Monday, November 25, 2013

A Favor to Ask



Nuit Blanche has had more than 2,500,000 page views so far and its ten year anniversary is coming up. If any of you has found the blog entries interesting, and most importantly insightful, or more, I would not mind if you were to say so in a recommendation on my LinkedIn profile.

Micro-modulated luminescence tomography


Micro-modulated luminescence tomography by Wenxiang Cong, Fenglin Liu, Chao Wang, Ge Wang

Imaging depth of optical microscopy has been fundamentally limited to millimeter or sub-millimeter due to light scattering. X-ray microscopy can resolve spatial details of few microns deeply inside a sample but the contrast resolution is still inadequate to depict heterogeneous features at cellular or sub-cellular levels. To enhance and enrich biological contrast at large imaging depth, various nanoparticles are introduced and become essential to basic research and molecular medicine. Nanoparticles can be functionalized as imaging probes, similar to fluorescent and bioluminescent proteins. LiGa5O8:Cr3+ nanoparticles were recently synthesized to facilitate luminescence energy storage with x-ray pre-excitation and the subsequently stimulated luminescence emission by visible/near-infrared (NIR) light. In this paper, we suggest a micro-modulated luminescence tomography (MLT) approach to quantify a nanophosphor distribution in a thick biological sample with high resolution. Our numerical simulation studies demonstrate the feasibility of the proposed approach.

the algorithm used was detailed in this behins a paywall paper: A few-view reweighted sparsity hunting (FRESH) method for CT image reconstruction by Ming Chang, Liang Li, Zhiqiang Chen, Yongshun Xiao, Li Zhang, Ge Wang

In recent years, the total variation (TV) minimization method has been widely used for compressed sensing (CS) based CT image reconstruction. In this paper, we propose a few-view reweighted sparsity hunting (FRESH) method for CT image reconstruction, and demonstrate the superior performance of this method. Specifically, the key of the purposed method is that a reweighted total variation (RwTV) measure is used to characterize image sparsity in the cost function, outperforming the conventional TV counterpart. To solve the RwTV minimization problem efficiently, the Split-Bregman method and other state-of-the-art L1 optimization methods are compared. Inspired by the fast iterative shrinkage/thresholding algorithm (FISTA), a predication step is incorporated for fast computation in the Split-Bregman framework. Extensive numerical experiments have shown that our FRESH approach performs significantly better than competing algorithms in terms of image quality and convergence speed for few-view CT. High-quality images were reconstructed by our FRESH method after 250 iterations using only 15 few-view projections of the Forbild head phantom while other competitors needed more than 800 iterations. Remarkable improvements in details in the experimental evaluation using actual sheep thorax data further indicate the potential real-world application of the FRESH method.



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Friday, November 22, 2013

Paris Machine Learning Meetup #6: Playing with Kaggle/ Botnet detection with Neural Networks. Jouer avec Kaggle / Detection de Botnets

Before I get to the announcement for the next Paris Machine Learning meetup #6, let me point to a meetup that will take place in about 9 hours in Silicon Valley on Compressed sensing techniques for sensor data using unsupervised learning by Song Cui. Coming back to the focus of this announcement, on December 11th, we will have the sixth Paris Machine Learning Meetup: Playing with Kaggle/ Botnet detection with Neural Networks. Jouer avec Kaggle / Detection de Botnets. Here is the announcement in French.

Mercredi 11 Decembre à 19h00 à DojoEvents, 41 Boulevard Saint-Martin, Paris 

Pour ce sixieme rendez-vous du Machine Learning à Paris nous aurons au moins deux présentateurs: Matthieu Scordia (Profil Kaggle: http://www.kaggle.com/users/70112/matt-sco ) et Joseph Ghafari ( http://www.josephghafari.com/ ) . Matthieu est classe 147eme sur 130,000 utilisateurs de Kaggle. Il nous parlera des différentes stratégies mises en place pour concourir dans les differents challenges de la plateforme Kaggle. Joseph, lui, nous parlera de l'utilisation d'un reseau de neurones pour la detection de bots sur les reseaux d'un exploitant telecom francais. Les présentations ainsi que le Champagne seront en français.

