WO2020191390A3 - Artificial intelligence-based quality scoring - Google Patents

Artificial intelligence-based quality scoring Download PDF

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Publication number
WO2020191390A3
WO2020191390A3 PCT/US2020/024091 US2020024091W WO2020191390A3 WO 2020191390 A3 WO2020191390 A3 WO 2020191390A3 US 2020024091 W US2020024091 W US 2020024091W WO 2020191390 A3 WO2020191390 A3 WO 2020191390A3
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WO
WIPO (PCT)
Prior art keywords
base
scores
quantized
quantized classification
classification scores
Prior art date
Application number
PCT/US2020/024091
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French (fr)
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WO2020191390A2 (en
Inventor
Kishore Jaganathan
John Randall GOBBEL
Amirali Kia
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Illumina, Inc.
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Publication date
Priority claimed from NL2023310A external-priority patent/NL2023310B1/en
Priority claimed from NL2023312A external-priority patent/NL2023312B1/en
Priority claimed from NL2023316A external-priority patent/NL2023316B1/en
Priority claimed from NL2023314A external-priority patent/NL2023314B1/en
Priority claimed from NL2023311A external-priority patent/NL2023311B9/en
Priority claimed from US16/825,991 external-priority patent/US11210554B2/en
Priority claimed from US16/826,126 external-priority patent/US11783917B2/en
Priority to KR1020217009877A priority Critical patent/KR20210143154A/en
Priority to EP20719294.9A priority patent/EP3942073A2/en
Application filed by Illumina, Inc. filed Critical Illumina, Inc.
Priority to JP2021517978A priority patent/JP2022524562A/en
Priority to CN202080005431.0A priority patent/CN112789680A/en
Priority to AU2020240383A priority patent/AU2020240383A1/en
Publication of WO2020191390A2 publication Critical patent/WO2020191390A2/en
Publication of WO2020191390A3 publication Critical patent/WO2020191390A3/en
Priority to IL281668A priority patent/IL281668A/en

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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
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F18/00—Pattern recognition
    • G06F18/20—Analysing
    • G06F18/23—Clustering techniques
    • G06F18/232—Non-hierarchical techniques
    • G06F18/2321—Non-hierarchical techniques using statistics or function optimisation, e.g. modelling of probability density functions
    • G06F18/23211—Non-hierarchical techniques using statistics or function optimisation, e.g. modelling of probability density functions with adaptive number of clusters
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F18/00—Pattern recognition
    • G06F18/20—Analysing
    • G06F18/24—Classification 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
    • G06N3/08—Learning methods
    • G06N3/084—Backpropagation, e.g. using gradient descent
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06V—IMAGE OR VIDEO RECOGNITION OR UNDERSTANDING
    • G06V10/00—Arrangements for image or video recognition or understanding
    • G06V10/20—Image preprocessing
    • G06V10/26—Segmentation of patterns in the image field; Cutting or merging of image elements to establish the pattern region, e.g. clustering-based techniques; Detection of occlusion
    • G06V10/267—Segmentation of patterns in the image field; Cutting or merging of image elements to establish the pattern region, e.g. clustering-based techniques; Detection of occlusion by performing operations on regions, e.g. growing, shrinking or watersheds
    • 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
    • G06V10/82—Arrangements for image or video recognition or understanding using pattern recognition or machine learning using neural networks
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR 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
    • 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
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06V—IMAGE OR VIDEO RECOGNITION OR UNDERSTANDING
    • G06V20/00—Scenes; Scene-specific elements
    • G06V20/40—Scenes; Scene-specific elements in video content
    • G06V20/46—Extracting features or characteristics from the video content, e.g. video fingerprints, representative shots or key frames
    • G06V20/47—Detecting features for summarising video content
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06V—IMAGE OR VIDEO RECOGNITION OR UNDERSTANDING
    • G06V2201/00—Indexing scheme relating to image or video recognition or understanding
    • G06V2201/03—Recognition of patterns in medical or anatomical images

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  • Engineering & Computer Science (AREA)
  • Theoretical Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • General Physics & Mathematics (AREA)
  • Evolutionary Computation (AREA)
  • General Health & Medical Sciences (AREA)
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  • Bioinformatics & Computational Biology (AREA)
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  • Biodiversity & Conservation Biology (AREA)
  • Bioethics (AREA)
  • Epidemiology (AREA)
  • Public Health (AREA)
  • Biotechnology (AREA)
  • Probability & Statistics with Applications (AREA)
  • Signal Processing (AREA)
  • Image Analysis (AREA)
  • Telephonic Communication Services (AREA)

