The AstroStat Slog » Imaging Weaving together Astronomy+Statistics+Computer Science+Engineering+Intrumentation, far beyond the growing borders Fri, 09 Sep 2011 17:05:33 +0000 en-US hourly 1 CAS 2010 Sat, 14 Aug 2010 18:50:05 +0000 chasc The schedule for the mini-Workshop on Computational AstroStatistics is set:

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[MADS] Kalman Filter Fri, 02 Oct 2009 03:18:32 +0000 hlee I decide to discuss Kalman Filter a while ago for the slog after finding out that this popular methodology is rather underrepresented in astronomy. However, it is not completely missing from ADS. I see that the fulltext search and all bibliographic source search shows more results. Their use of Kalman filter, though, looked similar to the usage of “genetic algorithms” or “Bayes theorem.” Probably, the broad notion of Kalman filter makes it difficult my finding Kalman Filter applications by its name in astronomy since often wheels are reinvented (algorithms under different names have the same objective).

When I learned “Kalman filter” for the first time, I was not sure how to distinguish it from “Yule-Walker equation” (time series), “Pade approximant, (unfortunately, the wiki page does not have its matrix form). Wiener Filter” (signal processing), etc. Here are those publications, specifically mentioned the name Kalman filter in their abstracts found from ADS.

The motivation of introducing Kalman filter although it is a very well known term is the recent Fisher Lecture given by Noel Cressie at the JSM 2009. He is the leading expert in spatial statistics. He is the author of a very famous book in Spatial Statistics. During his presentation, he described challenges from satellite data and how Kalman filter accelerated computing a gigantic covariance matrix in kriging. Satellite data of meteorology and geosciences may not exactly match with astronomical satellite data but from statistical modeling perspective, the challenges are similar. Namely, massive data, streaming data, multi dimensional, temporal, missing observations in certain areas, different exposure time, estimation and prediction, interpolation and extrapoloation, large image size, and so on. It’s not just focusing denoising/cleaning images. Statisticians want to find the driving force of certain features by modeling and to perform statistical inference. (They do not mind parametrization of interesting metric/measure/quantity for modeling or they approach the problem in a nonparametric fashion). I understood the use of Kalman filter for a fast solution to inverse problems for inference.

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More on Space Weather Tue, 22 Sep 2009 17:03:11 +0000 hlee Thanks to a Korean solar physicist[1] I was able to gather the following websites and some relevant information on Space Weather Forecast in action, not limited to literature nor toy data.

These seem quite informative and I believe more statisticians and data scientists (signal and image processing, machine learning, computer vision, and data mining) easily collaborate with solar physicists. All the complexity, as a matter of fact, comes from data processing to be fed in to (machine, statistical) learning algorithms and defining the objectives of learning. Once settled, one can easily apply numerous methods in the field to these time varying solar images.

I’m writing this short posting because I finally found those interesting articles that I collected for my previous post on Space Weather. After finding them and scanning through, I realized that methodology-wise they only made baby steps. You’ll see a limited number key words are repeated although there is a humongous society of scientists and engineers in the knowledge discovery and data mining.

Note that the objectives of these studies are quite similar. They described machine learning for the purpose of automatizing the procedure of detecting features of interest of the Sun and possible forecasting relevant phenomena that affects our own atmosphere due to associated solar activities.

  1. Automated Prediction of CMEs Using Machine Learning of CME – Flare Associations by Qahwaji et al. (2008) in Solar Phy. vol 248, pp.471-483.
  2. Automatic Short-Term Solar Flare Prediction using Machine Learning and Sunspot Associations by Qahwaji and Colak (2007) in Solar Phy. vol. 241, pp. 195-211

    Space weather is defined by the U.S. National Space Weather Probram (NSWP) as “conditions on the Sun and in the solar wind, magnetosphere, ionosphere, and thermosphere that can influence the performance and reliability of space-borne and ground-based technological systems and can endanger human life or health”

    Personally thinking, the section of “jackknife” needs to be replaced with “cross-validation.”

