LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 205

Search options

  1. Book ; Online: Unsupervised Learning of Deep Features for Music Segmentation

    McCallum, Matthew C.

    2021  

    Abstract: Music segmentation refers to the dual problem of identifying boundaries between, and labeling, distinct music segments, e.g., the chorus, verse, bridge etc. in popular music. The performance of a range of music segmentation algorithms has been shown to ... ...

    Abstract Music segmentation refers to the dual problem of identifying boundaries between, and labeling, distinct music segments, e.g., the chorus, verse, bridge etc. in popular music. The performance of a range of music segmentation algorithms has been shown to be dependent on the audio features chosen to represent the audio. Some approaches have proposed learning feature transformations from music segment annotation data, although, such data is time consuming or expensive to create and as such these approaches are likely limited by the size of their datasets. While annotated music segmentation data is a scarce resource, the amount of available music audio is much greater. In the neighboring field of semantic audio unsupervised deep learning has shown promise in improving the performance of solutions to the query-by-example and sound classification tasks. In this work, unsupervised training of deep feature embeddings using convolutional neural networks (CNNs) is explored for music segmentation. The proposed techniques exploit only the time proximity of audio features that is implicit in any audio timeline. Employing these embeddings in a classic music segmentation algorithm is shown not only to significantly improve the performance of this algorithm, but obtain state of the art performance in unsupervised music segmentation.
    Keywords Computer Science - Sound ; Computer Science - Machine Learning ; Computer Science - Multimedia ; Electrical Engineering and Systems Science - Audio and Speech Processing
    Subject code 780
    Publishing date 2021-08-29
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    More links

    Kategorien

  2. Book ; Online: On the Effect of Data-Augmentation on Local Embedding Properties in the Contrastive Learning of Music Audio Representations

    McCallum, Matthew C. / Davies, Matthew E. P. / Henkel, Florian / Kim, Jaehun / Sandberg, Samuel E.

    2024  

    Abstract: Audio embeddings are crucial tools in understanding large catalogs of music. Typically embeddings are evaluated on the basis of the performance they provide in a wide range of downstream tasks, however few studies have investigated the local properties ... ...

    Abstract Audio embeddings are crucial tools in understanding large catalogs of music. Typically embeddings are evaluated on the basis of the performance they provide in a wide range of downstream tasks, however few studies have investigated the local properties of the embedding spaces themselves which are important in nearest neighbor algorithms, commonly used in music search and recommendation. In this work we show that when learning audio representations on music datasets via contrastive learning, musical properties that are typically homogeneous within a track (e.g., key and tempo) are reflected in the locality of neighborhoods in the resulting embedding space. By applying appropriate data augmentation strategies, localisation of such properties can not only be reduced but the localisation of other attributes is increased. For example, locality of features such as pitch and tempo that are less relevant to non-expert listeners, may be mitigated while improving the locality of more salient features such as genre and mood, achieving state-of-the-art performance in nearest neighbor retrieval accuracy. Similarly, we show that the optimal selection of data augmentation strategies for contrastive learning of music audio embeddings is dependent on the downstream task, highlighting this as an important embedding design decision.

    Comment: Accepted to the International Conference on Acoustics, Speech and Signal Processing (ICASSP) 2024
    Keywords Computer Science - Sound ; Computer Science - Information Retrieval ; Computer Science - Machine Learning ; Computer Science - Multimedia ; Electrical Engineering and Systems Science - Audio and Speech Processing
    Subject code 780
    Publishing date 2024-01-16
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    More links

    Kategorien

  3. Book ; Online: Similar but Faster

    McCallum, Matthew C. / Henkel, Florian / Kim, Jaehun / Sandberg, Samuel E. / Davies, Matthew E. P.

    Manipulation of Tempo in Music Audio Embeddings for Tempo Prediction and Search

    2024  

    Abstract: Audio embeddings enable large scale comparisons of the similarity of audio files for applications such as search and recommendation. Due to the subjectivity of audio similarity, it can be desirable to design systems that answer not only whether audio is ... ...

