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ORCIDBibTeX records: Esben Jannik Bjerrum
@article{DBLP:journals/jcamd/BjerrumMBKC23,
author = {Esben Jannik Bjerrum and
Christian Margreitter and
Thomas Blaschke and
Simona Kolarova and
Raquel Lopez{-}Rios de Castro},
title = {Faster and more diverse de novo molecular optimization with double-loop
reinforcement learning using augmented {SMILES}},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {8},
pages = {373--394},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00512-6},
doi = {10.1007/S10822-023-00512-6},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BjerrumMBKC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/HeNTCPBE22,
author = {Jiazhen He and
Eva Nittinger and
Christian Tyrchan and
Werngard Czechtizky and
Atanas Patronov and
Esben Jannik Bjerrum and
Ola Engkvist},
title = {Transformer-based molecular optimization beyond matched molecular
pairs},
journal = {J. Cheminformatics},
volume = {14},
number = {1},
pages = {18},
year = {2022},
url = {https://doi.org/10.1186/s13321-022-00599-3},
doi = {10.1186/S13321-022-00599-3},
timestamp = {Wed, 27 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/HeNTCPBE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/SundinVXPBHPKE22,
author = {Iiris Sundin and
Alexey Voronov and
Haoping Xiao and
Kostas Papadopoulos and
Esben Jannik Bjerrum and
Markus Heinonen and
Atanas Patronov and
Samuel Kaski and
Ola Engkvist},
title = {Human-in-the-loop assisted de novo molecular design},
journal = {J. Cheminformatics},
volume = {14},
number = {1},
pages = {86},
year = {2022},
url = {https://doi.org/10.1186/s13321-022-00667-8},
doi = {10.1186/S13321-022-00667-8},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/SundinVXPBHPKE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/FialkovaZPEBKP22,
author = {Vendy Fialkov{\'{a}} and
Jiaxi Zhao and
Kostas Papadopoulos and
Ola Engkvist and
Esben Jannik Bjerrum and
Thierry Kogej and
Atanas Patronov},
title = {LibINVENT: Reaction-based Generative Scaffold Decoration for \emph{in
Silico} Library Design},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {9},
pages = {2046--2063},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.1c00469},
doi = {10.1021/ACS.JCIM.1C00469},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/FialkovaZPEBKP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/MercadoBE22,
author = {Roc{\'{\i}}o Mercado and
Esben Jannik Bjerrum and
Ola Engkvist},
title = {Exploring Graph Traversal Algorithms in Graph-Based Molecular Generation},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {9},
pages = {2093--2100},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.1c00777},
doi = {10.1021/ACS.JCIM.1C00777},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/MercadoBE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mlst/GenhedenEB22,
author = {Samuel Genheden and
Ola Engkvist and
Esben Jannik Bjerrum},
title = {Fast prediction of distances between synthetic routes with deep learning},
journal = {Mach. Learn. Sci. Technol.},
volume = {3},
number = {1},
pages = {15018},
year = {2022},
url = {https://doi.org/10.1088/2632-2153/ac4a91},
doi = {10.1088/2632-2153/AC4A91},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mlst/GenhedenEB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mlst/IrwinDHB22,
author = {Ross Irwin and
Spyridon Dimitriadis and
Jiazhen He and
Esben Jannik Bjerrum},
title = {Chemformer: a pre-trained transformer for computational chemistry},
journal = {Mach. Learn. Sci. Technol.},
volume = {3},
number = {1},
pages = {15022},
year = {2022},
url = {https://doi.org/10.1088/2632-2153/ac3ffb},
doi = {10.1088/2632-2153/AC3FFB},
timestamp = {Mon, 26 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mlst/IrwinDHB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bigdataconf/SvenssonBTEC22,
author = {Hampus Gummesson Svensson and
Esben Jannik Bjerrum and
Christian Tyrchan and
Ola Engkvist and
Morteza Haghir Chehreghani},
editor = {Shusaku Tsumoto and
Yukio Ohsawa and
Lei Chen and
Dirk Van den Poel and
Xiaohua Hu and
