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WO2001031579A3 - Methods and devices for identifying patterns in biological patterns - Google Patents

Methods and devices for identifying patterns in biological patterns Download PDF

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Publication number
WO2001031579A3
WO2001031579A3 PCT/US2000/029712 US0029712W WO0131579A3 WO 2001031579 A3 WO2001031579 A3 WO 2001031579A3 US 0029712 W US0029712 W US 0029712W WO 0131579 A3 WO0131579 A3 WO 0131579A3
Authority
WO
WIPO (PCT)
Prior art keywords
patterns
methods
devices
biological
identifying
Prior art date
Application number
PCT/US2000/029712
Other languages
French (fr)
Other versions
WO2001031579A2 (en
Inventor
Stephen D Barnhill
Isabelle Guyon
Jason Weston
Original Assignee
Barnhill Technologies Llc
Stephen D Barnhill
Isabelle Guyon
Jason Weston
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from US09/568,301 external-priority patent/US6427141B1/en
Priority claimed from US09/578,011 external-priority patent/US6658395B1/en
Priority claimed from US09/633,850 external-priority patent/US6789069B1/en
Application filed by Barnhill Technologies Llc, Stephen D Barnhill, Isabelle Guyon, Jason Weston filed Critical Barnhill Technologies Llc
Priority to AU13505/01A priority Critical patent/AU1350501A/en
Publication of WO2001031579A2 publication Critical patent/WO2001031579A2/en
Publication of WO2001031579A3 publication Critical patent/WO2001031579A3/en

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    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/70—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for mining of medical data, e.g. analysing previous cases of other patients
    • 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
    • G06F18/2115—Selection of the most significant subset of features by evaluating different subsets according to an optimisation criterion, e.g. class separability, forward selection or backward elimination
    • 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
    • G06F18/214—Generating training patterns; Bootstrap methods, e.g. bagging or boosting
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20—Supervised data analysis
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/30—Unsupervised data analysis
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H10/00—ICT specially adapted for the handling or processing of patient-related medical or healthcare data
    • G16H10/40—ICT specially adapted for the handling or processing of patient-related medical or healthcare data for data related to laboratory analysis, e.g. patient specimen analysis
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/20—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
    • 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
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
    • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Landscapes

  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Data Mining & Analysis (AREA)
  • Medical Informatics (AREA)
  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Public Health (AREA)
  • General Health & Medical Sciences (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Epidemiology (AREA)
  • Evolutionary Computation (AREA)
  • Artificial Intelligence (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Databases & Information Systems (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Bioethics (AREA)
  • Software Systems (AREA)
  • Primary Health Care (AREA)
  • Genetics & Genomics (AREA)
  • General Physics & Mathematics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biomedical Technology (AREA)
  • Pathology (AREA)
  • Molecular Biology (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The methods, systems and devices of the present invention comprise use of support vector machines for the identification of patterns that are important for medical diagnosis, prognosis and treatment. Such patterns may be found in many different datasets. The present invention also comprises methods and compositions for the treatment and diagnosis of medical conditions.
PCT/US2000/029712 1999-10-27 2000-10-27 Methods and devices for identifying patterns in biological patterns WO2001031579A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU13505/01A AU1350501A (en) 1999-10-27 2000-10-27 Methods and devices for identifying patterns in biological systems and methods for uses thereof

Applications Claiming Priority (16)

Application Number Priority Date Filing Date Title
US16180699P 1999-10-27 1999-10-27
US60/161,806 1999-10-27
US16870399P 1999-12-02 1999-12-02
US60/168,703 1999-12-02
US18459600P 2000-02-24 2000-02-24
US60/184,596 2000-02-24
US19121900P 2000-03-22 2000-03-22
US60/191,219 2000-03-22
US09/568,301 2000-05-09
US09/568,301 US6427141B1 (en) 1998-05-01 2000-05-09 Enhancing knowledge discovery using multiple support vector machines
US09/578,011 US6658395B1 (en) 1998-05-01 2000-05-24 Enhancing knowledge discovery from multiple data sets using multiple support vector machines
US09/578,011 2000-05-24
US20702600P 2000-05-25 2000-05-25
US60/207,026 2000-05-25
US09/633,850 2000-08-07
US09/633,850 US6789069B1 (en) 1998-05-01 2000-08-07 Method for enhancing knowledge discovered from biological data using a learning machine

Publications (2)

Publication Number Publication Date
WO2001031579A2 WO2001031579A2 (en) 2001-05-03
WO2001031579A3 true WO2001031579A3 (en) 2002-07-11

Family

ID=27575021

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/029712 WO2001031579A2 (en) 1999-10-27 2000-10-27 Methods and devices for identifying patterns in biological patterns

Country Status (2)

Country Link
AU (1) AU1350501A (en)
WO (1) WO2001031579A2 (en)

Families Citing this family (21)