Résumé des présentations:

* Les compétitions Kaggle, un moyen fun et instructif pour mesurer ses compétences en machine learning. Matthieu nous invitera à entrer dans un challenge et donnera quelques astuces/pièges à éviter. Matthieu Scordia (profil Kaggle: http://www.kaggle.com/users/70112/matt-sco ), sa bio: Master's degree in Artificial Intelligence @ UPMC.
Data Scientist Junior @ Dataiku.

* "Réseaux de neurones pour la détection de Botnets". Le but de cette etude est d'appliquer de nouveaux modèles de réseaux de neurones pour classifier des traces de trafic internet issues de serveurs DNS d'Orange. Un apprentissage supervisé est appliqué à ces données pour : détecter les traces issues de trafic malveillant (Botnets en particulier) et déterminer les paramètres réseaux les plus pertinents pour caractériser le passage d'un Bot sur le réseau. Joseph Ghafari ( http://www.josephghafari.com/ )

Si vous ou un collègue, voulez-vous inscrire a la liste du meetup, vous pouvez le faire directement à

http://www.meetup.com/Paris-Machine-learning-applications-group/

Pour s'inscrire au meetup #6 c'est ici: http://www.meetup.com/Paris-Machine-learning-applications-group/events/150851882/

Les archives des précédents meetups se trouvent ici:
http://nuit-blanche.blogspot.com/p/paris-based-meetups-on-machine-learning.html

Il y aussi un groupe Paris Machine Learning sur LinkedIn:
http://www.linkedin.com/groups?gid=6400776

Les organisateurs,

Franck Bardol, Frederick Demback, Igor Carron
 


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Randomized Items: $\ell_p$ Pooling Representations, the little Grothendieck Problem, Last 100 interesting entries.


Afonso Bandeira just sent me the following:

Hi Igor,
First of all, congrats on the great blog!
I noticed that you mentioned the Grothendieck problem a few days ago in your blog. I just wrote a blog post (about my work on a natural generalization of that problem) where I discuss that problem quite a bit. I thought you might want to take a look:
Keep up the good work with your blog!
Best,
Afonso
Thanks AfonsoAfonso restarted his blog in full force since September, here is a longer list of entries from his blog:

I did a small survey on the last 100 posts that received either more than a 1000 page views (a certain amount were just below that threshold) or received more than 8 Google+1, here there are below. I like the fact that the Sunday Morning Insight series does generate some readership and/or appreciation:


credit: ESA/NASA, SOHO Magnetogram

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Thursday, November 21, 2013

Signal Recovery from $\ell_p$ Pooling Representations

Happy Thanksgiving y'all.

In Sunday Morning Insight: A Quick Panorama of Sensing from Direct Imaging to Machine Learning, we saw that the main difference between neural networks these days and traditional sensing revolved around the acquisition stage: It is linear in compressive sensing while nonlinear in neural networks. At some point the two fields will collide (for one thing Imaging CMOSes are already nonlinear devices and there is this issue of quantization and 1bit compressive sensing lurking beneath). One of the question would be to ask how does the nonlinear aquisition stage permits some sort of recovery, which seems to be the question asked in the following paper (and it seems that there is a clear connection to phase retrieval.)


In this work we compute lower Lipschitz bounds of $\ell_p$ pooling operators for $p=1, 2, \infty$ as well as $\ell_p$ pooling operators preceded by half-rectification layers. These give sufficient conditions for the design of invertible neural network layers. Numerical experiments on MNIST and image patches confirm that pooling layers can be inverted with phase recovery algorithms. Moreover, the regularity of the inverse pooling, controlled by the lower Lipschitz constant, is empirically verified with a nearest neighbor regression.

