CA3098876A1 - Machine learning enabled biological polymer assembly - Google Patents

Machine learning enabled biological polymer assembly Download PDF

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Publication number
CA3098876A1
CA3098876A1 CA3098876A CA3098876A CA3098876A1 CA 3098876 A1 CA3098876 A1 CA 3098876A1 CA 3098876 A CA3098876 A CA 3098876A CA 3098876 A CA3098876 A CA 3098876A CA 3098876 A1 CA3098876 A1 CA 3098876A1
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Canada
Prior art keywords
assembly
locations
location
learning model
nucleotide
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Pending
Application number
CA3098876A
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English (en)
French (fr)
Inventor
Minh Duc Cao
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Quantum Si Inc
Original Assignee
Quantum Si 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 Quantum Si Inc filed Critical Quantum Si Inc
Publication of CA3098876A1 publication Critical patent/CA3098876A1/en
Pending legal-status Critical Current

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    • 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
    • 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 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
    • 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
    • G16B15/00—ICT specially adapted for analysing two-dimensional [2D] or three-dimensional [3D] molecular structures, e.g. structural or functional relations or structure alignment
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • 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
    • 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
    • G16B40/30—Unsupervised 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
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics

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  • Physics & Mathematics (AREA)
  • Engineering & Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Evolutionary Biology (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Data Mining & Analysis (AREA)
  • Chemical & Material Sciences (AREA)
  • Software Systems (AREA)
  • Evolutionary Computation (AREA)
  • Artificial Intelligence (AREA)
  • Bioethics (AREA)
  • Databases & Information Systems (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Epidemiology (AREA)
  • Public Health (AREA)
  • General Engineering & Computer Science (AREA)
  • Computing Systems (AREA)
  • General Physics & Mathematics (AREA)
  • Mathematical Physics (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Molecular Biology (AREA)
  • Computational Linguistics (AREA)
  • Biomedical Technology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Addition Polymer Or Copolymer, Post-Treatments, Or Chemical Modifications (AREA)
CA3098876A 2018-05-14 2019-05-13 Machine learning enabled biological polymer assembly Pending CA3098876A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201862671260P 2018-05-14 2018-05-14
US62/671,260 2018-05-14
US201862671884P 2018-05-15 2018-05-15
US62/671,884 2018-05-15
PCT/US2019/032065 WO2019222120A1 (en) 2018-05-14 2019-05-13 Machine learning enabled biological polymer assembly

Publications (1)

Publication Number Publication Date
CA3098876A1 true CA3098876A1 (en) 2019-11-21

Family

ID=66669118

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3098876A Pending CA3098876A1 (en) 2018-05-14 2019-05-13 Machine learning enabled biological polymer assembly

Country Status (10)

Country Link
US (1) US20190348152A1 (https=)
EP (1) EP3794596A1 (https=)
JP (1) JP2021523479A (https=)
KR (1) KR20210010488A (https=)
CN (1) CN112437961A (https=)
AU (1) AU2019270961A1 (https=)
BR (1) BR112020022257A2 (https=)
CA (1) CA3098876A1 (https=)
MX (1) MX2020012278A (https=)
WO (1) WO2019222120A1 (https=)

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3624068A1 (en) * 2018-09-14 2020-03-18 Covestro Deutschland AG Method for improving prediction relating to the production of a polymer-ic produc
US11664090B2 (en) * 2020-06-11 2023-05-30 Life Technologies Corporation Basecaller with dilated convolutional neural network
EP4211691A1 (en) * 2020-09-11 2023-07-19 F. Hoffmann-La Roche AG Deep-learning-based techniques for generating a consensus sequence from multiple noisy sequences
CA3214755A1 (en) * 2021-04-09 2022-10-13 Natalie CASTELLANA Method for antibody identification from protein mixtures

Family Cites Families (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2010127045A2 (en) * 2009-04-29 2010-11-04 Complete Genomics, Inc. Method and system for calling variations in a sample polynucleotide sequence with respect to a reference polynucleotide sequence
EP2718862B1 (en) * 2011-06-06 2018-10-31 Koninklijke Philips N.V. Method for assembly of nucleic acid sequence data
EP3084002A4 (en) * 2013-12-16 2017-08-23 Complete Genomics, Inc. Basecaller for dna sequencing using machine learning
CA2894317C (en) * 2015-06-15 2023-08-15 Deep Genomics Incorporated Systems and methods for classifying, prioritizing and interpreting genetic variants and therapies using a deep neural network

Also Published As

Publication number Publication date
MX2020012278A (es) 2021-01-29
JP2021523479A (ja) 2021-09-02
WO2019222120A1 (en) 2019-11-21
KR20210010488A (ko) 2021-01-27
AU2019270961A1 (en) 2020-11-19
BR112020022257A2 (pt) 2021-02-23
CN112437961A (zh) 2021-03-02
EP3794596A1 (en) 2021-03-24
US20190348152A1 (en) 2019-11-14

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