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Abstract Toward A Completely Automatic Neural Network Based

Abstract Toward A Completely Automatic Neural Network Based
Abstract Toward A Completely Automatic Neural Network Based

Toward A Completely Automatic Neural Network Based

Human Chromosome Analysis

Boaz Lerner

University of Cambridge Computer Laboratory

Cambridge CB2 3QG, UK

(email: boaz.lerner@https://www.doczj.com/doc/f018002857.html,)

Abstract

The application of neural networks (NNs) to automatic analysis of chromosome images is investigated in this paper. All aspects of the analysis, namely segmentation, feature description, selection and extraction and finally classification, are studied. As part of the segmentation process, the separation of clusters of partially occluded chromosomes, which is the critical stage that state-of-the-art chromosome analyzers usually fail to accomplish, is performed. First, a moment representation of the image pixels is clustered to create a binary image without a need for threshold selection. Based on the binary image, lines connecting cut points imply possible separations. These hypotheses are verified by a multilayer perceptron (MLP) NN that classifies the two segments created by each separating line. Use of a classification-driven segmentation process gives very promising results without a need for shape modelling or an excessive use of heuristics. In addition, an NN implementation of Sammon’s mapping using principal component based initialization is applied to feature extraction, significantly reducing the dimensionality of the feature space and allowing high classification capability. Finally, by applying MLP based hierarchical classification strategies to a well-explored chromosome database, we achieve a classification performance of 83.6%. This is higher than ever published on this database and an improvement of more than 10% in the error rate. Therefore, basing a chromosome analysis on the NN based techniques that are developed in this research leads toward a completely automatic human chromosome analysis.

Index Terms- Chromosomes, feature extraction, image classification, neural networks, partial occlusion, segmentation

Published in IEEE Transactions on Systems, Man, and Cybernetics Special issue on Artificail Neural Networks, vol. 28, pt. B, pp. 544-552, 1998.

1. Introduction

Human chromosome analysis is an essential task in cytogenetics, especially in prenatal screening and genetic syndrome diagnosis, cancer pathology research and environmentally induced mutagen dosimetry [2]. Cells used for chromosome analysis are taken mostly from amniotic fluid or blood samples. The stage at which the chromosomes are most suitable for analysis is the metaphase (Fig. 1). One of the aims of chromosome analysis is the creation of a karyotype, which is a layout of chromosome images organised by decreasing size in pairs (Fig. 2). The karyotype is obtained by cutting chromosome images from a photograph of a cell, taken using a microscope, and arranging the chromosomes into their appropriate places on the layout according to their visual classification by the cytotechnician. Karyotyping is a useful tool for detecting deviations from normal cell structure. Abnormal cells can have an excess or deficit of a chromosome and/or structural defects, like breaks, fragments or translocations (exchange of genetic material between chromosomes). However, even today, chromosome analysis and karyotyping are performed manually in most cytogenetic laboratories in a repetitive, time consuming and therefore expensive procedure.

Great efforts to develop automatic chromosome classification techniques have been made during the last 25 years. However, all have had limited success and have yielded poor classification results compared with those of a trained cytotechnician [2], [10]. Some of the reasons for the relatively poor performances are the inadequate use of expert knowledge and experience, and insufficient ability to make comparisons and/or elimination among chromosomes within the same metaphase. In addition, the systems always require operator interaction to separate touching and/or overlapping chromosomes and to verify the classification results.

During recent years we have developed [14]-[17] a capability to deal with the most important aspects of chromosome analysis, mainly through the application of NNs. The present study is an additional step to extend this capability by solving the very complex problem of separating images

of touching chromosomes and contributing to a compact representation and a highly accurate chromosome classification. Furthermore, we present here an NN based methodology for a complete automation of all the stages of human chromosome analysis. Therefore, the research aims to (a) resolve, reliably and simply, partial occlusion in a chromosome image, (b) improve chromosome classification performance compared with the current methods, (c) study the benefits of applying NNs to the analysis and (d) present a coherent methodology for automatic chromosome image analysis.

Section 2 of the paper introduces the traditional procedure for computerised chromosome analysis. Section 3 describes our methodology to automatic chromosome analysis while Section 4 presents the results of the application of this methodology.

2. Conventional Computerised Chromosome Analysis

Computerised chromosome analysis consists primarily of pre-processing, segmentation, intermediate processing, feature measurement and selection and finally, classification. The pre-processing stage aims to improve the quality of the cell image by techniques of noise removal, edge enhancement and/or contrast improvement. The segmentation’s purpose is to isolate the metaphase chromosomes from the background, undivided cell nuclei and irrelevant biological materials within the image and from each other. After segmentation, some intermediate processing, as the medial axis transform (MAT) and centromere finding, is usually needed to measure features. The result of feature selection, if applied, is a more condensed representation that still retains most of the important chromosome information. Finally, classification, usually using statistical methods, is performed. This section describes the traditional state-of-the-art techniques to accomplish chromosome analysis whereas Section 3 summarizes our suggested methodology. Although segmentation usually precedes all other stages of image analysis, in our

methodology it is based on them, therefore, we prefer to describe it at the end of the two sections.

