Computational Immunohistochemistry: Recipes for Standardization of Immunostaining. - Nuri Murat Arar; Pushpak Pati; Aditya Kashyap; Anna Fomitcheva Khartchenko; Orcun Goksel; Govind V. Kaigala; Maria Gabrani (MICCAI (2), 2017)

A Fast and Scalable Pipeline for Stain Normalization of Whole-Slide Images in Histopathology. - Milos Stanisavljevic; Andreea Anghel; Nikolaos Papandreou; Sonali Andani; Pushpak Pati; Jan Hendrik Rüschoff; Peter Wild; Maria Gabrani; Haralampos Pozidis (ECCV Workshops (6), 2018)

Deep positive-unlabeled learning for region of interest localization in breast tissue images. - Pushpak Pati; Sonali Andani; Matthew Pediaditis; Matheus Palhares Viana; Jan Hendrik Rüschoff; Peter Wild; Maria Gabrani (Digital Pathology, 2018)

A deep learning framework for context-aware mitotic activity estimation in whole slide images. - Pushpak Pati; Raúl Catena; Orcun Goksel; Maria Gabrani (Digital Pathology, 2019)

High-Quality Immunohistochemical Stains Through Computational Assay Parameter Optimization. - Nuri Murat Arar; Pushpak Pati; Aditya Kashyap; Anna Fomitcheva Khartchenko; Orcun Goksel; Govind V. Kaigala; Maria Gabrani (IEEE Trans. Biomed. Eng., 2019)

Mitosis Detection Under Limited Annotation: A Joint Learning Approach. - Pushpak Pati; Antonio Foncubierta-Rodríguez; Orçun Göksel; Maria Gabrani (ISBI, 2020)

HACT-Net: A Hierarchical Cell-to-Tissue Graph Neural Network for Histopathological Image Classification. - Pushpak Pati; Guillaume Jaume; Lauren Alisha Fernandes; Antonio Foncubierta-Rodríguez; Florinda Feroce; Anna Maria Anniciello; Giosue Scognamiglio; Nadia Brancati; Daniel Riccio; Maurizio Di Bonito; Giuseppe De Pietro; Gerardo Botti; et al. (UNSURE/GRAIL@MICCAI, 2020)

NINEPINS: Nuclei Instance Segmentation with Point Annotations. - Ting-An Yen; Hung-Chun Hsu; Pushpak Pati; Maria Gabrani; Antonio Foncubierta-Rodríguez; Pau-Choo Chung (CoRR, 2020)

Towards Explainable Graph Representations in Digital Pathology. - Guillaume Jaume; Pushpak Pati; Antonio Foncubierta-Rodríguez; Florinda Feroce; Giosue Scognamiglio; Anna Maria Anniciello; Jean-Philippe Thiran; Orcun Goksel; Maria Gabrani (CoRR, 2020)

Histocartography: a pipeline for histology image analysis. - Antonio Foncubierta-Rodríguez; Pushpak Pati; Guillaume Jaume; Maria Gabrani (AMIA, 2021)

HistoCartography: A Toolkit for Graph Analytics in Digital Pathology. - Guillaume Jaume; