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  1. Article ; Online: Understanding quantum machine learning also requires rethinking generalization.

    Gil-Fuster, Elies / Eisert, Jens / Bravo-Prieto, Carlos

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 2277

    Abstract: Quantum machine learning models have shown successful generalization performance even when trained with few data. In this work, through systematic randomization experiments, we show that traditional approaches to understanding generalization fail to ... ...

    Abstract Quantum machine learning models have shown successful generalization performance even when trained with few data. In this work, through systematic randomization experiments, we show that traditional approaches to understanding generalization fail to explain the behavior of such quantum models. Our experiments reveal that state-of-the-art quantum neural networks accurately fit random states and random labeling of training data. This ability to memorize random data defies current notions of small generalization error, problematizing approaches that build on complexity measures such as the VC dimension, the Rademacher complexity, and all their uniform relatives. We complement our empirical results with a theoretical construction showing that quantum neural networks can fit arbitrary labels to quantum states, hinting at their memorization ability. Our results do not preclude the possibility of good generalization with few training data but rather rule out any possible guarantees based only on the properties of the model family. These findings expose a fundamental challenge in the conventional understanding of generalization in quantum machine learning and highlight the need for a paradigm shift in the study of quantum models for machine learning tasks.
    Language English
    Publishing date 2024-03-13
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-45882-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Integrative description of two new species and two new subspecies of Lamprospilus Geyer (Lepidoptera: Lycaenidae).

    Prieto, Carlos / Faynel, Christophe / Lorenc-Brudecka, Jadwiga

    Zootaxa

    2023  Volume 5244, Issue 2, Page(s) 145–159

    Abstract: Lamprospilus stegmaier Prieto & Faynel sp. nov. is described from five specimens collected in sympatry with L. nicetus C. Felder & R. Felder on the northern central range of the Colombian Andes. Lamprospilus bicolor Faynel & Prieto sp. nov. is described ... ...

    Abstract Lamprospilus stegmaier Prieto & Faynel sp. nov. is described from five specimens collected in sympatry with L. nicetus C. Felder & R. Felder on the northern central range of the Colombian Andes. Lamprospilus bicolor Faynel & Prieto sp. nov. is described from specimens collected in Colombia, Peru and Bolivia. Lamprospilus bicolor mirador Faynel & Prieto ssp. nov. is described from specimens collected in Peru and Bolivia. Lamprospilus decorata valluna Prieto & Faynel ssp. nov. is described from specimens collected in Western Colombia. Male and female phenotypes are associated, and we present morphological and molecular diagnostic characters for the new species. We also evaluate the congruence between a priori morphology-based species identifications and Molecular Operational Taxonomic Units (MOTUs) delimitations based on Barcode Index Numbers (BINs) in the genus. DNA barcodes are in perfect agreement with morphology in 64% of the species. Interspecific distances were found to range from 3.22% to 8.42% (average 5.48%), whilst their mean intraspecific variation ranges from 0.0% to 4.30% (average 1.78%). Based on DNA barcodes evidence of topotypic individuals, the study of original descriptions and illustrations of the holotypes, we consider here that Lamprospilus occidentalis Johnson & Salazar 2004 is a new junior subjective synonym of L. draudti Lathy, 1932.
    MeSH term(s) Female ; Male ; Animals ; Butterflies
    Language English
    Publishing date 2023-02-17
    Publishing country New Zealand
    Document type Journal Article
    ISSN 1175-5334
    ISSN (online) 1175-5334
    DOI 10.11646/zootaxa.5244.2.3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Response to Kang et al.

    Garcia-Prieto, Carlos A / Davalos, Veronica / Esteller, Manel

    Journal of the National Cancer Institute

    2023  Volume 115, Issue 10, Page(s) 1234–1235

    Language English
    Publishing date 2023-08-18
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 2992-0
    ISSN 1460-2105 ; 0027-8874 ; 0198-0157
    ISSN (online) 1460-2105
    ISSN 0027-8874 ; 0198-0157
    DOI 10.1093/jnci/djad166
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Characterization of Nonribosomal Peptide Synthetases with NRPSsp.

    Prieto, Carlos

    Methods in molecular biology (Clifton, N.J.)

    2016  Volume 1401, Page(s) 273–278

    Abstract: Bioinformatic sequence analysis allows the functional characterization of newly sequenced proteins. Nonribosomal peptide synthetases (NRPSs) are multi-modular enzymes involved in the biosynthesis of natural products. The current omics era has enabled the ...