2.1 Chromosome description

The use of features rather than the image itself makes the classification procedure easier, faster and more accurate. Different features have been used to describe chromosomes, e.g., features of size (length, area, etc.) [2], [15], [21], band pattern descriptors (e.g., Fourier or Gaussian decomposition of an intensity profile along the chromosome [8]) or global features based on the histogram of gray levels or the 2D Fourier transform components [16]. Among the most discriminative chromosomal features we can find two geometrical features, the length [2], [15], [22] and the centromeric index (the ratio of the short arm length to the whole chromosome length) [2], [10], [15], [22]. Other most discriminative features are the density profile features, which are integral or average intensities along sections perpendicular to the medial axis of the chromosome [2], [10], [15], [22]. The MAT is generally employed to extract these later geometrical and intensity features.

2.2 Feature selection and extraction

It is convenient to distinguish between feature selection in the measurement space and feature selection in a projected space. Techniques belonging to the first category aim to accomplish dimensionality reduction by reducing the number of required measurements and are referred to as feature selection. Techniques belonging to the second category use all the information in the feature vector to yield a lower-dimensional vector and are referred to as feature extraction [4].

Feature selection for classification can be regarded as a search, among all possible transformations, for the one that preserves class separability in the lowest possible dimensional space. However, since the Bayes classifier compares a posteriori probabilities, which are hard to

obtain and their estimates normally have severe biases and variances [6], and since the search for the optimal subset is a combinatorial problem, a few sub-optimal selection techniques have been suggested [4]. Most of these techniques are based on the minimization of criteria of scatter matrices, which are conceptually simple and give systematic feature selection algorithms. These criteria are based on the within-class (W )

W x m x m i i i c i T

=??∈=∑∑ P x i x ()()1(1)

and between-class (B )

B P m m m m i i c i i T

=??=∑1()()(2)

scatter matrices, where m i is the mean of vectors x i in the i th class, m is the mean vector of the mixture distribution, c is the number of classes and P i is the i th class a priori probability.Intuitively, the criterion (e.g., J =trace(W -1.B )) should be larger when the between-class scatter is larger (the classes are distant from each other) and/or when the within-class scatter is smaller (the patterns in each class are concentrated around their centroid). Although many feature selection methods, which are based on different selection techniques and scatter criteria, are known from the literature [4], previous research in chromosomal feature selection has relied only on a very few approaches [9], [15].

In feature extraction, the original features (measurements) are mapped into fewer features which retain the main information of the data structure. A mapping f transforms a pattern y of a d -dimensional measurement space to a pattern x of an m -dimensional space, x =f (y ) and m

{}{})( min )(y g J g y f J =(3)

is determined among all the transformations g [4].

To our knowledge, feature extraction techniques were applied to chromosome analysis only once [17].

2.3 Chromosome classification

Chromosome classification is the most widely investigated stage of chromosome analysis. Over the years several classifiers have been tested, among them: distance and statistical [2], [10], [21], [22], nearest neighbour [10], NN based [7], [14], [27] and fuzzy [29] classifiers. Most of these classifiers have two flaws [10], [16], [22]: 1) lower level of performance than the human expert (~70-80% compared with ~99.7%) and 2) a requirement for an operator interaction to classify misclassified chromosomes. Some of the reasons for these flaws are: 1) inadequate use of the expert knowledge and methodology (e.g., chromosome comparison, elimination), 2) the use of features of limited quality and/or number compared with the very powerful feature synthesis mechanism of the expert brain, 3) the use of the same specific features to represent all chromosomes, and 4) the naive attempt to represent a very complex problem, involving highly context-sensitive patterns, which exhibit natural diversities, by a constrained mathematical and/or engineering framework.

2.4 Segmentation of a chromosome image

Most conventional image segmentation methods are based on either threshold selection, adaptive thresholding, edge detection or matching with a set of prototype shapes [20]. However, almost all of these methods tend to fail or lose accuracy when considering complicated images or those of partially occluded objects [13] as in the case of a chromosome image [16], [18]. Indeed, only a very few studies [1], [16], [18] deal successfully with automatic image segmentation of touching or overlapping chromosomes. Consequently, it is not surprising that in most of the published works concerning chromosome analysis, manually segmented databases are used.

Neither is it surprising to find that almost all the commercial “automatic” chromosome analysis systems are in fact “semi-automatic”and require a continuous interaction of the cytotechnician. In a comprehensive research to separate touching chromosomes, Liang [18] bases his approach on an analysis of concavities along the chromosome shape and on performing a heuristic search for a minimum density path between touching chromosomes. Although very efficient and superior to other techniques, Liang’s method uses a large number of empirical thresholds that might suit images taken from one laboratory (or using a specific preparation technique) but not necessarily others, involves a time-consuming procedure and depends critically on the origin of the split line. In another successful method [1] to separate touching chromosomes, an evaluation of the fit of the separated segments to some prototype shapes is made. However, this method strongly depends on heuristics and thresholds and make use of a multistage complex procedure. Therefore, a complete and efficient automatic segmentation of a chromosome image is a very ambitious goal.

