Mrukwa et al., 2022 - Google Patents

Finding significantly enriched cells in single-cell RNA sequencing by single-sample approaches

Mrukwa et al., 2022

Document ID
15326701463786083783
Author
Mrukwa A
Marczyk M
Zyla J
Publication year
Publication venue
International Work-Conference on Bioinformatics and Biomedical Engineering

External Links

Snippet

Gene set analysis is a leading bioinformatical technique allowing comparison of phenotypes on gene set level, which is applied to different transcriptome-wide gene expression platforms and omics levels. The aim of this study was to measure the performance of three …
Continue reading at link.springer.com (other versions)

Classifications

    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/30286—Information retrieval; Database structures therefor; File system structures therefor in structured data stores
    • G06F17/30587—Details of specialised database models
    • G06F17/30595—Relational databases
    • G06F17/30598—Clustering or classification
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/24—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for machine learning, data mining or biostatistics, e.g. pattern finding, knowledge discovery, rule extraction, correlation, clustering or classification
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/12—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for modelling or simulation in systems biology, e.g. probabilistic or dynamic models, gene-regulatory networks, protein interaction networks or metabolic networks
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/28—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for programming tools or database systems, e.g. ontologies, heterogeneous data integration, data warehousing or computing architectures
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/20—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for hybridisation or gene expression, e.g. microarrays, sequencing by hybridisation, normalisation, profiling, noise correction models, expression ratio estimation, probe design or probe optimisation
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/18—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06K—RECOGNITION OF DATA; PRESENTATION OF DATA; RECORD CARRIERS; HANDLING RECORD CARRIERS
    • G06K9/00—Methods or arrangements for reading or recognising printed or written characters or for recognising patterns, e.g. fingerprints
    • G06K9/62—Methods or arrangements for recognition using electronic means
    • G06K9/6267—Classification techniques
    • G06K9/6268—Classification techniques relating to the classification paradigm, e.g. parametric or non-parametric approaches
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06N—COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N99/00—Subject matter not provided for in other groups of this subclass
    • G06N99/005—Learning machines, i.e. computer in which a programme is changed according to experience gained by the machine itself during a complete run
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06K—RECOGNITION OF DATA; PRESENTATION OF DATA; RECORD CARRIERS; HANDLING RECORD CARRIERS
    • G06K9/00—Methods or arrangements for reading or recognising printed or written characters or for recognising patterns, e.g. fingerprints
    • G06K9/62—Methods or arrangements for recognition using electronic means
    • G06K9/6217—Design or setup of recognition systems and techniques; Extraction of features in feature space; Clustering techniques; Blind source separation
    • G06K9/6261—Design or setup of recognition systems and techniques; Extraction of features in feature space; Clustering techniques; Blind source separation partitioning the feature space
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06N—COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computer systems based on biological models
    • G06N3/02—Computer systems based on biological models using neural network models
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06K—RECOGNITION OF DATA; PRESENTATION OF DATA; RECORD CARRIERS; HANDLING RECORD CARRIERS
    • G06K9/00—Methods or arrangements for reading or recognising printed or written characters or for recognising patterns, e.g. fingerprints
    • G06K9/62—Methods or arrangements for recognition using electronic means
    • G06K9/6267—Classification techniques
    • G06K9/6279—Classification techniques relating to the number of classes
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06N—COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computer systems based on biological models
    • G06N3/12—Computer systems based on biological models using genetic models
    • G06N3/126—Genetic algorithms, i.e. information processing using digital simulations of the genetic system
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F15/00—Digital computers in general; Data processing equipment in general
    • G06F15/18—Digital computers in general; Data processing equipment in general in which a programme is changed according to experience gained by the computer itself during a complete run; Learning machines
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by the preceding groups
    • G01N33/48—Investigating or analysing materials by specific methods not covered by the preceding groups biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06N—COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N5/00—Computer systems utilising knowledge based models
    • G06N5/02—Knowledge representation
    • G06N5/022—Knowledge engineering, knowledge acquisition
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06K—RECOGNITION OF DATA; PRESENTATION OF DATA; RECORD CARRIERS; HANDLING RECORD CARRIERS
    • G06K9/00—Methods or arrangements for reading or recognising printed or written characters or for recognising patterns, e.g. fingerprints
    • G06K9/36—Image preprocessing, i.e. processing the image information without deciding about the identity of the image
    • G06K9/46—Extraction of features or characteristics of the image

Similar Documents

Publication Publication Date Title
Abdelaal et al. A comparison of automatic cell identification methods for single-cell RNA sequencing data
Alghunaim et al. On the scalability of machine-learning algorithms for breast cancer prediction in big data context
Shaham et al. Removal of batch effects using distribution-matching residual networks
Nguyen et al. Modified AHP for gene selection and cancer classification using type-2 fuzzy logic
Liu et al. An efficient semi-unsupervised gene selection method via spectral biclustering
Horng et al. An expert system to classify microarray gene expression data using gene selection by decision tree
Wang et al. Subtype dependent biomarker identification and tumor classification from gene expression profiles
Li et al. Pan-cancer classification based on self-normalizing neural networks and feature selection
Xu et al. CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis
Le et al. Machine learning for cell type classification from single nucleus RNA sequencing data
WO2021062198A1 (en) Single cell rna-seq data processing
US11270098B2 (en) Clustering methods using a grand canonical ensemble
Dash et al. Performance analysis of clustering techniques over microarray data: A case study
Zhuang et al. Deep learning on graphs for multi-omics classification of COPD
US12060578B2 (en) Systems and methods for associating compounds with physiological conditions using fingerprint analysis
Zhou et al. scDLC: a deep learning framework to classify large sample single-cell RNA-seq data
Sameer et al. Multi-objectives TLBO hybrid method to select the related risk features with rheumatism disease
Mukherjee et al. Determining clinically relevant features in cytometry data using persistent homology
Ghosh et al. Machine Learning in Biological Sciences
Mrukwa et al. Finding significantly enriched cells in single-cell RNA sequencing by single-sample approaches
He et al. Retracted: Overcoming the inadaptability of sparse group lasso for data with various group structures by stacking
Gönen Integrating gene set analysis and nonlinear predictive modeling of disease phenotypes using a Bayesian multitask formulation
Gunavathi et al. A survey on feature selection methods in microarray gene expression data for cancer classification
Ji et al. Optimal distance metrics for single-cell RNA-seq populations
Dutta et al. Predicting degree of relevance of pathway markers from gene expression data: A pso based approach