MX2022010273A - Compresion de datos para llamadas de base basadas en inteligencia artificial. - Google Patents

Compresion de datos para llamadas de base basadas en inteligencia artificial.

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Publication number
MX2022010273A
MX2022010273A MX2022010273A MX2022010273A MX2022010273A MX 2022010273 A MX2022010273 A MX 2022010273A MX 2022010273 A MX2022010273 A MX 2022010273A MX 2022010273 A MX2022010273 A MX 2022010273A MX 2022010273 A MX2022010273 A MX 2022010273A
Authority
MX
Mexico
Prior art keywords
sequencing cycles
window
output sets
spatial output
artificial intelligence
Prior art date
Application number
MX2022010273A
Other languages
English (en)
Inventor
Kishore Jaganathan
Dorna Kashefhaghighi
Amirali Kia
Anindita Dutta
Gery Vessere
Gavin Derek Parnaby
Original Assignee
Illumina Inc
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
Application filed by Illumina Inc filed Critical Illumina Inc
Publication of MX2022010273A publication Critical patent/MX2022010273A/es

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    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR 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
    • 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
    • G16B30/20—Sequence assembly
    • 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; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F18/00—Pattern recognition
    • G06F18/20—Analysing
    • G06F18/23—Clustering techniques
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR 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; CALCULATING OR 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; CALCULATING OR COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/06—Physical realisation, i.e. hardware implementation of neural networks, neurons or parts of neurons
    • G06N3/063—Physical realisation, i.e. hardware implementation of neural networks, neurons or parts of neurons using electronic means
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR 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
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR 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; CALCULATING OR 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
    • G06V10/762—Arrangements for image or video recognition or understanding using pattern recognition or machine learning using clustering, e.g. of similar faces in social networks
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR 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
    • G06V10/764—Arrangements for image or video recognition or understanding using pattern recognition or machine learning using classification, e.g. of video objects
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR 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
    • G06V10/77—Processing image or video features in feature spaces; using data integration or data reduction, e.g. principal component analysis [PCA] or independent component analysis [ICA] or self-organising maps [SOM]; Blind source separation
    • G06V10/7715—Feature extraction, e.g. by transforming the feature space, e.g. multi-dimensional scaling [MDS]; Mappings, e.g. subspace methods
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR 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
    • 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
    • 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

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  • Engineering & Computer Science (AREA)
  • Theoretical Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Evolutionary Computation (AREA)
  • General Health & Medical Sciences (AREA)
  • Artificial Intelligence (AREA)
  • General Physics & Mathematics (AREA)
  • Software Systems (AREA)
  • Data Mining & Analysis (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Medical Informatics (AREA)
  • Computing Systems (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • Biomedical Technology (AREA)
  • Databases & Information Systems (AREA)
  • General Engineering & Computer Science (AREA)
  • Multimedia (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Computational Linguistics (AREA)
  • Mathematical Physics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Chemical & Material Sciences (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biotechnology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Organic Chemistry (AREA)
  • Bioethics (AREA)
  • Epidemiology (AREA)
  • Public Health (AREA)
  • Wood Science & Technology (AREA)
  • Biodiversity & Conservation Biology (AREA)
  • Zoology (AREA)
  • Neurology (AREA)
  • Signal Processing (AREA)
  • Immunology (AREA)

Abstract

La tecnología descrita se relaciona con un método basado en inteligencia artificial de llamada de bases. En particular, se relaciona con el procesamiento, a través de una red espacial de un llamador de bases basado en red neural, una primera ventana de conjuntos de canales de analito por ciclo en para una primera ventana de ciclos de secuenciación de una ejecución de secuenciación, y generar secuencias de conjuntos de salidas espaciales respectivas para los ciclos de secuenciación respectivos en la primera ventana de ciclos de secuenciación, procesar, a través de una red de compresión del llamador de bases basado en red neural, conjuntos de salidas espaciales finales respectivos en las secuencias respectivas de conjuntos de salidas espaciales, y generar conjuntos de salidas espaciales comprimidas respectivos para los ciclos de secuenciación respectivos en la primera ventana de ciclos de secuenciación, y generar, basado en los conjuntos de salidas espaciales comprimidas respectivos, predicciones de llamadas de bases para uno o más ciclos de secuenciación en la primera ventana de ciclos de secuenciación.
MX2022010273A 2020-02-20 2021-02-19 Compresion de datos para llamadas de base basadas en inteligencia artificial. MX2022010273A (es)

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US202062979399P 2020-02-20 2020-02-20
US202062979411P 2020-02-20 2020-02-20
US17/179,395 US20210265016A1 (en) 2020-02-20 2021-02-18 Data Compression for Artificial Intelligence-Based Base Calling
US17/180,480 US20210264266A1 (en) 2020-02-20 2021-02-19 Split Architecture for Artificial Intelligence-Based Base Caller
US17/180,513 US20210264267A1 (en) 2020-02-20 2021-02-19 Bus Network for Artificial Intelligence-Based Base Caller
PCT/US2021/018913 WO2021168356A1 (en) 2020-02-20 2021-02-19 Data compression for artificial intelligence-based base calling

Publications (1)

Publication Number Publication Date
MX2022010273A true MX2022010273A (es) 2022-09-19

Family

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Family Applications (2)

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MX2022010272A MX2022010272A (es) 2020-02-20 2021-02-19 Arquitectura de division para llamador de base basado en inteligencia artificial.
MX2022010273A MX2022010273A (es) 2020-02-20 2021-02-19 Compresion de datos para llamadas de base basadas en inteligencia artificial.

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MX2022010272A MX2022010272A (es) 2020-02-20 2021-02-19 Arquitectura de division para llamador de base basado en inteligencia artificial.

Country Status (11)

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US (3) US20210265016A1 (es)
EP (3) EP4107740A1 (es)
JP (3) JP2023515500A (es)
KR (3) KR20220144373A (es)
CN (3) CN115398549A (es)
AU (3) AU2021224873A1 (es)
BR (2) BR112022016416A2 (es)
CA (1) CA3168731A1 (es)
IL (3) IL295587A (es)
MX (2) MX2022010272A (es)
WO (3) WO2021168356A1 (es)

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WO2023049212A2 (en) * 2021-09-22 2023-03-30 Illumina, Inc. State-based base calling
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Also Published As

Publication number Publication date
KR20220144375A (ko) 2022-10-26
JP2023515804A (ja) 2023-04-14
EP4107740A1 (en) 2022-12-28
EP4107739A1 (en) 2022-12-28
WO2021168356A1 (en) 2021-08-26
IL295587A (en) 2022-10-01
BR112022016495A2 (pt) 2022-10-11
BR112022016416A2 (pt) 2022-10-11
IL295584A (en) 2022-10-01
CN115398549A (zh) 2022-11-25
JP2023515092A (ja) 2023-04-12
EP4107738A1 (en) 2022-12-28
AU2021224872A1 (en) 2022-09-08
CN115280418A (zh) 2022-11-01
IL295585A (en) 2022-10-01
AU2021222050A1 (en) 2022-09-08
US20210265016A1 (en) 2021-08-26
MX2022010272A (es) 2022-09-19
JP2023515500A (ja) 2023-04-13
KR20220144373A (ko) 2022-10-26
US20210264267A1 (en) 2021-08-26
AU2021224873A1 (en) 2022-09-08
CN115443508A (zh) 2022-12-06
CA3168731A1 (en) 2021-08-26
US20210264266A1 (en) 2021-08-26
WO2021168360A1 (en) 2021-08-26
KR20220144374A (ko) 2022-10-26
WO2021168358A1 (en) 2021-08-26

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