3. A Methodology for Automatic Chromosome Analysis

3.1 Chromosome data

The suggested methodology is applied to two chromosome databases. In the first database, there are images of amniotic fluid cells which were acquired from the Institute of Genetics of Soroka Medical Center, Beer-Sheva, Israel. The images were digitized to yield 512 X 768 pixel pictures where each pixel was represented by 1 byte (256 gray levels). No pre-processing techniques were applied to the images. These images were used both for the automatic segmentation procedure (Section 3.6) and to segment manually five types of chromosomes (the “Soroka5 database”) [15] to evaluate the chromosome features (Section 3.2) and feature selection and extraction paradigms (Sections 3.3 and 3.4). The second database was kindly provided by Dr. Piper of the Medical Research Council in Edinburgh, Scotland. This database

[22] (the “Edinburgh database”) has two main advantages: first, it is huge and hence represents the variety of chromosome images very well. Moreover, its large size is a very crucial advantage when chromosomes are represented by a large number of features. Second, this database has been widely explored by researchers in the field [2], [7], [10], [21], [22], [27], [28] and is therefore very attractive for a comparative study of classification performances (Section 4.2). It contains around 5,500 chromosomes of 125 cells and is based on routinely acquired blood cell images. The characteristics of the two databases are summarized in Table 1.

3.2 Chromosome representation

Most of the chromosomal features described in sub-Section 2.1 were evaluated to select a good chromosome representation [15], [16]. Two geometrical features, the chromosome length (lng.) and centromeric index (ci) and 64 density profile (d.p.) features, which have previously found very discriminative for classification [15], are suggested in this methodology.

3.3 Feature selection

The “knock-out” algorithm [25], which is a sequential backward technique and a simplified scatter criterion which only relies on the within-class scatter matrix, J=trace(W) [15], are employed to find a sub-optimal subset of the 66-dimentional (64 d.p. + ci + lng.) feature space.

3.4 Feature extraction

Different mapping functions and optimization criteria have been suggested in the past for both exploratory data projection and classification. A specific choice of a mapping function and an optimization criterion could be very beneficial to one task but not necessarily to the other. Moreover, the number of features which are required for classification is usually higher than that required for data projection. Therefore, an evaluation of the projection maps and the probability

of correct classification based on several mappings that were applied to the chromosome feature space has been made here. This evaluation includes an NN implementation [19] of Sammon’s mapping [26] (unsupervised nonlinear paradigm) and an MLP [11] (supervised nonlinear), auto-associative NN [11] (unsupervised linear) and principal component (PC) [6] (unsupervised linear) feature extractors.

3.5 Classification

Classification of five types of chromosomes using a monolithic MLP NN was found to be both efficient and superior to that based on the Bayes piecewise linear classifier [14]. However, when classifying all the 24 chromosome types both classifiers yielded comparable results [7]. Therefore, when trying to accomplish a full karyotype using an NN based classifier, other, e.g. hierarchical, strategies may be considered apart from the monolithic MLP. Besides task simplification, which might improve generalization, hierarchical strategies cut training period drastically. When applying hierarchical classification, different classifiers could be trained independently, using independent data sets and/or feature sets, to possibly improve performance and to employ fewer resources. For example, chromosome identification by first classifying the patterns into groups followed by a classification in the groups and into types yields both a desired task decomposition and a compatibility with the common cytogenetic methodology [3], which partitions the twenty-four chromosome types into seven groups. Therefore, a “group classifier” is trained here independently of seven “type classifiers”, each one of them is employed for a different group. Furthermore, training of the “group classifier” could be based on typical “group” features while that of the “type classifiers” on “type” features.

3.6 Automatic segmentation of partially occluded chromosomes

While the problem of segmenting images of isolated chromosomes is easily solved by thresholding, the accuracy of separating images of touching chromosomes is not yet sufficient for a reliable completely automatic procedure [5]. Techniques which are based on threshold selection fail [16], [18], [22] and techniques which are “tailored” to the chromosome shape [1], [18] are complex, multistage procedures which highly depend on heuristics and initial conditions. However, clusters of touching chromosomes exist in almost every chromosome image. Hence, the separation of them is unavoidable to achieve a completely automatic chromosome image analysis, especially in low quality images (e.g., bone marrow) which can have many clusters of touching chromosomes [18].

A new approach called a classification-driven partially occluded object segmentation (CPOOS) method [16], is used here for separating clusters of touching chromosomes. The method aims to achieve a highly accurate separation of touching objects without a need for a tedious, usually unreliable experimentation with threshold selection or the excessive use of heuristics in locating the best separating path between touching objects.

