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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Zanzotto, F. M.; Onorati, D.; Tommasino, P.; Santilli, A.; +2 Authors
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Archivio della ricer...arrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Archivio della ricer...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Sanne van der Linden; Rita Sevastjanova; Mathias Funk; Mennatallah El-Assady;

    Healthcare systems are under pressure from an aging population, rising costs, and increasingly complex conditions and treatments. Although data are determined to play a bigger role in how doctors diagnose and prescribe treatments, they struggle due to a lack of time and an abundance of structured and unstructured information. To address this challenge, we introduce MediCoSpace, a visual decision-support tool for more efficient doctor-patient consultations. The tool links patient reports to past and present diagnoses, diseases, drugs, and treatments, both for the current patient and other patients in comparable situations. MediCoSpace uses textual medical data, deep-learning supported text analysis and concept spaces to facilitate a visual discovery process. The tool is evaluated by five medical doctors. The results show that MediCoSpace facilitates a promising, yet complex way to discover unlikely relations and thus suggests a path toward the development of interactive visual tools to provide physicians with more holistic diagnoses and personalized, dynamic treatments for patients. ACM Transactions on Management Information Systems, 14 (2) ISSN:2158-656X ISSN:2158-6578

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    Research Collection
    Article . 2023
    License: CC BY
    ACM Transactions on Management Information Systems
    Article . 2023 . Peer-reviewed
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      Article . 2023
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      Article . 2023 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Jensen, Lars Juhl; Gorodkin, Jan;

    TISSUES is a weekly updated web resource that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. We map all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unify it by assigning confidence scores that facilitate comparison of the different types and sources of evidence. We finally visualize these scores on a schematic human body to provide a convenient overview.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ bio.toolsarrow_drop_down
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    bio.tools
    Software . 2018
    License: CC-BY-4.0
    Data sources: bio.tools
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ bio.toolsarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      bio.tools
      Software . 2018
      License: CC-BY-4.0
      Data sources: bio.tools
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Jensen, Lars Juhl;

    COMPARTMENTS is a weekly updated web resource that integrates evidence on protein subcellular localization from manually curated literature, high-throughput screens, automatic text mining, and sequence-based prediction methods. We map all evidence to common protein identifiers and Gene Ontology terms, and further unify it by assigning confidence scores that facilitate comparison of the different types and sources of evidence and visualize these scores on a schematic cell.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ bio.toolsarrow_drop_down
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    bio.tools
    Software . 2018
    License: CC-BY-4.0
    Data sources: bio.tools
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ bio.toolsarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      bio.tools
      Software . 2018
      License: CC-BY-4.0
      Data sources: bio.tools
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Scheffel, Maren; Niemann, Katja; Leon Rojas, Sarah; Drachsler, Hendrik; +3 Authors

    The amount of literature within a research domain is ever growing, thus making it difficult to stay on top of everything. Getting a grasp on the important topics of and areas within a domain or even knowing where to start is often tough and tedious. This paper therefore presents a visualization, that is a cluster spiral, that offers a fast but plain and simple way of exploring the content of large text collections.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ NARCISarrow_drop_down
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Scheffel, Maren; Niemann, Katja; Leon Rojas, Sarah; Drachsler, Hendrik; +1 Authors

    The amount of literature within a research domain is ever growing, thus making it difficult to stay on top of everything. Getting a grasp on the important topics of and areas within a domain or even knowing where to start is often tough and tedious. This paper therefore presents a visualization, that is a cluster spiral, that offers a fast but plain and simple way of exploring the content of large text collections.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Open University of t...arrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Open University of t...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Sorger, Peter;

    Interactive pathway modeling using natural language with automated assembly.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ bio.toolsarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    bio.tools
    Software . 2019
    License: BSD-2-Clause
    Data sources: bio.tools
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ bio.toolsarrow_drop_down
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      bio.tools
      Software . 2019
      License: BSD-2-Clause
      Data sources: bio.tools
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/

    The amount of literature within a research domain is ever growing, thus making it difficult to stay on top of everything. Getting a grasp on the important topics of and areas within a domain or even knowing where to start is often tough and tedious. This paper therefore presents a visualization, that is a cluster spiral, that offers a fast but plain and simple way of exploring the content of large text collections.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ NARCISarrow_drop_down
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    NARCIS
    Conference object . 2014
    Data sources: NARCIS
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      Conference object . 2014
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Bogaert, Jérémie; Jean, Emmanuël; De Bodt, Cyril; Standaert, François-Xavier;

    Since their release, transformers, and in particular fine-tuned transformers are widely used for text related classification tasks. However, only a few studies try to understand how fine-tuning actually works and existing alternatives, such as feature-based transformers, are often overlooked. In this work, we study a French transformer model, CamemBERT, to compare the fine-tuned and feature-based approaches in terms of their performances, interpretability and embedding space. We observe that while fine-tuning has a limited impact on performances in our case study, it significantly affects the intepretability (by better isolating words that are intuitively connected to the classification task) and embedding space (by summarizing the majority of the relevant information into a fewer dimensions) of the results. We conclude by highlighting open questions regarding the generalization potential of fine-tuned embeddings.

