WO2001099043A1 - Heuristic method of classification - Google Patents
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- WO2001099043A1 WO2001099043A1 PCT/US2001/019376 US0119376W WO0199043A1 WO 2001099043 A1 WO2001099043 A1 WO 2001099043A1 US 0119376 W US0119376 W US 0119376W WO 0199043 A1 WO0199043 A1 WO 0199043A1
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- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06F—ELECTRIC DIGITAL DATA PROCESSING
- G06F18/00—Pattern recognition
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- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N3/00—Computing arrangements based on biological models
- G06N3/02—Neural networks
- G06N3/08—Learning methods
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- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06F—ELECTRIC DIGITAL DATA PROCESSING
- G06F18/00—Pattern recognition
- G06F18/20—Analysing
- G06F18/21—Design or setup of recognition systems or techniques; Extraction of features in feature space; Blind source separation
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- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06F—ELECTRIC DIGITAL DATA PROCESSING
- G06F18/00—Pattern recognition
- G06F18/20—Analysing
- G06F18/21—Design or setup of recognition systems or techniques; Extraction of features in feature space; Blind source separation
- G06F18/211—Selection of the most significant subset of features
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- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06F—ELECTRIC DIGITAL DATA PROCESSING
- G06F18/00—Pattern recognition
- G06F18/20—Analysing
- G06F18/24—Classification techniques
- G06F18/243—Classification techniques relating to the number of classes
- G06F18/2433—Single-class perspective, e.g. one-against-all classification; Novelty detection; Outlier detection
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- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10S706/00—Data processing: artificial intelligence
- Y10S706/90—Fuzzy logic
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- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10S706/00—Data processing: artificial intelligence
- Y10S706/902—Application using ai with detail of the ai system
- Y10S706/932—Mathematics, science, or engineering
Definitions
- the field of the invention concerns a method of analyzing and classifying objects which can be represented as character strings, such as documents, or strings or tables of numerical data, such as changes in stock market prices, the levels of expression of different genes in cells of a tissue detected by hybridization of mRNA to a gene chip, or the amounts of different proteins in a sample detected by mass spectroscopy. More specifically, the invention concerns a general method whereby a classification algorithm is generated and verified from a learning data set consisting of pre-classified examples of the class of objects that are to be classified. The pre- classified examples having been classified by reading in the case of documents, historical experience in the case of market data, or pathological examination in the case of biological data. The classification algorithm can then be used to classify previously unclassified examples.
- the invention uses genetic algorithms and self organizing adaptive pattern recognition algorithms. Genetic algorithms were described initially by Professor John H. Holland. (J.H. Holland, Adaptation in Natural and Artificial Systems, MIT Press 1992, see also U.S. patent No. 4,697,242 and No. 4,881,178). A use of a genetic algorithm for pattern recognition is described in U.S. patent No. 5,136,686 to Koza, see column 87.
- the invention consists of two related heuristic algorithms, a classifying algorithm and a learning algorithm, which are used to implement classifying methods and learning methods.
- the parameters of the classifying algorithm are determined by the application of the learning algorithm to a training or learning data set.
- the training data set is a data set in which each item has already been classified.
- the classifying method of the invention classifies Objects according to a data stream that is associated with the Object.
- Each Object in the invention is characterized by a data stream, which is a large number, at least about 100 data points, and can be 10,000 or more data points.
- a data stream is generated in a way that allows for the individual datum in data streams of different samples of the same type of Object to be correlated one with the other.
- Examples of Objects include texts, points in time in the context of predicting the direction of financial markets or the behavior of a complex processing facility, and biological samples for medical diagnosis.
- the associated data streams of these Objects are the distribution of trigrams in the text, the daily changes in price of publicly traded stocks or commodities, the instantaneous readings of a number of pressure, temperature and flow readings in the processing facility such as an oil refinery, and a mass spectrum of some subset of the proteins found in the sample, or the intensity mRNA hybridization to an array of different test polynucleotides.
- the invention can be used whenever it is desired to classify
- Objects into one of several categories e.g., which typically is two or three categories, and the Objects are associated with extensive amounts of data, e.g., typically thousands of data points.
- the term "Objects" is capitalized herein to indicate that Objects has a special meaning herein in that it refers collectively to tangible objects, e.g., specific samples, and intangible objects, e.g., writings or texts, and totally abstract objects, e.g., the moment in time prior to an untoward event in a complex processing facility or the movement in the price of a foreign currency.
- the first step of the classifying method is to calculate an Object vector, i.e., an ordered set of a small number of data points or sealers (between 4 and 100, more typically between 5 and 30) that is derived from the data stream associated with the Object to be classified.
