Esben Jannik Bjerrum

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 30

Top Topics

Mass Spectrometry

Tree Edit Distance

Top Venues

J. Cheminformatics

J. Chem. Inf. Model.

Mach. Learn. Sci. Technol.

Publications

Janosch Menke, Yasmine Nahal, Esben Jannik Bjerrum, Mikhail Kabeshov, Samuel Kaski, Ola Engkvist
Metis: a python-based user interface to collect expert feedback for generative chemistry models. J. Cheminformatics 16 (1) (2024)
Esben Jannik Bjerrum, Christian Margreitter, Thomas Blaschke, Simona Kolarova, Raquel Lopez-Rios de Castro
Faster and more diverse de novo molecular optimization with double-loop reinforcement learning using augmented SMILES. J. Comput. Aided Mol. Des. 37 (8) (2023)
Rocío Mercado, Esben Jannik Bjerrum, Ola Engkvist
Exploring Graph Traversal Algorithms in Graph-Based Molecular Generation. J. Chem. Inf. Model. 62 (9) (2022)
Hampus Gummesson Svensson, Esben Jannik Bjerrum, Christian Tyrchan, Ola Engkvist, Morteza Haghir Chehreghani
Autonomous Drug Design with Multi-armed Bandits. CoRR (2022)
Ross Irwin, Spyridon Dimitriadis, Jiazhen He, Esben Jannik Bjerrum
Chemformer: a pre-trained transformer for computational chemistry. Mach. Learn. Sci. Technol. 3 (1) (2022)
Samuel Genheden, Ola Engkvist, Esben Jannik Bjerrum
Fast prediction of distances between synthetic routes with deep learning. Mach. Learn. Sci. Technol. 3 (1) (2022)
Esben Jannik Bjerrum, Christian Margreitter, Thomas Blaschke, Raquel Lopez-Rios de Castro
Faster and more diverse de novo molecular optimization with double-loop reinforcement learning using augmented SMILES. CoRR (2022)
Jiazhen He, Eva Nittinger, Christian Tyrchan, Werngard Czechtizky, Atanas Patronov, Esben Jannik Bjerrum, Ola Engkvist
Transformer-based molecular optimization beyond matched molecular pairs. J. Cheminformatics 14 (1) (2022)
Iiris Sundin, Alexey Voronov, Haoping Xiao, Kostas Papadopoulos, Esben Jannik Bjerrum, Markus Heinonen, Atanas Patronov, Samuel Kaski, Ola Engkvist
Human-in-the-loop assisted de novo molecular design. J. Cheminformatics 14 (1) (2022)
Hampus Gummesson Svensson, Esben Jannik Bjerrum, Christian Tyrchan, Ola Engkvist, Morteza Haghir Chehreghani
Autonomous Drug Design with Multi-Armed Bandits. Big Data (2022)
Vendy Fialková, Jiaxi Zhao, Kostas Papadopoulos, Ola Engkvist, Esben Jannik Bjerrum, Thierry Kogej, Atanas Patronov
Library Design. J. Chem. Inf. Model. 62 (9) (2022)
Esben Jannik Bjerrum, Amol Thakkar, Ola Engkvist
Artificial applicability labels for improving policies in retrosynthesis prediction. Mach. Learn. Sci. Technol. 2 (1) (2021)
Rocío Mercado, Tobias Rastemo, Edvard Lindelöf, Günter Klambauer, Ola Engkvist, Hongming Chen, Esben Jannik Bjerrum
Graph networks for molecular design. Mach. Learn. Sci. Technol. 2 (2) (2021)
Samuel Genheden, Ola Engkvist, Esben Jannik Bjerrum
Clustering of Synthetic Routes Using Tree Edit Distance. J. Chem. Inf. Model. 61 (8) (2021)
Jiazhen He, Huifang You, Emil Sandström, Eva Nittinger, Esben Jannik Bjerrum, Christian Tyrchan, Werngard Czechtizky, Ola Engkvist
Molecular optimization by capturing chemist's intuition using deep neural networks. J. Cheminformatics 13 (1) (2021)
Josep Arús-Pous, Atanas Patronov, Esben Jannik Bjerrum, Christian Tyrchan, Jean-Louis Reymond, Hongming Chen, Ola Engkvist
SMILES-based deep generative scaffold decorator for de-novo drug design. J. Cheminformatics 12 (1) (2020)
Panagiotis-Christos Kotsias, Josep Arús-Pous, Hongming Chen, Ola Engkvist, Christian Tyrchan, Esben Jannik Bjerrum
Direct steering of de novo molecular generation with descriptor conditional recurrent neural networks. Nat. Mach. Intell. 2 (5) (2020)
Samuel Genheden, Amol Thakkar, Veronika Chadimová, Jean-Louis Reymond, Ola Engkvist, Esben Jannik Bjerrum
AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning. J. Cheminformatics 12 (1) (2020)
Josep Arús-Pous, Simon Johansson, Oleksii Prykhodko, Esben Jannik Bjerrum, Christian Tyrchan, Jean-Louis Reymond, Hongming Chen, Ola Engkvist
Improving Deep Generative Models with Randomized SMILES. ICANN (Workshop) (2019)
Boris Sattarov, Igor I. Baskin, Dragos Horvath, Gilles Marcou, Esben Jannik Bjerrum, Alexandre Varnek
De Novo Molecular Design by Combining Deep Autoencoder Recurrent Neural Networks with Generative Topographic Mapping. J. Chem. Inf. Model. 59 (3) (2019)
Oleksii Prykhodko, Simon Johansson, Panagiotis-Christos Kotsias, Josep Arús-Pous, Esben Jannik Bjerrum, Ola Engkvist, Hongming Chen
A de novo molecular generation method using latent vector based generative adversarial network. J. Cheminformatics 11 (1) (2019)
Amol Thakkar, Esben Jannik Bjerrum, Ola Engkvist, Jean-Louis Reymond
Neural Network Guided Tree-Search Policies for Synthesis Planning. ICANN (Workshop) (2019)
Josep Arús-Pous, Simon Johansson, Oleksii Prykhodko, Esben Jannik Bjerrum, Christian Tyrchan, Jean-Louis Reymond, Hongming Chen, Ola Engkvist
Randomized SMILES strings improve the quality of molecular generative models. J. Cheminformatics 11 (1) (2019)
Esben Jannik Bjerrum
Improving Chemical Autoencoder Latent Space and Molecular De novo Generation Diversity with Heteroencoders. CoRR (2018)
Esben Jannik Bjerrum
DeepIEP: a Peptide Sequence Model of Isoelectric Point (IEP/pI) using Recurrent Neural Networks (RNNs). CoRR (2017)
Esben Jannik Bjerrum, Jan H. Jensen, Jakob L. Tolborg
pICalculax: Improved Prediction of Isoelectric Point for Modified Peptides. J. Chem. Inf. Model. 57 (8) (2017)
Esben Jannik Bjerrum, Richard Threlfall
Molecular Generation with Recurrent Neural Networks (RNNs). CoRR (2017)
Esben Jannik Bjerrum
SMILES Enumeration as Data Augmentation for Neural Network Modeling of Molecules. CoRR (2017)
Esben Jannik Bjerrum, Mads Glahder, Thomas Skov
Data Augmentation of Spectral Data for Convolutional Neural Network (CNN) Based Deep Chemometrics. CoRR (2017)
Esben Jannik Bjerrum
Machine learning optimization of cross docking accuracy. Comput. Biol. Chem. 62 (2016)