specific to certain types of scene or object or signal so that one can operate additional operation such as classification or even reconstruction from the compressed measurement. This is an open question and one which NuMax is trying to answer in the following paper:
A Convex Approach for Learning Near-Isometric Linear Embeddings by Chinmay Hegde, Aswin C Sankaranarayanan , Wotao Yin, Richard G. Baraniuk. The abstract reads:
We propose a novel framework for the deterministic construction of linear, near-isometric embeddings of a nite set of data points. Given a set of training points X R N, we consider the secant set S(X ) that consists of all pairwise di erence vectors of X , normalized to lie on the unit sphere. We formulate an a ne rank minimization problem to construct a matrix that preserves the norms of all the vectors in S(X ) up to a distortion parameter .While a ne rank minimization is NP-hard, we show that this problem can be relaxed toa convex formulation that can be solved using a tractable semide nite program (SDP). In order to enable scalability of our proposed SDP to very large-scale problems, we adopt a two-stage approach. First, in order to reduce compute time, we develop a novel algorithm based on the Alternating Direction Method of Multipliers (ADMM) that we call Nuclear norm minimization with Max-norm constraints (NuMax) to solve the SDP. Second, we develop a greedy, approximate version of NuMax based on the column generation method commonly used to solve large-scale linear programs. We demonstrate that our framework is useful for a number of applications in machine learning and signal processing via a range of experiments on large-scale synthetic and real datasets.
The attendant code is here.


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Postdoc opening on developing advanced sparse machine learning and bioinformatics strategies

When was the last time you heard of a postdoc position advertized by somebody who is about to graduate. Wait no more, Zhilin who will have his thesis defense in a few days just sent me the following:

Hi ...Igor 
.....It's very nice to see that you have written a number of reviews on the progression of CS. I am waiting to see more.
Recently, one of my collaborative labs has a postdoc opening. The main job focuses on developing advanced sparse machine learning and bioinformatics strategies for multidimensional brain imaging genetics. The position description is copied below. The background on the medical stuff is not necessarily required. Like me, although I have no background on this field, I still successfully co-worked with that lab.
I would very much appreciate if  the announcement could be posted on your blog.
Best regards,
Zhilin

Here is the job announcement:


Applications are invited for a Postdoc Position in the Imaging Genomics Lab at the Indiana University School of Medicine (IUSM), funded by an NIH R01 grant. The project is focused on developing advanced sparse machine learning and bioinformatics strategies for multidimensional brain imaging genetics.

Requirements include a Ph.D. in computer science, informatics, statistics, or related disciplines, and a record of academic productivities. Preference will be given to candidates who have experience with advanced techniques for analyzing genome wide array data, complex phenotypic data, and/or systems biology data. A strong interest in integrative analysis of multimodal neuroimaging data, high throughput omics data, and other biomarker data, would be highly desirable, as would solid background in machine learning and bioinformatics, and strong programming experience using Matlab, R, Python, and/or C/C++.

The Imaging Genomics Lab (http://www.iupui.edu/~shenlab/) is affiliated with two multidisciplinary centers at IUSM: (1) Center for Neuroimaging, the hub for all neuroimaging research activities on campus, and (2) Center for Computational Biology and Bioinformatics, the bioinformatics core of IUSM. There is an excellent set of critical resources at IUSM, including (1) experts from neuroscience, imaging science, computer science, genetics, informatics, and statistics, (2) state-of-the-art imaging facilities, and (3) large scale computer systems and advanced software tools. The successful candidate will benefit from mentorship of a diverse research team and will be exposed to cutting-edge technology by collaborating on various genomic and imaging projects.

Interested candidates should email their CV, selected reprints and a list of three references to: Li Shen at shenli@iupui.edu.

Indiana University is an AA/EOE employer, M/F/D.

The approaches will be similar to those proposed in the following papers.

[1] Vounou M, Janousova E., Wolz R., Stein J. Thompson P., Rueckert D. and Montana G. (2011) Sparse reduced-rank regression detects genetic associations with voxel-wise longitudinal phenotypes in Alzheimer's disease. NeuroImage, 60(1):700-716

[2] T. Ge, J. Feng, D.P. Hibar, P.M. Thompson, and T.E. Nichols. Increasing power for voxel-wise genome-wide association studies: the random field theory, least square kernel machines and fast permutation procedures. NeuroImage, 63(2): 858-873, 2012.

[3] Witten DM, Tibshirani R, and T Hastie (2009) A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics 10(3): 515-534.

We will be dealing with data similar to those in the following papers.

