当前位置： SCI文献检索 > Nature Communications期刊下所有文献 > Cumulative learning enables convolutional neural network representations for small mass spectrometry data classification.

Cumulative learning enables convolutional neural network representations for small mass spectrometry data classification.

Abstract：

:Rapid and accurate clinical diagnosis remains challenging. A component of diagnosis tool development is the design of effective classification models with Mass spectrometry (MS) data. Some Machine Learning approaches have been investigated but these models require time-consuming preprocessing steps to remove artifacts, making them unsuitable for rapid analysis. Convolutional Neural Networks (CNNs) have been found to perform well under such circumstances since they can learn representations from raw data. However, their effectiveness decreases when the number of available training samples is small, which is a common situation in medicine. In this work, we investigate transfer learning on 1D-CNNs, then we develop a cumulative learning method when transfer learning is not powerful enough. We propose to train the same model through several classification tasks over various small datasets to accumulate knowledge in the resulting representation. By using rat brain as the initial training dataset, a cumulative learning approach can have a classification accuracy exceeding 98% for 1D clinical MS-data. We show the use of cumulative learning using datasets generated in different biological contexts, on different organisms, and acquired by different instruments. Here we show a promising strategy for improving MS data classification accuracy when only small numbers of samples are available.

journal_name

Nat Commun

journal_title

Nature communications

authors

Seddiki K,Saudemont P,Precioso F,Ogrinc N,Wisztorski M,Salzet M,Fournier I,Droit A

doi

10.1038/s41467-020-19354-z

subject

Has Abstract

pub_date

2020-11-05 00:00:00

pages

5595

issue

1

issn

2041-1723

pii

10.1038/s41467-020-19354-z

journal_volume

11

pub_type

杂志文章

相关文献

Nature Communications文献大全
  • Mechanisms of increased Trichodesmium fitness under iron and phosphorus co-limitation in the present and future ocean.

    abstract：:Nitrogen fixation by cyanobacteria supplies critical bioavailable nitrogen to marine ecosystems worldwide; however, field and lab data have demonstrated it to be limited by iron, phosphorus and/or CO2. To address unknown future interactions among these factors, we grew the nitrogen-fixing cyanobacterium Trichodesmium ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms12081

    authors： Walworth NG,Fu FX,Webb EA,Saito MA,Moran D,Mcllvin MR,Lee MD,Hutchins DA

    更新日期：2016-06-27 00:00:00

  • Active and dynamic mitochondrial S-depalmitoylation revealed by targeted fluorescent probes.

    abstract：:The reversible modification of cysteine residues by thioester formation with palmitate (S-palmitoylation) is an abundant lipid post-translational modification (PTM) in mammalian systems. S-palmitoylation has been observed on mitochondrial proteins, providing an intriguing potential connection between metabolic lipids ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-017-02655-1

    authors： Kathayat RS,Cao Y,Elvira PD,Sandoz PA,Zaballa ME,Springer MZ,Drake LE,Macleod KF,van der Goot FG,Dickinson BC

    更新日期：2018-01-23 00:00:00

  • Author Correction: Structural determinants and functional consequences of protein affinity for membrane rafts.

    abstract：:In the originally published version of this Article, financial support was not fully acknowledged. The PDF and HTML versions of the Article have now been corrected to include support from National Institute of General Medical Sciences, National Institutes of Health grant R01GM124072. ...

    journal_title：Nature communications

    pub_type： 杂志文章,已发布勘误

    doi：10.1038/s41467-018-04164-1

    authors： Lorent JH,Diaz-Rohrer B,Lin X,Spring K,Gorfe AA,Levental KR,Levental I

    更新日期：2018-05-01 00:00:00

  • Publisher Correction: Nitric oxide-dependent anaerobic ammonium oxidation.

    abstract：:The original HTML version of this Article had an incorrect Published online date of 20 March 2019; it should have been 18 March 2019. This has been corrected in the HTML version of the Article. The PDF version was correct from the time of publication. ...