  3. Automatic Detection and Classification of Coronal Mass Ejections by Qu et al. (2006) in Solar Phy. vol. 237, pp.419-431.
  4. Automatic Solar Filament Detection Using image Processing Techniques by Qu et al. (2005) in Solar Phy., vol. 228, pp. 119-135
  5. Automatic Solar Flare Tracking Using Image-Processing Techniques by Qu, et al. (2004) in Solar Phy. vol. 222, pp. 137-149
  6. Automatic Solar Flare Detection Using MLP, RBF, and SVM by Qu et al. (2003) in Solar Phy. vol. 217, pp.157-172. pp. 157-172

I’d like add a survey paper on another type of learning methods beyond Support Vector Machine (SVM) used in almost all articles above. Luckily, this survey paper happened to address my concern about the “practices of background subtraction” in high energy astrophysics.

A Survey of Manifold-Based Learning methods by Huo, Ni, Smith
[Excerpt] What is Manifold-Based Learning?
It is an emerging and promising approach in nonparametric dimension reduction. The article reviewed principle component analysis, multidimensional scaling (MDS), generative topological mapping (GTM), locally linear embedding (LLE), ISOMAP, Laplacian eigenmaps, Hessian eigenmaps, and local tangent space alignment (LTSA) Apart from these revisits and comparison, this survey paper is useful to understand the danger of background subtraction. Homogeneity does not mean constant background to be subtracted, often cause negative source observation.

More collaborations among multiple disciplines are desired in this relatively new field. For me, it is one of the best data and information scientific fields of the 21st century and any progress will be beneficial to human kind.

  1. I must acknowledge him for his kindness and patience. He was my wikipedia to questions while I was studying the Sun.
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[MADS] compressed sensing Fri, 11 Sep 2009 04:20:54 +0000 hlee Soon it’ll not be qualified for [MADS] because I saw some abstracts with the phrase, compressed sensing from Nonetheless, there’s one publication within refereed articles from ADS, so far.
Title:Compressed sensing imaging techniques for radio interferometry
Authors: Wiaux, Y. et al.
Abstract: Radio interferometry probes astrophysical signals through incomplete and noisy Fourier measurements. The theory of compressed sensing demonstrates that such measurements may actually suffice for accurate reconstruction of sparse or compressible signals. We propose new generic imaging techniques based on convex optimization for global minimization problems defined in this context. The versatility of the framework notably allows introduction of specific prior information on the signals, which offers the possibility of significant improvements of reconstruction relative to the standard local matching pursuit algorithm CLEAN used in radio astronomy. We illustrate the potential of the approach by studying reconstruction performances on simulations of two different kinds of signals observed with very generic interferometric configurations. The first kind is an intensity field of compact astrophysical objects. The second kind is the imprint of cosmic strings in the temperature field of the cosmic microwave background radiation, of particular interest for cosmology.

As discussed, reconstructing images from noisy observations is typically considered as an ill-posed problem or an inverse problem. Owing to the personal lack of comprehension in image reconstruction of radio interferometry observation based on sample from Fourier space via inverse Fourier transform, I cannot judge how good this new adaption of compressed sensing for radio astronomical imagery is. I think, however, compressed sensing will take over many of traditional image reconstruction tools due to their shortage in forgiving sparsely represented large data/images .

Please, check my old post on compressed sensing for more references to the subject like the Rice university repository in addition to references from Wiaux et al. It’s a new exciting field with countless applications, already enjoying wide popularity from many scientific and engineering fields. My thought is that well developed compressed sensing algorithms might resolve bandwidth issues in satellite observations/communication by transmiting more images within fractional temporal intervals for improved image reconstruction.

