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The context-tree kernel for strings.

We propose a new kernel for strings which borrows ideas and techniques from information theory and data compression. This kernel can be used in combination with any kernel method, in particular Support Vector Machines for string classification, with notable applications in proteomics. By using a Bayesian averaging framework with conjugate priors on a class of Markovian models known as probabilistic suffix trees or context-trees, we compute the value of this kernel in linear time and space while only using the information contained in the spectrum of the considered strings. This is ensured through an adaptation of a compression method known as the context-tree weighting algorithm. Encouraging classification results are reported on a standard protein homology detection experiment, showing that the context-tree kernel performs well with respect to other state-of-the-art methods while using no biological prior knowledge.

Algorithms↗

Three learning phases for radial-basis-function networks.

In this paper, learning algorithms for radial basis function (RBF) networks are discussed. Whereas multilayer perceptrons (MLP) are typically trained with backpropagation algorithms, starting the training procedure with a random initialization of the MLP's parameters, an RBF network may be trained in many different ways. We categorize these RBF training methods into one-, two-, and three-phase learning schemes. Two-phase RBF learning is a very common learning scheme. The two layers of an RBF network are learnt separately; first the RBF layer is trained, including the adaptation of centers and scaling parameters, and then the weights of the output layer are adapted. RBF centers may be trained by clustering, vector quantization and classification tree algorithms, and the output layer by supervised learning (through gradient descent or pseudo inverse solution). Results from numerical experiments of RBF classifiers trained by two-phase learning are presented in three completely different pattern recognition applications: (a) the classification of 3D visual objects; (b) the recognition hand-written digits (2D objects); and (c) the categorization of high-resolution electrocardiograms given as a time series (ID objects) and as a set of features extracted from these time series. In these applications, it can be observed that the performance of RBF classifiers trained with two-phase learning can be improved through a third backpropagation-like training phase of the RBF network, adapting the whole set of parameters (RBF centers, scaling parameters, and output layer weights) simultaneously. This, we call three-phase learning in RBF networks. A practical advantage of two- and three-phase learning in RBF networks is the possibility to use unlabeled training data for the first training phase. Support vector (SV) learning in RBF networks is a different learning approach. SV learning can be considered, in this context of learning, as a special type of one-phase learning, where only the output layer weights of the RBF network are calculated, and the RBF centers are restricted to be a subset of the training data. Numerical experiments with several classifier schemes including k-nearest-neighbor, learning vector quantization and RBF classifiers trained through two-phase, three-phase and support vector learning are given. The performance of the RBF classifiers trained through SV learning and three-phase learning are superior to the results of two-phase learning, but SV learning often leads to complex network structures, since the number of support vectors is not a small fraction of the total number of data points.

Algorithms↗

A hybrid neural network/genetic algorithm approach to optimizing feature extraction for signal classification.

In this paper, a hybrid neural network/genetic algorithm technique is presented, aiming at designing a feature extractor that leads to highly separable classes in the feature space. The application upon which the system is built, is the identification of the state of human peripheral vascular tissue (i.e., normal, fibrous and calcified). The system is further tested on the classification of spectra measured from the cell nucleii in blood samples in order to distinguish normal cells from those affected by Acute Lymphoblastic Leukemia. As advantages of the proposed technique we may encounter the algorithmic nature of the design procedure, the optimized classification results and the fact that the system performance is less dependent on the classifier type to be used.

Journal Article↗

A modified fuzzy C-means algorithm for bias field estimation and segmentation of MRI data.

In this paper, we present a novel algorithm for fuzzy segmentation of magnetic resonance imaging (MRI) data and estimation of intensity inhomogeneities using fuzzy logic. MRI intensity inhomogeneities can be attributed to imperfections in the radio-frequency coils or to problems associated with the acquisition sequences. The result is a slowly varying shading artifact over the image that can produce errors with conventional intensity-based classification. Our algorithm is formulated by modifying the objective function of the standard fuzzy c-means (FCM) algorithm to compensate for such inhomogeneities and to allow the labeling of a pixel (voxel) to be influenced by the labels in its immediate neighborhood. The neighborhood effect acts as a regularizer and biases the solution toward piecewise-homogeneous labelings. Such a regularization is useful in segmenting scans corrupted by salt and pepper noise. Experimental results on both synthetic images and MR data are given to demonstrate the effectiveness and efficiency of the proposed algorithm.

Algorithms↗

DSM-III-R as a taxonomy. A cluster analysis of diagnoses and symptoms.

While there have been many applications of cluster analysis in psychiatric classification research, there are no studies in which cluster analysis is used to discover the taxonomic structure implicit in the DSM-III itself. In order to do so, the symptom index in the DSM-III-R manual was summarized in a two-way matrix of disorders by symptoms and then analyzed using a hierarchical classes model and companion algorithm (HICLAS) that permits overlap among classes. A novel feature of this model is that superordinate-subordinate relationships among diagnostic and symptom classes are explicitly represented. The HICLAS analysis revealed that there are several discrete symptom classes in DSM-III-R and that many psychiatric disorders can be modeled as combinations of one or more of these classes. The disorders associated with these symptom classes tend to fit the hierarchical classes model relatively well, particularly the mood disorders and the psychotic disorders. However, disorders such as adjustment, personality, and sexual disorder fit the model poorly or not at all. The results are in line with the conjecture that the taxonomic model implicit in DSM-III-R is a hybrid of discrete symptom classes and some other structure, perhaps a dimensional one.

Algorithms↗

A fast T1 algorithm.

Multispectral tissue classification using magnetic resonance T1, T2, and rho images may be useful in diagnosing and locating certain pathology. Techniques for generating the T1 images necessary for this classification scheme often require longer data collection and post processing times than are practical. As a consequence, further development of this classification scheme may be limited. This paper addresses an improvement in the post processing time required to generate T1 images. A nonlinear least-squares algorithm is described for rapidly generating spin-lattice relaxation time images from variable repetition time magnetic resonance images. The algorithm generates a 256 x 256 pixel T1 image from nine variable repetition time images in approximately 60 sec on a VAX-6510 computer.

Algorithms↗

A signal processing pipeline for noninvasive imaging of ventricular preexcitation.

OBJECTIVES: Noninvasive imaging of the cardiac activation sequence in humans could guide interventional curative treatment of cardiac arrhythmias by catheter ablation. Highly automated signal processing tools are desirable for clinical acceptance. The developed signal processing pipeline reduces user interactions to a minimum, which eases the operation by the staff in the catheter laboratory and increases the reproducibility of the results. METHODS: A previously described R-peak detector was modified for automatic detection of all possible targets (beats) using the information of all leads in the ECG map. A direct method was applied for signal classification. The algorithm was tuned for distinguishing beats with an adenosine induced AV-nodal block from baseline morphology in Wolff-Parkinson-White (WPW) patients. Furthermore, an automatic identification of the QRS-interval borders was implemented. RESULTS: The software was tested with data from eight patients having overt ventricular preexcitation. The R-peak detector captured all QRS-complexes with no false positive detection. The automatic classification was verified by demonstrating adenosine-induced prolongation of ventricular activation with statistical significance (p <0.001) in all patients. This also demonstrates the performance of the automatic detection of QRS-interval borders. Furthermore, all ectopic or paced beats were automatically separated from sinus rhythm. Computed activation maps are shown for one patient localizing the accessory pathway with an accuracy of 1 cm. CONCLUSIONS: The implemented signal processing pipeline is a powerful tool for selecting target beats for noninvasive activation imaging in WPW patients. It robustly identifies and classifies beats. The small beat to beat variations in the automatic QRS-interval detection indicate accurate identification of the time window of interest.

Action Potentials↗

Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry serum protein profiling to identify nasopharyngeal carcinoma.

