CN117581304A - 基于压缩状态的碱基调用 - Google Patents

基于压缩状态的碱基调用 Download PDF

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Publication number
CN117581304A
CN117581304A CN202280045844.0A CN202280045844A CN117581304A CN 117581304 A CN117581304 A CN 117581304A CN 202280045844 A CN202280045844 A CN 202280045844A CN 117581304 A CN117581304 A CN 117581304A
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China
Prior art keywords
channel
sequencing
cluster
intensity
per
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Pending
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CN202280045844.0A
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English (en)
Chinese (zh)
Inventor
G·D·帕纳比
E·J·奥贾德
D·卡什夫哈吉吉
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Inmair Ltd
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Inmair Ltd
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Priority claimed from US17/944,948 external-priority patent/US20230087698A1/en
Application filed by Inmair Ltd filed Critical Inmair Ltd
Priority claimed from PCT/US2022/044293 external-priority patent/WO2023049215A1/en
Publication of CN117581304A publication Critical patent/CN117581304A/zh
Pending legal-status Critical Current

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    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06V—IMAGE OR VIDEO RECOGNITION OR UNDERSTANDING
    • G06V10/00—Arrangements for image or video recognition or understanding
    • G06V10/94—Hardware or software architectures specially adapted for image or video understanding
    • G06V10/955—Hardware or software architectures specially adapted for image or video understanding using specific electronic processors
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/04—Architecture, e.g. interconnection topology
    • G06N3/0464—Convolutional networks [CNN, ConvNet]
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; 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
    • G06N3/084—Backpropagation, e.g. using gradient descent
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; 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
    • G06N3/088—Non-supervised learning, e.g. competitive learning
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06V—IMAGE OR VIDEO RECOGNITION OR UNDERSTANDING
    • G06V10/00—Arrangements for image or video recognition or understanding
    • G06V10/40—Extraction of image or video features
    • G06V10/44—Local feature extraction by analysis of parts of the pattern, e.g. by detecting edges, contours, loops, corners, strokes or intersections; Connectivity analysis, e.g. of connected components
    • G06V10/443—Local feature extraction by analysis of parts of the pattern, e.g. by detecting edges, contours, loops, corners, strokes or intersections; Connectivity analysis, e.g. of connected components by matching or filtering
    • G06V10/449—Biologically inspired filters, e.g. difference of Gaussians [DoG] or Gabor filters
    • G06V10/451—Biologically inspired filters, e.g. difference of Gaussians [DoG] or Gabor filters with interaction between the filter responses, e.g. cortical complex cells
    • G06V10/454—Integrating the filters into a hierarchical structure, e.g. convolutional neural networks [CNN]
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06V—IMAGE OR VIDEO RECOGNITION OR UNDERSTANDING
    • G06V10/00—Arrangements for image or video recognition or understanding
    • G06V10/40—Extraction of image or video features
    • G06V10/56—Extraction of image or video features relating to colour
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06V—IMAGE OR VIDEO RECOGNITION OR UNDERSTANDING
    • G06V10/00—Arrangements for image or video recognition or understanding
    • G06V10/70—Arrangements for image or video recognition or understanding using pattern recognition or machine learning
    • G06V10/82—Arrangements for image or video recognition or understanding using pattern recognition or machine learning using neural networks
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06V—IMAGE OR VIDEO RECOGNITION OR UNDERSTANDING
    • G06V20/00—Scenes; Scene-specific elements
    • G06V20/60—Type of objects
    • G06V20/69—Microscopic objects, e.g. biological cells or cellular parts
    • G06V20/698—Matching; Classification
    • 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
    • G16B40/10—Signal processing, e.g. from mass spectrometry [MS] or from PCR
    • 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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/04—Architecture, e.g. interconnection topology
    • G06N3/044—Recurrent networks, e.g. Hopfield networks
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/04—Architecture, e.g. interconnection topology
    • G06N3/045—Combinations of networks
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/04—Architecture, e.g. interconnection topology
    • G06N3/048—Activation functions