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    https://doi.org/10.14428/esann...
    Conference object . 2023 . Peer-reviewed
    Data sources: Crossref
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      https://doi.org/10.14428/esann...
      Conference object . 2023 . Peer-reviewed
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  • Authors: Louis-Alexandre Dit Petit-Frere, Judith;

    In recent years, the importance of Natural Language Processing has been increasing with more and more fields of application. The word representations, such as word embedding or transformer models, used to transcribe the language are trained using large text corpora that may include stereotypes. These stereotypes may be learned by Natural Language Processing algorithms and lead to biases in their results. Extensive research has been performed on the detection, repair and visualization of the biases in the field of Natural Language Processing. Nevertheless, the methods developed so far mostly focus on word embeddings, or direct and binary biases.To fill the research gap regarding multi-class indirect biases learned by transformer models, this thesis proposes new visualisation interfaces to explore indirect and multi-class biases learned by BERT and XLNet models. These visualisations are based on an indirect quantitative method to measure the potential biases encapsulated in transformer models, the Indirect Logarithmic Probability Bias Score. This metric is adapted from an existing one, to enable the investigation of indirect biases. The evaluation of our new indirect method shows that it enables to reveal known biases and to discover new insights which could not be found using the direct method. Moreover, the user study performed on our visualization interfaces demonstrates that the visualizations supports the exploration of multi-class indirect biases, even though improvements may be needed to fully assist the investigation of the sources of the biases.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Zanzotto, F. M.; Onorati, D.; Tommasino, P.; Santilli, A.; +2 Authors
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    Authors: Sanne van der Linden; Rita Sevastjanova; Mathias Funk; Mennatallah El-Assady;

    Healthcare systems are under pressure from an aging population, rising costs, and increasingly complex conditions and treatments. Although data are determined to play a bigger role in how doctors diagnose and prescribe treatments, they struggle due to a lack of time and an abundance of structured and unstructured information. To address this challenge, we introduce MediCoSpace, a visual decision-support tool for more efficient doctor-patient consultations. The tool links patient reports to past and present diagnoses, diseases, drugs, and treatments, both for the current patient and other patients in comparable situations. MediCoSpace uses textual medical data, deep-learning supported text analysis and concept spaces to facilitate a visual discovery process. The tool is evaluated by five medical doctors. The results show that MediCoSpace facilitates a promising, yet complex way to discover unlikely relations and thus suggests a path toward the development of interactive visual tools to provide physicians with more holistic diagnoses and personalized, dynamic treatments for patients. ACM Transactions on Management Information Systems, 14 (2) ISSN:2158-656X ISSN:2158-6578

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    Research Collection
    Article . 2023
    License: CC BY
    ACM Transactions on Management Information Systems
    Article . 2023 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Jensen, Lars Juhl; Gorodkin, Jan;

    TISSUES is a weekly updated web resource that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. We map all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unify it by assigning confidence scores that facilitate comparison of the different types and sources of evidence. We finally visualize these scores on a schematic human body to provide a convenient overview.

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    bio.tools
    Software . 2018
    License: CC-BY-4.0
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      bio.tools
      Software . 2018
      License: CC-BY-4.0
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Jensen, Lars Juhl;

    COMPARTMENTS is a weekly updated web resource that integrates evidence on protein subcellular localization from manually curated literature, high-throughput screens, automatic text mining, and sequence-based prediction methods. We map all evidence to common protein identifiers and Gene Ontology terms, and further unify it by assigning confidence scores that facilitate comparison of the different types and sources of evidence and visualize these scores on a schematic cell.

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    bio.tools
    Software . 2018
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      bio.tools
      Software . 2018
      License: CC-BY-4.0
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Scheffel, Maren; Niemann, Katja; Leon Rojas, Sarah; Drachsler, Hendrik; +3 Authors

    The amount of literature within a research domain is ever growing, thus making it difficult to stay on top of everything. Getting a grasp on the important topics of and areas within a domain or even knowing where to start is often tough and tedious. This paper therefore presents a visualization, that is a cluster spiral, that offers a fast but plain and simple way of exploring the content of large text collections.

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    Authors: Scheffel, Maren; Niemann, Katja; Leon Rojas, Sarah; Drachsler, Hendrik; +1 Authors

    The amount of literature within a research domain is ever growing, thus making it difficult to stay on top of everything. Getting a grasp on the important topics of and areas within a domain or even knowing where to start is often tough and tedious. This paper therefore presents a visualization, that is a cluster spiral, that offers a fast but plain and simple way of exploring the content of large text collections.

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    Authors: Sorger, Peter;

    Interactive pathway modeling using natural language with automated assembly.

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    bio.tools
    Software . 2019
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      bio.tools
      Software . 2019
      License: BSD-2-Clause
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    The amount of literature within a research domain is ever growing, thus making it difficult to stay on top of everything. Getting a grasp on the important topics of and areas within a domain or even knowing where to start is often tough and tedious. This paper therefore presents a visualization, that is a cluster spiral, that offers a fast but plain and simple way of exploring the content of large text collections.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ NARCISarrow_drop_down
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    Conference object . 2014
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