Integration of Mechanistic Immunological Knowledge into a Machine Learning Pipeline Increases Predictive Power
暂无分享,去创建一个
Trevor Hastie | Robert Tibshirani | Martin Becker | Ramin Fallahzadeh | Nima Aghaeepour | Xiaoyuan Han | Sean Bendall | Garry P. Nolan | Sean C. Bendall | Huda Nassar | Natalie Stanley | Ivana Marić | Martin S. Angst | Anthony Culos | Athena Tanada | Dyani Gaudilliere | Kazuo Ando | Brice Gaudilliere | Edward Ganio | Thanaphong Phongpreecha | Wendy Fantl | Kara L. Davis | Amy S. Tsai | Mohammad S. Ghaemi | David R. Mcilwain | Laura Peterson | ina Stelzer | Alan L. Chang | Gary M. Shaw | David K. Stevenson | R. Tibshirani | T. Hastie | G. Nolan | K. Davis | G. Shaw | N. Aghaeepour | D. Gaudillière | D. Stevenson | A. Culos | A. Tsai | N. Stanley | M. Becker | M. S. Ghaemi | D. Mcilwain | R. Fallahzadeh | A. Tanada | Huda Nassar | E. Ganio | Laura S. Peterson | Xiaoyuan Han | I. Stelzer | K. Ando | T. Phongpreecha | I. Marić | A. Chang | W. Fantl | M. Angst | B. Gaudillière
[1] W. Ketterl. [Periodontal diseases]. , 1971, Der Zahnarzt; Colloquium med. dent.
[2] J. Hanley,et al. The meaning and use of the area under a receiver operating characteristic (ROC) curve. , 1982, Radiology.
[3] D. Levy,et al. Interferon-induced nuclear signalling by Jak protein tyrosine kinases , 1993, Nature.
[4] R. Tibshirani. Regression Shrinkage and Selection via the Lasso , 1996 .
[5] Anil K. Jain,et al. Statistical Pattern Recognition: A Review , 2000, IEEE Trans. Pattern Anal. Mach. Intell..
[6] A. E. Hoerl,et al. Ridge regression: biased estimation for nonorthogonal problems , 2000 .
[7] N. Kadowaki,et al. Subsets of Human Dendritic Cell Precursors Express Different Toll-like Receptors and Respond to Different Microbial Antigens , 2001, The Journal of experimental medicine.
[8] I. Caramalho,et al. Regulatory T Cells Selectively Express Toll-like Receptors and Are Activated by Lipopolysaccharide , 2003, The Journal of experimental medicine.
[9] Peter O. Krutzik,et al. Intracellular phospho‐protein staining techniques for flow cytometry: Monitoring single cell signaling events , 2003, Cytometry. Part A : the journal of the International Society for Analytical Cytology.
[10] P. Heinrich,et al. Principles of interleukin (IL)-6-type cytokine signalling and its regulation. , 2003, The Biochemical journal.
[11] Leo Breiman,et al. Random Forests , 2001, Machine Learning.
[12] D. Ruppert. The Elements of Statistical Learning: Data Mining, Inference, and Prediction , 2004 .
[13] Corinna Cortes,et al. Support-Vector Networks , 1995, Machine Learning.
[14] A. Hoffmann,et al. Signaling pathways and genes that inhibit pathogen-induced macrophage apoptosis--CREB and NF-kappaB as key regulators. , 2005, Immunity.
[15] N. Johnson,et al. Periodontal diseases , 2005, The Lancet.
[16] H. Zou,et al. Regularization and variable selection via the elastic net , 2005 .
[17] H. Zou,et al. Addendum: Regularization and variable selection via the elastic net , 2005 .
[18] Wei Pan,et al. Incorporating prior knowledge of gene functional groups into regularized discriminant analysis of microarray data , 2007, Bioinform..
[19] Naftali Tishby,et al. Incorporating Prior Knowledge on Features into Learning , 2007, AISTATS.
[20] Geoffrey E. Hinton,et al. Visualizing Data using t-SNE , 2008 .
[21] O. Ornatsky,et al. Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry. , 2009, Analytical chemistry.
[22] Klaus Nordhausen,et al. The Elements of Statistical Learning: Data Mining, Inference, and Prediction, Second Edition by Trevor Hastie, Robert Tibshirani, Jerome Friedman , 2009 .
[23] B. Beutler. TLRs and innate immunity. , 2009, Blood.
[24] William N. Venables,et al. Modern Applied Statistics with S , 2010 .
[25] Chris Hans. Elastic Net Regression Modeling With the Orthant Normal Prior , 2011 .
[26] I. Glad,et al. Weighted Lasso with Data Integration , 2011, Statistical applications in genetics and molecular biology.
[27] Sean C. Bendall,et al. Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum , 2011, Science.
[28] J. Scheller,et al. The pro- and anti-inflammatory properties of the cytokine interleukin-6. , 2011, Biochimica et biophysica acta.
[29] Sean C. Bendall,et al. Extracting a Cellular Hierarchy from High-dimensional Cytometry Data with SPADE , 2011, Nature Biotechnology.
[30] A. Bagg,et al. Chimeric antigen receptor-modified T cells in chronic lymphoid leukemia. , 2011, The New England journal of medicine.
[31] J. Sprent,et al. The role of interleukin-2 during homeostasis and activation of the immune system , 2012, Nature Reviews Immunology.