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[ArXiv] Statistical Analysis of fMRI Data Wed, 02 Sep 2009 00:43:13 +0000 hlee

[arxiv:0906.3662] The Statistical Analysis of fMRI Data by Martin A. Lindquist
Statistical Science, Vol. 23(4), pp. 439-464

This review paper offers some information and guidance of statistical image analysis for fMRI data that can be expanded to astronomical image data. I think that fMRI data contain similar challenges of astronomical images. As Lindquist said, collaboration helps to find shortcuts. I hope that introducing this paper helps further networking and collaboration between statisticians and astronomers.

List of similarities

  • data acquisition: data read in frequency domain and image reconstruction via inverse Fourier transform. (To my naive eyes, It looks similar to Power Spectrum Analysis for cosmic microwave background (CMB) data).
  • amplitudes or coefficients are cared and analyzed, not phase nor wavelets.
  • understanding data:brain physiology or physics like cosmological models that describe data generating mechanism.
  • limits in/trade-off between spatial and temporal resolution.
  • understanding/modeling noise and signal.

These similarities seem common for statistically analyzing images from fMRI or telescopes. Notwithstanding, no astronomers can (or want) to carry out experimental design. This can be a huge difference between medical and astronomical image analysis. My emphasis is that because of these commonalities, strategies in preprocessing and data analysis for fMRI data can be shared for astronomical observations and vise versa. Some sloggers would like to check Section 6 that covers various statistical models and methods for spatial and temporal data.

I’d rather simply end this posting with the following quotes, saying that statisticians play a critical role in scientific image analysis. :)

There are several common objectives in the analysis of fMRI data. These include localizing regions of the brain activated by a task, determining distributed networks that correspond to brain function and making predictions about psychological or disease states. Each of these objectives can be approached through the application of suitable statistical methods, and statisticians play an important role in the interdisciplinary teams that have been assembled to tackle these problems. This role can range from determining the appropriate statistical method to apply to a data set, to the development of unique statistical methods geared specifically toward the analysis of fMRI data. With the advent of more sophisticated experimental designs and imaging techniques, the role of statisticians promises to only increase in the future.

A full spatiotemporal model of the data is generally not considered feasible and a number of short cuts are taken throughout the course of the analysis. Statisticians play an important role in determining which short cuts are appropriate in the various stages of the analysis, and determining their effects on the validity and power of the statistical analysis.

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[MADS] Kriging Wed, 26 Aug 2009 02:19:26 +0000 hlee Kriging is the first thing that one learns from a spatial statistics course. If an astronomer sees its definition and application, almost every astronomer will say, “Oh, I know this! It is like the 2pt correlation function!!” At least this was my first impression when I first met kriging.

There are three distinctive subjects in spatial statistics: geostatistics, lattice data analysis, and spatial point pattern analysis. Because of the resemblance between the spatial distribution of observations in coordinates and the notion of spatially random points, spatial statistics in astronomy has leaned more toward the spatial point pattern analysis than the other subjects. In other fields from immunology to forestry to geology whose data are associated spatial coordinates of underlying geometric structures or whose data were sampled from lattices, observations depend on these spatial structures and scientists enjoy various applications from geostatistics and lattice data analysis. Particularly, kriging is the fundamental notion in geostatistics whose application is found many fields.

Hitherto, I expected that the term kriging can be found rather frequently in analyzing cosmic micro-wave background (CMB) data or large extended sources, wide enough to assign some statistical models for understanding the expected geometric structure and its uncertainty (or interpolating observations via BLUP, best linear unbiased prediction). Against my anticipation, only one referred paper from ADS emerged:

Topography of the Galactic disk – Z-structure and large-scale star formation
by Alfaro, E. J., Cabrera-Cano, J., and Delgado (1991)
in ApJ, 378, pp. 106-118

I attribute this shortage of applying kriging in astronomy to missing data and differential exposure time across the sky. Both require underlying modeling to fill the gap or to convolve with observed data to compensate this unequal sky coverage. Traditionally the kriging analysis is only applied to localized geological areas where missing and unequal coverage is no concern. As many survey and probing missions describe the wide sky coverage, we always see some gaps and selection biases in telescope pointing directions. So, once this characteristics of missing is understood and incorporated into models of spatial statistics, I believe statistical methods for spatial data could reveal more information of our Galaxy and universe.

