Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

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Transformer-based methods for novel active chemical compounds

2019/35/N/ST6/02125

Keywords:

deep learning neural networks cheminformatics chemical compounds generation graph convolutional neural networks transformer architecture self-attention mechanism reinforcement learning

Descriptors:

  • ST6_011:
  • ST6_007:

Panel:

ST6 - Computer science and informatics: informatics and information systems, computer science, scientific computing, intelligent systems

Host institution :

Uniwersytet Jagielloński, Wydział Matematyki i Informatyki

woj. małopolskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

Łukasz Andrzej Maziarka 

Number of co-investigators in the project: 3

Call: PRELUDIUM 18 - announced on 2019-09-16

Amount awarded: 94 332 PLN

Project start date (Y-m-d): 2020-08-10

Project end date (Y-m-d): 2024-01-09

Project duration:: 41 months (the same as in the proposal)

Project status: Project settled

Project description

Download the project description in a pdf file

Note - project descriptions were prepared by the authors of the applications themselves and placed in the system in an unchanged form.

Information in the final report

  • Publication in academic press/journals (4)
  • Articles in post-conference publications (8)
  1. Relative molecule self-attention transformer
    Authors:
    Łukasz Maziarka, Dawid Majchrowski, Tomasz Danel, Piotr Gaiński, Jacek Tabor, Igor Podolak, Paweł Morkisz, Stanisław Jastrzębski
    Academic press:
    Journal of Cheminformatics (rok: 2024, tom: 16, strony: 3), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1186/s13321-023-00789-7 - link to the publication
  2. Extended study on atomic featurization in graph neural networks for molecular property prediction
    Authors:
    Agnieszka Wojtuch, Tomasz Danel, Sabina Podlewska, Łukasz Maziarka
    Academic press:
    Journal of Cheminformatics (rok: 2023, tom: 15, strony: 81), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1186/s13321-023-00751-7 - link to the publication
  3. Multi-Label Conditional Generation From Pre-Trained Models
    Authors:
    Magdalena Proszewska, Maciej Wołczyk, Maciej Zieba, Patryk Wielopolski, Łukasz Maziarka, Marek Śmieja
    Academic press:
    IEEE Transactions on Pattern Analysis and Machine Intelligence (rok: 2024, tom: Early Access, strony: 45671), Wydawca: IEEE
    Status:
    Published
    DOI:
    10.1109/TPAMI.2024.3382008 - link to the publication
  4. Extended study on atomic featurization in graph neural networks for molecular property prediction
    Authors:
    Agnieszka Wojtuch, Tomasz Danel, Sabina Podlewska, Łukasz Maziarka
    Academic press:
    Journal of Cheminformatics (rok: 2023, tom: 15, strony: 81), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1186/s13321-023-00751-7 - link to the publication
  1. Spatial Graph Convolutional Networks
    Authors:
    Tomasz Danel; Przemysław Spurek; Jacek Tabor; Marek Śmieja; Łukasz Struski; Agnieszka Słowik; Łukasz Maziarka
    Conference:
    International Conference on Neural Information Processing 2020 (rok: 2020, tom: ICONIP 2020, strony: 668-675), Wydawca: Springer, Cham
    Data:
    konferencja 18-22.11.2020
    Status:
    Published
    DOI:
    10.1007/978-3-030-63823-8_76 - link to the publication
  2. On the relationship between disentanglement and multi-task learning
    Authors:
    Łukasz Maziarka, Aleksandra Nowak, Maciej Wołczyk, Andrzej Bedychaj
    Conference:
    Machine Learning and Knowledge Discovery in Databases, European Conference, ECML PKDD 2022, Grenoble, France, September 19–23, 2022, Proceedings, Part I (rok: 2023, tom: Machine Learning and Knowledge Discovery in Databases. ECML PKDD 2022., strony: 625–641), Wydawca: Springer, Cham
    Data:
    konferencja 19-23.09.2022
    Status:
    Published
    DOI:
    10.1007/978-3-031-26387-3_38 - link to the publication
  3. Multitask Learning Using BERT with Task-Embedded Attention
    Authors:
    Łukasz Maziarka; Tomasz Danel
    Conference:
    2021 International Joint Conference on Neural Networks (IJCNN) (rok: 2021, tom: IJCNN 2021, strony: ), Wydawca: IEEE
    Data:
    konferencja 18-22.07.2021
    Status:
    Published
    DOI:
    10.1109/IJCNN52387.2021.9533990 - link to the publication
  4. Comparison of Atom Representations in Graph Neural Networks for Molecular Property Prediction
    Authors:
    Agnieszka Pocha; Tomasz Danel; Sabina Podlewska; Jacek Tabor; Łukasz Maziarka
    Conference:
    2021 International Joint Conference on Neural Networks (IJCNN) (rok: 2021, tom: IJCNN 2021, strony: ), Wydawca: IEEE
    Data:
    konferencja 18-22.07.2021
    Status:
    Published
    DOI:
    10.1109/IJCNN52387.2021.9533698 - link to the publication
  5. Spatial Graph Convolutional Networks
    Authors:
    Tomasz Danel; Przemysław Spurek; Jacek Tabor; Marek Śmieja; Łukasz Struski; Agnieszka Słowik; Łukasz Maziarka
    Conference:
    International Conference on Neural Information Processing 2020 (rok: 2020, tom: ICONIP 2020, strony: 668-675), Wydawca: Springer, Cham
    Data:
    konferencja 18-22.11.2020
    Status:
    Published
    DOI:
    10.1007/978-3-030-63823-8_76 - link to the publication
  6. PluGeN: Multi-Label Conditional Generation From Pre-Trained Models
    Authors:
    Maciej Wołczyk; Magdalena Proszewska; Łukasz Maziarka; Maciej Zieba; Patryk Wielopolski; Rafał Kurczab; Marek Śmieja
    Conference:
    The Thirty-Sixth AAAI Conference on Artificial Intelligence (AAAI-21) (rok: 2022, tom: AAAI 2022, strony: 8647-8656), Wydawca: Association for the Advancement of Artificial Intelligence
    Data:
    konferencja 22.02.2022 - 01.03.2022
    Status:
    Published
    DOI:
    10.1609/aaai.v36i8.20843 - link to the publication
  7. HuggingMolecules: An Open-Source Library for Transformer-Based Molecular Property Prediction
    Authors:
    Piotr Gaiński; Łukasz Maziarka; Tomasz Danel; Stanisław Jastrzębski
    Conference:
    The Thirty-Sixth AAAI Conference on Artificial Intelligence (AAAI-21) (Student Abstract) (rok: 2022, tom: AAAI 2022, strony: 12949-12950), Wydawca: Association for the Advancement of Artificial Intelligence
    Data:
    konferencja 22.02.2022 - 01.03.2022
    Status:
    Published
    DOI:
    10.1609/aaai.v36i11.21611 - link to the publication
  8. On the relationship between disentanglement and multi-task learning
    Authors:
    Łukasz Maziarka, Aleksandra Nowak, Maciej Wołczyk, Andrzej Bedychaj
    Conference:
    Machine Learning and Knowledge Discovery in Databases, European Conference, ECML PKDD 2022, Grenoble, France, September 19–23, 2022, Proceedings, Part I (rok: 2023, tom: Machine Learning and Knowledge Discovery in Databases. ECML PKDD 2022., strony: 625–641), Wydawca: Springer, Cham
    Data:
    konferencja 19-23.09.2022
    Status:
    Published
    DOI:
    10.1007/978-3-031-26387-3_38 - link to the publication

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