- the transformation of the data steam into an Object vector is termed "abstraction.”
- the most simple abstraction process is to select a number of points of the data stream. However, in principle the abstraction process can be performed on any function of the data stream. In the embodiments presented below abstraction is performed by selection of a small number of specific intensities from the data stream.
- the second step of the classifying method is to determine in which data cluster, if any, the vector rests.
- Data clusters are mathematical constructs that are the multidimensional equivalents of non-overlapping "hyperspheres" of fixed size in the vector space.
- the location and associated classification or "status" of each data cluster is determined by the learning algorithm from the training data set.
- the extent or size of each data cluster and the number of dimensions of the vector space is set as a matter of routine experimentation by the operator prior to the operation of the learning algorithm. If the vector lies within a known data cluster, the Object is given the classification associated with that cluster. In the most simple embodiments the number of dimensions of the vector space is equal to the number of data points that is selected in the abstraction process. Alternatively, however, each sealer of the Object vector can be calculated using multiple data points of the data stream. If the Obj ect vector rests outside of any known cluster, a classification can be made of atypia, or atypical sample.
- the match parameter p is also termed a normalized "fuzzy" AND.
- the Object is then classified according to the classification of the preformed vector to which it is most similar by this metric.
- the match parameter is 1 when the Object vector and the preformed vector are identical and less than 1 in all other cases.
- the learning algorithm determines both the details of abstraction process and the identity of the data clusters by utilizing a combination of known mathematical techniques and two pre-set parameters.
- a user pre-sets the number of dimensions of the vector space and the size of the data clusters or, alternatively, the minimum acceptable level of the "fuzzy AND” match parameter p.
- data cluster refers to both a hypersphere using a Euclidean metric and preformed classified vectors using a "fuzzy AND” metric.
- the vector space in which the data clusters lie is a normalized vector space so that the variation of intensities in each dimension is constant. So expressed the size of the data cluster using a Euclidean metric can be expressed as minimum percent similarity among the vectors resting within the cluster.
- the learning algorithm can be implemented by combining two different types of publicly available generic software, which have been developed by others and are well known in the field: (1) a genetic algorithm (J.H. Holland, Adaptation in Natural and Artificial Systems, MIT Press 1992) that processes a set of logical chromosomes 1 to identify an optimal logical chromosome that controls the abstraction of the data steam and (2) an adaptive self-organizing pattern recognition system (see, T. Kohonen, Self Organizing and Associative Memory, 8 Series in
- logical chromosome is used in connection with genetic learning algorithms because the logical operations of the algorithm are analogous to reproduction, selection, recombination and mutation. There is, of course, no biological embodiment of a logical chromosome in DNA or otherwise.
- the genetic learning algorithms of the invention are purely computational devices, and should not be confused with schemes for biologically-based information processing. Information Sciences, Springer Nerlag, 1984; Kohonen, T, Self-organizing Maps, Springer Nerlag, Heidelberg 1997 ), available from Group One Software, Greenbelt, MD, which identifies a set of data clusters based on any set of vectors generated by a logical chromosome. Specifically the adaptive pattern recognition software maximizes the number of vectors that rest in homogeneous data clusters, i.e., clusters that contain vectors of the learning set having only one classification type.
- each logical chromosome must be assigned a "fitness.”
- the fitness of each logical chromosome is determined by the number of vectors in the training data set that rest in homogeneous clusters of the optimal set of data clusters for that chromosome.
- the learning algorithm of the invention combines a genetic algorithm to identify an optimal logical chromosome and an adaptive pattern recognition algorithm to generate an optimal set of data clusters and a the fitness calculation based on the number of sample vectors resting in homogeneous clusters.
- the learning algorithm of the invention consists of the combination of a genetic algorithm, a pattern recognition algorithm and the use of a fitness function that measures the homogeneity of the output of the pattern recognition algorithm to control the genetic algorithm.
- the number of data clusters is much greater than the number of categories.
- the classifying algorithms of the examples below sorted Objects into two categories, e.g., documents into those of interest and those not of interest, or the clinical samples into benign or malignant. These classifying algorithms, however, utilize multiple data clusters to perform the classification.
- the classifying algorithm may utilize more than two categories. For example, when the invention is used as a predictor of foreign exchange rates, a tripartite scheme corresponding to rising, falling and mixed outlooks would be appropriate. Again, such a tripartite classifying algorithm would be expected to have many more than three data clusters. IN. Detailed Description of the Invention
- routine practitioner In order to practice the invention the routine practitioner must develop a classifying algorithm by employing the learning algorithm. As with any heuristic method, some routine experimentation is required. To employ the learning algorithm, the routine practitioner uses a training data set and must experimentally optimize two parameters, the number of dimensions and the data cluster size.
