JP2024534302A - 圧縮された状態ベースのベースコール - Google Patents

圧縮された状態ベースのベースコール Download PDF

Info

Publication number
JP2024534302A
JP2024534302A JP2023579830A JP2023579830A JP2024534302A JP 2024534302 A JP2024534302 A JP 2024534302A JP 2023579830 A JP2023579830 A JP 2023579830A JP 2023579830 A JP2023579830 A JP 2023579830A JP 2024534302 A JP2024534302 A JP 2024534302A
Authority
JP
Japan
Prior art keywords
sequencing
channel
cluster
state
intensity
Prior art date
Legal status (The legal status 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 status listed.)
Pending
Application number
JP2023579830A
Other languages
English (en)
Japanese (ja)
Inventor
ギャヴィン・デレク・パーナビー
エリック・ジョン・オジャード
ドルナ・カシェファギギ
Original Assignee
イルミナ インコーポレイテッド
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 US17/944,948 external-priority patent/US20230087698A1/en
Application filed by イルミナ インコーポレイテッド filed Critical イルミナ インコーポレイテッド
Priority claimed from PCT/US2022/044293 external-priority patent/WO2023049215A1/en
Publication of JP2024534302A publication Critical patent/JP2024534302A/ja
Pending legal-status Critical Current

Links

Classifications

    • 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
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • 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)
JP2023579830A 2021-09-22 2022-09-21 圧縮された状態ベースのベースコール Pending JP2024534302A (ja)

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
US63/247,301 2021-09-22
US63/247,296 2021-09-22
US17/944,948 2022-09-14
US17/944,809 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
PCT/US2022/044293 WO2023049215A1 (en) 2021-09-22 2022-09-21 Compressed state-based base calling

Publications (1)

Publication Number Publication Date
JP2024534302A true JP2024534302A (ja) 2024-09-20

Family

ID=88067183

Family Applications (2)

Application Number Title Priority Date Filing Date
JP2023579830A Pending JP2024534302A (ja) 2021-09-22 2022-09-21 圧縮された状態ベースのベースコール
JP2023579829A Pending JP2024536665A (ja) 2021-09-22 2022-09-21 状態ベースのベースコール

Family Applications After (1)

Application Number Title Priority Date Filing Date
JP2023579829A Pending JP2024536665A (ja) 2021-09-22 2022-09-21 状態ベースのベースコール

Country Status (4)

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

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
CN117581304A (zh) 2024-02-20
EP4405955A1 (en) 2024-07-31
US20230298339A1 (en) 2023-09-21
EP4405956A2 (en) 2024-07-31
US12412387B2 (en) 2025-09-09

Similar Documents

Publication Publication Date Title
JP7581190B2 (ja) 人工知能ベースの品質スコアリング
JP7754822B2 (ja) 人工知能ベースのベースコーラの知識蒸留及び勾配プルーニングに基づく圧縮
US11347965B2 (en) Training data generation for artificial intelligence-based sequencing
WO2020205296A1 (en) Artificial intelligence-based generation of sequencing metadata
NL2023311B9 (en) Artificial intelligence-based generation of sequencing metadata
US20230343414A1 (en) Sequence-to-sequence base calling
NL2023310B1 (en) Training data generation for artificial intelligence-based sequencing
US12412387B2 (en) State-based base calling
US20230087698A1 (en) Compressed state-based base calling
WO2023049212A2 (en) State-based base calling
JP2024532004A (ja) ベースコールのための補間及び適合による強度抽出
HK40076748B (en) Knowledge distillation and gradient pruning-based compression of artificial intelligence-based base caller
HK40076748A (en) Knowledge distillation and gradient pruning-based compression of artificial intelligence-based base caller
HK40058973A (en) Training data generation for artificial intelligence-based sequencing

Legal Events

Date Code Title Description
A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20240325