    journal_title：Nature communications

    pub_type： 已发布勘误

    doi：10.1038/s41467-019-09797-4

    authors： Hu Z,Wessels HJCT,van Alen T,Jetten MSM,Kartal B

    更新日期：2019-04-18 00:00:00

  • ROW1 maintains quiescent centre identity by confining WOX5 expression to specific cells.

    abstract：:The quiescent centre (QC) in the Arabidopsis root apical meristem is essential for stem cell organization. Here we show that the loss of REPRESSOR OF WUSCHEL1 (ROW1), a PHD domain-containing protein, leads to QC failure, defects in cell differentiation and ectopic expression of WUSCHEL-RELATED HOMEOBOX 5 (WOX5) in cel...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms7003

    authors： Zhang Y,Jiao Y,Liu Z,Zhu YX

    更新日期：2015-01-29 00:00:00

  • Publisher Correction: Parallel evolution in the emergence of highly pathogenic avian influenza A viruses.

    abstract：:A Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20006-5. ...

    journal_title：Nature communications

    pub_type： 已发布勘误

    doi：10.1038/s41467-020-20006-5

    authors： Escalera-Zamudio M,Golden M,Gutiérrez B,Thézé J,Keown JR,Carrique L,Bowden TA,Pybus OG

    更新日期：2020-11-23 00:00:00

  • Thymosin β4-sulfoxide attenuates inflammatory cell infiltration and promotes cardiac wound healing.

    abstract：:The downstream consequences of inflammation in the adult mammalian heart are formation of a non-functional scar, pathological remodelling and heart failure. In zebrafish, hydrogen peroxide released from a wound is the initial instructive chemotactic cue for the infiltration of inflammatory cells, however, the identity...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms3081

    authors： Evans MA,Smart N,Dubé KN,Bollini S,Clark JE,Evans HG,Taams LS,Richardson R,Lévesque M,Martin P,Mills K,Riegler J,Price AN,Lythgoe MF,Riley PR

    更新日期：2013-01-01 00:00:00

  • Targeted production of reactive oxygen species in mitochondria to overcome cancer drug resistance.

    abstract：:Multidrug resistance is a major challenge to cancer chemotherapy. The multidrug resistance phenotype is associated with the overexpression of the adenosine triphosphate (ATP)-driven transmembrane efflux pumps in cancer cells. Here, we report a lipid membrane-coated silica-carbon (LSC) hybrid nanoparticle that targets ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-02915-8

    authors： Wang H,Gao Z,Liu X,Agarwal P,Zhao S,Conroy DW,Ji G,Yu J,Jaroniec CP,Liu Z,Lu X,Li X,He X

    更新日期：2018-02-08 00:00:00

  • Physiological constraints to climate warming in fish follow principles of plastic floors and concrete ceilings.

    abstract：:Understanding the resilience of aquatic ectothermic animals to climate warming has been hindered by the absence of experimental systems experiencing warming across relevant timescales (for example, decades). Here, we examine European perch (Perca fluviatilis, L.) from the Biotest enclosure, a unique coastal ecosystem ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms11447

    authors： Sandblom E,Clark TD,Gräns A,Ekström A,Brijs J,Sundström LF,Odelström A,Adill A,Aho T,Jutfelt F

    更新日期：2016-05-17 00:00:00

  • H3 ubiquitination by NEDD4 regulates H3 acetylation and tumorigenesis.

    abstract：:Dynamic changes in histone modifications under various physiological cues play important roles in gene transcription and cancer. Identification of new histone marks critical for cancer development is of particular importance. Here we show that, in a glucose-dependent manner, E3 ubiquitin ligase NEDD4 ubiquitinates his...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms14799

    authors： Zhang X,Li B,Rezaeian AH,Xu X,Chou PC,Jin G,Han F,Pan BS,Wang CY,Long J,Zhang A,Huang CY,Tsai FJ,Tsai CH,Logothetis C,Lin HK

    更新日期：2017-03-16 00:00:00

  • Interrogating the protein interactomes of RAS isoforms identifies PIP5K1A as a KRAS-specific vulnerability.