Yoichi Motomura and
Takuya Takagi and
Lingfei Wu and
Ying Xie and
Akihiro Abe and
Vijay Raghavan},
title = {Autonomous Drug Design with Multi-Armed Bandits},
booktitle = {{IEEE} International Conference on Big Data, Big Data 2022, Osaka,
Japan, December 17-20, 2022},
pages = {5584--5592},
publisher = {{IEEE}},
year = {2022},
url = {https://doi.org/10.1109/BigData55660.2022.10020357},
doi = {10.1109/BIGDATA55660.2022.10020357},
timestamp = {Fri, 18 Aug 2023 17:39:03 +0200},
biburl = {https://dblp.org/rec/conf/bigdataconf/SvenssonBTEC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2207-01393,
author = {Hampus Gummesson Svensson and
Esben Jannik Bjerrum and
Christian Tyrchan and
Ola Engkvist and
Morteza Haghir Chehreghani},
title = {Autonomous Drug Design with Multi-armed Bandits},
journal = {CoRR},
volume = {abs/2207.01393},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2207.01393},
doi = {10.48550/ARXIV.2207.01393},
eprinttype = {arXiv},
eprint = {2207.01393},
timestamp = {Wed, 06 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2207-01393.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2210-12458,
author = {Esben Jannik Bjerrum and
Christian Margreitter and
Thomas Blaschke and
Raquel Lopez{-}Rios de Castro},
title = {Faster and more diverse de novo molecular optimization with double-loop
reinforcement learning using augmented {SMILES}},
journal = {CoRR},
volume = {abs/2210.12458},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2210.12458},
doi = {10.48550/ARXIV.2210.12458},
eprinttype = {arXiv},
eprint = {2210.12458},
timestamp = {Fri, 28 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2210-12458.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/HeYSNBTCE21,
author = {Jiazhen He and
Huifang You and
Emil Sandstr{\"{o}}m and
Eva Nittinger and
Esben Jannik Bjerrum and
Christian Tyrchan and
Werngard Czechtizky and
Ola Engkvist},
title = {Molecular optimization by capturing chemist's intuition using deep
neural networks},
journal = {J. Cheminformatics},
volume = {13},
number = {1},
pages = {26},
year = {2021},
url = {https://doi.org/10.1186/s13321-021-00497-0},
doi = {10.1186/S13321-021-00497-0},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/HeYSNBTCE21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/GenhedenEB21,
author = {Samuel Genheden and
Ola Engkvist and
Esben Jannik Bjerrum},
title = {Clustering of Synthetic Routes Using Tree Edit Distance},
journal = {J. Chem. Inf. Model.},
volume = {61},
number = {8},
pages = {3899--3907},
year = {2021},
url = {https://doi.org/10.1021/acs.jcim.1c00232},
doi = {10.1021/ACS.JCIM.1C00232},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/GenhedenEB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mlst/BjerrumTE21,
author = {Esben Jannik Bjerrum and
Amol Thakkar and
Ola Engkvist},
title = {Artificial applicability labels for improving policies in retrosynthesis
prediction},
journal = {Mach. Learn. Sci. Technol.},
volume = {2},
number = {1},
pages = {17001},
year = {2021},
url = {https://doi.org/10.1088/2632-2153/abcf90},
doi = {10.1088/2632-2153/ABCF90},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mlst/BjerrumTE21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mlst/MercadoRLKECB21,
author = {Roc{\'{\i}}o Mercado and
Tobias Rastemo and
Edvard Lindel{\"{o}}f and
G{\"{u}}nter Klambauer and
Ola Engkvist and
Hongming Chen and
Esben Jannik Bjerrum},
title = {Graph networks for molecular design},
journal = {Mach. Learn. Sci. Technol.},
volume = {2},
number = {2},
pages = {25023},
year = {2021},
url = {https://doi.org/10.1088/2632-2153/abcf91},
doi = {10.1088/2632-2153/ABCF91},
timestamp = {Fri, 16 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/mlst/MercadoRLKECB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/Arus-PousPBTRCE20,
author = {Josep Ar{\'{u}}s{-}Pous and
Atanas Patronov and
Esben Jannik Bjerrum and
Christian Tyrchan and
Jean{-}Louis Reymond and
Hongming Chen and
Ola Engkvist},
title = {SMILES-based deep generative scaffold decorator for de-novo drug design},
journal = {J. Cheminformatics},
volume = {12},
number = {1},