Tuesday, November 19, 2013

Learning Intuitive Compressive Sensing


I was talking recently to someone about the fact that one of the interesting thing to come out of  the whole Compressive Sensing research effort is how the community has grown fast because of the sharing of codes in order to adhere to some reproducible research standards. In that vein, Gary Ballantyne and Martin Clark sent me the following intriguing email on the learning side of things:

As a start-up we're finding our feet in the world of community-based modelling and computation. As part of that process we'd like to offer the compressive sensing community a place to host an interactive tutorial--as a resource for newcomers, students and teachers--on puzlet.com. We've made a start (in two parts): 
There is code to run on the site (in sandboxes), and for navigation try the escape key and reading the "Keyboard shortcuts and tips".
However, we're not experts and we'd welcome any feedback. Our goal was to take someone with a basic technical background to the point where they could appreciate the broad stokes of a journal paper (in that sense, we wrote it for ourselves). Ultimately the tutorial will be community edited, but for now we will just use info@haulashore.com for requests and feedback.
Many thanks,
Gary
Thanks Gary !

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The STONE Transform: Multi-Resolution Image Enhancement and Real-Time Compressive Video

This is an interesting direction especially coming from some of the inventors of the single pixel camera. The following paper does compressive sensing on images and video but it does so by allowing what they call a preview capability, i.e. the ability to produce, with very little computation, a low resolution image without the complexity required to go faster than a blink of an eye. This is significant in two ways:
  • the way the measurement matrix is designed opens the door to numerous different implementations
  • the approach provides a way for hybrid systems and more importantly lends credence to the work on infinite dimensional work/generalized sampling which points to a requirement to sample 'normally' in the low frequency range (which is what those previews are).

without further due here is the paper:



Compressed sensing enables the reconstruction of high-resolution signals from under-sampled data. While compressive methods simplify data acquisition, they require the solution of difficult recovery problems to make use of the resulting measurements. This article presents a new sensing framework that combines the advantages of both conventional and compressive sensing. Using the proposed \stone transform, measurements can be reconstructed instantly at Nyquist rates at any power-of-two resolution. The same data can then be "enhanced" to higher resolutions using compressive methods that leverage sparsity to "beat" the Nyquist limit. The availability of a fast direct reconstruction enables compressive measurements to be processed on small embedded devices. We demonstrate this by constructing a real-time compressive video camera.

Monday, November 18, 2013

Around the blogs in 78 summer hours

In no particular order:


Sebastien

Guest post by Dan Garber and Elad Hazan: The Conditional Gradient Method, A Linear Convergent Algorithm – Part II/II

Guest post by Dan Garber and Elad Hazan: The Conditional Gradient Method, A Linear Convergent Algorithm – Part I/II

5 announcements

Thomas
There’s a new journal in town…
Academia.edu acquires Plasmyd to bring peer review into the 21st century
More on anonymity in peer review
An emerging consensus for open evaluation: 18 visions for the future of scientific publishing
Science Publishing Laboratory
Third-party review platforms
A look at the process of submitting articles to OA journals | Open Science

Steve
CRISPR


ML
Metric Learning: Some Quantum Statistical Mechanics
Music Recommendations and the Logistic Metric Embedding


Petros

Publication List Update: Signal Representations and Embeddings
Internship Openings


Larry
Stein’s Method

Jordan

RANDOM SIMPLICIAL COMPLEXES
SEBASTIAN THRUN, MOOC SKEPTIC

Djalil

About the Jensen inequality
Confined particles with singular pair repulsion

Vladimir

Nokia Emulates Pelican and Lytro Refocusing Function
SiOnyx Says Black Silicon Sensors with 2e Read Noise Possible
Superconducting Image Sensor Measures Energy of Each Photon, with Timestamp
ISORG Demos 96x96 Pixel on Plastic Sensor
Pelican Imaging Presentation
Omnivision Announces 13MP/30fps 1.12um PureCel Low Power Sensor

Christian

Bayesian essentials with R available on amazon
machine learning as buzzword
arXiv bonanza!
MCMC for non-linear state space models using ensembles of latent sequences


Herve

La cuisine note à note à la bbc :
La notion d'innovation

Muthu

Data as a Quantifiable Asset

Greg
First look at the Quonset Microwave Coffee Can Radar Kit, on sale now
Small and Short-Range Radar Systems, coming out spring 2014!
First look at the Quonset Microwave Coffee Can Radar Kit!