    Abstract Bioinformatic sequence analysis allows the functional characterization of newly sequenced proteins. Nonribosomal peptide synthetases (NRPSs) are multi-modular enzymes involved in the biosynthesis of natural products. The current omics era has enabled the exponential growth of the sequenced NRPS, and it is important to characterize the final product of these synthetases. Here, how to achieve the prediction of substrates which bind to adenylation domains in NRPS with NRPSsp (www.nrpssp.com) bioinformatic tool is described.
    MeSH term(s) Bacteria/chemistry ; Bacteria/enzymology ; Bacteria/metabolism ; Internet ; Models, Biological ; Peptide Synthases/chemistry ; Peptide Synthases/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Proteomics/methods ; Software ; Substrate Specificity
    Chemical Substances Peptide Synthases (EC 6.3.2.-) ; non-ribosomal peptide synthase (EC 6.3.2.-)
    Language English
    Publishing date 2016
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-3375-4_17
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Size Effects in Single- and Few-Layer MoS

    Cortijo-Campos, Sandra / Prieto, Carlos / De Andrés, Alicia

    Nanomaterials (Basel, Switzerland)

    2022  Volume 12, Issue 8

    Abstract: The high optical absorption and emission of bidimensional ... ...

    Abstract The high optical absorption and emission of bidimensional MoS
    Language English
    Publishing date 2022-04-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662255-5
    ISSN 2079-4991
    ISSN 2079-4991
    DOI 10.3390/nano12081330
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: SingleCAnalyzer: Interactive Analysis of Single Cell RNA-Seq Data on the Cloud.

    Prieto, Carlos / Barrios, David / Villaverde, Angela

    Frontiers in bioinformatics

    2022  Volume 2, Page(s) 793309

    Abstract: Single-cell RNA sequencing (scRNA-Seq) enables researchers to quantify the transcriptomes of individual cells. The capacity of researchers to perform this type of analysis has allowed researchers to undertake new scientific goals. The usefulness of scRNA- ...

    Abstract Single-cell RNA sequencing (scRNA-Seq) enables researchers to quantify the transcriptomes of individual cells. The capacity of researchers to perform this type of analysis has allowed researchers to undertake new scientific goals. The usefulness of scRNA-Seq has depended on the development of new computational biology methods, which have been designed to meeting challenges associated with scRNA-Seq analysis. However, the proper application of these computational methods requires extensive bioinformatics expertise. Otherwise, it is often difficult to obtain reliable and reproducible results. We have developed SingleCAnalyzer, a cloud platform that provides a means to perform full scRNA-Seq analysis from FASTQ within an easy-to-use and self-exploratory web interface. Its analysis pipeline includes the demultiplexing and alignment of FASTQ files, read trimming, sample quality control, feature selection, empty droplets detection, dimensional reduction, cellular type prediction, unsupervised clustering of cells, pseudotime/trajectory analysis, expression comparisons between groups, functional enrichment of differentially expressed genes and gene set expression analysis. Results are presented with interactive graphs, which provide exploratory and analytical features. SingleCAnalyzer is freely available at https://singleCAnalyzer.eu.
    Language English
    Publishing date 2022-05-23
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2673-7647
    ISSN (online) 2673-7647
    DOI 10.3389/fbinf.2022.793309
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Book ; Online: Understanding quantum machine learning also requires rethinking generalization

    Gil-Fuster, Elies / Eisert, Jens / Bravo-Prieto, Carlos

    2023  

    Abstract: Quantum machine learning models have shown successful generalization performance even when trained with few data. In this work, through systematic randomization experiments, we show that traditional approaches to understanding generalization fail to ... ...

    Abstract Quantum machine learning models have shown successful generalization performance even when trained with few data. In this work, through systematic randomization experiments, we show that traditional approaches to understanding generalization fail to explain the behavior of such quantum models. Our experiments reveal that state-of-the-art quantum neural networks accurately fit random states and random labeling of training data. This ability to memorize random data defies current notions of small generalization error, problematizing approaches that build on complexity measures such as the VC dimension, the Rademacher complexity, and all their uniform relatives. We complement our empirical results with a theoretical construction showing that quantum neural networks can fit arbitrary labels to quantum states, hinting at their memorization ability. Our results do not preclude the possibility of good generalization with few training data but rather rule out any possible guarantees based only on the properties of the model family. These findings expose a fundamental challenge in the conventional understanding of generalization in quantum machine learning and highlight the need for a paradigm shift in the design of quantum models for machine learning tasks.