A good news for astronomers is that nowadays more statisticians and geo-scientists working on spatial data, particularly from satellites. These data are not much different compared to traditional astronomical data except the direction to which a satellite aims (inward or outward). Therefore, data of these scientists has typical properties of astronomical data: missing, unequal sky coverage or exposure and sparse but gigantic images. Due to the increment of computational power and the developments in hierarchical modeling, techniques in geostatistics are being developed to handle these massive, but sparse images for statistical inference. Not only denoising images but they also aim to produce a measure of uncertainty associated with complex spatial data.

For those who are interested in what spatial statistics does, there are a few books I’d like to recommend.

  • Cressie, N (1993) Statistics for spatial data
    (the bible of statistical statistics)
  • Stein, M.L. (2002) Interpolation of Spatial Data: Some Theory for Kriging
    (it’s about Kriging and written by one of scholarly pinnacles in spatial statistics)
  • Banerjee, Carlin, and Gelfand (2004) Hierarchical Modeling and Analysis for Spatial Data
    (Bayesian hierarchical modeling is explained. Very pragmatic but could give an impression that it’s somewhat limited for applications in astronomy)
  • Illian et al (2008) Statistical Analysis and Modelling of Spatial Point Patterns
    (Well, I still think spatial point pattern analysis is more dominant in astronomy than geostatistics. So… I feel obliged to throw a book for that. If so, I must mention Peter Diggle’s books too.)
  • Diggle (2004) Statistical Analysis of Spatial Point Patterns
    Diggle and Ribeiro (2007) Model-based Geostatistics
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Astroinformatics Mon, 13 Jul 2009 00:21:53 +0000 hlee Approximately for a decade, there have been journals dedicated to bioinformatics. On the other hand, there is none in astronomy although astronomers have a long history of comprising a huge volume of catalogs and data archives. Prof. Bickel’s comment during his plenary lecture at the IMS-APRM particularly on sparse matrix and philosophical issues on choosing principal components led me to wonder why astronomers do not discuss astroinformatics.

Nevertheless, I’ve noticed a few astronomers rigorously apply principle component analysis (PCA) in order to reduce the dimensionality of a data set. An evident example of PCA applications in astronomy is photo-z. In contrast to the wide PCA application, almost no publication about statistical adequacy studies is found by investigating the properties of covariance matrix and its estimation method particularly when it is sparse. Even worse, the notion of measurement errors are improperly implemented since statistician’s dimension reduction methodology never confronted astronomers’ measurement errors. How to choose components is seldom discussed since the significance in physics model is rarely agreeing with statistical significance. This disagreement often elongates scientific writings hard to please readers. As a compromise, statistical parts are omitted, which makes me feel the publication incomplete.

Due to its easy visualization via intuitive scales, in wavelet multiscale imaging, the coarse scale to fine scale approach and the assumption of independent noise enables to clean the noisy image and to accentuate features in it. Likewise, principle components and other dimension reduction methods in statistics capture certain features via transformed metrics and regularized, or penalized objective functions. These features are not necessary to match the important features in astrophysics unless the likelihood function and selected priors match physics models. To my knowledge, astronomical literature exploiting PCA for dimension reduction for prediction rarely explains why PCA is chosen for dimensionality reduction, how to compensate the sparsity in covariance matrix, and other questions, often the major topics in bioinformatics. In the literature, these questions are explored to explain the particular selection of gene attributes or bio-markers under a certain response like blood pressures and types of cancers. Instead of binning and chi-square minimization, statisticians explore strategies how to compensate sparsity in the data set to get unbiased best fits and righteous error bars based on data matching assumptions and theory.

