Publications

Patents

1. Processing Multimodal Images of Tissue for Medical Evaluation
   P. Pati, G. Jaume, K. Thandiackal, A. Foncubierta‑Rodríguez, and M. Gabrani
   US Patent App. 17/346,195 (2022)
2. Interpretation of Whole‑slide Images in Digital Pathology
   P. Pati, G. Jaume, A. Foncubierta‑Rodríguez, and M. Gabrani
   US Patent App. 16/953,377 (2022)
3. Biomarker Quantification in a Tissue Sample
   G. Kaigala, A. Fomitcheva‑Khartchenko, A. Kashyap, M. Gabrani, and P. Pati
   US Patent App. 15/924,745 (2022)
4. Tissue Staining Quality Determination
   N. Arar, P. Pati, M. Gabrani, G. Kaigala, A. Kashyap, and A. Fomitcheva‑Khartchenko
   US Patent App. 15/699,204 (2020)

Preprints

1. Multi-scale Feature Alignment for Continual Learning of Unlabeled Domains
   K. Thandiackal*, L. Piccinelli*, P. Pati, and O. Goksel
   arXiv:2302.01287 (2023)
2. Weakly Supervised Joint Whole‑Slide Segmentation and Classification in Prostate Cancer
   P. Pati*, G. Jaume, B. Bozorgtabar, M. Gabrani, and O. Goksel
   arXiv:2301.02933 (2023)
3. Generative appearance replay for continual unsupervised domain adaptation
   B. Chen*, K. Thandiackal*, P. Pati, and O. Goksel
   arXiv:2301.01211 (2023)

Journals

1. Matching Single Cells across Modalities with Contrastive Learning and Optimal Transport
   F. Gossi, P. Pati, A. Martinelli, and M. Rapsomaniki
   Briefings in Bioinformatics (2023) [Code]
2. BRACS: A Dataset for Breast Carcinoma Subtyping in H&E Histology Images
   N. Brancati, A. Anniciello, P. Pati, D. Riccio, G. Scognamiglio, G. Jaume, G. De Pietro, M. Di Bonito, A. Foncubierta, G. Botti, M. Gabrani, F. Feroce, and M. Frucci
   Database (2022)
3. Hierarchical Graph Representations in Digital Pathology
   P. Pati*, G. Jaume*, A. Foncubierta‑Rodríguez, F. Feroce, A. Anniciello, G. Scognamiglio, N. Brancati, M. Fiche, E. Dubruc, D. Riccio, M. Di Bonito, G. De Pietro, G. Botti, J. Thiran, M. Frucci, O. Goksel, and M. Gabrani
   Medical image analysis (2022) [Code]
4. Reducing Annotation Effort in Digital Pathology: A Co‑Representation Learning Framework for Classification
   P. Pati, A. Foncubierta‑Rodríguez, O. Goksel, and M. Gabrani
   Medical image analysis (2021)
5. High‑Quality Immunohistochemical Stains through Assay Parameter Optimization
   N. Arar*, P. Pati*, A. Kashyap, A. Fomitcheva‑Khartchenko, O. Goksel, G. Kaigala, and M. Gabrani
   IEEE Transactions on Biomedical Engineering (2019)
6. Quantitative Microimmunohistochemistry for The Grading of Immunostains on Tumour Tissues
   A. Kashyap*, A. Fomitcheva‑Khartchenko*, P. Pati, M. Gabrani, P. Schraml, and G. Kaigala
   Nature Biomedical Engineering (2019)
7. Multi‑organ Gland Segmentation using Deep Learning
   T. Binder, E.M. Tantaoui, P. Pati, R. Catena, A. Set‑Aghayan, and M. Gabrani
   Frontiers in Medicine (2019)

Conferences

1. Differentiable Zooming for Multiple Instance Learning on Whole‑Slide Image
   K. Thandiackal, B. Chen, P. Pati, G. Jaume, D. Williamson, M. Gabrani, and O. Goksel
   In European Conference on Computer Vision (ECCV) (2022) [Code]
2. Learning Whole‑Slide Segmentation from Inexact and Incomplete Labels using Tissue Graphs
   V. Anklin*, P. Pati*, G. Jaume*, B. Bozorgtabar, A. Foncubierta‑Rodríguez, J. Thiran, M. Sibony, M. Gabrani, and O. Goksel
   In Medical Image Computing and Computer Assisted Intervention (MICCAI) (2021) [Code]
3. Quantifying Explainers of Graph Neural Networks in Computational Pathology
   G. Jaume*, P. Pati*, B. Bozorgtabar, A. Rodriguez, F. Feroce, A. Anniciello, T. Rau, J. Thiran, M. Gabrani, and O. Goksel
   In Conference on Computer Vision and Pattern Recognition (CVPR) (2021) [Code]
4. Mitosis detection under limited annotation: A joint learning approach
   P. Pati, A. Foncubierta-Rodríguez, O. Goksel, and M. Gabrani
   In IEEE International Symposium on Biomedical Imaging (ISBI) (2018)
5. A deep learning framework for context-aware mitotic activity estimation in whole slide images
   P. Pati, R. Catena, O. Goksel, and M. Gabrani
   In SPIE Medical Imaging (2019)
6. Deep positive-unlabeled learning for region of interest localization in breast tissue images
   P. Pati, S. Andani, M. Pediaditis, M.P. Viana, J.H. Ruschoff, P. Wild, and M. Gabrani
   In SPIE Medical Imaging (2018)
7. Computational Immunohistochemistry: Recipes for Standardization of Immunostaining
   N.M. Arar, P. Pati, A. Kashyap, A. Fomitcheva-Khartchenko, O. Goksel, G.V. Kaigala, and M. Gabrani
   In Medical Image Computing and Computer Assisted Intervention (MICCAI) (2017)

Workshops

1. MatchCLOT: Single-Cell Modality Matching with Contrastive Learning and Optimal Transport
   F. Gossi, P. Pati, A. Martinelli, and M. Rapsomaniki
   Neural Information Processing Systems (NeurIPS) - Learning Meaningful Representations of Life (2022) [Code]
2. ChromFormer: A Transformer‑based Model for 3D Genome Structure Prediction
   H. Valeyre*, P. Pati*, F. Gossi, V. Somnath, A. Martinelli, and M. Rapsomaniki
   Neural Information Processing Systems (NeurIPS) - Learning Meaningful Representations of Life (2022) [Code]
3. HistoCartography: A Toolkit for Graph Analytics in Digital Pathology
   G. Jaume*, P. Pati*, V. Anklin, A. Rodríguez, and M. Gabrani
   Medical Image Computing and Computer Assisted Intervention (MICCAI) - Computational Pathology (2021) [Code]
4. HACT‑Net: Hierarchical Cell‑to‑Tissue Graph Neural Network for Histology Image Classification
   P. Pati*, G. Jaume*, L. Fernandes, A. Rodríguez, F. Feroce, A. Anniciello, G. Scognamiglio, N. Brancati, D. Riccio, M. Di Bonito, G. De Pietro, G. Botti, O. Goksel, J. Thiran, M. Frucci, and M. Gabrani
   Medical Image Computing and Computer Assisted Intervention (MICCAI) - Graphs in Biomedical Image analysis (2020) [Code]
5. Towards Explainable Graph Representations in Digital Pathology
   G. Jaume*, P. Pati*, A. Foncubierta‑Rodríguez, F. Feroce, G. Scognamiglio, A. Anniciello, J. Thiran, O. Goksel, and M. Gabrani
   International Conference on Machine Learning (ICML) - Computational Biology (2020) [Code]