    Abstract Audio embeddings enable large scale comparisons of the similarity of audio files for applications such as search and recommendation. Due to the subjectivity of audio similarity, it can be desirable to design systems that answer not only whether audio is similar, but similar in what way (e.g., wrt. tempo, mood or genre). Previous works have proposed disentangled embedding spaces where subspaces representing specific, yet possibly correlated, attributes can be weighted to emphasize those attributes in downstream tasks. However, no research has been conducted into the independence of these subspaces, nor their manipulation, in order to retrieve tracks that are similar but different in a specific way. Here, we explore the manipulation of tempo in embedding spaces as a case-study towards this goal. We propose tempo translation functions that allow for efficient manipulation of tempo within a pre-existing embedding space whilst maintaining other properties such as genre. As this translation is specific to tempo it enables retrieval of tracks that are similar but have specifically different tempi. We show that such a function can be used as an efficient data augmentation strategy for both training of downstream tempo predictors, and improved nearest neighbor retrieval of properties largely independent of tempo.

    Comment: Accepted to the International Conference on Acoustics, Speech and Signal Processing (ICASSP) 2024
    Keywords Computer Science - Sound ; Computer Science - Digital Libraries ; Computer Science - Information Retrieval ; Computer Science - Machine Learning ; Electrical Engineering and Systems Science - Audio and Speech Processing
    Subject code 006
    Publishing date 2024-01-16
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    More links

    Kategorien

  4. Book ; Online: Tempo estimation as fully self-supervised binary classification

    Henkel, Florian / Kim, Jaehun / McCallum, Matthew C. / Sandberg, Samuel E. / Davies, Matthew E. P.

    2024  

    Abstract: This paper addresses the problem of global tempo estimation in musical audio. Given that annotating tempo is time-consuming and requires certain musical expertise, few publicly available data sources exist to train machine learning models for this task. ... ...

    Abstract This paper addresses the problem of global tempo estimation in musical audio. Given that annotating tempo is time-consuming and requires certain musical expertise, few publicly available data sources exist to train machine learning models for this task. Towards alleviating this issue, we propose a fully self-supervised approach that does not rely on any human labeled data. Our method builds on the fact that generic (music) audio embeddings already encode a variety of properties, including information about tempo, making them easily adaptable for downstream tasks. While recent work in self-supervised tempo estimation aimed to learn a tempo specific representation that was subsequently used to train a supervised classifier, we reformulate the task into the binary classification problem of predicting whether a target track has the same or a different tempo compared to a reference. While the former still requires labeled training data for the final classification model, our approach uses arbitrary unlabeled music data in combination with time-stretching for model training as well as a small set of synthetically created reference samples for predicting the final tempo. Evaluation of our approach in comparison with the state-of-the-art reveals highly competitive performance when the constraint of finding the precise tempo octave is relaxed.

    Comment: Accepted to the International Conference on Acoustics, Speech and Signal Processing (ICASSP) 2024
    Keywords Computer Science - Sound ; Computer Science - Machine Learning ; Electrical Engineering and Systems Science - Audio and Speech Processing
    Subject code 006
    Publishing date 2024-01-16
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    More links

    Kategorien

  5. Article: Human coronavirus HKU1 recognition of the TMPRSS2 host receptor.

    McCallum, Matthew / Park, Young-Jun / Stewart, Cameron / Sprouse, Kaitlin R / Brown, Jack / Tortorici, M Alejandra / Gibson, Cecily / Wong, Emily / Ieven, Margareta / Telenti, Amalio / Veesler, David

    bioRxiv : the preprint server for biology

    2024  

    Abstract: The human coronavirus HKU1 spike (S) glycoprotein engages host cell surface sialoglycans and transmembrane protease serine 2 (TMPRSS2) to initiate infection. The molecular basis of HKU1 binding to TMPRSS2 and determinants of host receptor tropism remain ... ...