Alex

A useful trick for computing gradients w.r.t. matrix arguments, with some examples
Quick note on the Chen, Chi, Goldsmith covariance sketching paper

Laurent
Marseille: from the Vieux Port with hole

Kaggle
Mining data on the 'Data wizards'

Anand

the MAP perturbation framework
expected time for an optimal game of memory
dismissing research communities is counterproductive


Andrew

BDA class G+ hangout another try
Statistics is the least important part of data science
“What are some situations in which the classical approach (or a naive implementation of it, based on cookbook recipes) gives worse results than a Bayesian approach, results that actually impeded the science?”
Why ask why? Forward causal inference and reverse causal questions
I’m negative on the expression “false positives”
“Marginally significant”
Shlemiel the Software Developer and Unknown Unknowns
Doing Data Science: What’s it all about?
My talk in Amsterdam tomorrow (Wed 29 Oct): Can we use Bayesian methods to resolve the current crisis of statistically-significant research findings that don’t hold up?
Uncompressing the concept of compressed sensing

Dustin

Phase retrieval from coded diffraction patterns
A geometric intuition for the null space property
A fully automatic problem solver with human-style output
Probably Approximately Correct


Bob

The final lecture schedule
Paper of the Day (Po'D): Towards a universal representation for audio information retrieval and analysis Edition
Paper of the Day (Po'D): Multi-label sparse coding for automatic image annotation Edition
Deconstructing statistical questions and vacuous papers

Larry

Nonparametric Regression, ABC and CNN
PubMed Commons

Dirk
TGV minimizers in 1D and conditional gradient methods
The Kurdyka-Łojasiewicz inequality and gradient descent methods
Post-it for convex optimization for optimal transport, value functions, accelerated forward backward and Bayesion inversion

Tim

DBD1 — initial post

Hein

Simple Fact about Maximizing a Gaussian
Ali Rahimi’s “Random Kitchen Sinks” Video
Assorted Links

Danny

PowerLyra
Online Machine Learning Course by Alex Smola & Geoff Gordon (CMU)
Hunch's Taste Graph
Notable presentation: Datapad @ Strata NY+ PyData
The 3rd GraphLab Conference is coming!
Notable presentation: Mark Levy's Recsys talk
LSRS 2013 - A great success!
Jason

FAA Releases UAS Integration Roadmap


While on Nuit Blanche, we had:




Image Credit: NASA/JPL/Space Science Institute
W00084967.jpg was taken on November 16, 2013 and received on Earth November 18, 2013. The camera was pointing toward SATURN-RINGS at approximately 1,998,613 miles (3,216,456 kilometers) away, and the image was taken using the CL1 and CL2 filters. This image has not been validated or calibrated. 


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Sunday, November 17, 2013

Sunday Morning Insight: Exploring Further the Limits of Admissibility

It was only on his fourth voyage that Christopher Columbus actually set foot on what I would call the real American continent (not far from where the Panama canal would stand 400 years or so later).



If one is to look at last Sunday Morning Insight's (The Map Makers) and this week's entries, one can witness how the navitational maps are being used:
and how they potentially constrain technologies:
and how they should be compared to previous work (see [2] Compressive Phase Retrieval via Generalized Approximate Message Passing)

In all these cases, the issue generally revolves around the performance of the solver or how the sharp phase transitions can be seen as a rule of thumb for dimensionality studies. One of the most important element of these sharp phase transitions can be thought along a different line of investigation: Ever since 2004, the whole reasoning for the admissibility conditions for measurement matrices or the size of an underdetermined system of linear equations, has revolved around conditions like RIP, NSP, etc...It certainly is a problem when one tries to map the discretization of an inverse problem and find out if it fits a compressive approach. None of these conditions help in providing an insight. In particular, one does not know how to locate sensors or even how to operate them.

If a matrix doesn't fit any of these conditions: is there some hope to extract the possibly sparsest solution ? It turns out, the only way to quantify this is through the study of the sharp phase transitions. In the past two weeks, we had two arxiv preprints trying to address this issue of too coherent measurement matrices and how phase transitions establish the performance of the actual sensing. 