Luckily, there are efforts among some renown astronomers to form a community of astroinformatics. At the dawn of bioinformatics, genetic scientists were responsible for the bio part and statisticians were responsible for the informatics until young scientists are educated enough to carry out bioinformatics by themselves. Observing this trend partially from statistics conferences created an urge in me that it is my responsibility to ponder why there has been shortage of statisticians’ involvement in astronomy regardless of plethora of catalogs and data archives with long history. A few postings will follow what I felt while working among astronomers. I hope this small bridging effort to narrow the gap between two communities. My personal wish is to see prospering astroinformatics like bioinformatics.

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Wavelet-regularized image deconvolution Fri, 12 Jun 2009 20:47:36 +0000 hlee

A Fast Thresholded Landweber Algorithm for Wavelet-Regularized Multidimensional Deconvolution
Vonesch and Unser (2008)
IEEE Trans. Image Proc. vol. 17(4), pp. 539-549

Quoting the authors, I also like to say that the recovery of the original image from the observed is an ill-posed problem. They traced the efforts of wavelet regularization in deconvolution back to a few relatively recent publications by astronomers. Therefore, I guess the topic and algorithm of this paper could drag some attentions from astronomers.

They explain the wavelet based reconstruction procedure in a simple term. The matrix-vector product wx= Wx yields the coefficients of x in the wavelet basis, and WTWx reconstructs the signal from these coefficients.

Their assumed model is

y=Hxorig + b,

where y and x_{orig} are vectors containing uniform samples of the original and measured signals; b represents the measurement error. H is a square (block) circulant matrix that approximates the convolution with the PSF. Then, the problem of deconvolution is to find an estimate that maximizes the cost function

J(x) = Jdata(x)+ λ Jreg(x)

They described that “this functional can also interpreted as a (negative) log-likelihood in a Bayesian statistical framework, and deconvolution can then be seen as a maximum a posteriori (MAP) estimation problem.” Also the description of the cost function is applicable to the frequently appearing topic in regression or classification problems such as ridge regression, quantile regression, LASSO, LAR, model/variable selection, state space models from time series and spatial statistics, etc.

The observed image is the d-dimensional covolution of an origianl image (the characteristic function of the object of interest) with the impulse response (or PSF). of the imaging system.

The notion of regularization or penalizing the likelihood seems not well received among astronomers based on my observation that often times the chi-square minimization (the simple least square method) without penalty is suggested and used in astronomical data analysis. Since image analysis with wavelets popular in astronomy, the fast algorithm for wavelet regularized variational deconvolution introduced in this paper could bring faster results to astronomers and could offer better insights of the underlying physical processes by separating noise and background more in a model according fashion, not simple background subtraction.

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space weather Thu, 21 May 2009 22:55:26 +0000 hlee Among billion objects in our Galaxy, outside the Earth, our Sun drags most attention from astronomers. These astronomers go by solar physicists, who enjoy the most abundant data including 400 year long sunspot counts. Their joy is not only originated from the fascinating, active, and unpredictable characteristics of the Sun but also attributed to its influence on our daily lives. Related to the latter, sometimes studying the conditions on the Sun is called space weather forecast.

With my limited knowledge, I cannot lay out all important aspects in solar physics, climate changes (not limited to our lower atmosphere but covering the space between the sun and the earth) due to solar activities, and the most important issues of recent years related to space weather. Only I can emphasize that compared to earth climate/atmosphere or meteorology, contribution from statisticians to space weather is almost none existing. I’ve witnessed frequently that crude eyeballing instead of statistics in analyzing data and quantifying images occurs in Solar Physics. Luckily, a few articles discussing statistics are found and my discussion is rather focused on these papers while leaving a room for solar physicists to chip in how space weather is dealt statistically for collaborating with statisticians.