    abstract：:In human cancers, oncogenic mutations commonly occur in the RAS genes KRAS, NRAS, or HRAS, but there are no clinical RAS inhibitors. Mutations are more prevalent in KRAS, possibly suggesting a unique oncogenic activity mediated by KRAS-specific interaction partners, which might be targeted. Here, we determine the spec...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-05692-6

    authors： Adhikari H,Counter CM

    更新日期：2018-09-07 00:00:00

  • Publisher Correction: Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy.

    abstract：:Affiliation 4 incorrectly read 'University of the Basque Country (Ikerbasque), University of the Basque Country and Donostia International Physics Center, San Sebastian 20018, Spain.'Also, the affiliations of Ignacio Arganda-Carreras with 'IKERBASQUE, Basque Foundation for Science, Bilbao, 48013, Spain' and 'Donostia ...

    journal_title：Nature communications

    pub_type： 已发布勘误

    doi：10.1038/s41467-019-10225-w

    authors： Abdeladim L,Matho KS,Clavreul S,Mahou P,Sintes JM,Solinas X,Arganda-Carreras I,Turney SG,Lichtman JW,Chessel A,Bemelmans AP,Loulier K,Supatto W,Livet J,Beaurepaire E

    更新日期：2019-05-09 00:00:00

  • Exosomes harbor B cell targets in pancreatic adenocarcinoma and exert decoy function against complement-mediated cytotoxicity.

    abstract：:Although B cell response is frequently found in cancer, there is little evidence that it alters tumor development or progression. The process through which tumor-associated antigens trigger humoral response is not well delineated. We investigate the repertoire of antigens associated with humoral immune response in pan...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-08109-6

    authors： Capello M,Vykoukal JV,Katayama H,Bantis LE,Wang H,Kundnani DL,Aguilar-Bonavides C,Aguilar M,Tripathi SC,Dhillon DS,Momin AA,Peters H,Katz MH,Alvarez H,Bernard V,Ferri-Borgogno S,Brand R,Adler DG,Firpo MA,Mulvihill S

    更新日期：2019-01-16 00:00:00

  • Real-space observation of spin-split molecular orbitals of adsorbed single-molecule magnets.

    abstract：:A key challenge in the field of molecular spintronics, and for the design of single-molecule magnet-based devices in particular, is the understanding and control of the molecular coupling at the electrode interfaces. It was demonstrated for the field of molecular electronics that the characterization of the molecule-m...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms1953

    authors： Schwöbel J,Fu Y,Brede J,Dilullo A,Hoffmann G,Klyatskaya S,Ruben M,Wiesendanger R

    更新日期：2012-07-17 00:00:00

  • Weakening of the stratospheric polar vortex by Arctic sea-ice loss.

    abstract：:Successive cold winters of severely low temperatures in recent years have had critical social and economic impacts on the mid-latitude continents in the Northern Hemisphere. Although these cold winters are thought to be partly driven by dramatic losses of Arctic sea-ice, the mechanism that links sea-ice loss to cold w...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms5646

    authors： Kim BM,Son SW,Min SK,Jeong JH,Kim SJ,Zhang X,Shim T,Yoon JH

    更新日期：2014-09-02 00:00:00

  • The vectorial control of magnetization by light.

    abstract：:Application of coherent light-matter interactions has recently been extended to the ultrafast control of magnetization. An important but unrealized technique is the manipulation of magnetization vector motion to make it follow an arbitrarily designed multidimensional trajectory. Here we demonstrate a full manipulation...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms1366

    authors： Kanda N,Higuchi T,Shimizu H,Konishi K,Yoshioka K,Kuwata-Gonokami M

    更新日期：2011-06-21 00:00:00

  • Structure of tRNA splicing enzyme Tpt1 illuminates the mechanism of RNA 2'-PO4 recognition and ADP-ribosylation.

    abstract：:Tpt1 is an essential agent of fungal tRNA splicing that removes the 2'-PO4 at the splice junction generated by fungal tRNA ligase. Tpt1 catalyzes a unique two-step reaction whereby the 2'-PO4 attacks NAD+ to form an RNA-2'-phospho-ADP-ribosyl intermediate that undergoes transesterification to yield 2'-OH RNA and ADP-r...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-08211-9

    authors： Banerjee A,Munir A,Abdullahu L,Damha MJ,Goldgur Y,Shuman S

    更新日期：2019-01-15 00:00:00

  • Author Correction: A systems biology approach uncovers cell-specific gene regulatory effects of genetic associations in multiple sclerosis.

    abstract：:An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    journal_title：Nature communications

    pub_type： 已发布勘误

    doi：10.1038/s41467-019-10951-1

    authors： International Multiple Sclerosis Genetics Consortium.