The first paper uses tomography as defined in [1] but instead of going the traditional route of the synthesis approach, the paper studies the phase transition of the co-sparse problem instead. 



Back in 2010, I wondered (and still do) if, in order to map tomogaphic problems, we shouldn't use Boogie-Woogie grids in order to bring back some randomization in the problematic. The first paper seems to have the beginning of an answer to this question and it looks like it is mildly negative (see result for perturbed matrices). It certainly is the beginning of an answer but I wonder if this holds for CT-like tomography which gets to be nonlinear as soon as you make it a source coding system (think about it, a linear problem becomes nonlinear as soon as the excitation sources are used simultaneously, mmmmhhhhh).

Here are the papers:



We study unique recovery of cosparse signals from limited-angle tomographic measurements of two- and three-dimensional domains. Admissible signals belong to the union of subspaces defined by all cosupports of maximal cardinality ℓ with respect to the discrete gradient operator. We relate ℓ both to the number of measurements and to a nullspace condition with respect to the measurement matrix, so as to achieve unique recovery by linear programming. These results are supported by comprehensive numerical experiments that show a high correlation of performance in practice and theoretical predictions. Despite poor properties of the measurement matrix from the viewpoint of compressed sensing, the class of uniquely recoverable signals basically seems large enough to cover practical applications, like contactless quality inspection of compound solid bodies composed of few materials.
From the paper

Several observations are in order.
  • Perturbation of projection matrices brings no significant advantage in the practically relevant case of unknown co-support. The empirical transitions will remain the same for perturbed and unperturbed matrices. This is very different to the `1-minimization problem (1.1), where perturbation boosts the recovery performance significantly as shown in [PS13].
  • In the case of known co-support, when Bu = 0 is added as additional constraint, unperturbed matrices perform better. We notice that the empirical phase transition is above the red curve, and deduce that linear dependencies might be beneficial when the co-support is known.
  • When increasing the number of projecting directions (4,5,6 or more) the differences between estimated (dashed) and theoretical (continuous line) phase transition become smaller. This might be due to the fact that linear dependencies between the columns (and rows) of A become “rare”, and the assumptions of Propositions 4.1 and 4.2 are more likely to be satisfied.
  • In 3D the difference between empirical phase transitions for 3 and 4 projecting directions is very small, i.e. relative phase transitions are almost equal. This is different to the 2D case above. We currently do not have an explanation for this phenomenon.
  • The log-log plot in Figure 15 shows that phase transitions in 3D exhibit a power law behavior, similar to the theoretical phase transitions for `1-recovery from [PS13], [PSS13]. Moreover, the plot also shows the scaling exponent of the green and red curves is higher, which results in significantly higher sparsity levels of the image gradient then image sparsity which allow exact recovery for big volumes and large d.

The second paper maps how a new solver perform with these highly coherent matrices.



Compressive sensing is a methodology for the reconstruction of sparse or compressible signals using far fewer samples than required by the Nyquist criterion. However, many of the results in compressive sensing concern random sampling matrices such as Gaussian and Bernoulli matrices. In common physically feasible signal acquisition and reconstruction scenarios such as super-resolution of images, the sensing matrix has a non-random structure with highly correlated columns. Here we present a compressive sensing type recovery algorithm, called Partial Inversion (PartInv), that overcomes the correlations among the columns. We provide theoretical justification as well as empirical comparisons.

References:
The reconstruction of three-dimensional sparse volume functions from few tomographic projections constitutes a challenging problem in image reconstruction and turns out to be a particular instance problem of compressive sensing. The tomographic measurement matrix encodes the incidence relation of the imaging process, and therefore is not subject to design up to small perturbations of non-zero entries. We present an average case analysis of the recovery properties and a corresponding tail bound to establish weak thresholds, in excellent agreement with numerical experiments. Our result improve the state-of-the-art of tomographic imaging in experimental fluid dynamics by a factor of three.

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