Patents by Inventor Pablo Tamayo

Pablo Tamayo has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Patent number: 9593377
    Abstract: The present invention provides methods of detecting cancer using biomarkers.
    Type: Grant
    Filed: November 30, 2011
    Date of Patent: March 14, 2017
    Assignees: Dana-Farber Cancer Institute, Inc., The Broad Institute, Inc.
    Inventors: William C. Hahn, Pablo Tamayo, Jesse S. Boehm, Jill P. Mesirov
  • Patent number: 8775466
    Abstract: A method for projection mining comprises performing a first projection on a first data object of a first type comprising a plurality of data entries and a second data object of a second type comprising a plurality of data entries to create definitions of attributes of the first data object and definitions of attributes of the second data object, performing a second projection of the definitions of the attributes of the first data object and the definitions of the attributes of the second data object into a space of meta-attributes based on semantic relationships among the attributes of the first data object and the second data object, learning relationships between the space of meta-attributes formed by the projections of the first data object and the second data object and a space of meta-attributes relating to new data not included in the first data object and the second data object, and generating at least one new data object of the first or second type based on the new data using the learned relationships
    Type: Grant
    Filed: May 1, 2013
    Date of Patent: July 8, 2014
    Assignee: Oracle International Corporation
    Inventors: Pablo Tamayo, Mark Hornick, Marcos C. Campos, Boriana Milenova
  • Publication number: 20130323744
    Abstract: The present invention provides methods of detecting cancer using biomarkers.
    Type: Application
    Filed: November 30, 2011
    Publication date: December 5, 2013
    Applicants: The Broad Institute, Inc., Dana-Farber Cancer Institute, Inc.
    Inventors: William C. Hahn, Pablo Tamayo, Jesse S. Boehm, Jill P. Mesirov
  • Publication number: 20130246319
    Abstract: A method for projection mining comprises performing a first projection on a first data object of a first type comprising a plurality of data entries and a second data object of a second type comprising a plurality of data entries to create definitions of attributes of the first data object and definitions of attributes of the second data object, performing a second projection of the definitions of the attributes of the first data object and the definitions of the attributes of the second data object into a space of meta-attributes based on semantic relationships among the attributes of the first data object and the second data object, learning relationships between the space of meta-attributes formed by the projections of the first data object and the second data object and a space of meta-attributes relating to new data not included in the first data object and the second data object, and generating at least one new data object of the first or second type based on the new data using the learned relationships
    Type: Application
    Filed: May 1, 2013
    Publication date: September 19, 2013
    Applicant: Oracle International Corporation
    Inventors: Pablo Tamayo, Mark Hornick, Marcos C. Campos, Boriana Milenova
  • Patent number: 7734652
    Abstract: An implementation of NMF functionality integrated into a relational database management system provides the capability to apply NMF to relational datasets and to sparse datasets. A database management system comprises a multi-dimensional data table operable to store data and a processing unit operable to perform non-negative matrix factorization on data stored in the multi-dimensional data table and to generate a plurality of data tables, each data table being smaller than the multi-dimensional data table and having reduced dimensionality relative to the multi-dimensional data table. The multi-dimensional data table may be a relational data table.
    Type: Grant
    Filed: August 27, 2004
    Date of Patent: June 8, 2010
    Assignee: Oracle International Corporation
    Inventors: Pablo Tamayo, George G. Tang, Mark A. McCracken, Mahesh K. Jagannath, Marcos M. Campos, Boriana L. Milenova, Joseph S. Yarmus, Pavani Kuntala
  • Publication number: 20090276403
    Abstract: A method for projection mining comprises performing a first projection on a first data object of a first type comprising a plurality of data entries and a second data object of a second type comprising a plurality of data entries to create definitions of attributes of the first data object and definitions of attributes of the second data object, performing a second projection of the definitions of the attributes of the first data object and the definitions of the attributes of the second data object into a space of meta-attributes based on semantic relationships among the attributes of the first data object and the second data object, learning relationships between the space of meta-attributes formed by the projections of the first data object and the second data object and a space of meta-attributes relating to new data not included in the first data object and the second data object, and generating at least one new data object of the first or second type based on the new data using the learned relationships
    Type: Application
    Filed: November 26, 2008
    Publication date: November 5, 2009
    Inventors: Pablo Tamayo, Mark Hornick, Marcos M. Campos, Boriana Milenova
  • Patent number: 7324926
    Abstract: Methods and apparatus for classifying or predicting the classes for samples based on gene expression are described. Also described are methods and apparatus for ascertaining or discovering new, previously unknown classes based on gene expression. Methods, computer systems and apparatus for classifying or predicting whether a sample is treatment sensitive (e.g., chemosensitive) or treatment resistant (e.g., chemoresistant) are also provided. Classification occurs based on analysis of gene expression data from samples that have been subjected to one or more compounds.