The CPOOS method consists of three main stages. The first stage is K-means clustering(1) of an algebraic moment representation of the image pixels. The algebraic moments, as other statistical features, provide a more comprehensive characterisation than the pixel gray level itself. Although moment invariants are invariant to translation, rotation and scale changes [12], they are more sensitive to noise and sometimes yield inferior classification performance compared with the

algebraic moments [23], therefore the latter are preferred here. The (p,q)-th moment, m

pq

, of a

pixel (x

0,y

) of an image T which is measured in an N x N neighbourhood around the pixel is:

(1) The term “cluster” is usually used to describe both the aggregation of partially occluded objects [18] and the operation of grouping similar patterns (pixels) into groups (clustering) [20].

pq p q y N x N m x y x x y y T x y (,)()()(,)000011=??==∑∑ , p,q =0,1,2, (4)

It has been proved [12] that the double moment sequence, m pq , is uniquely determined by T and vice versa . Only very few moments are required here for two reasons. First, a large number of moments have not been found to be superior to a small number [23]. Second, we look for a rapid implementation, hence the smaller the number of moments that provides fair results the better.Therefore, only two moments (m 01 and m 02) which are calculated in a 3x3 neighbourhood around the central pixel are extracted and found to provide a robust B/W segmentation (K=2).

In the second stage, clusters of touching chromosomes are identified by their size and following a failure to classify them to one of the chromosome types. A cluster is identified if the probability of classifying it to each of the types is less than the inverse of the number of types.The contour of a cluster is found based on the 8-connected neighborhood of each contour pixel and tracked so that the image interior is located to the left of the contour. Following Rosenfeld and Kak [24], we define the left and right “k -slope” of a digital contour S =(p 0, .., p n ), where p i and p i+1 are adjacent points, as the directions from p i to p i-k and from p i to p i+k , respectively,where k ≥1. Based on this definition, the “k -curvature” (the angle between left and right “k -slopes”) of each contour point is computed and points are ordered by their curvatures. The r most concave points are selected and suggested as cut points to draw possible separating lines between touching chromosomes. A point, among these r potential cut points, which is closer than a distance s from a more acutely concave point is eliminated. The values of these experimentally found parameters remain unchanged throughout the experiments reported.

In the final stage, each pair of cut points creates a potential separating line. When the line connecting cut point(i ) and cut point(j ) is hypothesized, the two segments created by drawing this line are suspected of being the touching chromosomes. Each of the segments is rotated based on its first principal axis to be aligned to the x =0 axis, and the “straight” segment is transformed to

its medial axis (MA) [15] to extract the chromosomal features (ci, lng., and the 64-dimensional d.p. features of Section 3.2). Following the normalization of the feature vectors of the training segments (see later) to zero mean and unit variance the density profile feature vectors (only) are projected onto their principal axes. This feature extraction stage enables the use of approximately 90% of the variance in the density profiles with only one sixteenth of the number of original features (see later in Fig. 3) and without any performance degradation. An MLP, trained by the backpropogation (BP) learning algorithm [11], classifies the two reduced vectors (four eigenfeatures plus two geometrical features) and thereby achieves hypothesis verification and the selection of the “correct” separation line. The MLP and the BP provide simple but very reliable means of classification. Additionally, when implemented in a modest configuration which is therefore trained for only very short periods they accomplish a very cost-effective “tool” for hypothesis verification. The classifier is trained beforehand based on a priori knowledge of the identity of the two types of chromosomes which compose the cluster. This knowledge is gained following the classifiation of the isolated chromosomes in the beginning and the application of a simple elimination criterion. We assume that only one cluster of touching chromosomes exists in the image. When the image consists of several clusters and/or clusters of more than two chromosomes, the method would be applied hierarchically using complementary heuristics.

The classification is based on three classes. The first two are the two expected types of chromosomes which compose the cluster (the “wholes”) and the third is of those images created by any arbitrary “wrong” separating line (the “brokens”). The expected output vectors of the first two classes are (100) and (010) (or in opposite order for the opposite order of inputs) for a “correct” separating line and (001) and (001) for a “wrong” one. During the test, the first output value of the first output vector and the second output value of the second output vector are averaged to yield a score, which is an estimation of the average maximum a posteriori probability of the two input vectors. Therefore, a line that creates segments which are largely (or entirely)

composed of the expected chromosomes yields a high score where a line between two “wrong”cut points yields a low score. The highest score which is assigned by the classifier indicates the “correct” separating line and thereby verifies the corresponding hypothesis.

In addition, a “geometrical constraint” is obtatined from the training set using the maximum and minimum values of the length and centromeric index. A separating line in a test image that creates two segments such that at least one of them yields a length or a centromeric index which is either larger than one of the above maxima or smaller than one of the above minima is rejected and is not checked by the classifier.

