11 Research products

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Research software
2019-2023
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BioVAE
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2022 Shell bio.tools
Authors: Trieu, Hai-Long;
Trieu, Hai-Long;
BioVAE is a pre-trained latent variable language model for biomedical text mining. Large scale pre-trained language models (PLMs) have advanced state-of-the-art (SOTA) performance on various biomedical text mining tasks. The power of such PLMs can be combined with the advantages of deep generative models. These are examples of these combinations. However, they are trained only on general domain text, and biomedical models are still missing. In this work, we describe BioVAE, the first large scale pre-trained latent variable language model for the biomedical domain, which uses the OPTIMUS framework to train on large volumes of biomedical text. The model shows SOTA performance on several biomedical text mining tasks when compared to existing publicly available biomedical PLMs.
bio.toolsarrow_drop_down
bio.tools
Software . 2022
License: Apache-2.0
Data sources: bio.tools
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bio.tools
Software . 2022
License: Apache-2.0
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BERT-Kcr
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2022bio.tools
Authors: Zhu, Xiaolei;
Zhu, Xiaolei;
BERT-Kcr is a tool for prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models.
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bio.tools
Software . 2022
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bio.tools
Software . 2022
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ProtTrans
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2022 Python bio.tools
Authors: Elnaggar, Ahmed; Heinzinger, Michael; Dallago, Christian; Wang, Yu;
Elnaggar, Ahmed; Heinzinger, Michael; Dallago, Christian; Wang, Yu;
ProtTrans is providing state of the art pre-trained models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using various Transformers Models.
bio.toolsarrow_drop_down
bio.tools
Software . 2022
License: AFL-3.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2022
License: AFL-3.0
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VIQoR
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 R bio.tools
Authors: Tsiamis, Vasileios; Schwämmle, Veit;
Tsiamis, Vasileios; Schwämmle, Veit;
VIQoR, is a user-friendly web service for Visually supervised protein Inference and protein Quantification implemented in R. The Shiny web interface integrates the post-identification processes involved in protein inference and relative protein abundance summarization, along with smart and novel interactive visualization modules to support the common researchers with a straight-forward tool for protein quantification, data browsing and data inspection.
bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: Apache-2.0
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bio.tools
Software . 2021
License: Apache-2.0
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ImmunoCluster
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 R bio.tools
Authors: Arnold, James N.; Kordasti, Shahram;
Arnold, James N.; Kordasti, Shahram;
A computational framework for the non-specialist to profile cellular heterogeneity in cytometry datasets. The immunoCluster package uses the scDataViz bioconductor package’s vizualization tools and adaptation of the SingleCellExperiment data structure to build simple and flexible cytometry analysis workflows like those outlined in Nowicka et al. (2017) CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets.
bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: MIT
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: MIT
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DigChem
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019bio.tools
Authors: Lee, Hyunju;
Lee, Hyunju;
Identification of disease-gene-chemical relationships from Medline abstracts.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Unlicense
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Unlicense
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rREST
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 MATLAB bio.tools
Authors: Yao, Dezhong; ValdÃ©s Sosa, Pedro A.;
Yao, Dezhong; ValdÃ©s Sosa, Pedro A.;
Regularized reference electrode standardization technique.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: GPL-3.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: GPL-3.0
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CollaboNet
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 Python bio.tools
Authors: Kang, Jaewoo;
Kang, Jaewoo;
Collaboration of deep neural networks for biomedical named entity recognition.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: MIT
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: MIT
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ODAE
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019bio.tools NIH | Ontology-based Informatio...
NIH| Ontology-based Information Network to Support Vaccine Research
Authors: He, Oliver;
He, Oliver;
Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Unlicense
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Unlicense
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AlvisIR
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 PHP bio.tools EC | OpenMinTeD
EC| OpenMinTeD
Authors: Bossy, Robert;
Bossy, Robert;
Text mining tool for extracting information about microbial biodiversity in food.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Apache-2.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Apache-2.0
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11 Research products