BACKGROUND: Diagnosis of nasopharyngeal carcinoma (NPC) at an early disease stage is important for successful treatment and improving the outcome of patients. The use of serum protein profiles and a classification tree algorithm were explored to distinguish NPC from noncancer. METHODS: Serum samples were applied to metal affinity protein chips to generate mass spectra by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS). Protein peak identification and clustering were performed using the Biomarker Wizard software. Proteomic spectra of serum samples from 50 NPC patients and 54 noncancer controls were used as a training set and a classification tree with 6 distinct protein masses was generated by using Biomarker Pattern software. The validity of the classification tree was then challenged with a blind test set including another 20 NPC patients and 25 noncancer controls. RESULTS: The software identified an average of 93 mass peaks/spectrum and 6 of the identified peaks were used to construct the classification tree. The classification tree correctly determined 83% (123 of 149) of the test samples with 83% (58 of 70) of the NPC samples and 82% (65 of 79) of the noncancer samples. In a combination of the serum protein profiles with Epstein-Barr (EBV) nuclear antigen 1 (EBNA1 IgA) test, the diagnostic sensitivity and specificity were increased to 99% and 96%, respectively. CONCLUSIONS: The results suggest that SELDI-TOF-MS serum protein profiles could discriminate NPC from noncancer. The combination of serum protein profiles with an EBV antibody serology test could further improve the accuracy of NPC screening.

Adult↗

On classification with incomplete data.

We address the incomplete-data problem in which feature vectors to be classified are missing data (features). A (supervised) logistic regression algorithm for the classification of incomplete data is developed. Single or multiple imputation for the missing data is avoided by performing analytic integration with an estimated conditional density function (conditioned on the observed data). Conditional density functions are estimated using a Gaussian mixture model (GMM), with parameter estimation performed using both Expectation-Maximization (EM) and Variational Bayesian EM (VB-EM). The proposed supervised algorithm is then extended to the semisupervised case by incorporating graph-based regularization. The semisupervised algorithm utilizes all available data-both incomplete and complete, as well as labeled and unlabeled. Experimental results of the proposed classification algorithms are shown.

Algorithms↗

Adaptive threshold-based block classification in medical image compression for teleradiology.

Telemedicine, among other things, involves storage and transmission of medical images, popularly known as teleradiology. Due to constraints on bandwidth and storage capacity, a medical image may be needed to be compressed before transmission/storage. Among various compression techniques, transform-based techniques that convert an image in spatial domain into the data in spectral domain are very effective. Discrete cosine transform (DCT) is possibly the most popular transform used in compression of images in standards like Joint Photographic Experts Group (JPEG). In DCT-based compression the image is split into smaller blocks for computational simplicity. The blocks are classified on the basis of information content to maximize compression ratio without sacrificing diagnostic information. The present paper presents a technique along with computational algorithm for classification of blocks on the basis of an adaptive threshold value of variance. The adaptive approach makes the classification technique applicable across the board to all medical images. Its efficacy is demonstrated by applying it to CT, X-ray and ultrasound images and by comparing the results against the JPEG in terms of various objective quality indices.

Algorithms↗

Improved learning algorithms for mixture of experts in multiclass classification.

Mixture of experts (ME) is a modular neural network architecture for supervised learning. A double-loop Expectation-Maximization (EM) algorithm has been introduced to the ME architecture for adjusting the parameters and the iteratively reweighted least squares (IRLS) algorithm is used to perform maximization in the inner loop [Jordan, M.I., Jacobs, R.A. (1994). Hierarchical mixture of experts and the EM algorithm, Neural Computation, 6(2), 181-214]. However, it is reported in literature that the IRLS algorithm is of instability and the ME architecture trained by the EM algorithm, where IRLS algorithm is used in the inner loop, often produces the poor performance in multiclass classification. In this paper, the reason of this instability is explored. We find out that due to an implicitly imposed incorrect assumption on parameter independence in multiclass classification, an incomplete Hessian matrix is used in that IRLS algorithm. Based on this finding, we apply the Newton-Raphson method to the inner loop of the EM algorithm in the case of multiclass classification, where the exact Hessian matrix is adopted. To tackle the expensive computation of the Hessian matrix and its inverse, we propose an approximation to the Newton-Raphson algorithm based on a so-called generalized Bernoulli density. The Newton-Raphson algorithm and its approximation have been applied to synthetic data, benchmark, and real-world multiclass classification tasks. For comparison, the IRLS algorithm and a quasi-Newton algorithm called BFGS have also been applied to the same tasks. Simulation results have shown that the use of the proposed learning algorithms avoids the instability problem and makes the ME architecture produce good performance in multiclass classification. In particular, our approximation algorithm leads to fast learning. In addition, the limitation of our approximation algorithm is also empirically investigated in this paper.