[4] Meda SA, Narayanan B, Liu J, Perrone-Bizzozero NI,Stevens MC,Calhoun VD, Glahn DC, Shen L, Risacher SL, Saykin AJ, Pearlson GD (2012) A large scale multivariate parallel ICA method reveals novel imaging-genetic relationships for Alzheimer's disease in the ADNI cohort. Neuroimage, 60(3):1608-1621. doi:10.1016/j.neuroimage.2011.12.076

[5] Shen L, Kim S, Risacher SL, Nho K, Swaminathan S, West JD, Foroud TM, Pankratz ND, Moore JH, Sloan CD, Huentelman MJ, Craig DW, DeChairo BM, Potkin SG, Jack CR, Weiner MW, Saykin AJ, and ADNI. Whole genome association study of brain-wide imaging phenotypes for identifying quantitative trait loci in MCI and AD: A study of the ADNI cohort. NeuroImage, 53:1051-1063, 2010. http://dx.doi.org/10.1016/j.neuroimage.2010.01.042.



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Wednesday, December 05, 2012

Blind Deconvolution using Convex Programming - implementation -

Blind Deconvolution using Convex Programming by Ali Ahmed, Benjamin Recht, and Justin Romberg. The abstract reads:
We consider the problem of recovering two unknown vectors, w and x, of length L from their circular convolution. We make the structural assumption that the two vectors are members known subspaces, one with dimension N and the other with dimension K. Although the observed convolution is nonlinear in both w and x, it is linear in the rank-1 matrix formed by their outer product wx. This observation allows us to recast the deconvolution problem as low-rank matrix recovery problem from linear measurements, whose natural convex relaxation is a nuclear norm minimization program. We prove the eff ectiveness of this relaxation by showing that for \generic" signals, the program can deconvolve w and x exactly when the maximum of N and K is almost on the order of L. That is, we show that if x is drawn from a random subspace of dimension N, and w is a vector in a subspace of dimension K whose basis vectors are \spread out" in the frequency domain, then nuclear norm minimization recovers wx without error. We discuss this result in the context of blind channel estimation in communications. If we
have a message of length N which we code using a random L N coding matrix, and the encoded message travels through an unknown linear time-invariant channel of maximum length
K, then the receiver can recover both the channel response and the message when L & N + K, to within constant and log factors.

The attendant code implementing examples of this paper is here.


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Tuesday, December 04, 2012

Additional insights on the Q&A with Ben Adcock and Anders Hansen


Hi Igor,

Thanks for turning our email correspondence into a blog post - it's great that you've taken the time to understand what we're doing.

A couple of comments:

(i) In the second paragraph you mention the Gibbs phenomenon. However, this is not the fundamental issue. More precisely, the issue arises because of the discretization involved when replacing the continuous WT and FT by their discrete versions. This can be thought of as `data mismatch'. Although the Gibbs phenomenon is a result of this discretization, what is more important for compressed sensing is the loss of sparsity as Anders mentioned.

(ii) Regarding the TV-norm and Justin Romberg's approach. Your sentence "Except of course in Ben and Anders's approach we don't need the heuristics of the TV-norm" might possibly be construed to mean that we're advocates of l^1 over TV. This is not the case: so far we've studied l^1 because it's more fundamental and widespread in CS (and also easier to analyze than TV). However, certainly TV minimization will be more effective in some problems, and the same phenomenon (asymptotic incoherence) should explain empirical results for schemes such as Justin Romberg's.

Best wishes, and thanks again,

Ben
Thanks Ben .

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A Q&A with Ben Adcock and Anders Hansen: Infinite Dimensional Compressive Sensing, Generalized Sampling, Wavelet Crimes, Safe Zones and the Incoherence Barrier.


Part of the answer to "what is missing" pointed to the work [1,2,3] by Ben Adcok, Anders Hansen and others.  They deal with this issue of Gibbs phenomenon that could be the basis of some problematic we face in different areas touched by compressive sensing, especially hardware development. Here what I initially sent both Ben and Anders

Dear Ben and Anders,
I write a small blog on compressive sensing (http://nuit-blanche.blogspot.com/) and I was recently re- reading some of your recent papers and presentation about generalized sampling and compressive sensing. I am not sure I understand what the uneven section is and how it is chosen and was wondering if you had a toy example I could run in order to get a sense of how your discretization is different from the traditional one used in compressive sensing ?
For instance, would you have this numerical example 1 in http://www.math.purdue.edu/~adcock/Presentations/AdcockFields2012.pdf
Thanks in advance for your time,
Igor.