    Comment: 13+4 pages, 3 figures
    Keywords Quantum Physics ; Condensed Matter - Quantum Gases ; Computer Science - Machine Learning ; Statistics - Machine Learning
    Subject code 006
    Publishing date 2023-06-23
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article: Congruence between morphology-based species and Barcode Index Numbers (BINs) in Neotropical Eumaeini (Lycaenidae).

    Prieto, Carlos / Faynel, Christophe / Robbins, Robert / Hausmann, Axel

    PeerJ

    2021  Volume 9, Page(s) e11843

    Abstract: Background: With about 1,000 species in the Neotropics, the Eumaeini (Theclinae) are one of the most diverse butterfly tribes. Correct morphology-based identifications are challenging in many genera due to relatively little interspecific differences in ... ...

    Abstract Background: With about 1,000 species in the Neotropics, the Eumaeini (Theclinae) are one of the most diverse butterfly tribes. Correct morphology-based identifications are challenging in many genera due to relatively little interspecific differences in wing patterns. Geographic infraspecific variation is sometimes more substantial than variation between species. In this paper we present a large DNA barcode dataset of South American Lycaenidae. We analyze how well DNA barcode BINs match morphologically delimited species.
    Methods: We compare morphology-based species identifications with the clustering of molecular operational taxonomic units (MOTUs) delimitated by the RESL algorithm in BOLD, which assigns Barcode Index Numbers (BINs). We examine intra- and interspecific divergences for genera represented by at least four morphospecies. We discuss the existence of local barcode gaps in a genus by genus analysis. We also note differences in the percentage of species with barcode gaps in groups of lowland and high mountain genera.
    Results: We identified 2,213 specimens and obtained 1,839 sequences of 512 species in 90 genera. Overall, the mean intraspecific divergence value of CO1 sequences was 1.20%, while the mean interspecific divergence between nearest congeneric neighbors was 4.89%, demonstrating the presence of a barcode gap. However, the gap seemed to disappear from the entire set when comparing the maximum intraspecific distance (8.40%) with the minimum interspecific distance (0.40%). Clear barcode gaps are present in many genera but absent in others. From the set of specimens that yielded COI fragment lengths of at least 650 bp, 75% of the
    Language English
    Publishing date 2021-08-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2703241-3
    ISSN 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.11843
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: RaNA-Seq: Interactive RNA-Seq analysis from FASTQ files to functional analysis.

    Prieto, Carlos / Barrios, David

    Bioinformatics (Oxford, England)

    2019  

    Abstract: Summary: RaNA-Seq is a cloud platform for the rapid analysis and visualization of RNA-Seq data. It performs a full analysis in minutes by quantifying FASTQ files, calculating quality control metrics, running differential expression analyses and enabling ...

    Abstract Summary: RaNA-Seq is a cloud platform for the rapid analysis and visualization of RNA-Seq data. It performs a full analysis in minutes by quantifying FASTQ files, calculating quality control metrics, running differential expression analyses and enabling the explanation of results with functional analyses. Our analysis pipeline applies generally accepted and reproducible protocols that can be applied with two simple steps in its web interface. Analysis results are presented as interactive graphics and reports, ready for their interpretation and publication.
    Availability: RaNA-Seq web service is freely available online at https://ranaseq.eu.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    Language English
    Publishing date 2019-11-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btz854
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: An Integrated Process Analysis for Producing Glycerol Carbonate from CO

    Del-Mazo-Alvarado, Octavio / Prieto, Carlos / Sánchez, Antonio / Ramírez-Márquez, César / Bonilla-Petriciolet, Adrián / Martín, Mariano

    ChemSusChem

    2024  Volume 17, Issue 8, Page(s) e202301546

    Abstract: Glycerol carbonate (GC) is one of the most attractive green chemicals involved in several applications such as polymer synthesis, e. g., the production of polyurethanes and polycarbonates. This relevant chemical can be produced, in a green way, using ... ...

    Abstract Glycerol carbonate (GC) is one of the most attractive green chemicals involved in several applications such as polymer synthesis, e. g., the production of polyurethanes and polycarbonates. This relevant chemical can be produced, in a green way, using CO
    Language English
    Publishing date 2024-03-21
    Publishing country Germany
    Document type Journal Article
    ISSN 1864-564X
    ISSN (online) 1864-564X
    DOI 10.1002/cssc.202301546
    Database MEDical Literature Analysis and Retrieval System OnLINE

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