pages = {38},
year = {2020},
url = {https://doi.org/10.1186/s13321-020-00441-8},
doi = {10.1186/S13321-020-00441-8},
timestamp = {Fri, 16 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/Arus-PousPBTRCE20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/GenhedenTCREB20,
author = {Samuel Genheden and
Amol Thakkar and
Veronika Chadimov{\'{a}} and
Jean{-}Louis Reymond and
Ola Engkvist and
Esben Jannik Bjerrum},
title = {AiZynthFinder: a fast, robust and flexible open-source software for
retrosynthetic planning},
journal = {J. Cheminformatics},
volume = {12},
number = {1},
pages = {70},
year = {2020},
url = {https://doi.org/10.1186/s13321-020-00472-1},
doi = {10.1186/S13321-020-00472-1},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/GenhedenTCREB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/natmi/KotsiasACETB20,
author = {Panagiotis{-}Christos Kotsias and
Josep Ar{\'{u}}s{-}Pous and
Hongming Chen and
Ola Engkvist and
Christian Tyrchan and
Esben Jannik Bjerrum},
title = {Direct steering of de novo molecular generation with descriptor conditional
recurrent neural networks},
journal = {Nat. Mach. Intell.},
volume = {2},
number = {5},
pages = {254--265},
year = {2020},
url = {https://doi.org/10.1038/s42256-020-0174-5},
doi = {10.1038/S42256-020-0174-5},
timestamp = {Fri, 16 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/natmi/KotsiasACETB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/Arus-PousJPBTRC19,
author = {Josep Ar{\'{u}}s{-}Pous and
Simon Johansson and
Oleksii Prykhodko and
Esben Jannik Bjerrum and
Christian Tyrchan and
Jean{-}Louis Reymond and
Hongming Chen and
Ola Engkvist},
title = {Randomized {SMILES} strings improve the quality of molecular generative
models},
journal = {J. Cheminformatics},
volume = {11},
number = {1},
pages = {71:1--71:13},
year = {2019},
url = {https://doi.org/10.1186/s13321-019-0393-0},
doi = {10.1186/S13321-019-0393-0},
timestamp = {Fri, 16 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/Arus-PousJPBTRC19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/PrykhodkoJKABEC19,
author = {Oleksii Prykhodko and
Simon Johansson and
Panagiotis{-}Christos Kotsias and
Josep Ar{\'{u}}s{-}Pous and
Esben Jannik Bjerrum and
Ola Engkvist and
Hongming Chen},
title = {A de novo molecular generation method using latent vector based generative
adversarial network},
journal = {J. Cheminformatics},
volume = {11},
number = {1},
pages = {74},
year = {2019},
url = {https://doi.org/10.1186/s13321-019-0397-9},
doi = {10.1186/S13321-019-0397-9},
timestamp = {Fri, 16 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/PrykhodkoJKABEC19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/SattarovBHMBV19,
author = {Boris Sattarov and
Igor I. Baskin and
Dragos Horvath and
Gilles Marcou and
Esben Jannik Bjerrum and
Alexandre Varnek},
title = {De Novo Molecular Design by Combining Deep Autoencoder Recurrent Neural
Networks with Generative Topographic Mapping},
journal = {J. Chem. Inf. Model.},
volume = {59},
number = {3},
pages = {1182--1196},
year = {2019},
url = {https://doi.org/10.1021/acs.jcim.8b00751},
doi = {10.1021/ACS.JCIM.8B00751},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/SattarovBHMBV19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icann/ThakkarBER19,
author = {Amol Thakkar and
Esben Jannik Bjerrum and
Ola Engkvist and
Jean{-}Louis Reymond},
editor = {Igor V. Tetko and
Vera Kurkov{\'{a}} and
Pavel Karpov and
Fabian J. Theis},
title = {Neural Network Guided Tree-Search Policies for Synthesis Planning},
booktitle = {Artificial Neural Networks and Machine Learning - {ICANN} 2019 - 28th
International Conference on Artificial Neural Networks, Munich, Germany,
September 17-19, 2019, Proceedings - Workshop and Special Sessions},
series = {Lecture Notes in Computer Science},
volume = {11731},
pages = {721--724},
publisher = {Springer},
year = {2019},
url = {https://doi.org/10.1007/978-3-030-30493-5\_64},
doi = {10.1007/978-3-030-30493-5\_64},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icann/ThakkarBER19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icann/Arus-PousJPBTRC19,
author = {Josep Ar{\'{u}}s{-}Pous and
Simon Johansson and
Oleksii Prykhodko and
Esben Jannik Bjerrum and
Christian Tyrchan and
Jean{-}Louis Reymond and
Hongming Chen and
Ola Engkvist},
editor = {Igor V. Tetko and
Vera Kurkov{\'{a}} and
Pavel Karpov and
Fabian J. Theis},
title = {Improving Deep Generative Models with Randomized {SMILES}},
booktitle = {Artificial Neural Networks and Machine Learning - {ICANN} 2019 - 28th
International Conference on Artificial Neural Networks, Munich, Germany,
September 17-19, 2019, Proceedings - Workshop and Special Sessions},
series = {Lecture Notes in Computer Science},
volume = {11731},
pages = {747--751},
publisher = {Springer},
year = {2019},
url = {https://doi.org/10.1007/978-3-030-30493-5\_68},
doi = {10.1007/978-3-030-30493-5\_68},
timestamp = {Fri, 16 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icann/Arus-PousJPBTRC19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1806-09300,
author = {Esben Jannik Bjerrum},
title = {Improving Chemical Autoencoder Latent Space and Molecular De novo
Generation Diversity with Heteroencoders},
journal = {CoRR},
volume = {abs/1806.09300},
year = {2018},
url = {http://arxiv.org/abs/1806.09300},
eprinttype = {arXiv},
eprint = {1806.09300},
timestamp = {Sat, 23 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1806-09300.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/BjerrumJT17,
author = {Esben Jannik Bjerrum and
Jan H. Jensen and
Jakob L. Tolborg},
title = {pICalculax: Improved Prediction of Isoelectric Point for Modified
Peptides},
journal = {J. Chem. Inf. Model.},
volume = {57},
number = {8},
pages = {1723--1727},
year = {2017},
url = {https://doi.org/10.1021/acs.jcim.7b00030},
doi = {10.1021/ACS.JCIM.7B00030},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/BjerrumJT17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/Bjerrum17,
author = {Esben Jannik Bjerrum},
title = {{SMILES} Enumeration as Data Augmentation for Neural Network Modeling
of Molecules},
journal = {CoRR},
volume = {abs/1703.07076},
year = {2017},
url = {http://arxiv.org/abs/1703.07076},
eprinttype = {arXiv},
eprint = {1703.07076},
timestamp = {Sat, 23 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/Bjerrum17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/BjerrumT17,
author = {Esben Jannik Bjerrum and
Richard Threlfall},
title = {Molecular Generation with Recurrent Neural Networks (RNNs)},
journal = {CoRR},
volume = {abs/1705.04612},
year = {2017},
url = {http://arxiv.org/abs/1705.04612},
eprinttype = {arXiv},
eprint = {1705.04612},
timestamp = {Sat, 23 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/BjerrumT17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1710-01927,
author = {Esben Jannik Bjerrum and
Mads Glahder and
Thomas Skov},
title = {Data Augmentation of Spectral Data for Convolutional Neural Network
{(CNN)} Based Deep Chemometrics},
journal = {CoRR},
volume = {abs/1710.01927},
year = {2017},
url = {http://arxiv.org/abs/1710.01927},
eprinttype = {arXiv},
eprint = {1710.01927},
timestamp = {Sat, 23 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1710-01927.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1712-09553,
author = {Esben Jannik Bjerrum},
title = {DeepIEP: a Peptide Sequence Model of Isoelectric Point (IEP/pI) using
Recurrent Neural Networks (RNNs)},
journal = {CoRR},
volume = {abs/1712.09553},
year = {2017},
url = {http://arxiv.org/abs/1712.09553},
eprinttype = {arXiv},
eprint = {1712.09553},
timestamp = {Sat, 23 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1712-09553.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/Bjerrum16,
author = {Esben Jannik Bjerrum},
title = {Machine learning optimization of cross docking accuracy},
journal = {Comput. Biol. Chem.},
volume = {62},
pages = {133--144},
year = {2016},
url = {https://doi.org/10.1016/j.compbiolchem.2016.04.005},
doi = {10.1016/J.COMPBIOLCHEM.2016.04.005},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/candc/Bjerrum16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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