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Publication number Priority date Publication date Assignee Title
WO2003040949A1 (en) * 2001-11-07 2003-05-15 Biowulf Technologies, Llc Pre-processed Feature Ranking for a support Vector Machine
CN1741036A (en) 2000-06-19 2006-03-01 科雷洛吉克系统公司 Method of constructing a model for classifying biological samples belonging to different states
WO2002006829A2 (en) 2000-07-18 2002-01-24 Correlogic Systems, Inc. A process for discriminating between biological states based on hidden patterns from biological data
AU2002245043B2 (en) 2000-11-16 2006-10-26 Bio-Rad Laboratories, Inc. Method for analyzing mass spectra
WO2003015001A2 (en) * 2001-08-03 2003-02-20 Synt:Em S.A. Method for identification of protein function
JP3896868B2 (en) 2002-02-27 2007-03-22 日本電気株式会社 Pattern feature selection method, classification method, determination method, program, and apparatus
AU2003304161A1 (en) 2002-07-29 2005-01-21 Correlogic Systems, Inc. Quality assurance/quality control for high throughput bioassay process
WO2004061410A2 (en) 2002-12-18 2004-07-22 Ciphergen Biosystems, Inc. Serum biomarkers in lung cancer
US7072772B2 (en) 2003-06-12 2006-07-04 Predicant Bioscience, Inc. Method and apparatus for modeling mass spectrometer lineshapes
EP1709442A4 (en) 2003-12-11 2010-01-20 Correlogic Systems Inc Method of diagnosing biological states through the use of a centralized, adaptive model, and remote sample processing
WO2009006439A1 (en) 2007-06-29 2009-01-08 Correlogic Systems, Inc. Predictive markers for ovarian cancer
AU2009212193B2 (en) * 2008-02-08 2015-08-27 Health Discovery Corporation Method and system for analysis of flow cytometry data using support vector machines
KR20110110247A (en) 2008-12-30 2011-10-06 센토코 오르토 바이오테크 인코포레이티드 Serum Markers Predicting Clinical Responses to Anti-NTFα Antibodies in Patients with Ankylosing Spondylitis
US8972899B2 (en) 2009-02-10 2015-03-03 Ayasdi, Inc. Systems and methods for visualization of data analysis
US8738303B2 (en) 2011-05-02 2014-05-27 Azure Vault Ltd. Identifying outliers among chemical assays
US8660968B2 (en) 2011-05-25 2014-02-25 Azure Vault Ltd. Remote chemical assay classification
US10288626B2 (en) 2012-09-14 2019-05-14 University Of Kentucky Research Foundation Secreted tumor-associated cytochrome as a blood-based biomarker for cancer
US10776760B2 (en) 2017-11-17 2020-09-15 The Boeing Company Machine learning based repair forecasting
CN109460420A (en) * 2018-09-28 2019-03-12 北京赛博贝斯数据科技有限责任公司 The Knowledge Discovery Method and system of structural data
CN111612231B (en) * 2020-05-13 2023-09-01 云南电网有限责任公司电力科学研究院 A distribution network line re-hopping model fusion processing method and device
US11958632B2 (en) * 2020-07-22 2024-04-16 The Boeing Company Predictive maintenance model design system

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1999022019A1 (en) * 1997-10-29 1999-05-06 Rutgers, The State University Of New Jersey Linking gene sequence to gene function by three-dimensional (3d) protein structure determination
WO1999053101A1 (en) * 1998-04-13 1999-10-21 Isis Pharmaceuticals, Inc. Identification of genetic targets for modulation by oligonucleotides and generation of oligonucleotides for gene modulation
WO1999057622A2 (en) * 1998-05-01 1999-11-11 Barnhill Technologies, Llc Pre-processing and post-processing for enhancing knowledge discovery using support vector machines

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1999022019A1 (en) * 1997-10-29 1999-05-06 Rutgers, The State University Of New Jersey Linking gene sequence to gene function by three-dimensional (3d) protein structure determination
WO1999053101A1 (en) * 1998-04-13 1999-10-21 Isis Pharmaceuticals, Inc. Identification of genetic targets for modulation by oligonucleotides and generation of oligonucleotides for gene modulation
WO1999057622A2 (en) * 1998-05-01 1999-11-11 Barnhill Technologies, Llc Pre-processing and post-processing for enhancing knowledge discovery using support vector machines

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
AMARI S ET AL: "Improving support vector machine classifiers by modifying kernel functions", NEURAL NETWORKS, ELSEVIER SCIENCE PUBLISHERS, BARKING, GB, vol. 12, no. 6, July 1999 (1999-07-01), pages 783 - 789, XP004174075, ISSN: 0893-6080 *
MORIK K ET AL: "COMBINING STATISTICAL LEARNING WITH A KNOWLEDGE-BASED APPROACH -A CASE STUDY IN INTENSIVE CARE MONITORING", MACHINE LEARNING. PROCEEDINGS OF THE INTERNATIONAL CONFERENCE, XX, XX, 27 June 1999 (1999-06-27), pages 268 - 277, XP001030158 *
SUGAYA S ET AL: "Support vector machines for knowledge discovery", PRINCIPLES OF DATA MINING AND KNOWLEDGE DISCOVERY. THIRD EUROPEAN CONFERENCE, PKDD'99. PROCEEDINGS. (LECTURE NOTES IN ARTIFICIAL INTELLIGENCE VOL.1704), PRINCIPLES OF DATA MINING AND KNOWLEDGE DISCOVERY. THIRD EUROPEAN CONFERENCE, PKDD'99, PRAGUE, CZ, 1999, Berlin, Germany, Springer-Verlag, Germany, pages 561 - 567, XP001030152, ISBN: 3-540-66490-4 *

Also Published As

Publication number Publication date
AU1350501A (en) 2001-05-08
WO2001031579A2 (en) 2001-05-03

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