Ben kindly responded with:

Dear Igor,
Thanks for getting in touch.

> I write a small blog on compressive sensing (http://nuit-blanche.blogspot.com/) and I was >recently re- reading some of your recent papers and presentation about generalized sampling >and compressive sensing. I am not sure i understand what the uneven section is and how it is >chosen 
I'm an active reader of your blog (which is by no means small in my opinion): it's a great resource for the CS community. I was pleased to see you mention our work over the weekend.

> and was wondering if you had a toy example I could run in order to get a sense of how your >discretization is different from the traditional one used in compressive sensing ?
> For instance, would you have this numerical example 1 inhttp://www.math.purdue.edu/~adcock/Presentations/AdcockFields2012.pdf 
Anders has most of the code, so I will leave that up to him.
The key idea is that discretization comes, as you say, from an uneven, as opposed to a finite (i.e. square) section. This ensures that isometric structure is preserved.
The height of the uneven section (N in the slides) is chosen by satisfying the so-called balancing property (slide 45). The question of how large N needs to be (for a given M) to satisfy this property depends completely on the sampling and sparsity bases. However, we have some results which say that for Fourier sampling with (most types of) wavelets as the sparsity basis that one can take N = O(M). As you can see in slide 43 though, N=M doesn't work. One needs N to be roughly twice M in this case.
The balancing property is described in more detail in our paper "Generalized sampling and infinite-dimensional compressed sensing", and the analysis for wavelets can be found in:
"On optimal wavelet reconstructions from Fourier samples: linearity and universality of the stable sampling rate"
There we consider only the nonsparse case with l^2 minimization, and analyze a simpler quantity known as the stable sampling rate. But this is the first step towards the analysis of the full balancing property in this case.
I hope that helps. Please let me know if you have questions or comments.
Best wishes,
Ben

I was intrigued so I responded with:

Hello Ben,

Thanks for being a reader of the blog. ......

I am looking at slide 43 and the rule of thumb I am getting out of it is that you need to sample in a wider set of "frequencies" than the largest frequency of the actual sparse signal in order to get a good reconstruction. This is a very rough idea but is that the gist of it ?

In the affirmative, and those are not mathematically well defined term but when you are faced with a compressible signal (as opposed to a sparse one), the idea is that when you are sampling to a certain high "frequency", you can reconstruct well only the truncated series expansion with a much lower top "frequency" number ?

Cheers,

Igor.

To what Ben, once again, kindly replied:

Hi Igor,

....
>I am looking at slide 43 and the rule of thumb I am getting out of it is that you need to sample >in a wider set of "frequencies" than the largest frequency of the actual sparse signal in order to >get a good reconstruction. This is a very rough idea but is that the gist of it ? 
Yes. The range of frequencies N needs to be larger than the bandwidth of the sparse signal M.


>In the affirmative, and those are not mathematically well defined term but when you are faced >with a compressible signal (as opposed to sparse), the idea is that when you are sampling to a >certain high "frequency", you can reconstruct well only the truncated series expansion with a >much lower top "frequency" number ? 
That's correct. Although in many case `much lower' can often by, say, about half of the sampling frequency.

By the way, this is not an issue that arises due to sparsity or subsampling, or our method. We have have results that say that the dependence of M with N in our method is in some senses universal barrier that one will encounter regardless of the method used. In other words, there is a fundamental limit on `how far out' one can go in reconstruction basis given a finite frequency range N in the sampling. This is explained in the wavelet paper I sent you, and also the following paper:

"Beyond consistent reconstructions: optimality and sharp bounds for generalized sampling, and application to the uniform resampling problem"

Best wishes,

Ben
In the meantime, Anders Hansen also sent a response: 