Journal Article↗

Automated evaluation of Her-2/neu status in breast tissue from fluorescent in situ hybridization images.

The evaluation of fluorescent in situ hybridization (FISH) images is one of the most widely used methods to determine Her-2/neu status of breast samples, a valuable prognostic indicator. Conventional evaluation is a difficult task since it involves manual counting of dots in multiple images. In this paper, we present a multistage algorithm for the automated classification of FISH images from breast carcinomas. The algorithm focuses not only on the detection of FISH dots per image, but also on combining results from multiple images taken from a slice for overall case classification. The algorithm includes mainly two stages for nuclei and dot detection respectively. The dot segmentation consists of a top-hat filtering stage followed by template matching to separate real signals from noise. Nuclei segmentation includes a nonlinearity correction step, global thresholding to identify candidate regions, and a geometric rule to distinguish between holes within a nucleus and holes between nuclei. Finally, the marked watershed transform is used to segment cell nuclei with markers detected as regional maxima of the distance transform. Combining the two stages allows the measurement of FISH signals ratio per cell nucleus and the collective classification of cases as positive or negative. The system was evaluated with receiver operating characteristic analysis and the results were encouraging for the further development of this method.

Algorithms↗

Clustering protein sequences--structure prediction by transitive homology.

MOTIVATION: It is widely believed that for two proteins Aand Ba sequence identity above some threshold implies structural similarity due to a common evolutionary ancestor. Since this is only a sufficient, but not a necessary condition for structural similarity, the question remains what other criteria can be used to identify remote homologues. Transitivity refers to the concept of deducing a structural similarity between proteins A and C from the existence of a third protein B, such that A and B as well as B and C are homologues, as ascertained if the sequence identity between A and B as well as that between B and C is above the aforementioned threshold. It is not fully understood if transitivity always holds and whether transitivity can be extended ad infinitum. RESULTS: We developed a graph-based clustering approach, where transitivity plays a crucial role. We determined all pair-wise similarities for the sequences in the SwissProt database using the Smith-Waterman local alignment algorithm. This data was transformed into a directed graph, where protein sequences constitute vertices. A directed edge was drawn from vertex A to vertex B if the sequences A and B showed similarity, scaled with respect to the self-similarity of A, above a fixed threshold. Transitivity was important in the clustering process, as intermediate sequences were used, limited though by the requirement of having directed paths in both directions between proteins linked over such sequences. The length dependency-implied by the self-similarity-of the scaling of the alignment scores appears to be an effective criterion to avoid clustering errors due to multi-domain proteins. To deal with the resulting large graphs we have developed an efficient library. Methods include the novel graph-based clustering algorithm capable of handling multi-domain proteins and cluster comparison algorithms. Structural Classification of Proteins (SCOP) was used as an evaluation data set for our method, yielding a 24% improvement over pair-wise comparisons in terms of detecting remote homologues. AVAILABILITY: The software is available to academic users on request from the authors. CONTACT: e.bolten@science-factory.com; schliep@zpr.uni-koeln.de; s.schneckener@science-factory.com; d.schomburg@uni-koeln.de; schrader@zpr.uni-koeln.de. SUPPLEMENTARY INFORMATION: http://www.zaik.uni-koeln.de/~schliep/ProtClust.html.

Algorithms↗

A template matching algorithm for sperm tracking and classification.