4. Experiments and Results

4.1 Feature measurement, selection and extraction

Although global features are very easily computed and suitable for hardware implementation [16], a combination of geometrical ((lng.) and (ci)) and intensity (d.p.) features (Section 3.2) is shown in Table 2 to provide better chromosome discrimination when classifying five types of chromosomes (similar conclusions are made in [22] for 24 types). The latter features are used throughout this study and measuring them is part of the suggested methodology. In all the experiments of this sub-section, a two-layer perceptron trained by the backpropagation (BP) algorithm is employed as a classifier.

When the “knock-out” algorithm and the scatter criterion of Section 3.3 are applied to the “Soroka5 database” to choose a feature subset from the above 66 features, the length and centromeric index of the chromosome and points of the d.p. which correspond to the chromosome upper tip are selected as the most significant features [15].

When different mapping paradigms are applied to the chromosome features, superior paradigms for exploratory data projection are often found to be superior paradigms for classification and vice versa [17]. An experiment to evaluate the four mappings of Section 3.4 is

performed with a data set of 300 patterns of three types of chromosomes (types “13”, “19” and “x”), using 100 patterns of each type. The patterns are derived from the “Soroka5 database”, represented by 64 d.p. features and mapped into 1 to 10 dimensional patterns. The experiment is repeated with ten randomly initialized classifiers and fourty randomly chosen training and test sets derived from the database. The average probability of correct classification of the test set is shown in Fig. 3 (for details on the paradigm parameters see [17]). Only very few features (around one sixteenth of the original number) are required to achieve almost the ultimate performance, therefore contributing to a substantial reduction of the feature space dimensionality. Although Sammon’s mapping aims at data visualization, we can extract an arbitrary number of features by the mapping and therefore apply it also to classification. Fig. 3 reveals an impressive chromosome classification performance based on the unsupervised Sammon’s mapping which is comparable with that based on the supervised MLP feature extractor, and superior to those of the auto-associative NN and PC feature extractors. Furthermore, we initialise the input-hidden weight matrix of the NN implementation of the mapping by the eigenvectors of the covariance matrix of the data [17]. Besides improved classification capability, the eigenvector based initialisation of Sammon’s mapping provides a reduced training period, a lower mapping error and requires fewer experiments compared with the random initialisation.

4.2 Classification

The classification accuracy of two monolithic configurations and two hierarchical strategies, all of them based on an MLP, is compared for the “Edinburgh database” and for classifying the full karyotype (24 chromosome types). The feature space is 17-dimensional and it includes 15 selected out of the 64 d.p. features along with the length and centromeric index of the chromosome. Classification performance is the average of two experiments, where in the first training is made on one half of the data and testing on the other half and in the second the

procedure is reversed (i.e., the cross-validation technique). This technique is common in the cytogenetic community [21], [22], and therefore it is also applied here for a comparison.

In the first hierarchical strategy the chromosomes are first classified into seven groups and then in each of the seven groups (Section 3.5). The same features are used by all the classifiers. The configurations of the classifiers are: 17:hidden:7 for the “group classifier” and 17:hidden:output for the “type classifiers”, where “hidden” is the number of hidden units (selected to prevent overtraining) and “output” is 2 to 8 (according to the number of chromosome types in each group). Table 3 shows the probabilities of correct classification of the test set for each of the eight classifiers (one “group classifier” and seven (A to G) “type classifiers”). The first row of Table 3 shows the population of chromosomes in the seven groups. The second and third rows give, respectively, the above probabilities of the “group classifier” and “type classifiers”. The classification probabilities of the “type classifiers” are calculated for only those chromosomes that are correctly classified by the “group classifier”. The overall performance of the first hierarchical classifier is calculated, based on the relative population of chromosomes in the groups, to be 83.6%. When this experiment is repeated using only the two geometrical (ci + lng.) features to classify chromosomes into their groups and only the intensity (d.p.) features to classify chromosomes into their types, a performance degradation of all the eight classifiers (~2-10%) is observed.

In the second hierarchical strategy, a “group classifier” is trained using only the geometrical features (configuration of 2:hidden:7), and its outputs, as well as the fifteen selected d.p. features, are used as the inputs of a “type classifier” (configuration of 22:hidden:24). The probability of correct classification to “groups” is 89.4% and that to “types”, which is also the overall probability, is 81.6%, which is lower by 1.3% than that reported by Graham et al. [7] for a similar strategy.