Dear Igor
I am a great fan of your blog, and I think you are doing an excellent job for the community. Apologies for the late reply, but last week was the final week of term. Anyway, attached is a demo to show how the standard discretization using DFT and DWT fails dramatically for the simplest case of recovering the Haar wavelet. The reason why is that any discretization based on the DFT will yield a rasterized version of the truncated Fourier series. Thus, applying the DWT to that will (at best give you the wavelet coefficients of the truncated Fourier series). The truncated Fourier series of the Haar wavelet is infinitely smooth and hence it must have infinitely many Haar coefficients. This is why this approach breaks down.
Note also that if one uses a DWT based on other wavelets than Haar, then one is doing the wavelet crime, and the coefficients produced by the DWT are not even the wavelet coefficients of the truncated Fourier series.
The correct way of doing the discretization is to create a matrix whose elements are inner products of the Fourier basis and the Haar basis. This yields an infinite matrix and then one must use uneven sections.
I'll send you some codes that can produce these matrices if you would like to try this "infinite dimensional compressed sensing", just let me know if you want some more stuff. Let me know how the demo worked.
Best wishes,
Anders, 
P.S. You need to download spgl1 from the spgl1 webpage to run the demo.
After witnessing the Gibbs phenomenon first hand, I asked Anders some further explanation:
..... 
> Can you clarify this wavelet crime statement ?
> 
Indeed, the wavelet crime term was introduced by Gil Strang (I believe) and is the following phenomenon: The Discrete wavelet transform is an infinite dimensional operation that takes the coefficients of the expansion of the function corresponding to the scaling function. The output of the discrete wavelet transform are the wavelet coefficients as well as the scaling coefficients corresponding to the next level. When working in a discrete framework the input of the discrete wavelet transform can only be finite. So what does it mean to take the discrete wavelet transform of say an image. Let's start with the Haar wavelet for simplicity. The Haar wavelet has the characteristic function as its scaling function, that means that we may view an image as a sum of characteristic functions, in fact we may view an image as an infinite sum of characteristic functions with only finitely many non-zero coefficients. Plugging this into the discrete wavelet transform now gives us the correct output, in particular, in the Haar case there is no wavelet crime.
So if y is a vector of Fourier coefficients of a function f and we let
x = DWT \times DFTy, (DWT is the discrete wavelet transform corresponding to the Haar wavelet)
then, since DFTy is a rasterized version of the truncated Fourier series of f, then x is essentially the Haar coefficients of the truncated Fourier series (this is why the example I sent you fails so dramatically)
However, it is in the non-Haar case the wavelet crime occurs. The problem is that for, say DB4, the scaling function is not the characteristic function. So the discrete wavelet transform of an image should be the output of the transform getting the coefficients corresponding to the scaling function as the input. The wavelet crime is when the image itself is plugged into the discrete wavelet transform (as in the Haar case). Thus, when the wavelet crime is committed, the output has very little to do with the actual wavelet coefficients.
In our framework there is no wavelet crime as we go directly for the wavelet coefficients (there is no use of the discrete wavelet transform).



While some of us were bothered by the results of the Matlab Programming Contest results, the real genesis of this conversation stemmed initially from Leslie Smith's recent quest on how to compare bicubic interpolation with compressive sensing reconstruction on the Compressive Sensing LinkedIn group. During the thread, he wrote the following: 
....I recently read a paper by Romberg called "Imaging via CS" in which he simulates CS and he made his code available. I downloaded his code and started running it yesterday. It gets better PSNR results for CS than anything else I've tried. I don't understand the camera architecture he is simulated but this is an encouraging line of inquiry.

in that paper, Justin wrote about an intriguing scheme

The second scheme, which we call “compressive imaging,” again sketches the image by measuring the first 1,000 DCT coefficients but then switches to pseudorandom φk to acquire the details

This is an intriguing approach for many reasons, not the least is that it is hardly listed as a generic scheme in compressive sensing. Of specific interest this scheme, that seems to be doing extra well, parallels the approach of Ben and Anders except of course for the application of the TV norm for the final reconstruction.. How is it similar ? take a look at the six slides below extracted from reference [3]. The first three slides talk about the safe zone that Ben and Anders discussed initially at the top of this entry, then on slide 4, 5 and 6, we get to see the beginning of an explanation as to why Justin's second scheme may be right on the money. Except of course that in Ben and Anders's approach we don't need the heuristics of the TV-norm.










And then, the incoherence property is only a sufficient condition.....

Thank you to both Ben and Anders for being good sports and answering my dumb questions.

References:
[1] Ben Adcok, Anders Hansen,; E. Herrholz,; G. Teschke, "Generalized sampling, infinite-dimensional compressed sensing, and semi-random sampling for asymptotically incoherent dictionaries".
[2] Ben Adcok ,  Anders Hansen, "Generalized Sampling and Infinite Dimensional Compressed Sensing".
[4] "Beyond consistent reconstructions: optimality and sharp bounds for generalized sampling, and application to the uniform resampling problem" Ben Adcok, Anders Hansen, Clarice Poon
[5]  Ben Adcok, Anders Hansen and Clarice Poon. On optimal wavelet reconstructions from Fourier samples: linearity and universality of the stable sampling rate,
[6] Ben Adcok, Anders Hansen and Clarice Poon. Beyond consistent reconstructions: optimality and sharp bounds for generalized sampling, and application to the uniform resampling problem,




