23,002 research outputs found
A Convex Formulation for Spectral Shrunk Clustering
Spectral clustering is a fundamental technique in the field of data mining
and information processing. Most existing spectral clustering algorithms
integrate dimensionality reduction into the clustering process assisted by
manifold learning in the original space. However, the manifold in
reduced-dimensional subspace is likely to exhibit altered properties in
contrast with the original space. Thus, applying manifold information obtained
from the original space to the clustering process in a low-dimensional subspace
is prone to inferior performance. Aiming to address this issue, we propose a
novel convex algorithm that mines the manifold structure in the low-dimensional
subspace. In addition, our unified learning process makes the manifold learning
particularly tailored for the clustering. Compared with other related methods,
the proposed algorithm results in more structured clustering result. To
validate the efficacy of the proposed algorithm, we perform extensive
experiments on several benchmark datasets in comparison with some
state-of-the-art clustering approaches. The experimental results demonstrate
that the proposed algorithm has quite promising clustering performance.Comment: AAAI201
Analyzing and clustering neural data
This thesis aims to analyze neural data in an overall effort by the Charles Stark
Draper Laboratory to determine an underlying pattern in brain activity in healthy
individuals versus patients with a brain degenerative disorder. The neural data comes from ECoG (electrocorticography) applied to either humans or primates. Each ECoG array has electrodes that measure voltage variations which neuroscientists claim correlates to neurons transmitting signals to one another. ECoG differs from the less invasive technique of EEG (electroencephalography) in that EEG electrodes are placed above a patients scalp while ECoG involves drilling small holes in the skull to allow electrodes to be closer to the brain. Because of this ECoG boasts an exceptionally high signal-to-noise ratio and less susceptibility to artifacts than EEG [6]. While wearing the ECoG caps, the patients are asked to perform a range of different tasks.
The tasks performed by patients are partitioned into different levels of mental stress
i.e. how much concentration is presumably required. The specific dataset used in
this thesis is derived from cognitive behavior experiments performed on primates at
MGH (Massachusetts General Hospital).
The content of this thesis can be thought of as a pipelined process. First the
data is collected from the ECoG electrodes, then the data is pre-processed via signal processing techniques and finally the data is clustered via unsupervised learning techniques. For both the pre-processing and the clustering steps, different techniques are applied and then compared against one another. The focus of this thesis is to evaluate clustering techniques when applied to neural data.
For the pre-processing step, two types of bandpass filters, a Butterworth Filter
and a Chebyshev Filter were applied. For the clustering step three techniques were
applied to the data, K-means Clustering, Spectral Clustering and Self-Tuning Spectral Clustering. We conclude that for pre-processing the results from both filters are very similar and thus either filter is sufficient. For clustering we conclude that K- means has the lowest amount of overlap between clusters. K-means is also the most time-efficient of the three techniques and is thus the ideal choice for this application.2016-10-27T00:00:00
Poisson noise reduction with non-local PCA
Photon-limited imaging arises when the number of photons collected by a
sensor array is small relative to the number of detector elements. Photon
limitations are an important concern for many applications such as spectral
imaging, night vision, nuclear medicine, and astronomy. Typically a Poisson
distribution is used to model these observations, and the inherent
heteroscedasticity of the data combined with standard noise removal methods
yields significant artifacts. This paper introduces a novel denoising algorithm
for photon-limited images which combines elements of dictionary learning and
sparse patch-based representations of images. The method employs both an
adaptation of Principal Component Analysis (PCA) for Poisson noise and recently
developed sparsity-regularized convex optimization algorithms for
photon-limited images. A comprehensive empirical evaluation of the proposed
method helps characterize the performance of this approach relative to other
state-of-the-art denoising methods. The results reveal that, despite its
conceptual simplicity, Poisson PCA-based denoising appears to be highly
competitive in very low light regimes.Comment: erratum: Image man is wrongly name pepper in the journal versio
Manifold Learning in MR spectroscopy using nonlinear dimensionality reduction and unsupervised clustering
Purpose To investigate whether nonlinear dimensionality reduction improves unsupervised classification of 1H MRS brain tumor data compared with a linear method. Methods In vivo single-voxel 1H magnetic resonance spectroscopy (55 patients) and 1H magnetic resonance spectroscopy imaging (MRSI) (29 patients) data were acquired from histopathologically diagnosed gliomas. Data reduction using Laplacian eigenmaps (LE) or independent component analysis (ICA) was followed by k-means clustering or agglomerative hierarchical clustering (AHC) for unsupervised learning to assess tumor grade and for tissue type segmentation of MRSI data. Results An accuracy of 93% in classification of glioma grade II and grade IV, with 100% accuracy in distinguishing tumor and normal spectra, was obtained by LE with unsupervised clustering, but not with the combination of k-means and ICA. With 1H MRSI data, LE provided a more linear distribution of data for cluster analysis and better cluster stability than ICA. LE combined with k-means or AHC provided 91% accuracy for classifying tumor grade and 100% accuracy for identifying normal tissue voxels. Color-coded visualization of normal brain, tumor core, and infiltration regions was achieved with LE combined with AHC. Conclusion Purpose To investigate whether nonlinear dimensionality reduction improves unsupervised classification of 1H MRS brain tumor data compared with a linear method. Methods In vivo single-voxel 1H magnetic resonance spectroscopy (55 patients) and 1H magnetic resonance spectroscopy imaging (MRSI) (29 patients) data were acquired from histopathologically diagnosed gliomas. Data reduction using Laplacian eigenmaps (LE) or independent component analysis (ICA) was followed by k-means clustering or agglomerative hierarchical clustering (AHC) for unsupervised learning to assess tumor grade and for tissue type segmentation of MRSI data. Results An accuracy of 93% in classification of glioma grade II and grade IV, with 100% accuracy in distinguishing tumor and normal spectra, was obtained by LE with unsupervised clustering, but not with the combination of k-means and ICA. With 1H MRSI data, LE provided a more linear distribution of data for cluster analysis and better cluster stability than ICA. LE combined with k-means or AHC provided 91% accuracy for classifying tumor grade and 100% accuracy for identifying normal tissue voxels. Color-coded visualization of normal brain, tumor core, and infiltration regions was achieved with LE combined with AHC. Conclusion The LE method is promising for unsupervised clustering to separate brain and tumor tissue with automated color-coding for visualization of 1H MRSI data after cluster analysis
Local Component Analysis
Kernel density estimation, a.k.a. Parzen windows, is a popular density
estimation method, which can be used for outlier detection or clustering. With
multivariate data, its performance is heavily reliant on the metric used within
the kernel. Most earlier work has focused on learning only the bandwidth of the
kernel (i.e., a scalar multiplicative factor). In this paper, we propose to
learn a full Euclidean metric through an expectation-minimization (EM)
procedure, which can be seen as an unsupervised counterpart to neighbourhood
component analysis (NCA). In order to avoid overfitting with a fully
nonparametric density estimator in high dimensions, we also consider a
semi-parametric Gaussian-Parzen density model, where some of the variables are
modelled through a jointly Gaussian density, while others are modelled through
Parzen windows. For these two models, EM leads to simple closed-form updates
based on matrix inversions and eigenvalue decompositions. We show empirically
that our method leads to density estimators with higher test-likelihoods than
natural competing methods, and that the metrics may be used within most
unsupervised learning techniques that rely on such metrics, such as spectral
clustering or manifold learning methods. Finally, we present a stochastic
approximation scheme which allows for the use of this method in a large-scale
setting
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