Multispectral magnetic resonance images segmentation using fuzzy Hopfield neural network

Hope4Genes: a Hopfield-like class prediction algorithm for transcriptomic data

After its introduction in 1982, the Hopfield model has been extensively applied for classification and pattern recognition. Recently, its great potential in gene expression patterns retrieval has also been shown. Following this line, we develop Hope4Genes a single-sample class prediction algorithm based on a Hopfield-like model. Differently from previous works, we here tested the performances of the algorithm for class prediction, a task of fundamental importance for precision medicine and therapeutic decision-making. Hope4Genes proved better performances than the state-of-art methodologies in the field independently of the size of the input dataset, its profiling platform, the number of classes and the typical class-imbalance present in biological data. Our results provide encoraging evidence that the Hopfield model, together with the use of its energy for the estimation of the false discoveries, is a particularly promising tool for precision medicine.

SEGMENTATION OF BRAIN MRIs BY SUPPORT VECTOR MACHINE: DETECTION AND CHARACTERIZATION OF STROKES

The aim of our work is the segmentation of healthy and pathological brains to obtain brain structures and extract strokes. We used real magnetic resonance (MR) images weighted on diffusion. The brain was isolated, and the images were filtered by an anisotropic filter, and then segmented by support vector machines (SVMs). We first applied the method on synthetic images to test the performance of the algorithm and adjust the parameters. Then, we compared our results with those obtained by a cooperative approach proposed in a previous paper.

A COMPENSATED FUZZY HOPFIELD NEURAL NETWORK FOR CODEBOOK DESIGN IN VECTOR QUANTIZATION

In this paper, a new Hopfield-model net called Compensated Fuzzy Hopfield Neural Network (CFHNN) is proposed for vector quantization in image compression. In CFHNN, the compensated fuzzy c-means algorithm, modified from penalized fuzzy c-means, is embedded into Hopfield neural network so that the parallel implementation for codebook design is feasible. The vector quantization can be cast as an optimal problem that may also be regarded as a minimization of a criterion defined as a function of the average distortion between training vector and codevector. The CFHNN is trained to classify the divided vectors on a real image into feasible class to generate an available codebook when the defined energy function converges to near global minimum. The training vectors on a divided image are mapped to a two-dimensional Hopfield neural network. Also the compensated fuzzy c-means technique is used to update the quantization performance and to eliminate searching for the weighting factors. In the context of vector quantization, each training vector on the divided image is represented by a neuron which is fully connected by the other neurons. After a number of iterations, neuron states are refined to reach near optimal result when the defined energy function is converged.

Automated classification of multi-spectral MR images using Linear Discriminant Analysis

Magnetic resonance imaging (MRI) is a valuable instrument in medical science owing to its capabilities in soft tissue characterization and 3D visualization. A potential application of MRI in clinical practice is brain parenchyma classification. This work proposes a novel approach called "Unsupervised Linear Discriminant Analysis (ULDA)" to classify and segment the three major tissues, i.e. gray matter (GM), white matter (WM) and cerebral spinal fluid (CSF), from a multi-spectral MR image of the human brain. The ULDA comprises two processes, namely Target Generation Process (TGP) and Linear Discriminant Analysis (LDA) classification. TGP is a fuzzy-set process that generates a set of potential targets from unknown information, and applies these targets to train the optimal division boundary by LDA, such that three tissues GM, WM and CSF are separated. Finally, two sets of images, namely computer-generated phantom images and real MR images are used in the experiments to evaluate the effectiveness of ULDA. Experiment results reveal that UDLA segments a multi-spectral MR image much more effectively than either FMRIB's Automated Segmentation Tool (FAST) or Fuzzy C-means (FC).