The conventional assessment of human semen, especially sperm movement characteristics, is a highly subjective assessment, with considerable intra- and inter-technician variability. Computer-assisted sperm analysis (CASA) systems provide a rapid and automated assessment of the parameters of sperm motion, together with improved standardization and quality control. However, it should be noted that the measurement of the sperm head motion by CASA is sensitive to the technique of experimentation. While conventional CASA systems use digital microscopes with phase-contrast accessories that make the sperm's head appear brighter and sharper than the other parts, in this research, a regular light microscope was used with a digital camera directly attached to its eyepiece. One of the drawbacks of this method is that the images lack proper contrast and sharpness. To remedy this, we have proposed an algorithm for sperm tracking that is insensitive to image acquisition conditions. This tracking algorithm was used after the background and extra particles were successfully removed through a two-step enhancement algorithm. Additionally, in this research, a template matching method was used for finding the sperm's path. Upon examination, it was proven that our tracking algorithm worked well with different image acquisition conditions. This paper explains how this method reduces error probability in finding and tracking sperm in various frames.

Algorithms↗

[Clinical and experimental bases of the algorithm of treatment in colon injuries].

The results of a retrospective analysis of treatment of 1106 patients with injuries of the colon in peace and war time as well as experimental investigations in 160 dogs have shown the lethality and amount of complications to depend on the size, amount and localization of the colon injuries, trauma shock degree, volume of blood loss, severity of concomitant injuries, the presence and phase of peritonitis by the moment of operation and on the method of treatment. The extension of the operation volume and putting the injured part out onto the anterior abdominal wall are most frequently followed by complications and higher lethality. The one-row precision sero-muscular-submucous interrupted intestinal sutures as well as the early peritoneal sorption with liquid colloid sorbents give better results of the surgical treatment. A classification and algorithm of the surgeon's actions for wounds of the colon are proposed.

Algorithms↗

Trends and pitfalls with nomenclatures and classifications in medicine.

This paper reflects some of the main points in the history and the trends of classifications, nomenclatures and knowledge representation models in medicine. The relations with philosophical background are briefly related. The contributions in this field during the Medical Informatics Europe (MIE) conference in 1997 are presented. International collaborations in the field of lexico-semantic resources and inter-disciplinary partnership in natural language processing technologies are necessary steps to achieve definitive results that will lead to applications in the daily medical practice.

Algorithms↗

A cluster pattern algorithm for the analysis of multiparametric cell assays.

The issue of multiparametric analysis of complex single cell assays of both static and flow cytometry (SC and FC, respectively) has become common in recent years. In such assays, the analysis of changes, applying common statistical parameters and tests, often fails to detect significant differences between the investigated samples. The cluster pattern similarity (CPS) measure between two sets of gated clusters is based on computing the difference between their density distribution functions' set points. The CPS was applied for the discrimination between two observations in a four-dimensional parameter space. The similarity coefficient (r) ranges between 0 (perfect similarity) to 1 (dissimilar). Three CPS validation tests were carried out: on the same stock samples of fluorescent beads, yielding very low r's (0, 0.066); and on two cell models: mitogenic stimulation of peripheral blood mononuclear cells (PBMC), and apoptosis induction in Jurkat T cell line by H2O2. In both latter cases, r indicated similarity (r < 0.23) within the same group, and dissimilarity (r > 0.48) otherwise. This classification and algorithm approach offers a measure of similarity between samples. It relies on the multidimensional pattern of the sample parameters. The algorithm compensates for environmental drifts in this apparatus and assay; it also may be applied to more than four dimensions.

Algorithms↗

[Classification approach to prognostication of the severity of bronchial asthma].

To define the severity of bronchial asthma, to predict its subsequent course, and to prescribe adequate glucocorticosteroid therapy, a mathematical model based on the cluster analysis was used. The authors' algorithm of the classification of bronchial asthma was based on the cluster analysis was used. The authors' algorithm of the classification of bronchial asthma was based on the mean distance value between the objects characterizing patients' status and hyperspatial signs. Each patient was described using a set of 15 clinical, functional, and immunological indices which had a meaning of signs describing the objects. Three clusters corresponding to the groups identified a priori up to two patients were formed to make the classification by the algorithm proposed. The findings make it possible to efficiently analyze the baseline indices in a particular patient from his entrance into or highest relationship to a definite cluster. This may define the severity of bronchial obstruction and predict its progression.

Algorithms↗