IL295568B1 - Compression of an AI-based base reader by knowledge refining and gradient reduction - Google Patents

Compression of an AI-based base reader by knowledge refining and gradient reduction

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Publication number
IL295568B1
IL295568B1 IL295568A IL29556822A IL295568B1 IL 295568 B1 IL295568 B1 IL 295568B1 IL 295568 A IL295568 A IL 295568A IL 29556822 A IL29556822 A IL 29556822A IL 295568 B1 IL295568 B1 IL 295568B1
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IL
Israel
Prior art keywords
base
cluster
neural network
data
caller
Prior art date
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IL295568A
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English (en)
Hebrew (he)
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IL295568A (en
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Illumina Inc
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Publication date
Application filed by Illumina Inc filed Critical Illumina Inc
Publication of IL295568A publication Critical patent/IL295568A/en
Publication of IL295568B1 publication Critical patent/IL295568B1/en

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    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; 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
    • 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
    • G06N3/044—Recurrent networks, e.g. Hopfield networks
    • G06N3/0442—Recurrent networks, e.g. Hopfield networks characterised by memory or gating, e.g. long short-term memory [LSTM] or gated recurrent units [GRU]
    • 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
    • G06N3/0464—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
    • G06N3/04—Architecture, e.g. interconnection topology
    • G06N3/0475—Generative 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
    • 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
    • G06N3/0495—Quantised networks; Sparse networks; Compressed 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
    • G06N3/06—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 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
    • 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
    • G06N3/082—Learning methods modifying the architecture, e.g. adding, deleting or silencing nodes or connections
    • 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
    • G06N3/09—Supervised learning
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N5/00—Computing arrangements using knowledge-based models
    • G06N5/04—Inference or reasoning models
    • 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
    • G06V10/70—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
    • 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

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  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Theoretical Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Evolutionary Computation (AREA)
  • Artificial Intelligence (AREA)
  • Data Mining & Analysis (AREA)
  • General Health & Medical Sciences (AREA)
  • Software Systems (AREA)
  • General Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Biomedical Technology (AREA)
  • Computing Systems (AREA)
  • Molecular Biology (AREA)
  • General Engineering & Computer Science (AREA)
  • Mathematical Physics (AREA)
  • Computational Linguistics (AREA)
  • Medical Informatics (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Databases & Information Systems (AREA)
  • Biotechnology (AREA)
  • Multimedia (AREA)
  • Bioethics (AREA)
  • Public Health (AREA)
  • Epidemiology (AREA)
  • Biodiversity & Conservation Biology (AREA)
  • Neurology (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Signal Processing (AREA)
  • Image Analysis (AREA)
  • Compression, Expansion, Code Conversion, And Decoders (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
IL295568A 2020-02-20 2021-02-17 Compression of an AI-based base reader by knowledge refining and gradient reduction IL295568B1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US202062979385P 2020-02-20 2020-02-20
US17/176,151 US12354008B2 (en) 2020-02-20 2021-02-15 Knowledge distillation and gradient pruning-based compression of artificial intelligence-based base caller
PCT/US2021/018422 WO2021168014A1 (en) 2020-02-20 2021-02-17 Knowledge distillation and gradient pruning-based compression of artificial intelligence-based base caller

Publications (2)

Publication Number Publication Date
IL295568A IL295568A (en) 2022-10-01
IL295568B1 true IL295568B1 (en) 2026-01-01

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IL295568A IL295568B1 (en) 2020-02-20 2021-02-17 Compression of an AI-based base reader by knowledge refining and gradient reduction

Country Status (12)

Country Link
US (2) US12354008B2 (https=)
EP (1) EP4107737B1 (https=)
JP (1) JP7754822B2 (https=)
KR (1) KR20220144372A (https=)
CN (1) CN115136245A (https=)
AU (1) AU2021224592A1 (https=)
BR (1) BR112022016409A2 (https=)
CA (1) CA3168451A1 (https=)
IL (1) IL295568B1 (https=)
MX (1) MX2022010275A (https=)
MY (1) MY209788A (https=)
WO (1) WO2021168014A1 (https=)

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CN113987187B (zh) * 2021-11-09 2024-06-28 重庆大学 基于多标签嵌入的舆情文本分类方法、系统、终端及介质
CN114170599B (zh) * 2021-12-14 2024-08-23 华中科技大学 一种基于蒸馏比较的异常物体分割方法
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