Artificial neural network: border detection in echocardiography

Being non-invasive and low cost, the echocardiography has become a diagnostic technique largely applied for the determination of the left ventricle systolic and diastolic volumes, which are used indirectly to calculate the left ventricle ejection volume, the cardiac cavities muscular contraction, the regional ejection fraction, the myocardial thickness, and the ventricular mass, etc. However, the image is very noisy, which renders the delineation of the borders of the left ventricle very difficult. While there are many techniques image segmentation, this work chooses the artificial neural network (ANN) since it is not very sensitive to noise. In order to reduce the processing time, the operator selects the region of interest where the neural network will identify the borders. Neighborhood and gradient search techniques are then employed to link the points and the left ventricle contour is traced. The present method has been efficient in detecting the left ventricle borders echocardiography images compared to those whose borders were delineated by the specialists. For good results, it is important to choose properly the areas to be analyzed and the central points of these areas.

Registration and machine learning-based automated segmentation of subcortical and cerebellar brain structures

The large amount of imaging data collected in several ongoing multi-center studies requires automated methods to delineate brain structures of interest. We have previously reported on using artificial neural networks (ANN) to define subcortical brain structures. Here we present several automated segmentation methods using multidimensional registration. A direct comparison between template, probability, artificial neural network (ANN) and support vector machine (SVM)-based automated segmentation methods is presented. Three metrics for each segmentation method are reported in the delineation of subcortical and cerebellar brain regions. Results show that the machine learning methods outperform the template and probability-based methods. Utilization of these automated segmentation methods may be as reliable as manual raters and require no rater intervention.

Segmentation of magnetic resonance brain images through discriminant analysis

Segmentation (tissue classification) of medical images obtained from a magnetic resonance (MR) system is a primary step in most applications of medical image post-processing. This paper describes nonparametric discriminant analysis methods to segment multispectral MR images of the brain. Starting from routinely available spin-lattice relaxation time, spin-spin relaxation time, and proton density weighted images (T1w, T2w, PDw), the proposed family of statistical methods is based on: (i) a transform of the images into components that are statistically independent from each other; (ii) a nonparametric estimate of probability density functions of each tissue starting from a training set; (iii) a classic Bayes 0-1 classification rule. Experiments based on a computer built brain phantom (brainweb) and on eight real patient data sets are shown. A comparison with parametric discriminant analysis is also reported. The capability of nonparametric discriminant analysis in improving brain tissue classification of parametric methods is demonstrated. Finally, an assessment of the role of multispectrality in classifying brain tissues is discussed.

Multivariate statistical model for 3D image segmentation with application to medical images

In this article we describe a statistical model that was developed to segment brain magnetic resonance images. The statistical segmentation algorithm was applied after a pre-processing stage involving the use of a 3D anisotropic filter along with histogram equalization techniques. The segmentation algorithm makes use of prior knowledge and a probability-based multivariate model designed to semi-automate the process of segmentation. The algorithm was applied to images obtained from the Center for Morphometric Analysis at Massachusetts General Hospital as part of the Internet Brain Segmentation Repository (IBSR). The developed algorithm showed improved accuracy over the k-means, adaptive Maximum Apriori Probability (MAP), biased MAP, and other algorithms. Experimental results showing the segmentation and the results of comparisons with other algorithms are provided. Results are based on an overlap criterion against expertly segmented images from the IBSR. The algorithm produced average results of approximately 80% overlap with the expertly segmented images (compared with 85% for manual segmentation and 55% for other algorithms).

Detection of spectral signatures in multispectral MR images for classification

This paper presents a new spectral signature detection approach to magnetic resonance (MR) image classification. It is called constrained energy minimization (CEM) method, which is derived from the minimum variance distortionless response in passive sensor array processing. It considers a bank of spectral channels as an array of sensors where each spectral channel represents a sensor and object spectral signature in multispectral MR images are viewed as signals impinging upon the array. The strength of the CEM lies on its ability in detection of spectral signatures of interest without knowing image background. The detected spectral signatures are then used for classification. The CEM makes use of a finite impulse response (FIR) filter to linearly constrain a desired object while minimizing interfering effects caused by other unknown signal sources. Unlike most spatial-based classification techniques, the proposed CEM takes advantage of spectral characteristics to achieve object detection and classification. A series of experiments is conducted and compared with the commonly used c-means method for performance evaluation. The results show that the CEM method is a promising and effective spectral technique for MR image classification.