Table 4 compares our classification performances using the monolithic classifiers (two and three layer perceptron in columns 1 and 2, respectively) and the two hierarchical strategies (columns 3 and 4) with the published best classification performances [2], [7], [22], [28]. Our classification methods, as the maximum likelihood classifier (column 5), belong to the context-free classification methods, in which the data set is classified as is and without a posteriori rearrangement of the chromosomes. Context-dependent classification procedures (columns 6 and 7), on the other hand, make use of a priori knowledge that each normal cell has exactly two chromosomes from each type. A classification procedure which results in a different arrangement of the chromosomes (e.g., three or more chromosomes of a specific cell are allocated to the same type) is followed by rearranging the chromosomes to meet the expected pattern [22], [28]. These classification procedures are found to provide a higher probability of correct classification by about 3% than context-free classification [2], [22], [28] but they are only useful if the cells are known to be taken from a normal sample. The first context-dependent classification method (column 6) is based on the maximum likelihood classifier (column 5) and a penalty for “implausible” assignments [22]. The second method (column 7), called the “transportation method” [28], finds a globally optimal solution to the constrained allocation problem. A third context-dependent classifier based on a probabilistic NN [27] yields very similar results to the first two. Table 4 reveals that the first hierarchical strategy (column 3) is slightly superior to the other context-free classification methods (columns 1, 2, 4 and 5) and even comparable with the context-dependent classification methods (columns 6 and 7).

4.3 Automatic segmentation

One of the novelties of using the CPOOS method for separating partially occluded chromosomes is that it is a classification-driven segmentation procedure. A necessary condition

for a successful application of the CPOOS method is, therefore, a demonstrated chromosome classification capability, such as the one described so far.

Only sub-images of cell images that include clusters of touching chromosomes are selected and analysed here. Training and test images are gathered for different combinations of two touching chromosomes. Since there are many as p(p-1)/2 such combinations (p=24) and there is no standard database of cell images, we are able to collect only very few images with the same combination of touching chromosomes. Therefore, in most of our experiments only one image is used for training and another one for the test, although there are a few examples where we have two training images. Using each training image and the cluster’s potential separating lines we create segment images of arbitrary cluster separation which define the data set of images of the third class (the “brokens”) for a specific combination. The images of the first two classes (the “wholes”) are collected from a manually segmented database (sub-Section 3.1). The two sets (“brokens” and “wholes”) are combined to one data set of around 300 vectors (~100 from each class) and the procedure repeats itself for all the p(p-1)/2 combinations (networks). The 66-dimensional feature vectors, one from each image of each class, are measured, normalised and projected into the first four principal axes (the quickest mapping among the four of Fig. 3) to define the training set for the classifier. During the test, the classifier is similarly used to verify each hypothesis which is posed by each separating line in the test image. In addition, these lines are checked to satisfy the “geometrical constraint”.

To cover all the possible combinations of two touching chromosomes p(p-1)/2 networks are required. However, each one of these networks is of a very modest configuration (6:2:3) and is therefore trained for a very short period (100 epochs). Moreover, since the classifier training is done beforehand, the verification procedure (test) is very rapid and only involves a multiplication of a 2x6 feature matrix by two weight (6x2 and 2x3) matrices.

Fig. 4 shows two examples of training and test images of clusters of touching chromosomes along with the cluster contours and cut points of the test images. The two training images (Fig. 4a) are c107 (top) and c159 (bottom) and the two test images (Fig. 4b) are c121 (top ) and c163 (bottom). The clusters in the first and second examples are composed of chromosome types “2”and “x” and “2” and “4”, respectively.

Tables 5 and 6 outline the separation results for each test image of Fig. 4 using lines connecting each pair of cut points. These results are represented by the classifier score and the satisfaction (or not) of the “geometrical constraint” (sub-Section 3.6). When a separating line does not satisfy the constraint no use of the classifier is made (not applicable (NA) in Tables 5 and 6). In the first test image (c121, Table 5) three lines begin at the same cut point (#8) and end at a relatively very close cut points (#1, #2, #3). However, the classifier ranks the “correct”separating line (2-8) higher than the other two lines (1-8 and 3-8) and with a score close to 1, since it is the only line which creates two segments that are classified as the chromosomes. Lines 1-8 and 3-8, however, create segments of which only one is classified as a chromosome. All the other lines create two segments which are both classified as belonging to the third class (and hence yield a zero score) or do not satisfy the “geometrical constraint”. In the second case (c163, Table 6), a few lines that are connected to point #5 pass near the second correct point (#3) but create slightly different segments, and therefore fail to outperform the score of the “correct” line (3-5). In this test image fewer lines are rejected by the “geometrical constraint” compared with the first image. When applied to a relatively small database of 46 human cell images, the CPOOS method achieves over 90% probability of correct segmentation when it is allowed to reject 8.7% of the images.

5. Toward a Completely Automatic Neural Network Based Human Chromosome Analysis-

a Discussion

The research has had four major goals: (a) to accomplish a reliable but simple segmentation of a chromosome image that contains partial occlusion, (b) to try to improve chromosome classification performance compared with the current methods, (c) to study the benefits of applying NNs to all stages of chromosome analysis and (d) to present a coherent methodology toward a completely automatic chromosome image analysis.

