CA3142888A1 - Techniques for protein identification using machine learning and related systems and methods - Google Patents

Techniques for protein identification using machine learning and related systems and methods

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Publication number
CA3142888A1
CA3142888A1 CA3142888A CA3142888A CA3142888A1 CA 3142888 A1 CA3142888 A1 CA 3142888A1 CA 3142888 A CA3142888 A CA 3142888A CA 3142888 A CA3142888 A CA 3142888A CA 3142888 A1 CA3142888 A1 CA 3142888A1
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CA
Canada
Prior art keywords
data
learning model
machine learning
amino acids
training
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Pending
Application number
CA3142888A
Other languages
English (en)
French (fr)
Inventor
Zhizhuo ZHANG
Sabrina RASHID
Bradley Robert Parry
Michael Meyer
Brian Reed
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
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Application filed by Quantum Si Inc filed Critical Quantum Si Inc
Publication of CA3142888A1 publication Critical patent/CA3142888A1/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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/20—Sequence assembly
    • 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
    • G06N3/045—Combinations of networks
    • G06N3/0455—Auto-encoder networks; Encoder-decoder 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
    • G06N3/08—Learning methods
    • G06N3/088—Non-supervised learning, e.g. competitive learning
    • 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
    • G06N3/0895—Weakly supervised learning, e.g. semi-supervised or self-supervised learning
    • 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
    • G06N7/00—Computing arrangements based on specific mathematical models
    • G06N7/01—Probabilistic graphical models, e.g. probabilistic 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
    • G16B40/30—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
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic 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)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Data Mining & Analysis (AREA)
  • Software Systems (AREA)
  • Artificial Intelligence (AREA)
  • Evolutionary Computation (AREA)
  • General Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Computing Systems (AREA)
  • General Engineering & Computer Science (AREA)
  • Mathematical Physics (AREA)
  • Biomedical Technology (AREA)
  • Computational Linguistics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Evolutionary Biology (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Physiology (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Bioethics (AREA)
  • Public Health (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Algebra (AREA)
  • Computational Mathematics (AREA)
  • Mathematical Analysis (AREA)
  • Mathematical Optimization (AREA)
  • Pure & Applied Mathematics (AREA)
  • Probability & Statistics with Applications (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
CA3142888A 2019-06-12 2020-06-12 Techniques for protein identification using machine learning and related systems and methods Pending CA3142888A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201962860750P 2019-06-12 2019-06-12
US62/860,750 2019-06-12
PCT/US2020/037541 WO2020252345A1 (en) 2019-06-12 2020-06-12 Techniques for protein identification using machine learning and related systems and methods

Publications (1)

Publication Number Publication Date
CA3142888A1 true CA3142888A1 (en) 2020-12-17

Family

ID=71409529

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3142888A Pending CA3142888A1 (en) 2019-06-12 2020-06-12 Techniques for protein identification using machine learning and related systems and methods

Country Status (10)

Country Link
US (1) US20200395099A1 (https=)
EP (1) EP3966824A1 (https=)
JP (1) JP2022536343A (https=)
KR (1) KR20220019778A (https=)
CN (1) CN115989545A (https=)
AU (1) AU2020290510A1 (https=)
BR (1) BR112021024915A2 (https=)
CA (1) CA3142888A1 (https=)
MX (1) MX2021015347A (https=)
WO (1) WO2020252345A1 (https=)

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BR112021008098A2 (pt) 2018-11-15 2021-08-10 Quantum-Si Incorporated métodos e composições para o sequenciamento de proteínas
US11126890B2 (en) * 2019-04-18 2021-09-21 Adobe Inc. Robust training of large-scale object detectors with a noisy dataset
CN114929897A (zh) * 2019-10-28 2022-08-19 宽腾矽公司 制备用于多肽测序的富集样品的方法
JP7592737B2 (ja) 2020-03-06 2024-12-02 ボストンジーン コーポレイション 多重免疫蛍光イメージングを使用する組織特性の決定
WO2021236983A2 (en) 2020-05-20 2021-11-25 Quantum-Si Incorporated Methods and compositions for protein sequencing
CA3227592A1 (en) * 2021-09-22 2023-03-30 Gregory KAPP Methods and systems for determining polypeptide interactions
CN114118366B (zh) * 2021-11-15 2025-04-22 国网浙江省电力有限公司电力科学研究院 基于长短期记忆神经网络的生命体触电电流检测方法
CN114093415B (zh) * 2021-11-19 2022-06-03 中国科学院数学与系统科学研究院 肽段可检测性预测方法及系统
CN114456926A (zh) * 2022-03-15 2022-05-10 常州市环境科学研究院 一种可预测生长趋势的浮游植物自动培养装置及方法
US12587274B2 (en) 2023-03-28 2026-03-24 Quantum Generative Materials Llc Satellite optimization management system based on natural language input and artificial intelligence
WO2025057424A1 (ja) 2023-09-15 2025-03-20 富士通株式会社 情報処理プログラム，情報処理装置および情報処理方法
WO2025128525A1 (en) * 2023-12-11 2025-06-19 Research Development Foundation System and method for predicting microproteins
WO2025123211A1 (zh) * 2023-12-12 2025-06-19 深圳华大生命科学研究院 一种多肽分类器的构建与应用
WO2025123212A1 (zh) * 2023-12-12 2025-06-19 深圳华大生命科学研究院 一种基于目标检测模型的多肽信号提取方法
US12368503B2 (en) 2023-12-27 2025-07-22 Quantum Generative Materials Llc Intent-based satellite transmit management based on preexisting historical location and machine learning
US12603701B2 (en) 2023-12-27 2026-04-14 Quantum Generative Materials Llc Distributed satellite constellation management and control system
CN117744748B (zh) * 2024-02-20 2024-04-30 北京普译生物科技有限公司 一种神经网络模型训练、碱基识别方法及装置、电子设备

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Also Published As

Publication number Publication date
WO2020252345A9 (en) 2022-02-10
BR112021024915A2 (pt) 2022-01-18
JP2022536343A (ja) 2022-08-15
CN115989545A (zh) 2023-04-18
KR20220019778A (ko) 2022-02-17
MX2021015347A (es) 2022-04-06
US20200395099A1 (en) 2020-12-17
WO2020252345A1 (en) 2020-12-17
AU2020290510A1 (en) 2022-02-03
EP3966824A1 (en) 2022-03-16

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