Evaluation of inherent performance of intelligent medical decision support systems: utilising neural networks as an example

Researchers who design intelligent systems for medical decision support, are aware of the need for response to real clinical issues, in particular the need to address the specific ethical problems that the medical domain has in using black boxes. This means such intelligent systems have to be thoroughly evaluated, for acceptability. Attempts at compliance, however, are hampered by lack of guidelines. This paper addresses the issue of inherent performance evaluation, which researchers have addressed in part, but a Medline search, using neural networks as an example of intelligent systems, indicated that only about 12.5% evaluated inherent performance adequately. This paper aims to address this issue by concentrating on the possible evaluation methodology, giving a framework and specific suggestions for each type of classification problem. This should allow the developers of intelligent systems to produce evidence of a sufficiency of output performance evaluation.

Implementation of intelligent decision support systems in health care

The full implementation of any intelligent system in health care, which is designed for decision support, has several stages, from initial problem identification through development and, finally, cost-benefit analysis. Central to this is formal objectivist evaluation with its core component of inherent performance of the outputs from these systems. A Medline survey of one type of intelligent system is presented, which demonstrates that this issue is not being addressed adequately. Lack of criteria for dealing with the outputs from these "black box" systems to prescribe adequate levels of inherent performance may be preventing their being accepted by those in the health-care domain and, thus, their being applied widely in the field.

Estimation of expiratory time constants via fuzzy clustering

OBJECTIVE

In mechanically ventilated patients the expiratory time constant provides information about respiratory mechanics. In the present study a new method, fuzzy clustering, is proposed to determine expiratory time constants. Fuzzy clustering differs from other methods since it neither interferes with expiration nor presumes any functional relationship between the variables analysed. Furthermore, time constant behaviour during expiration can be assessed, instead of an average time constant. The time constants obtained with fuzzy clustering are compared to time constants conventionally calculated from the same expirations.

METHODS

20 mechanically ventilated patients, including 10 patients with COPD, were studied. The data of flow, volume and pressure were sampled. From these data, four local linear models were detected by fuzzy clustering. The time constants (tau) of the local linear models (clusters) were calculated by a least-squares technique. Time constant behaviour was analysed. Time constants obtained with fuzzy clustering were compared to time constants calculated from flow-volume curves using a conventional method.

RESULTS

Fuzzy clustering revealed two patterns of expiratory time constant behaviour. In the patients with COPD an initial low time constant was found (mean tau1: 0.33 s, SD 0.21) followed by higher time constants; mean tau2: 2.00 s (SD 0.91s), mean tau3: 3.45 s (SD 1.44) and mean tau4: 5.47 s (SD 2.93). In the other patients only minor changes in time constants were found; mean tau1: 0.74 s (SD 0.30), mean tau2: 0.90 s (SD 0.23), mean tau3: 1.04 s (SD 0.42) and mean tau4: 1.74 s (SD 0.78). Both the pattern of expiratory time constants, as well as the time constants calculated from the separate clusters, were significantly different between the patients with and without COPD. Time constants obtained with fuzzy clustering for cluster 2, 3 and 4 correlated well with time constants obtained from the flow-volume curves.

CONCLUSIONS

In mechanically ventilated patients, expiratory time constant behaviour can be accurately assessed by fuzzy clustering. A good correlation was found between time constants obtained with fuzzy clustering and time constants obtained by conventional analysis. On the basis of the time constants obtained with fuzzy clustering, a clear distinction was made between patients with and without

FLAIR histogram segmentation for measurement of leukoaraiosis volume

The purposes of this study were to develop a method to measure brain and white matter hyperintensity (leukoaraiosis) volume that is based on the segmentation of the intensity histogram of fluid-attenuated inversion recovery (FLAIR) images and to assess the accuracy and reproducibility of the method. Whole-head synthetic image phantoms with manually introduced leukoaraiosis lesions of varying severity were constructed. These synthetic image phantom sets incorporated image contrast and anatomic features that mimicked leukoaraiosis found in real life. One set of synthetic image phantoms was used to develop the segmentation algorithm (FLAIR-histoseg). A second set was used to measure its accuracy. Test retest reproducibility was assessed in 10 elderly volunteers who were imaged twice. The mean absolute error of the FLAIR-histoseg method was 6.6% for measurement of leukoaraiosis volume and 1.4% for brain volume. The mean test retest coefficient of variation was 1.4% for leukoaraiosis volume and 0.3% for brain volume. We conclude that the FLAIR-histoseg method is an accurate and reproducible method for measuring leukoaraiosis and whole-brain volume in elderly subjects.