Segmentation of partially occluded chromosomes has been efficiently accomplished in this research using the CPOOS method. First, clustering of the image pixels provides a separation of chromosomes and chromosome clusters from background without a need to search for an optimum threshold. Thereafter, cut points are located at the most concave points along a cluster curvature. Finally, an MLP is used to score and verify hypotheses, which are lines connecting each pair of cut points, by classifying the two segments created by each line. Using this method, modeling of the object’s shape or curvature is not necessary nor is the traditional excessive use of heuristics and pre-processing. Moreover, being a classification-driven segmentation procedure, the CPOOS method is able to apply the (a priori known) information necessary for object classification during the segmentation and thereby to achieve very promising results. The next step in the research is the modification of the CPOOS method to handle more than one cluster in an image and clusters of more than two chromosomes, through hierarchical application of the method combined with suitable heuristics. A modified system such as this could automatically and very reliably segment and classify most of the normal cells (about 97% of the cells) in each cytogenetic laboratory, leaving the human expert only the most difficult cases and the abnormal cells. Although the CPOOS method is applied here to chromosome analysis we believe it is suitable to images with partial occlusion coming from other applications, as well.

Efficient chromosome description is found to depend on a few geometrical features and on the density profile of the chromosome. Global features, although very easily computed, fail to achieve the high discriminative power of the former features. Furthermore, several NN based feature extraction techniques are found, in this research, to be very useful in reducing the feature space dimensionality while retaining high chromosome classification performance.

MLP based hierarchical classification strategies reduce the training period and improve human chromosome classification beyond any known method. Using a very well explored database, an NN based hierarchical classifier has classified 5,500 chromosomes with a success rate of 83.6% compared with 81.7% of a maximum likelihood classifier [2], [21], [22] and 82.9% of another NN based classifier [7]. This is an improvement of more than ten and 4% in the error rate compared with the statistical and the other NN classifier, respectively.

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Finally, although applied to human chromosome analysis, our methodology is well suited to other real-world image analysis applications and therefore, contributes to the generic research of image analysis.

Acknowledgement The author would like to thank Dr. Romem, previously of the Soroka Medical Center, Beer-Sheva, Israel, and Dr. Piper of the Medical Research Council, Edinburgh, UK, for providing the “Soroka” and “Edinburgh” databases, respectively. This work was supported in part by the Paul Ivanier Center for Robotics and Production Management, Ben-Gurion University, Beer-Sheva, Israel.

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1简介2 2.4.3中文数字转换 (7) 2.5高级设置 (8) 2.5.1章节标题设置 (9) 2.5.2部分修改标题格式 (12) 2.5.3附录标题设置 (12) 2.5.4其他标题设置 (13) 2.5.5其他设置 (13) 2.6配置文件 (14) 3版本更新15 4开发人员17 1简介 这个宏包的部分原始代码来自于由王磊编写cjkbook.cls文档类,还有一小部分原始代码来自于吴凌云编写的GB.cap文件。原来的这些工作都是零零碎碎编写的,没有认真、系统的设计,也没有用户文档,非常不利于维护和改进。2003年,吴凌云用doc和docstrip工具重新编写了整个文档,并增加了许多新的功能。2007年,oseen和王越在ctex宏包基础上增加了对UTF-8编码的支持,开发出了ctexutf8宏包。2009年5月,我们在Google Code建立了ctex-kit项目1,对ctex宏包及相关宏包和脚本进行了整合,并加入了对XeT E X的支持。该项目由https://www.doczj.com/doc/f018002857.html,社区的开发者共同维护,新版本号为v0.9。在开发新版本时,考虑到合作开发和调试的方便,我们不再使用doc和docstrip工具,改为直接编写宏包文件。 最初Knuth设计开发T E X的时候没有考虑到支持多国语言,特别是多字节的中日韩语言。这使得T E X以至后来的L A T E X对中文的支持一直不是很好。即使在CJK解决了中文字符处理的问题以后,中文用户使用L A T E X仍然要面对许多困难。最常见的就是中文化的标题。由于中文习惯和西方语言的不同,使得很难直接使用原有的标题结构来表示中文标题。因此需要对标准L A T E X宏包做较大的修改。此外,还有诸如中文字号的对应关系等等。ctex宏包正是尝试着解决这些问题。中间很多地方用到了在https://www.doczj.com/doc/f018002857.html,论坛上的讨论结果,在此对参与讨论的朋友们表示感谢。 ctex宏包由五个主要文件构成:ctexart.cls、ctexrep.cls、ctexbook.cls和ctex.sty、ctexcap.sty。ctex.sty主要是提供整合的中文环境,可以配合大多数文档类使用。而ctexcap.sty则是在ctex.sty的基础上对L A T E X的三个标准文档类的格式进行修改以符合中文习惯,该宏包只能配合这三个标准文档类使用。ctexart.cls、ctexrep.cls、ctexbook.cls则是ctex.sty、ctexcap.sty分别和三个标准文档类结合产生的新文档类,除了包含ctex.sty、ctexcap.sty的所有功能,还加入了一些修改文档类缺省设置的内容(如使用五号字体为缺省字体)。 1https://www.doczj.com/doc/f018002857.html,/p/ctex-kit/