- the learning algorithm itself inherently limits the number of dimensions in each implementation. If the number of dimensions is too low or the size of the cluster is too large, the learning algorithm fails to generate any logical chromosomes that correctly classify all samples with an acceptable level of homogeneity. Conversely, the number of dimensions can be too large. Under this circumstance, the learning algorithm generates many logical chromosomes that have the maximum possible fitness early in the learning process and, accordingly, there is only abortive selection.
- the number of clusters will be found to approach the number of samples in the training data set and, again, the routine practitioner will find that a large number of logical chromosomes will yield a set of completely homogeneous data clusters.
- the invention provides a method for the computerized classification documents. For example, one may want to extract the documents of interest from a data base consisting of a number of documents too large to review individually. For these circumstances, the invention provides a computerized algorithm to identify a subset of the database most likely to contain the documents of interest.
- Each document is an Object
- the data stream for each document consists of the histogram representing the frequency of each of the 17576 (26 3 ) three letter combinations (trigrams) found in the document after removal of spaces and punctuation.
- a histogram of the 9261 trigrams of consonants can be prepared after the further removal of vowels from the document.
- the training data set consists of a sample of the appropriate documents that have been classified as "of interest” or “not of interest,” according to the needs of the user.
- Financial Markets It is self-evident that financial markets respond to external events and are interrelated to each other in a consistent fashion; for example, foreign exchange rates are influenced by the attractiveness of investment opportunities. However, the direction and extent of the response to an individual event can be difficult to predict.
- the invention provides an algorithm computerized prediction of prices in one market based on the movement in prices in another.
- Each point in time is an Object, for example hourly intervals
- the data stream for hour consists of the histogram of the change in price of publicly traded securities in the major stock markets in the relevant countries, e.g., the New York and London stock exchanges where the exchange rate of the pound and dollar are of interest.
- the training data set consists of the historical record such price changes that has been classified as preceding a rise or fall in the dolla ⁇ pound rate.
- the present invention provides a computerized algorithm to classify each point in time as either a high-risk or normal- risk time point.
- the data stream consists of the status values for each point in time.
- the training data set consists of the historical record of the status values classified as either preceding an untoward event or as preceding normal operation.
- the invention can be used in the analysis of a tissue sample for medical diagnosis, e.g.,, for analysis of serum or plasma.
- the data stream can be any reproducible physical analysis of the tissue sample that results in 2,000 or more measurements that can be quantified to at least 1 part per thousand (three significant figures).
- Time of flight mass spectra of proteins are particularly suitable for the practice of the invention. More specifically, matrix assisted laser desorption ionization time of flight (MALDI-TOF) and surface enhanced laser desorption ionization time of flight (SELDI-TOF) spectroscopy. See generally WO 00/49410.
- the data stream can also include measurements that are not inherently organized by a single ordered parameter such as molecular weight, but have an
- DNA microarray data that simultaneously measures the expression levels of 2,000 or more genes can be used as a data stream when the tissue sample is a biopsy specimen, recognizing that the order of the individual genes is the data stream is arbitrary.
- Specific diseases where the present invention is particularly valuable occur when early diagnosis is important, but technically difficult because of the absence of symptoms and the disease may be expected to produce differences that are detectable in the serum because of the metabolic activity of the pathological tissue.
- the early diagnosis of malignancies are a primary focus of the use of the invention.
- the working example illustrates the diagnosis of prostatic carcinoma, similar trials for the diagnosis of ovarian cancers have been performed.
- the first step in the classifying process of the invention is the transformation or abstraction of the data stream into a characteristic vector.
- the data may be conveniently normalized prior to abstraction by assigning the overall peak a arbitrary value of 1.0 and all other points given fractional values.
- the most simple abstraction of a data stream consists of the selection of a small number of data points.
- more complex functions of multiple points could be constructed such as averages over intervals or more complex sums or differences between data points that are at predetermined distance from a selected prototype data point.
- Such functions of the intensity values of the data stream could also be used and
- a feature of the invention is the use of a genetic algorithm to determine the data points which are used to calculate the characteristic vector.
- the list of the specific points to be selected is termed a logical chromosome.
- the logical chromosomes contain as many "genes" as there are dimensions of the characteristic vector. Any set of the appropriate number of data points can be a logical chromosome, provided only that no gene of a chromosome is duplicated. The order of the genes has no significance to the invention.