Orthogonal subspace projection-based approaches to classification of MR image sequences

Orthogonal subspace projection (OSP) approach has shown success in hyperspectral image classification. Recently, the feasibility of applying OSP to multispectral image classification was also demonstrated via SPOT (Satellite Pour 1'Observation de la Terra) and Landsat (Land Satellite) images. Since an MR (magnetic resonance) image sequence is also acquired by multiple spectral channels (bands), this paper presents a new application of OSP in MR image classification. The idea is to model an MR image pixel in the sequence as a linear mixture of substances (such as white matter, gray matter, cerebral spinal fluid) of interest from which each of these substances can be classified by a specific subspace projection operator followed by a desired matched filter. The experimental results show that OSP provides a promising alternative to existing MR image classification techniques.

Estimation of respiratory parameters via fuzzy clustering

The results of monitoring respiratory parameters estimated from flow-pressure-volume measurements can be used to assess patients' pulmonary condition, to detect poor patient-ventilator interaction and consequently to optimize the ventilator settings. A new method is proposed to obtain detailed information about respiratory parameters without interfering with the expiration. By means of fuzzy clustering, the available data set is partitioned into fuzzy subsets that can be well approximated by linear regression models locally. Parameters of these models are then estimated by least-squares techniques. By analyzing the dependence of these local parameters on the location of the model in the flow-volume-pressure space, information on patients' pulmonary condition can be gained. The effectiveness of the proposed approaches is demonstrated by analyzing the dependence of the expiratory time constant on the volume in patients with chronic obstructive pulmonary disease (COPD) and patients without COPD.

A modified fuzzy clustering algorithm for operator independent brain tissue classification of dual echo MR images

Methods for brain tissue classification or segmentation of structural magnetic resonance imaging (MRI) data should ideally be independent of human operators for reasons of reliability and tractability. An algorithm is described for fully automated segmentation of dual echo, fast spin-echo MRI data. The method is used to assign fuzzy-membership values for each of four tissue classes (gray matter, white matter, cerebrospinal fluid and dura) to each voxel based on partition of a two dimensional feature space. Fuzzy clustering is modified for this application in two ways. First, a two component normal mixture model is initially fitted to the thresholded feature space to identify exemplary gray and white matter voxels. These exemplary data protect subsequently estimated cluster means against the tendency of unmodified fuzzy clustering to equalize the number of voxels in each class. Second, fuzzy clustering is implemented in a moving window scheme that accommodates reduced image contrast at the axial extremes of the transmitting/receiving coil. MRI data acquired from 5 normal volunteers were used to identify stable values for three arbitrary parameters of the algorithm: feature space threshold, relative weight of exemplary gray and white matter voxels, and moving window size. The modified algorithm incorporating these parameter values was then used to classify data from simulated images of the brain, validating the use of fuzzy-membership values as estimates of partial volume. Gray:white matter ratios were estimated from 20 twenty normal volunteers (mean age 32.8 years). Processing time for each three-dimensional image was approximately 30 min on a 170 MHz workstation. Mean cerebral gray and white matter volumes estimated from these automatically segmented images were very similar to comparable results previously obtained by operator dependent methods, but without their inherent unreliability.

Magnetic resonance image segmentation using pattern recognition, and applied to image registration and quantitation

This review highlights various magnetic resonance image (MRI) segmentation algorithms that employ pattern recognition. The procedures are grouped into two categories: low- to intermediate-level, and high-level image processing. The former consists of grey level histogram analysis, texture definition, edge identification, region growing, and contour following. The roles of significant prior knowledge, neural networks and cluster analysis are examined by producing objective identification of anatomical structures. The application of the segmented anatomical structures in image registration, to monitor the disease progression or growth of anatomy in normal volunteers and patients, is highlighted. The use of the segmented anatomy in measuring volumes of structures in normals and patients is also examined.