    Abstract The human coronavirus HKU1 spike (S) glycoprotein engages host cell surface sialoglycans and transmembrane protease serine 2 (TMPRSS2) to initiate infection. The molecular basis of HKU1 binding to TMPRSS2 and determinants of host receptor tropism remain elusive. Here, we designed an active human TMPRSS2 construct enabling high-yield recombinant production in human cells of this key therapeutic target. We determined a cryo-electron microscopy structure of the HKU1 RBD bound to human TMPRSS2 providing a blueprint of the interactions supporting viral entry and explaining the specificity for TMPRSS2 among human type 2 transmembrane serine proteases. We found that human, rat, hamster and camel TMPRSS2 promote HKU1 S-mediated entry into cells and identified key residues governing host receptor usage. Our data show that serum antibodies targeting the HKU1 RBD TMPRSS2 binding-site are key for neutralization and that HKU1 uses conformational masking and glycan shielding to balance immune evasion and receptor engagement.
    Language English
    Publishing date 2024-01-09
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.01.09.574565
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  6. Article ; Online: Structure and design of Langya virus glycoprotein antigens.

    Wang, Zhaoqian / McCallum, Matthew / Yan, Lianying / Gibson, Cecily A / Sharkey, William / Park, Young-Jun / Dang, Ha V / Amaya, Moushimi / Person, Ashley / Broder, Christopher C / Veesler, David

    Proceedings of the National Academy of Sciences of the United States of America

    2024  Volume 121, Issue 16, Page(s) e2314990121

    Abstract: Langya virus (LayV) is a recently discovered henipavirus (HNV), isolated from febrile patients in China. HNV entry into host cells is mediated by the attachment (G) and fusion (F) glycoproteins which are the main targets of neutralizing antibodies. We ... ...

    Abstract Langya virus (LayV) is a recently discovered henipavirus (HNV), isolated from febrile patients in China. HNV entry into host cells is mediated by the attachment (G) and fusion (F) glycoproteins which are the main targets of neutralizing antibodies. We show here that the LayV F and G glycoproteins promote membrane fusion with human, mouse, and hamster target cells using a different, yet unknown, receptor than Nipah virus (NiV) and Hendra virus (HeV) and that NiV- and HeV-elicited monoclonal and polyclonal antibodies do not cross-react with LayV F and G. We determined cryoelectron microscopy structures of LayV F, in the prefusion and postfusion states, and of LayV G, revealing their conformational landscape and distinct antigenicity relative to NiV and HeV. We computationally designed stabilized LayV G constructs and demonstrate the generalizability of an HNV F prefusion-stabilization strategy. Our data will support the development of vaccines and therapeutics against LayV and closely related HNVs.
    MeSH term(s) Humans ; Animals ; Mice ; Cryoelectron Microscopy ; Nipah Virus ; Hendra Virus ; Glycoproteins ; Henipavirus Infections ; Virus Internalization ; Henipavirus
    Chemical Substances Glycoproteins
    Language English
    Publishing date 2024-04-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2314990121
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  7. Article ; Online: Time-Resolved Photoionization Detection of a Single Er

    Hu, Guangchong / de Boo, Gabriele G / Johnson, Brett Cameron / McCallum, Jeffrey Colin / Sellars, Matthew J / Yin, Chunming / Rogge, Sven

    Nano letters

    2022  Volume 22, Issue 1, Page(s) 396–401

    Abstract: The detection of charge trap ionization induced by resonant excitation enables spectroscopy on single ... ...