- the first illustrative example concerns a corpus of 100 documents, which were randomly divided into a training set of 46 documents and a testing set of 54
- the documents consisted of State of the Union addresses, selections from the book The Art of War and articles from the Financial Times. The distribution of trigrams for each document was calculated. A vector space of 25 dimensions and a data cluster size in each dimension of 0.35 times the range of values in that dimension was selected.
- the genetic algorithms were initialized with about 1,500 randomly chosen logical chromosomes. As the algorithm progressed the more fit logical chromosomes are duplicated and the less fit are terminated. There is recombination between chromosomes and mutation, which occurs by the random replacement of an element of a chromosome. It is not an essential feature of the invention that the initially selected collection of logical chromosome be random.
- Certain prescreening of the total set of data streams to identify those data points having the highest variability may be useful, although such techniques may also introduce an unwanted initialization bias.
- the initial set of chromosomes, the mutation rate and other boundary conditions for the genetic algorithm are not critical to its function.
- the fitness score of each of the logical chromosomes that are generated by the genetic algorithm is calculated.
- the calculation of the fitness score requires an optimal set of data clusters be generated for each logical chromosome that is tested.
- Data clusters are simply the volumes in the vector space in which the Object vectors of the training data set rest.
- the method of generating the optimal set of data clusters is not critical to the invention and will be considered below. However, whatever method is used to generate the data cluster map, the map is constrained by the following rules: each data cluster should be located at the centroid of the data points that lie within the data cluster, no two data clusters may overlap and the dimension of each cluster in the normalized vector space is fixed prior to the generation of the map.
- the size of the data cluster is set by the user during the training process. Setting the size too large results in a failure find any chromosomes that can successfully classify the entire training set, conversely setting the size to low results in a set of optimal data clusters in which the number of clusters approaches the number of data points in the training set. More importantly, a too small setting of the size of the data cluster results in "overfitting,” which is discussed below.
- the method used to define the size of the data cluster is a part of the invention.
- the cluster size can be defined by the maximum of the equivalent of the Euclidean distance (root sum of the squares) between any two members of the data cluster.
- a data cluster size that corresponds to a requirement of 90% similarity is suitable for the invention when the data stream is generated by SELDI-TOF mass spectroscopy data. Somewhat large data clusters have been found useful for the classification of texts.
- 90% similarity is defined by requiring that the distance between any two members of a cluster is less than 0.1 of the maximum distance between two points in a normalized vector space.
- the vector space is normalized so that the range of each scalar of the vectors within the training data set is between 0.0 and 1.0.
- the maximal possible distance between any two vectors in the vector space is then root N, where N is the number of dimensions.
- the Euclidean diameter of each cluster is then 0.1 x root(N).
- Non-Euclidean metrics such as vector product metrics can be used.
- the data stream may be converted into logarithmic form if the distribution of values within the data stream is log normal and not normally distributed.
- the fitness score for that chromosome can be calculated.
- the fitness score of the chromosome roughly corresponds to the number of vectors of the training data set that rest in clusters that are homogeneous, i.e., clusters that contain the characteristic vectors from samples having a single classification. More precisely, the fitness score is calculated by assigning to each cluster a homogeneity score, which varies from 0.0 for homogeneous clusters to 0.5 for clusters that contain equal numbers of malignant and benign sample vectors.
- the fitness score of the chromosome is the average fitness score of the data clusters. Thus, a fitness score of 0.0 is the most fit.
- An alternative embodiment of the invention utilizes a non-Euclidean metric to establish the boundaries of the data clusters.
- a metric refers to a method of measuring distance in a vector space.
- the alternative metric for the invention can be based on a normalized "fuzzy AND” as defined above.
- Soft ware that implements an adaptive pattern recognition algorithm based on the "fuzzy AND” metric is available from Boston University under the name Fuzzy ARTMAP.
- Boolean based search and retrieval methods have proven inadequate when faced with the rigors of the current production volume of textual material. Furthermore, Boolean searches do not capture conceptual information.
- a suggested approach to the problem has been to somehow extract conceptual information in a manner that is amenable to numeric analysis.
- One such method is the coding of a document as a collection of trigrams and their frequency of occurrence recorded.
- a trigram is a collection of any three characters, such as AFV, KLF, OID, etc. There are therefore 26 3 trigrams. White space and punctuation are not included.
- a document can then be represented as segmented into a specific set of trigrams
- the learning algorithm searched through the trigram set and identified a set of trigrams that separated the two classes of documents.
- the resultant model was in 25 dimensions with the decision boundary set at 0.35 the maximal distance allowed in the space.