    更新日期：2019-07-01 00:00:00

  • Identification of serum metabolites associating with chronic kidney disease progression and anti-fibrotic effect of 5-methoxytryptophan.

    abstract：:Early detection and accurate monitoring of chronic kidney disease (CKD) could improve care and retard progression to end-stage renal disease. Here, using untargeted metabolomics in 2155 participants including patients with stage 1-5 CKD and healthy controls, we identify five metabolites, including 5-methoxytryptophan ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-09329-0

    authors： Chen DQ,Cao G,Chen H,Argyopoulos CP,Yu H,Su W,Chen L,Samuels DC,Zhuang S,Bayliss GP,Zhao S,Yu XY,Vaziri ND,Wang M,Liu D,Mao JR,Ma SX,Zhao J,Zhang Y,Shang YQ,Kang H,Ye F,Cheng XH,Li XR,Zhang L,Meng MX,G

    更新日期：2019-04-01 00:00:00

  • Scanning STED-FCS reveals spatiotemporal heterogeneity of lipid interaction in the plasma membrane of living cells.

    abstract：:The interaction of lipids and proteins plays an important role in plasma membrane bioactivity, and much can be learned from their diffusion characteristics. Here we present the combination of super-resolution STED microscopy with scanning fluorescence correlation spectroscopy (scanning STED-FCS, sSTED-FCS) to characte...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms6412

    authors： Honigmann A,Mueller V,Ta H,Schoenle A,Sezgin E,Hell SW,Eggeling C

    更新日期：2014-11-20 00:00:00

  • Chaperone-mediated ordered assembly of the SAGA and NuA4 transcription co-activator complexes in yeast.

    abstract：:Transcription initiation involves the coordinated activities of large multimeric complexes, but little is known about their biogenesis. Here we report several principles underlying the assembly and topological organization of the highly conserved SAGA and NuA4 co-activator complexes, which share the Tra1 subunit. We s...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-13243-w

    authors： Elías-Villalobos A,Toullec D,Faux C,Séveno M,Helmlinger D

    更新日期：2019-11-20 00:00:00

  • Biochemical mechanisms determine the functional compatibility of heterologous genes.

    abstract：:Elucidating the factors governing the functional compatibility of horizontally transferred genes is important to understand bacterial evolution, including the emergence and spread of antibiotic resistance, and to successfully engineer biological systems. In silico efforts and work using single-gene libraries have sugg...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-02944-3

    authors： Porse A,Schou TS,Munck C,Ellabaan MMH,Sommer MOA

    更新日期：2018-02-06 00:00:00

  • D-Glucosamine supplementation extends life span of nematodes and of ageing mice.

    abstract：:D-Glucosamine (GlcN) is a freely available and commonly used dietary supplement potentially promoting cartilage health in humans, which also acts as an inhibitor of glycolysis. Here we show that GlcN, independent of the hexosamine pathway, extends Caenorhabditis elegans life span by impairing glucose metabolism that a...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms4563

    authors： Weimer S,Priebs J,Kuhlow D,Groth M,Priebe S,Mansfeld J,Merry TL,Dubuis S,Laube B,Pfeiffer AF,Schulz TJ,Guthke R,Platzer M,Zamboni N,Zarse K,Ristow M

    更新日期：2014-04-08 00:00:00

  • BAP1 complex promotes transcription by opposing PRC1-mediated H2A ubiquitylation.