Abstract

The technology disclosed assigns quality scores to bases called by a neural network-based base caller by (i) quantizing classification scores of predicted base calls produced by the neural network-based base caller in response to processing training data during training, (ii) selecting a set of quantized classification scores, (iii) for each quantized classification score in the set, determining a base calling error rate by comparing its predicted base calls to corresponding ground truth base calls, (iv) determining a fit between the quantized classification scores and their base calling error rates, and (v) correlating the quality scores to the quantized classification scores based on the fit.
PCT/US2020/024091 2019-03-21 2020-03-21 Artificial intelligence-based quality scoring WO2020191390A2 (en)

Priority Applications (6)

Application Number Priority Date Filing Date Title
AU2020240383A AU2020240383A1 (en) 2019-03-21 2020-03-21 Artificial intelligence-based quality scoring
CN202080005431.0A CN112789680A (en) 2019-03-21 2020-03-21 Artificial intelligence based quality scoring
JP2021517978A JP2022524562A (en) 2019-03-21 2020-03-21 Artificial intelligence-based quality scoring
KR1020217009877A KR20210143154A (en) 2019-03-21 2020-03-21 Artificial intelligence-based quality scoring
EP20719294.9A EP3942073A2 (en) 2019-03-21 2020-03-21 Artificial intelligence-based quality scoring
IL281668A IL281668A (en) 2019-03-21 2021-03-21 Artificial intelligence-based quality scoring

Applications Claiming Priority (30)

Application Number Priority Date Filing Date Title
US201962821602P 2019-03-21 2019-03-21
US201962821618P 2019-03-21 2019-03-21
US201962821724P 2019-03-21 2019-03-21
US201962821681P 2019-03-21 2019-03-21
US201962821766P 2019-03-21 2019-03-21
US62/821,681 2019-03-21
US62/821,602 2019-03-21
US62/821,618 2019-03-21
US62/821,724 2019-03-21
US62/821,766 2019-03-21
NL2023310A NL2023310B1 (en) 2019-03-21 2019-06-14 Training data generation for artificial intelligence-based sequencing
NL2023311A NL2023311B9 (en) 2019-03-21 2019-06-14 Artificial intelligence-based generation of sequencing metadata
NL2023314 2019-06-14
NL2023310 2019-06-14
NL2023314A NL2023314B1 (en) 2019-03-21 2019-06-14 Artificial intelligence-based quality scoring
NL2023316A NL2023316B1 (en) 2019-03-21 2019-06-14 Artificial intelligence-based sequencing
NL2023312 2019-06-14
NL2023312A NL2023312B1 (en) 2019-03-21 2019-06-14 Artificial intelligence-based base calling
NL2023311 2019-06-14
NL2023316 2019-06-14
US16/825,991 2020-03-20
US16/826,126 2020-03-20
US16/825,987 2020-03-20
US16/826,126 US11783917B2 (en) 2019-03-21 2020-03-20 Artificial intelligence-based base calling
US16/826,134 2020-03-20
US16/826,134 US11676685B2 (en) 2019-03-21 2020-03-20 Artificial intelligence-based quality scoring
US16/825,991 US11210554B2 (en) 2019-03-21 2020-03-20 Artificial intelligence-based generation of sequencing metadata
US16/825,987 US11347965B2 (en) 2019-03-21 2020-03-20 Training data generation for artificial intelligence-based sequencing
US16/826,168 US11436429B2 (en) 2019-03-21 2020-03-21 Artificial intelligence-based sequencing
US16/826,168 2020-03-21

Publications (2)

Publication Number Publication Date
WO2020191390A2 WO2020191390A2 (en) 2020-09-24
WO2020191390A3 true WO2020191390A3 (en) 2020-11-12

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PCT/US2020/024091 WO2020191390A2 (en) 2019-03-21 2020-03-21 Artificial intelligence-based quality scoring
PCT/US2020/024087 WO2020205296A1 (en) 2019-03-21 2020-03-21 Artificial intelligence-based generation of sequencing metadata
PCT/US2020/024088 WO2020191387A1 (en) 2019-03-21 2020-03-21 Artificial intelligence-based base calling
PCT/US2020/024090 WO2020191389A1 (en) 2019-03-21 2020-03-21 Training data generation for artificial intelligence-based sequencing
PCT/US2020/024092 WO2020191391A2 (en) 2019-03-21 2020-03-22 Artificial intelligence-based sequencing

Family Applications After (4)

Application Number Title Priority Date Filing Date
PCT/US2020/024087 WO2020205296A1 (en) 2019-03-21 2020-03-21 Artificial intelligence-based generation of sequencing metadata
PCT/US2020/024088 WO2020191387A1 (en) 2019-03-21 2020-03-21 Artificial intelligence-based base calling
PCT/US2020/024090 WO2020191389A1 (en) 2019-03-21 2020-03-21 Training data generation for artificial intelligence-based sequencing
PCT/US2020/024092 WO2020191391A2 (en) 2019-03-21 2020-03-22 Artificial intelligence-based sequencing

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