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Friday, February 27, 2015

Approximate Message Passing with Restricted Boltzmann Machine Priors

The great convergence is upon us. From the following paper:

The present paper demonstrates the first steps in incorporating deep learned priors into generalized linear problems such as compressed sensing.


 
Approximate Message Passing with Restricted Boltzmann Machine Priors by Eric W. Tramel, Angélique Drémeau, Florent Krzakala
Approximate Message Passing (AMP) has been shown to be an excellent statistical approach to signal inference and compressed sensing problem. The AMP framework provides modularity in the choice of signal prior; here we propose a hierarchical form of the Gauss-Bernouilli prior which utilizes a Restricted Boltzmann Machine (RBM) trained on the signal support to push reconstruction performance beyond that of simple iid priors for signals whose support can be well represented by a trained binary RBM. We present and analyze two methods of RBM factorization and demonstrate how these affect signal reconstruction performance within our proposed algorithm. Finally, using the MNIST handwritten digit dataset, we show experimentally that using an RBM allows AMP to approach oracle-support performance.  
 
 
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Gaussian Phase Transitions and Conic Intrinsic Volumes: Steining the Steiner Formula

 
 
Stéphane Chrétien just sent me the following:
 
Dear Igor,
 
I hope you are doing fine !
 
I recently read the following paper:

http://arxiv.org/abs/1411.6265

which uses techniques such as the Stein method for proving a CLT explaining precisely the asymptotical phase transition phenomenon in compressed sensing with gaussian measurements. The readers of Nuit Blanche might also be interested in this research.

Best regards, 
Thank you Stéphane !


Intrinsic volumes of convex sets are natural geometric quantities that also play important roles in applications, such as linear inverse problems with convex constraints, and constrained statistical inference. It is a well-known fact that, given a closed convex cone C⊂Rd, its conic intrinsic volumes determine a probability measure on the finite set {0,1,...d}, customarily denoted by L(VC). The aim of the present paper is to provide a Berry-Esseen bound for the normal approximation of L(VC), implying a general quantitative central limit theorem (CLT) for sequences of (correctly normalised) discrete probability measures of the type L(VCn), n≥1. This bound shows that, in the high-dimensional limit, most conic intrinsic volumes encountered in applications can be approximated by a suitable Gaussian distribution. Our approach is based on a variety of techniques, namely: (1) Steiner formulae for closed convex cones, (2) Stein's method and second order Poincar\'e inequality, (3) concentration estimates, and (4) Fourier analysis. Our results explicitly connect the sharp phase transitions, observed in many regularised linear inverse problems with convex constraints, with the asymptotic Gaussian fluctuations of the intrinsic volumes of the associated descent cones. In particular, our findings complete and further illuminate the recent breakthrough discoveries by Amelunxen, Lotz, McCoy and Tropp (2014) and McCoy and Tropp (2014) about the concentration of conic intrinsic volumes and its connection with threshold phenomena. As an additional outgrowth of our work we develop total variation bounds for normal approximations of the lengths of projections of Gaussian vectors on closed convex sets.  
 
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Thursday, February 26, 2015

Tutorial: Submodularity in Machine Learning Applications

Here is a tutorial on Submodularity in Machine Learning Applications by Jeff Bilmes.
 
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RSVDPACK: Subroutines for computing partial singular value decompositions via randomized sampling on single core, multi core, and GPU architectures - implementation -


RSVDPACK: Subroutines for computing partial singular value decompositions via randomized sampling on single core, multi core, and GPU architectures by Sergey Voronin, Per-Gunnar Martinsson

This document describes an implementation in C of a set of randomized algorithms for computing partial Singular Value Decompositions (SVDs). The techniques largely follow the prescriptions in the article "Finding structure with randomness: Probabilistic algorithms for constructing approximate matrix decompositions," N. Halko, P.G. Martinsson, J. Tropp, SIAM Review, 53(2), 2011, pp. 217-288, but with some modifications to improve performance. The codes implement a number of low rank SVD computing routines for three different sets of hardware: (1) single core CPU, (2) multi core CPU, and (3) massively multicore GPU.  
The implementations are on Sergey Voronin's GitHub: More specifically here.
 
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Wednesday, February 25, 2015

Unsupervised Learning of Acoustic Features Via Deep Canonical Correlation Analysis





It has been previously shown that, when both acoustic and articulatory training data are available, it is possible to improve phonetic recognition accuracy by learning acoustic features from this multi-view data with canonical correlation analysis (CCA). In contrast with previous work based on linear or kernel CCA, we use the recently proposed deep CCA, where the functional form of the feature mapping is a deep neural network. We apply the approach on a speaker-independent phonetic recognition task using data from the University of Wisconsin X-ray Microbeam Database. Using a tandem-style recognizer on this task, deep CCA features improve over earlier multi-view approaches as well as over articulatory inversion and typical neural network-based tandem features. We also present a new stochastic training approach for deep CCA, which produces both faster training and better-performing features.
 