    Abstract The detection of charge trap ionization induced by resonant excitation enables spectroscopy on single Er
    Language English
    Publishing date 2022-01-03
    Publishing country United States
    Document type Journal Article
    ISSN 1530-6992
    ISSN (online) 1530-6992
    DOI 10.1021/acs.nanolett.1c04072
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  8. Article ; Online: Correction to "Time-Resolved Photoionization Detection of a Single Er

    Hu, Guangchong / de Boo, Gabriele G / Johnson, Brett Cameron / McCallum, Jeffrey Colin / Sellars, Matthew J / Yin, Chunming / Rogge, Sven

    Nano letters

    2022  Volume 22, Issue 3, Page(s) 1456

    Language English
    Publishing date 2022-01-28
    Publishing country United States
    Document type Published Erratum
    ISSN 1530-6992
    ISSN (online) 1530-6992
    DOI 10.1021/acs.nanolett.2c00173
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  9. Article ; Online: The Dynamic Structures of the Type IV Pilus.

    McCallum, Matthew / Burrows, Lori L / Howell, P Lynne

    Microbiology spectrum

    2019  Volume 7, Issue 2

    Abstract: Type IV pilus (T4P)-like systems have been identified in almost every major phylum of prokaryotic life. They include the type IVa pilus (T4aP), type II secretion system (T2SS), type IVb pilus (T4bP), Tad/Flp pilus, Com pilus, and archaeal flagellum ( ... ...

    Abstract Type IV pilus (T4P)-like systems have been identified in almost every major phylum of prokaryotic life. They include the type IVa pilus (T4aP), type II secretion system (T2SS), type IVb pilus (T4bP), Tad/Flp pilus, Com pilus, and archaeal flagellum (archaellum). These systems are used for adhesion, natural competence, phage adsorption, folded-protein secretion, surface sensing, swimming motility, and twitching motility. The T4aP allows for all of these functions except swimming and is therefore a good model system for understanding T4P-like systems. Recent structural analyses have revolutionized our understanding of how the T4aP machinery assembles and functions. Here we review the structure and function of the T4aP.
    MeSH term(s) Fimbriae Proteins/chemistry ; Fimbriae Proteins/metabolism ; Fimbriae, Bacterial/chemistry ; Fimbriae, Bacterial/metabolism ; Flagella/chemistry ; Flagella/metabolism ; Protein Transport ; Type II Secretion Systems
    Chemical Substances Type II Secretion Systems ; Fimbriae Proteins (147680-16-8)
    Language English
    Publishing date 2019-02-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ISSN 2165-0497
    ISSN (online) 2165-0497
    DOI 10.1128/microbiolspec.PSIB-0006-2018
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  10. Article: Closing coronavirus spike glycoproteins by structure-guided design.

    McCallum, Matthew / Walls, Alexandra C / Corti, Davide / Veesler, David

    bioRxiv : the preprint server for biology

    2020  

    Abstract: The recent spillover of SARS-CoV-2 in the human population resulted in the ongoing COVID-19 pandemic which has already caused 4.9 million infections and more than 326,000 fatalities. To initiate infection the SARS-CoV-2 spike (S) glycoprotein promotes ... ...

    Abstract The recent spillover of SARS-CoV-2 in the human population resulted in the ongoing COVID-19 pandemic which has already caused 4.9 million infections and more than 326,000 fatalities. To initiate infection the SARS-CoV-2 spike (S) glycoprotein promotes attachment to the host cell surface, determining host and tissue tropism, and fusion of the viral and host membranes. Although SARS-CoV-2 S is the main target of neutralizing antibodies and the focus of vaccine design, its stability and conformational dynamics are limiting factors for developing countermeasures against this virus. We report here the design of a prefusion SARS-CoV-2 S ectodomain trimer construct covalently stabilized in the closed conformation. Structural and antigenicity analysis showed we successfully shut S in the closed state without otherwise altering its architecture. Finally, we show that this engineering strategy is applicable to other β-coronavirus S glycoproteins and might become an important tool for vaccine design, structural biology, serology and immunology studies.
    Keywords covid19
    Language English
    Publishing date 2020-06-03
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2020.06.03.129817
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

To top