    Type: Grant
    Filed: October 1, 2001
    Date of Patent: January 29, 2008
    Assignees: Whitehead Institute for Biomedical Research, Dana-Farber Cancer Institute, Inc.
    Inventors: Pablo Tamayo, Jane E. Staunton, Donna K. Slonim, Hilary A. Coller, Todd R. Golub, Eric S. Lander, Jill P. Mesirov
  • Patent number: 7239986
    Abstract: Methods and apparatus for classifying or predicting the classes for samples based on gene expression are described. Also described are methods and apparatus for ascertaining or discovering new, previously unknown classes based on gene expression.
    Type: Grant
    Filed: February 12, 2002
    Date of Patent: July 3, 2007
    Assignees: Whitehead Institute for Biomedical Research, Dana-Farber Cancer Institute, Inc.
    Inventors: Todd R. Golub, Eric S. Lander, Jill Mesirov, Donna Slonim, Pablo Tamayo
  • Patent number: 7117208
    Abstract: An enterprise-wide web data mining system, computer program product, and method of operation thereof, that uses Internet based data sources, and which operates in an automated and cost effective manner. The enterprise web mining system comprises: a database coupled to a plurality of data sources, the database operable to store data collected from the data sources; a data mining engine coupled to the web server and the database, the data mining engine operable to generate a plurality of data mining models using the collected data; a server coupled to a network, the server operable to: receive a request for a prediction or recommendation over the network, generate a prediction or recommendation using the data mining models, and transmit the generated prediction or recommendation.
    Type: Grant
    Filed: December 17, 2004
    Date of Patent: October 3, 2006
    Assignee: Oracle Corporation
    Inventors: Pablo Tamayo, Jacek Myczkowski, Marcos Campos
  • Patent number: 7105293
    Abstract: Sets of genetic markers for specific tumor classes are described, as well as methods of identifying a biological sample based on these markers. Also described are diagnostic, prognostic, and therapeutic screening uses for these markers, as well as oligonucleotide arrays comprising these markers.
    Type: Grant
    Filed: September 19, 2001
    Date of Patent: September 12, 2006
    Assignees: Whitehead Institute for Biomedical Research, Dana-Farber Cancer Institute, Inc.
    Inventors: Sridhar Ramaswamy, Todd R. Golub, Pablo Tamayo, Michael Angelo
  • Publication number: 20050246354
    Abstract: An implementation of NMF functionality integrated into a relational database management system provides the capability to apply NMF to relational datasets and to sparse datasets. A database management system comprises a multi-dimensional data table operable to store data and a processing unit operable to perform non-negative matrix factorization on data stored in the multi-dimensional data table and to generate a plurality of data tables, each data table being smaller than the multi-dimensional data table and having reduced dimensionality relative to the multi-dimensional data table. The multi-dimensional data table may be a relational data table.
    Type: Application
    Filed: August 27, 2004
    Publication date: November 3, 2005
    Inventors: Pablo Tamayo, George Tang, Mark McCracken, Mahesh Jagannath, Marcos Campos, Boriana Milenova, Joseph Yarmus, Pavani Kuntala
  • Patent number: 6941318
    Abstract: A method, system, and computer program product for generating a representation of a data mining model that improves the transparency of data mining models so as to be more easily interpretable by human users. The method comprises the steps of: receiving a dataset, generating a callable version of the data mining model, and generating a tree representing decisional logic of the data mining model using the dataset.
    Type: Grant
    Filed: May 10, 2002
    Date of Patent: September 6, 2005
    Assignee: Oracle International Corporation
    Inventors: Pablo Tamayo, Gary Drescher
  • Publication number: 20050102292
    Abstract: An enterprise-wide web data mining system, computer program product, and method of operation thereof, that uses Internet based data sources, and which operates in an automated and cost effective manner. The enterprise web mining system comprises: a database coupled to a plurality of data sources, the database operable to store data collected from the data sources; a data mining engine coupled to the web server and the database, the data mining engine operable to generate a plurality of data mining models using the collected data; a server coupled to a network, the server operable to: receive a request for a prediction or recommendation over the network, generate a prediction or recommendation using the data mining models, and transmit the generated prediction or recommendation.