Landscapes

  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Theoretical Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • General Health & Medical Sciences (AREA)
  • Evolutionary Computation (AREA)
  • General Physics & Mathematics (AREA)
  • Software Systems (AREA)
  • Artificial Intelligence (AREA)
  • Medical Informatics (AREA)
  • Biophysics (AREA)
  • Data Mining & Analysis (AREA)
  • Molecular Biology (AREA)
  • Biomedical Technology (AREA)
  • Multimedia (AREA)
  • Computing Systems (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Evolutionary Biology (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Mathematical Physics (AREA)
  • General Engineering & Computer Science (AREA)
  • Computational Linguistics (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Bioethics (AREA)
  • Public Health (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Chemical & Material Sciences (AREA)
  • Biodiversity & Conservation Biology (AREA)
  • Signal Processing (AREA)
  • Image Analysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
CN202280045844.0A 2021-09-22 2022-09-21 基于压缩状态的碱基调用 Pending CN117581304A (zh)

Applications Claiming Priority (9)

Application Number Priority Date Filing Date Title
US202163247301P 2021-09-22 2021-09-22
US202163247296P 2021-09-22 2021-09-22
US63/247296 2021-09-22
US63/247301 2021-09-22
US17/944948 2022-09-14
US17/944,948 US20230087698A1 (en) 2021-09-22 2022-09-14 Compressed state-based base calling
US17/944,809 US12412387B2 (en) 2021-09-22 2022-09-14 State-based base calling
US17/944809 2022-09-14
PCT/US2022/044293 WO2023049215A1 (en) 2021-09-22 2022-09-21 Compressed state-based base calling

Publications (1)

Publication Number Publication Date
CN117581304A true CN117581304A (zh) 2024-02-20

Family

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Family Applications (2)

Application Number Title Priority Date Filing Date
CN202280045844.0A Pending CN117581304A (zh) 2021-09-22 2022-09-21 基于压缩状态的碱基调用
CN202280046324.1A Pending CN117581305A (zh) 2021-09-22 2022-09-21 基于状态的碱基调用

Family Applications After (1)

Application Number Title Priority Date Filing Date
CN202280046324.1A Pending CN117581305A (zh) 2021-09-22 2022-09-21 基于状态的碱基调用

Country Status (4)

Country Link
US (1) US12412387B2 (https=)
EP (2) EP4405956A2 (https=)
JP (2) JP2024534302A (https=)
CN (2) CN117581304A (https=)

Families Citing this family (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2023197153A1 (en) * 2022-04-12 2023-10-19 Orange Systems and methods to accelerate creation of and/or searching for digital twins on a computerized platform
US20250021801A1 (en) * 2023-07-12 2025-01-16 Canon Medical Systems Corporation Mapping method and apparatus

Family Cites Families (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA3181696A1 (en) 2013-12-03 2015-06-11 Paul BELITZ Methods and systems for analyzing image data
EP3084002A4 (en) * 2013-12-16 2017-08-23 Complete Genomics, Inc. Basecaller for dna sequencing using machine learning
US11378544B2 (en) * 2018-01-08 2022-07-05 Illumina, Inc. High-throughput sequencing with semiconductor-based detection
US12073922B2 (en) * 2018-07-11 2024-08-27 Illumina, Inc. Deep learning-based framework for identifying sequence patterns that cause sequence-specific errors (SSEs)
US11783917B2 (en) 2019-03-21 2023-10-10 Illumina, Inc. Artificial intelligence-based base calling
WO2020191389A1 (en) 2019-03-21 2020-09-24 Illumina, Inc. Training data generation for artificial intelligence-based sequencing
US11593649B2 (en) 2019-05-16 2023-02-28 Illumina, Inc. Base calling using convolutions
US20210265009A1 (en) 2020-02-20 2021-08-26 Illumina, Inc. Artificial Intelligence-Based Base Calling of Index Sequences
CN121034400A (zh) * 2020-02-20 2025-11-28 因美纳有限公司 基于人工智能的多对多碱基判读
US12591780B2 (en) * 2020-02-20 2026-03-31 Illumina, Inc. Data compression for artificial intelligence-based base calling

Also Published As

Publication number Publication date
JP2024536665A (ja) 2024-10-08
CN117581305A (zh) 2024-02-20
EP4405955A1 (en) 2024-07-31
US20230298339A1 (en) 2023-09-21
EP4405956A2 (en) 2024-07-31
JP2024534302A (ja) 2024-09-20
US12412387B2 (en) 2025-09-09

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