[32] Sean C. Bendall,et al. Normalization of mass cytometry data with bead standards , 2013, Cytometry. Part A : the journal of the International Society for Analytical Cytology.
[33] P. Arck,et al. Fetomaternal immune cross-talk and its consequences for maternal and offspring's health , 2013, Nature Medicine.
[34] L. Ivashkiv,et al. Regulation of type I interferon responses , 2013, Nature Reviews Immunology.
[35] Greg Finak,et al. Critical assessment of automated flow cytometry data analysis techniques , 2013, Nature Methods.
[36] M. Adib-Conquy,et al. TLR‐mediated activation of NK cells and their role in bacterial/viral immune responses in mammals , 2014, Immunology and cell biology.
[37] S. Fisher,et al. Preterm labor: One syndrome, many causes , 2014, Science.
[38] Shriprakash Sinha. Integration of prior biological knowledge and epigenetic information enhances the prediction accuracy of the Bayesian Wnt pathway. , 2014, Integrative biology : quantitative biosciences from nano to macro.
[39] C. Murray,et al. Global Burden of Severe Periodontitis in 1990-2010 , 2014, Journal of dental research.
[40] Sean C. Bendall,et al. Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis , 2015, Cell.
[41] Piet Demeester,et al. FlowSOM: Using self‐organizing maps for visualization and interpretation of cytometry data , 2015, Cytometry. Part A : the journal of the International Society for Analytical Cytology.
[42] Eli R. Zunder,et al. Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm , 2015, Nature Protocols.
[43] Kurt Hornik,et al. Misc Functions of the Department of Statistics, ProbabilityTheory Group (Formerly: E1071), TU Wien , 2015 .
[44] C. Hunter,et al. IL-6 as a keystone cytokine in health and disease , 2015, Nature Immunology.
[45] Yiming Zuo,et al. Integrating prior biological knowledge and graphical LASSO for network inference , 2015, 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
[46] P. Eke,et al. Update on Prevalence of Periodontitis in Adults in the United States: NHANES 2009 to 2012. , 2015, Journal of periodontology.
[47] A. Metidji,et al. IFN-α/β Receptor Signaling Promotes Regulatory T Cell Development and Function under Stress Conditions , 2015, The Journal of Immunology.
[48] G. Nolan,et al. Automated Mapping of Phenotype Space with Single-Cell Data , 2016, Nature Methods.
[49] E. Coccia,et al. IFN‐α promotes rapid human Treg contraction and late Th1‐like Treg decrease , 2016, Journal of leukocyte biology.
[50] J. P. McCoy,et al. Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium , 2016, Scientific Reports.
[51] E. Newell,et al. Mass cytometry: blessed with the curse of dimensionality , 2016, Nature Immunology.
[52] R. Tibshirani,et al. An immune clock of human pregnancy , 2017, Science Immunology.
[53] Mark M. Davis,et al. Systems immunology: just getting started , 2017, Nature Immunology.
[54] Marco Gori,et al. Integrating Prior Knowledge into Deep Learning , 2017, 2017 16th IEEE International Conference on Machine Learning and Applications (ICMLA).
[55] S. Shen-Orr,et al. Social network architecture of human immune cells unveiled by quantitative proteomics , 2017, Nature Immunology.
[56] Alexandros Kalousis,et al. Regularising Non-linear Models Using Feature Side-information , 2017, ICML.
[57] Alexander R. Pico,et al. Fibrin-targeting immunotherapy protects against neuroinflammation and neurodegeneration , 2018, Nature Immunology.
[58] E. Saphire,et al. Antibody-mediated protection against Ebola virus , 2018, Nature Immunology.
[59] P. Chattopadhyay,et al. OMIP‐050: A 28‐color/30‐parameter Fluorescence Flow Cytometry Panel to Enumerate and Characterize Cells Expressing a Wide Array of Immune Checkpoint Molecules , 2018, Cytometry. Part A : the journal of the International Society for Analytical Cytology.
[60] Lucie Abeler-Dörner,et al. flowLearn: fast and precise identification and quality checking of cell populations in flow cytometry , 2018, Bioinform..
[61] Jeffrey A. Wiser,et al. Immune-centric network of cytokines and cells in disease context identified by computational mining of PubMed , 2018, Nature Biotechnology.
[62] Ralf Eggeling,et al. Weighted elastic net for unsupervised domain adaptation with application to age prediction from DNA methylation data , 2019, Bioinform..
[63] P. Chattopadhyay,et al. High-Parameter Single-Cell Analysis. , 2019, Annual review of analytical chemistry.
[64] Cynthia Rudin,et al. Stop explaining black box machine learning models for high stakes decisions and use interpretable models instead , 2018, Nature Machine Intelligence.
[65] Bruno Agard,et al. Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy , 2018, Bioinform..
[66] H. Deshmukh,et al. Immunological Basis for Recurrent Fetal Loss and Pregnancy Complications. , 2019, Annual review of pathology.
[67] Brandon LeBeau. Simulate Models Based on the Generalized Linear Model [R package simglm version 0.8.0] , 2020 .
[68] B. Rost,et al. Validity of machine learning in biology and medicine increased through collaborations across fields of expertise , 2020, Nature Machine Intelligence.
[69] Jiuyong Li,et al. Accurate data-driven prediction does not mean high reproducibility , 2020, Nature Machine Intelligence.
[70] L. Hood,et al. Deep phenotyping during pregnancy for predictive and preventive medicine , 2020, Science Translational Medicine.