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Monday, December 03, 2012

PDRank: Penalty Decomposition Methods for Rank Minimization (and more) - implementation -



Penalty Decomposition Methods for Rank Minimization by Zhaosong Lu, Yong Zhang. The abstract reads:
In this paper we consider general rank minimization problems with rank appearing in either objective function or constraint. We first establish that a class of special rank minimization problems has closed-form solutions. Using this result, we then propose penalty decomposition methods for general rank minimization problems in which each subproblem is solved by a block coordinate descend method. Under some suitable assumptions, we show that any accumulation point of the sequence generated by the penalty decomposition methods satisfies the first-order optimality conditions of a nonlinear reformulation of the problems. Finally, we test the performance of our methods by applying them to the matrix completion and nearest low-rank correlation matrix problems. The computational results demonstrate that our methods are generally comparable or superior to the existing methods in terms of solution quality
The PDRank package can be dowloaded here. Also of interest, the PDSparse package is here.

Other papers from the same author include: Iterative Hard Thresholding Methods for l0 Regularized Convex Cone Programming by Zhaosong Lu. The abstract reads:

In this paper we consider l0 regularized convex cone programming problems. In particular, we first propose an iterative hard thresholding (IHT) method and its variant for solving l0 regularized box constrained convex programming. We show that the sequence generated by these methods converges to a local minimizer. Also, we establish the iteration complexity of the IHT method for finding an -local-optimal solution. We then propose a method for solving l0 regularized convex cone programming by applying the IHT method to its quadratic penalty relaxation and establish its iteration complexity for fi nding an -approximate local minimizer. Finally, we propose a variant of this method in which the associated penalty parameter is dynamically updated, and show that every accumulation point is a local minimizer of the problem.
 

In this paper we study general lp regularized unconstrained minimization problems. In particular, we derive lower bounds for nonzero entries of rst- and second-order stationary points, and hence also of local minimizers of the lp minimization problems. We extend some existing iterative reweighted l1 (IRL1) and l2 (IRL2) minimization methods to solve these problems and proposed new variants for them in which each subproblem has a closed form solution. Also, we provide a uni ed convergence analysis for these methods. In addition, we propose a novel Lipschitz continuous -approximation to kxkpp. Using this result, we develop new IRL1 methods for the lp minimization problems and showed that any accumulation point of the sequence generated by these methods is a rst-order stationary point, provided that the approximation parameter is below a computable threshold value. This is a remarkable result since all existing iterative reweighted minimization methods require that be dynamically updated and approach zero. Our computational results demonstrate that the new IRL1 method is generally more stable than the existing IRL1 methods [21, 18] in terms of objective function value and CPU time.






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Saturday, December 01, 2012

Nuit Blanche in Review (November 2012 Edition)

Ever since the last Nuit Blanche's Month in Review, things got going in many areas

First, It looks like I am getting the hang of writing these Sunday Morning Insights, so much so that now they have a tag. It's a little bit like in Aggieland, every time you do something twice it becomes a tradition. I don't know how much time I will be able to keep up on those or if they are useful but this is an interesting area to explore. There were three entries for this month.  It will not have escaped the ever sharp and attentive reader that there were more than three Sundays this month. I agree but the these entries are called Sunday Morning Insight, the last word being as important as the first two:
At some point in time, people will have to notice that our community is at the forefront of open scientific  inquiry not because of the substantial contribution it brings to the world but rather by the natural way of doing things , i.e. share their codes with the rest of the world. I have also noted a burgeoning trend in setting up some of these efforts on GitHub starting with SPGL1. When you talk to your colleagues let them know you are part of that trend, you are sending a very strong signal. Here are the implementation that were listed this month: 


I, for one, am stunned by the quality of the diversity of the algorithms that are proposed. This month we had a few entries related to hardware hacking. This is a trend that will not die. When you go to some of these meetings, you are generally asked to provide three tags that somehow define your interests. The latest tags I used were: Dumb Sensors, Really Dumb Sensors, Really Really Dumb Sensors. It definitely is an attention getter but I suppose it can turn people off too. In light of these trends I wonder if I should not add "the Internet of Things" to the Wondering Star blog theme. The reason I started that blog was to talk about sensors that were the size of a planet. Most were government owned projects but I see how the arrival of Arduino, OpenPicus could change this altogether, stay tuned: Anyway, here are the entries on this theme this month:

Other entries that are difficult to sum in one or two themes are listed below. Several received some unusual large traffic:

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