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中排布。年份、序号用阿拉伯数字标识,年份用全称,用六角括号“〔〕”括入。序号不用虚位,不用“第”。发文字号距离红色反线4mm。 (六)签发人 上行文需要标识签发人,平行排列于发文字号右侧,发文字号居左空一字,签发人居右空一字。“签发人”用3号方正仿宋_GBK,后标全角冒号,冒号后用3号方正楷体_GBK标识签发人姓名。多个签发人的,主办单位签发人置于第一行,其他从第二行起排在主办单位签发人下,下移红色反线,最后一个签发人与发文字号在同一行。 二、主体部分 (一)标题 由“发文机关+事由+文种”组成,标识在红色反线下空两行,用2号方正小标宋_GBK,可一行或多行居中排布。 (二)主送机关 在标题下空一行,用3号方正仿宋_GBK字体顶格标识。回行是顶格,最后一个主送机关后面用全角冒号。 (三)正文 主送机关后一行开始,每段段首空两字,回行顶格。公文中的数字、年份用阿拉伯数字,不能回行,阿拉伯数字:用3号Times New Roman。正文用3号方正仿宋_GBK,小标题按照如下排版要求进行排版:

tabularx宏包中改变弹性列的宽度

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2-1论文写作要求与格式规范(2009年修订)

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4.对本研究课题有创造性见解,并取得显著的科研成果。 5.学位论文必须是作者本人独立完成,与他人合作的只能提出本人完成的部分。 6.论文字数不少于5万字,中、英摘要3000字;详细中文摘要(单行本)1万字左右。 (四)临床专业学位博士论文要求 1.要求论文课题紧密结合中医临床或中西结合临床实际,研究结果对临床工作具有一定的应用价值。 2.论文表明研究生具有运用所学知识解决临床实际问题和从事临床科学研究的能力。 3.论文字数一般不少于3万字,中、英文摘要2000字;详细中文摘要(单行本)5000字左右。 二、学位论文的格式要求 (一)学位论文的组成 博士、硕士学位论文一般应由以下几部分组成,依次为:1.论文封面;2. 原创性声明及关于学位论文使用授权的声明;3.中文摘要;4.英文摘要;5.目录; 6.引言; 7.论文正文; 8.结语; 9.参考文献;10.附录;11.致谢。 1.论文封面:采用研究生处统一设计的封面。论文题目应以恰当、简明、引人注目的词语概括论文中最主要的内容。避免使用不常见的缩略词、缩写字,题名一般不超过30个汉字。论文封面“指导教师”栏只写入学当年招生简章注明、经正式遴选的指导教师1人,协助导师名字不得出现在论文封面。 2.原创性声明及关于学位论文使用授权的声明(后附)。 3.中文摘要:要说明研究工作目的、方法、成果和结论。并写出论文关键词3~5个。 4.英文摘要:应有题目、专业名称、研究生姓名和指导教师姓名,内容与中文提要一致,语句要通顺,语法正确。并列出与中文对应的论文关键词3~5个。 5.目录:将论文各组成部分(1~3级)标题依次列出,标题应简明扼要,逐项标明页码,目录各级标题对齐排。 6.引言:在论文正文之前,简要说明研究工作的目的、范围、相关领域前人所做的工作和研究空白,本研究理论基础、研究方法、预期结果和意义。应言简

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(公文写作)毕业论文写作要求和格式规范

中国农业大学继续教育学院 毕业论文写作要求和格式规范 壹、写作要求 (壹)文体 毕业论文文体类型壹般分为:试验论文、专题论文、调查方案、文献综述、个案评述、计算设计等。学生根据自己的实际情况,能够选择适合的文体写作。 (二)文风 符合科研论文写作的基本要求:科学性、创造性、逻辑性、实用性、可读性、规范性等。写作态度要严肃认真,论证主题应有壹定理论或应用价值;立论应科学正确,论据应充实可靠,结构层次应清晰合理,推理论证应逻辑严密。行文应简练,文笔应通顺,文字应朴实,撰写应规范,要求使用科研论文特有的科学语言。 (三)论文结构和排列顺序 毕业论文,壹般由封面、独创性声明及版权授权书、摘要、目录、正文、后记、参考文献、附录等部分组成且按前后顺序排列。 1.封面:毕业论文(设计)封面(见文件5)具体要求如下: (1)论文题目应能概括论文的主要内容,切题、简洁,不超过30字,可分俩行排列; (2)层次:高起本,专升本,高起专; (3)专业名称:现开设园林、农林经济管理、会计学、工商管理等专业,应按照标准表述填写; (4)密级:涉密论文注明相应保密年限; (5)日期:毕业论文完成时间。 2.独创性声明和关于论文使用授权的说明:(略)。

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