    abstract：:In Drosophila, a complex consisting of Calypso and ASX catalyzes H2A deubiquitination and has been reported to act as part of the Polycomb machinery in transcriptional silencing. The mammalian homologs of these proteins (BAP1 and ASXL1/2/3, respectively), are frequently mutated in various cancer types, yet their preci...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-08255-x

    authors： Campagne A,Lee MK,Zielinski D,Michaud A,Le Corre S,Dingli F,Chen H,Shahidian LZ,Vassilev I,Servant N,Loew D,Pasmant E,Postel-Vinay S,Wassef M,Margueron R

    更新日期：2019-01-21 00:00:00

  • Rapid cost decrease of renewables and storage accelerates the decarbonization of China's power system.

    abstract：:The costs for solar photovoltaics, wind, and battery storage have dropped markedly since 2010, however, many recent studies and reports around the world have not adequately captured such dramatic decrease. Those costs are projected to decline further in the near future, bringing new prospects for the widespread penetr...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-020-16184-x

    authors： He G,Lin J,Sifuentes F,Liu X,Abhyankar N,Phadke A

    更新日期：2020-05-19 00:00:00

  • CTCF orchestrates the germinal centre transcriptional program and prevents premature plasma cell differentiation.

    abstract：:In germinal centres (GC) mature B cells undergo intense proliferation and immunoglobulin gene modification before they differentiate into memory B cells or long-lived plasma cells (PC). GC B-cell-to-PC transition involves a major transcriptional switch that promotes a halt in cell proliferation and the production of s...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms16067

    authors： Pérez-García A,Marina-Zárate E,Álvarez-Prado ÁF,Ligos JM,Galjart N,Ramiro AR

    更新日期：2017-07-05 00:00:00

  • Efficient near-infrared up-conversion photoluminescence in carbon nanotubes.

    abstract：:Photoluminescence phenomena normally obey Stokes' law of luminescence according to which the emitted photon energy is typically lower than its excitation counterparts. Here we show that carbon nanotubes break this rule under one-photon excitation conditions. We found that the carbon nanotubes exhibit efficient near-in...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms9920

    authors： Akizuki N,Aota S,Mouri S,Matsuda K,Miyauchi Y

    更新日期：2015-11-16 00:00:00

  • Subduction of the oceanic Hikurangi Plateau and its impact on the Kermadec arc.

    abstract：:Large igneous province subduction is a rare process on Earth. A modern example is the subduction of the oceanic Hikurangi Plateau beneath the southern Kermadec arc, offshore New Zealand. This segment of the arc has the largest total lava volume erupted and the highest volcano density of the entire Kermadec arc. Here w...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms5923

    authors： Timm C,Davy B,Haase K,Hoernle KA,Graham IJ,de Ronde CE,Woodhead J,Bassett D,Hauff F,Mortimer N,Seebeck HC,Wysoczanski RJ,Caratori-Tontini F,Gamble JA

    更新日期：2014-09-17 00:00:00

  • Nrl knockdown by AAV-delivered CRISPR/Cas9 prevents retinal degeneration in mice.

    abstract：:In retinitis pigmentosa, loss of cone photoreceptors leads to blindness, and preservation of cone function is a major therapeutic goal. However, cone loss is thought to occur as a secondary event resulting from degeneration of rod photoreceptors. Here we report a genome editing approach in which adeno-associated virus...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms14716

    authors： Yu W,Mookherjee S,Chaitankar V,Hiriyanna S,Kim JW,Brooks M,Ataeijannati Y,Sun X,Dong L,Li T,Swaroop A,Wu Z

    更新日期：2017-03-14 00:00:00

  • Wildlife population trends in protected areas predicted by national socio-economic metrics and body size.

    abstract：:Ensuring that protected areas (PAs) maintain the biodiversity within their boundaries is fundamental in achieving global conservation goals. Despite this objective, wildlife abundance changes in PAs are patchily documented and poorly understood. Here, we use linear mixed effect models to explore correlates of populati...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms12747

    authors： Barnes MD,Craigie ID,Harrison LB,Geldmann J,Collen B,Whitmee S,Balmford A,Burgess ND,Brooks T,Hockings M,Woodley S

    更新日期：2016-09-01 00:00:00