    Type: Application
    Filed: December 17, 2004
    Publication date: May 12, 2005
    Inventors: Pablo Tamayo, Jacek Myczkowski, Marcos Campos
  • Patent number: 6836773
    Abstract: An enterprise-wide web data mining system, computer program product, and method of operation thereof, that uses Internet based data sources, and which operates in an automated and cost effective manner. The enterprise web mining system comprises: a database coupled to a plurality of data sources, the database operable to store data collected from the data sources; a data mining engine coupled to the web server and the database, the data mining engine operable to generate a plurality of data mining models using the collected data; a server coupled to a network, the server operable to: receive a request for a prediction or recommendation over the network, generate a prediction or recommendation using the data mining models, and transmit the generated prediction or recommendation.
    Type: Grant
    Filed: September 27, 2001
    Date of Patent: December 28, 2004
    Assignee: Oracle International Corporation
    Inventors: Pablo Tamayo, Jacek Myczkowski, Marcos Campos
  • Publication number: 20040098367
    Abstract: Systems and methods for across platform and multiple dataset classification. In one embodiment the systems combine a Large Bayes classification framework, constructed from discovered itemsets or common patterns of data, with a definition of combined relative features to represent the original values. One realization of this method is that different datasets representing the same biological system display some amount of invariant biological characteristics independent of the idiosyncrasies of sample sources, preparation and the technological platform used to obtain the measurements.
    Type: Application
    Filed: August 6, 2003
    Publication date: May 20, 2004
    Applicants: Whitehead Institute for Biomedical Research, Dana-Farber Cancer Institute
    Inventors: Pablo Tamayo, Jill P. Mesirov, Todd Golub
  • Publication number: 20040010481
    Abstract: A neural network system and method for analyzing data sets, especially microarray gene expression data. The neural network is trained to generate time-dependent outcome predictions based on input features and outcome functions for a number of subjects. The features may be highly dimensional relative to the number of subjects, and feature selection is applied to the input feature data for training the neural network. A trained neural network processes input features from a subject to generate an outcome function that reflects the probability of the occurrence of an event at a given time point for that subject.
    Type: Application
    Filed: December 9, 2002
    Publication date: January 15, 2004
    Applicant: Whitehead Institute for Biomedical Research
    Inventors: D.R. Mani, Pablo Tamayo, Jill Mesirov, Todd R. Golub, Eric Lander
  • Publication number: 20030225526
    Abstract: Methods are provided for the clssification of disease types (e.g., cancer types), outcome predictions, and treatment classes based on algorithmic classifiers used to analyze large datasets.
    Type: Application
    Filed: November 14, 2002
    Publication date: December 4, 2003
    Inventors: Todd R. Golub, Sayan Mukherjee, Sridhar Ramaswamy, Ryan Rifkin, Pablo Tamayo
  • Patent number: 6647341
    Abstract: Methods and apparatus for classifying or predicting the classes for samples based on gene expression are described. Also described are methods and apparatus for ascertaining or discovering new, previously unknown classes based on gene expression.
    Type: Grant
    Filed: April 6, 2000
    Date of Patent: November 11, 2003
    Assignees: Whitehead Institute for Biomedical Research, Dana-Farber Cancer Institute, Inc.
    Inventors: Todd R. Golub, Eric S. Lander, Jill Mesirov, Donna Slonim, Pablo Tamayo
  • Publication number: 20030194701
    Abstract: Methods for predicting phenotypic classes of lymphomas, such as lymphoma type or treatment outcome, for lymphoma samples based on gene expression profiles are described.
    Type: Application
    Filed: November 20, 2001
    Publication date: October 16, 2003
    Inventors: Todd R. Golub, Pablo Tamayo, Margaret Shipp, Eric S. Lander, Jon C. Aster
  • Publication number: 20030073083
    Abstract: Methods and apparatus for classifying or predicting the classes for samples based on gene expression are described. Also described are methods and apparatus for ascertaining or discovering new, previously unknown classes based on gene expression. Methods, computer systems and apparatus for classifying or predicting whether a sample is treatment sensitive (e.g., chemosensitive) or treatment resistant (e.g., chemoresistant) are also provided. Classification occurs based on analysis of gene expression data from samples that have been subjected to one or more compounds.
    Type: Application
    Filed: October 1, 2001
    Publication date: April 17, 2003
    Inventors: Pablo Tamayo, Jane E. Staunton, Donna K. Slonim, Hilary A. Coller, Todd R. Golub, Eric S. Lander, Jill P. Mesirov