Health Discovery Corporation

André Elisseeff

Isabelle Guyon

Jason Aaron Edward Weston

Olivier Chapelle

Bernhard Schoelkopf

Asa Ben-Hur

Fernando Perez-Cruz

Jason Edward Weston

Bernhard Schölkopf

Peter L Bartlett

Asa Ben Hur

Fernando Pérez-Cruz

A method is provided for unsupervised clustering of gene expression data to identify co-regulation patterns. A clustering algorithm randomly divides the data into k different subsets and measures the similarity between pairs of datapoints within the subsets, assigning a score to the pairs based on similarity, with the greatest similarity giving the highest correlation score. A distribution of the scores is plotted for each k. The highest value of k that has a distribution that remains concentrated near the highest correlation score corresponds to the number of co-regulation patterns.

Identification of co-regulation patterns by unsupervised cluster analysis of gene expression data

Support vector machines are used to classify data contained within a structured dataset such as a plurality of signals generated by a spectral analyzer. The signals are pre-processed to ensure alignment of peaks across the spectra. Similarity measures are constructed to provide a basis for comparison of pairs of samples of the signal. A support vector machine is trained to discriminate between different classes of the samples. to identify the most predictive features within the spectra. In a preferred embodiment feature selection is performed to reduce the number of features that must be considered.

Support vector machine-based method for analysis of spectral data

A group of features that has been identified as 'significant' in being able to separate data into classes is evaluated using a support vector machine which separates the dataset into classes one feature at a time. After separation, an extremal margin value is assigned to each feature based on the distance between the lowest feature value in the first class and the highest feature value in the second class. Separately, extremal margin values are calculated for a normal distribution within a large number of randomly drawn example sets for the two classes to determine the number of examples within the normal distribution that would have a specified extremal margin value. Using p-values calculated for the normal distribution, a desired p-value is selected. The specified extremal margin value corresponding to the selected p-value is compared to the calculated extremal margin values for the group of features. The features in the group that have a calculated extremal margin value less than the specified margin value are labeled as falsely significant.

Method for feature selection and for evaluating features identified as significant for classifying data

A model selection method is provided for choosing the number of clusters, or more generally the parameters of a clustering algorithm. The algorithm is based on comparing the similarity between pairs of clustering runs on sub-samples or other perturbations of the data. High pairwise similarities show that the clustering represents a stable pattern in the data. The method is applicable to any clustering algorithm, and can also detect lack of structure. We show results on artificial and real data using a hierarchical clustering algorithm.

Model selection for cluster data analysis

In a pre-processing step prior to training a learning machine, pre-processing includes reducing the quantity of features to be processed using feature selection methods selected from the group consisting of recursive feature elimination (RFE), minimizing the number of non-zero parameters of the system (l-norm minimization), evaluation of cost function to identify a subset of features that are compatible with constraints imposed by the learning set, unbalanced correlation score, transductive feature selection and single feature using margin-based ranking. The features remaining after feature selection are then used to train a learning machine for purposes of pattern classification, regression, clustering and/or novelty detection.

Method for feature selection in a support vector machine using feature ranking

Learning machines, such as support vector machines, are used to analyze datasets to recognize patterns within the dataset using kernels that are selected according to the nature of the data to be analyzed. Where the datasets possesses structural characteristics, locational kernels can be utilized to provide measures of similarity among data points within the dataset. The locational kernels are then combined to generate a decision function, or kernel, that can be used to analyze the dataset. Where an invariance transformation or noise is present, tangent vectors are defined to identify relationships between the invariance or noise and the data points. A covariance matrix is formed using the tangent vectors, then used in generation of the kernel.

Kernels and methods for selecting kernels for use in learning machines

Selection of features predictive of biological conditions using protein mass spectrographic data

Kernels and kernel methods for spectral data

A computer-implemented method is provided for ranking features within a large dataset containing a large number of features according to each feature's ability to separate data into classes. For each feature, a support vector machine separates the dataset into two classes and determines the margins between extremal points in the two classes. The margins for all of the features are compared and the features are ranked based upon the size of the margin, with the highest ranked features corresponding to the largest margins. A subset of features for classifying the dataset is selected from a group of the highest ranked features. In one embodiment, the method is used to identify the best genes for disease prediction and diagnosis using gene expression data from micro-arrays.

Pre-processed feature ranking for a support vector machine

Learning machines, such as support vector machines, are used to analyze datasets to recognize patterns within the dataset using kernels that are selected according to the nature of the data to be analyzed. Where the datasets possesses structural characteristics, locational kernels can be utilized to provide measures of similarity among data points within the dataset. The locational kernels are then combined to generate a decision function, or kernel, that can be used to analyze the dataset. Where invariance transformations or noise is present, tangent vectors are defined to identify relationships between the invariance or noise and the data points. A covariance matrix is formed using the tangent vectors, then used in generation of the kernel for recognizing patterns in the dataset.

In a pre-processing step prior to training a learning machine, pre-processing includes reducing the quantity of features to be processed using feature selection methods selected from the group consisting of recursive feature elimination (RFE), minimizing the number of non-zero parameters of the system (l-norm minimization), evaluation of cost function to identify a subset of features that are compatible with constraints imposed by the learning set, unbalanced correlation score and transductive feature selection. The features remaining after feature selection are then used to train a learning machine for purposes of pattern classification, regression, clustering and/or novelty detection. (, 300, 301, 302, 304, 306, 308, 309, 310, 311, 312, 314)

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Thalwil, Switzerland

André Elisseeff