- the classifying algorithm utilizes only 25 of the possible 17,576 trigrams. On testing the results in the table obtained.
- Ta e Con us on atr x. ctua va ues are rea vert ca y an t e resu ts o an algorithm according to the invention are read horizontally.
- the above-described learning algorithm was employed to develop a classification for prostatic cancer using SELDI-TOF mass spectra (MS) of 55 patient serum samples, 30 having biopsy diagnosed prostatic cancer and prostatic serum antigen (PSA) levels greater than 4.0 ng/ml and 25 normals having PSA levels below 1 ng/ml.
- MS data was abstracted by selection of 7 molecular weight values.
- a cluster map that assigned each vector in the training data set to a homogeneous data cluster was generated.
- the cluster map contained 34 clusters, 17 benign and 17 malignant.
- Table 1 shows the location of each of data cluster of the map and the number of samples of the training set assigned to each cluster.
- the classifying algorithm was tested using 231 samples that were excluded from the training data set. Six sets of samples from patients with various clinical and pathological diagnoses were used. The clinical and pathological description and the algorithm results were as follows: 1) 24 patients with PSA >4 ng/ml and biopsy proven cancer, 22 map to diseased data clusters, 2 map to no cluster; 2) 6 normal, all map to healthy clusters; 3) 39 with benign prostatic hypertrophy (BPH) or prostatitis and PSA ⁇ 4 ng/ml, 7 map to diseased data clusters, none to healthy data clusters and 32 to no data cluster; 4) 139 with BPH or prostatitis and PSA >4 and ⁇ 10 ng/ml, 42 map to diseased data clusters, 2 to healthy data clusters and 95 to no data cluster; 5) 19 with BPH or prostatitis and PSA > 10 ng/ml, 9 map to diseased data clusters none to healthy and 10 to no data cluster.
- a sixth set of data was developed by taking pre- and post-prostatectomy samples from patients having biopsy proven carcinoma and PSA > 10 ng/ml. As expected each of the 7 pre-surgical samples was assigned to a diseased data set. However, none of the sample taken 6 weeks post surgery, at a time when the PSA levels had fallen to below 1 ng/ml were not assignable to any data set.
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CA002411906A CA2411906A1 (en) | 2000-06-19 | 2001-06-19 | Heuristic method of classification |
MXPA02012167A MXPA02012167A (en) | 2000-06-19 | 2001-06-19 | Heuristic method of classification. |
KR1020097002829A KR101047575B1 (en) | 2000-06-19 | 2001-06-19 | Heuristic Method of Classification |
AU2001269877A AU2001269877A1 (en) | 2000-06-19 | 2001-06-19 | Heuristic method of classification |
EA200300035A EA006272B1 (en) | 2000-06-19 | 2001-06-19 | Heuristic method of classification |
EP01948425A EP1292912B1 (en) | 2000-06-19 | 2001-06-19 | Heuristic method of classification |
IL15318901A IL153189A0 (en) | 2000-06-19 | 2001-06-19 | Heuristic method of classification |
DE60135549T DE60135549D1 (en) | 2000-06-19 | 2001-06-19 | HEURISTIC CLASSIFICATION PROCEDURE |
BR0111742-4A BR0111742A (en) | 2000-06-19 | 2001-06-19 | Heuristic Classification Method |
NZ522859A NZ522859A (en) | 2000-06-19 | 2001-06-19 | Heuristic method of classifying objects using a vector space having multiple preclassified data clusters |
JP2002503811A JP2003536179A (en) | 2000-06-19 | 2001-06-19 | Heuristic classification method |
NO20026087A NO20026087L (en) | 2000-06-19 | 2002-12-18 | Heuristic method of classification |
HK04102275A HK1059494A1 (en) | 2000-06-19 | 2004-03-29 | Heuristic method of classification |
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KR101047575B1 (en) | 2011-07-13 |
EA200300035A1 (en) | 2003-10-30 |
EA006272B1 (en) | 2005-10-27 |
JP2003536179A (en) | 2003-12-02 |
CA2411906A1 (en) | 2001-12-27 |
US20070185824A1 (en) | 2007-08-09 |
CN1446344A (en) | 2003-10-01 |
KR20030051435A (en) | 2003-06-25 |
NO20026087L (en) | 2003-02-13 |
US7499891B2 (en) | 2009-03-03 |
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HK1059494A1 (en) | 2004-07-02 |
US7240038B2 (en) | 2007-07-03 |
CN1741036A (en) | 2006-03-01 |
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US20020046198A1 (en) | 2002-04-18 |
ZA200209845B (en) | 2003-10-21 |
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