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Scalable audio separation with light Kernel Additive Modelling - implementation -

Using randomization to scale some capabilities on low power systems, this is what we have today: Scalable audio separation with light Kernel Additive Modelling by Antoine Liutkus, Derry Fitzgerald, Zafar Rafii
Recently, Kernel Additive Modelling (KAM) was proposed as a unified framework to achieve multichannel audio source separation. Its main feature is to use kernel models for locally describing the spectrograms of the sources. Such kernels can capture source features such as repetitivity, stability over time and/or frequency, self-similarity, etc. KAM notably subsumes many popular and effective methods from the state of the art, including REPET and harmonic/percussive separation with median filters. However, it also comes with an important drawback in its initial form: its memory usage badly scales with the number of sources. Indeed, KAM requires the storage of the full-resolution spectrogram for each source, which may become prohibitive for full-length tracks or many sources. In this paper, we show how it can be combined with a fast compression algorithm of its parameters to address the scalability issue, thus enabling its use on small platforms or mobile devices.  
The implementation is one Antoine Liutkus' KAML page.
 
 
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Tuesday, February 24, 2015

Crossing the P-river (follow-up)

A follow up to yesterday's blog entry. How much time did it take to gather all the information from the entire bacterial genome using a USB connected instrument that looks like a large memory stick and featured in the paper in Crossing the P-river: A complete bacterial genome assembled de novo using only nanopore sequencing data ?

 


Wow ! You're seeing history in the making.
 
Credit photo: this forum thread
 
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Compressive spectrum sensing of radar pulses based on photonic techniques

 
 
Here is another instance of Compressive Sensing hardware: Compressive spectrum sensing of radar pulses based on photonic techniques by Qiang Guo, Yunhua Liang, Minghua Chen, Hongwei Chen, and Shizhong Xie

We present a photonic-assisted compressive sampling (CS) system which can acquire about 106 radar pulses per second spanning from 500 MHz to 5 GHz with a 520-MHz analog-to-digital converter (ADC). A rectangular pulse, a linear frequency modulated (LFM) pulse and a pulse stream is respectively reconstructed faithfully through this system with a sliding window-based recovery algorithm, demonstrating the feasibility of the proposed photonic-assisted CS system in spectral estimation for radar pulses. 
 
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Monday, February 23, 2015

Crossing the P-river: A complete bacterial genome assembled de novo using only nanopore sequencing data

 
 
We interrupt our regularly scheduled program, you probably remember this entry from fifteen days ago:
 Here is a new piece of that puzzle, with the right sensor (the Oxford Nanopre MinION instrument a long read sequencer), things that used to be difficult are enabling the flooding of a new tsunami: A complete bacterial genome assembled de novo using only nanopore sequencing data by Nicholas James Loman , Joshua Quick , Jared T Simpson

A method for de novo assembly of data from the Oxford Nanopore MinION instrument is presented which is able to reconstruct the sequence of an entire bacterial chromosome in a single contig. Initially, overlaps between nanopore reads are detected. Reads are then subjected to one or more rounds of error correction by a multiple alignment process employing partial order graphs. After correction, reads are assembled using the Celera assembler. We show that this method is able to assemble nanopore reads from Escherichia coli K-12 MG1655 into a single contig of length 4.6Mb permitting a full reconstruction of gene order. The resulting assembly has 98.4% nucleotide identity compared to the finished reference genome.
The software pipeline used to generate these assemblies is freely available online at https://github.com/jts/nanocorrect.
 
 
 
Related blog entries:

 

 

 
 
 
 
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X-Ray Vision with Only WiFi Power Measurements Using Rytov Wave Models

We continue our series of Hardware related compressive sensing blog entries with this tomography using WiFi and robots to cover the area of interest from different angles.




In this paper, unmanned vehicles are tasked with seeing a completely unknown area behind thick walls based on only wireless power measurements using WLAN cards. We show that a proper modeling of wave propagation that considers scattering and other propagation phenomena can result in a considerable improvement in see-through imaging. More specifically, we develop a theoretical and experimental framework for this problem based on Rytov wave models, and integrate it with sparse signal processing and robotic path planning. Our experimental results show high-resolution imaging of three different areas, validating the proposed framework. Moreover, they show considerable performance improvement over the state-of-the-art that only considers the Line Of Sight (LOS) path, allowing us to image more complex areas not possible before. Finally, we show the impact of robot positioning and antenna alignment errors on our see-through imaging framework. 

In the end, I note their use of TV as a way to regularize their signals and I wonder if by modulating the power level of the emitters and having more than one receivers (they seem to have only two robots, one emitting the other receiving), then the results might be even more beautiful than what they have. While the system is indeed linear, it seems to rely on much trajectory design for both robots. With additional receivers, one would think that some of the trajectory issues might become less important but then additional receivers woud also mean that the system is not linear anymore as is the case of CT (traditional CT is linear, source coding CT is not).

On a totally unrelated note, I wonder if using monocular camera SLAM would simplify some of the embedded coding that goes into this current set up.

The project page is here.
 
 
 
another Wifi related project:

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