DREAMER-S: Deep leaRning-Enabled Attention-based Multiple-instance approaches with Explainable Representations for Spatial biology

M. Rifqi Rafsanjani; Alison Dooney; Rahul Suresh; Alice C. O’Farrell; Monika A. Jarzabek; Liam Shiels; Annette T. Byrne; Jochen H. M. Prehn; Aidan D. Meade

doi:10.1371/journal.pcbi.1013581

Loading metrics

Open Access

Peer-reviewed

DREAMER-S: Deep leaRning-Enabled Attention-based Multiple-instance approaches with Explainable Representations for Spatial biology

M. Rifqi Rafsanjani,

Roles Data curation, Formal analysis, Investigation, Methodology, Software, Visualization, Writing – original draft, Writing – review & editing

Affiliations Radiation and Environmental Science Centre, Physical to Life Sciences Research Hub, Technological University Dublin, Dublin, Ireland, School of Physics, Clinical & Optometric Sciences, Technological University Dublin, Dublin, Ireland
⨯
Alison Dooney,

Roles Software, Writing – original draft, Writing – review & editing

Affiliation School of Physics, Clinical & Optometric Sciences, Technological University Dublin, Dublin, Ireland
⨯
Rahul Suresh,

Roles Software, Writing – original draft, Writing – review & editing

Affiliations Radiation and Environmental Science Centre, Physical to Life Sciences Research Hub, Technological University Dublin, Dublin, Ireland, School of Physics, Clinical & Optometric Sciences, Technological University Dublin, Dublin, Ireland
⨯
Alice C. O’Farrell,

Roles Data curation, Methodology, Project administration, Investigation, Resources, Writing – original draft, Writing – review & editing

Affiliation Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
⨯
Monika A. Jarzabek,

Roles Data curation, Investigation, Writing – original draft, Writing – review & editing

Affiliation Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
⨯
Liam Shiels,

Roles Data curation, Investigation, Writing – original draft, Writing – review & editing

Affiliation Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
⨯
Annette T. Byrne,

Roles Data curation, Funding acquisition, Investigation, Project administration, Supervision, Writing – original draft, Writing – review & editing

Affiliation Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
⨯
Jochen H. M. Prehn,

Roles Conceptualization, Funding acquisition, Investigation, Project administration, Resources, Supervision, Writing – original draft, Writing – review & editing

Affiliation Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
⨯
Aidan D. Meade

Roles Conceptualization, Data curation, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Writing – original draft, Writing – review & editing

* E-mail: aidan.meade@tudublin.ie

Affiliations Radiation and Environmental Science Centre, Physical to Life Sciences Research Hub, Technological University Dublin, Dublin, Ireland, School of Physics, Clinical & Optometric Sciences, Technological University Dublin, Dublin, Ireland

https://orcid.org/0000-0003-0353-9768

⨯

DREAMER-S: Deep leaRning-Enabled Attention-based Multiple-instance approaches with Explainable Representations for Spatial biology

M. Rifqi Rafsanjani,
Alison Dooney,
Rahul Suresh,
Alice C. O’Farrell,
Monika A. Jarzabek,
Liam Shiels,
Annette T. Byrne,
Jochen H. M. Prehn,
Aidan D. Meade

Published: May 26, 2026
https://doi.org/10.1371/journal.pcbi.1013581
See the preprint

Reader Comments (0)

Post a new comment on this article

Subject Areas
?

For more information about PLOS Subject Areas, click here.
We want your feedback. Do these Subject Areas make sense for this article? Click the target next to the incorrect Subject Area and let us know. Thanks for your help!

Amides
Is the Subject Area "Amides" applicable to this article?

Thanks for your feedback.
Apoptosis
Is the Subject Area "Apoptosis" applicable to this article?

Thanks for your feedback.
Infrared spectroscopy
Is the Subject Area "Infrared spectroscopy" applicable to this article?

Thanks for your feedback.
Optimization
Is the Subject Area "Optimization" applicable to this article?

Thanks for your feedback.
Body weight
Is the Subject Area "Body weight" applicable to this article?

Thanks for your feedback.
Deep learning
Is the Subject Area "Deep learning" applicable to this article?

Thanks for your feedback.
Protein expression
Is the Subject Area "Protein expression" applicable to this article?

Thanks for your feedback.
Lipids
Is the Subject Area "Lipids" applicable to this article?

Thanks for your feedback.