By the way, I have no intention of degrading “eyeballing” in data analysis by astronomers. Statistical methods under EDA, exploratory data analysis whose counterpart is CDA, confirmatory data analysis, or statistical inference, is basically “eyeballing” with technical jargon and basics from probability theory. EDA is important to doubt every step in astronomers’ chi-square methods. Without those diagnostics and visualization, choosing right statistical strategies is almost impossible with real data sets. I used “crude” because instead of using “edge detection” algorithms, edges are drawn by hand via eyeballing. Also, my another disclaimer is that there are brilliant image processing/computer vision strategies developed by astronomers, which I’m not going to present. I’m focusing on small areas in statistics related to space weather and its forecasting.

Statistical Assessment of Photospheric Magnetic Features in Imminent Solar Flare Predictions by Song et al. (2009) SoPh. v. 254, p.101.

Their forte is “logistic regression” a statistical model that is not often used in astronomy. It is seen when modeling binary responses (or categorical responses like head or tail; agree, neutral, or disgree) and bunch of predictors, i.e. classification with multiple features or variables (astronomers might like to replace these lexicons with parameters). Also, the issue of variable selection is discussed like L_{gnl} to be the most powerful predictor. Their training set was carefully discussed from the solar physical perspective. Against their claim that they used “logistic regression” to predict solar flares for the first time, there was another paper a few years back discussing “logistic regression” to predict geomagnetic storms or coronal mass ejections. This statement can be wrong if flares and CMEs are exclusive events.

The Challenge of Predicting the Occurrence of Intense Storms by Srivastava (2006) J.Astrophys. Astr. v.27, pp.237-242

Probability of the storm occurrence is response in logistic regression model, of which predictors are CME related variables including latitude and longitude of the origin of CME, and interplanetary inputs like shock speeds, ram pressure, and solar wind related measures. Cross-validation was performed. A comment that the initial speed of a CME might be the most reliable predictor is given but no extensive discussion of variable selection/model selection.

Personally speaking, both publications[1] can be more statistically rigorous to discuss various challenges in logistic regression from the statistical learning/classification perspective and from the model/variable selection aspect to define more well behaving and statistically rigorous classifiers.

Often times we plan our days according to the weather forecast (although we grumble weather forecasts are not right, almost everyone relies on numbers and predictions from weather people). Although it may not be 100% reliable, those forecasts make our lives easier. Also, more reliable models are under developing. On the other hand, forecasting space weather with the help of statistics is yet unthinkable. However, scientists and engineers understand that the reliable space weather models help planning space missions and controlling satellites into safety mode. At least I know is that with the presence of flare or CME forecasting models, fewer scientists/engineers need to wake up in the middle of night, because of, otherwise unforeseen storms from the sun.

  1. I thought I collected more papers under “statistics” and “space weather,” not just these two. A few more probably are buried somewhere. It’s hard to believe such rich field is not touched by statisticians. I’d appreciate very much your kind forwarding those relevant papers. I’ll gradually add them.
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[ArXiv] Sparse Poisson Intensity Reconstruction Algorithms Thu, 07 May 2009 16:14:39 +0000 hlee One of [ArXiv] papers from yesterday whose title might drag lots of attentions from astronomers. Furthermore, it’s a short paper.
[arxiv:math.CO:0905.0483] by Harmany, Marcia, and Willet.

Estimating f under “Sparse Poisson Intensity” condition is an frequently appearing topic in high energy astrophysics data analysis. Some might like to check references in the paper, which offer solutions to compressed sensing problems with different kinds of sparsity, minimization approaches, and constraints on f.

Apart from the technical details, the first two sentences from the conclusion,

We have developed computational approaches for signal reconstruction from photon-limited measurements – a situation prevalent in many practical settings. Our method optimizes a regularized Poisson likelihood under nonnegativity constraints

tempt me to study and try their algorithm.

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