BioVAE
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2022 Shell bio.tools
Authors: Trieu, Hai-Long;
Trieu, Hai-Long;
BioVAE is a pre-trained latent variable language model for biomedical text mining. Large scale pre-trained language models (PLMs) have advanced state-of-the-art (SOTA) performance on various biomedical text mining tasks. The power of such PLMs can be combined with the advantages of deep generative models. These are examples of these combinations. However, they are trained only on general domain text, and biomedical models are still missing. In this work, we describe BioVAE, the first large scale pre-trained latent variable language model for the biomedical domain, which uses the OPTIMUS framework to train on large volumes of biomedical text. The model shows SOTA performance on several biomedical text mining tasks when compared to existing publicly available biomedical PLMs.
bio.toolsarrow_drop_down
bio.tools
Software . 2022
License: Apache-2.0
Data sources: bio.tools
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citeCite
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bio.toolsarrow_drop_down
bio.tools
Software . 2022
License: Apache-2.0
Data sources: bio.tools
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BERT-Kcr
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2022bio.tools
Authors: Zhu, Xiaolei;
Zhu, Xiaolei;
BERT-Kcr is a tool for prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models.
bio.toolsarrow_drop_down
bio.tools
Software . 2022
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2022
Data sources: bio.tools
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ProtTrans
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2022 Python bio.tools
Authors: Elnaggar, Ahmed; Heinzinger, Michael; Dallago, Christian; Wang, Yu;
Elnaggar, Ahmed; Heinzinger, Michael; Dallago, Christian; Wang, Yu;
ProtTrans is providing state of the art pre-trained models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using various Transformers Models.
bio.toolsarrow_drop_down
bio.tools
Software . 2022
License: AFL-3.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2022
License: AFL-3.0
Data sources: bio.tools
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VIQoR
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 R bio.tools
Authors: Tsiamis, Vasileios; Schwämmle, Veit;
Tsiamis, Vasileios; Schwämmle, Veit;
VIQoR, is a user-friendly web service for Visually supervised protein Inference and protein Quantification implemented in R. The Shiny web interface integrates the post-identification processes involved in protein inference and relative protein abundance summarization, along with smart and novel interactive visualization modules to support the common researchers with a straight-forward tool for protein quantification, data browsing and data inspection.
bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: Apache-2.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: Apache-2.0
Data sources: bio.tools
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ImmunoCluster
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 R bio.tools
Authors: Arnold, James N.; Kordasti, Shahram;
Arnold, James N.; Kordasti, Shahram;
A computational framework for the non-specialist to profile cellular heterogeneity in cytometry datasets. The immunoCluster package uses the scDataViz bioconductor package’s vizualization tools and adaptation of the SingleCellExperiment data structure to build simple and flexible cytometry analysis workflows like those outlined in Nowicka et al. (2017) CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets.
bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: MIT
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: MIT
Data sources: bio.tools
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DigChem
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019bio.tools
Authors: Lee, Hyunju;
Lee, Hyunju;
Identification of disease-gene-chemical relationships from Medline abstracts.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Unlicense
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Unlicense
Data sources: bio.tools
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rREST
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 MATLAB bio.tools
Authors: Yao, Dezhong; ValdÃ©s Sosa, Pedro A.;
Yao, Dezhong; ValdÃ©s Sosa, Pedro A.;
Regularized reference electrode standardization technique.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: GPL-3.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: GPL-3.0
Data sources: bio.tools
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CollaboNet
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 Python bio.tools
Authors: Kang, Jaewoo;
Kang, Jaewoo;
Collaboration of deep neural networks for biomedical named entity recognition.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: MIT
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: MIT
Data sources: bio.tools
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ODAE
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019bio.tools NIH | Ontology-based Informatio...
NIH| Ontology-based Information Network to Support Vaccine Research
Authors: He, Oliver;
He, Oliver;
Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Unlicense
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Unlicense
Data sources: bio.tools
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AlvisIR
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 PHP bio.tools EC | OpenMinTeD
EC| OpenMinTeD
Authors: Bossy, Robert;
Bossy, Robert;
Text mining tool for extracting information about microbial biodiversity in food.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Apache-2.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Apache-2.0
Data sources: bio.tools
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Digital Humanities and Cultural Heritage
Knowmad Institut

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Publications
Research software
2019-2023
Open Source
Digital Humanities and Cultural Heritage
Knowmad Institut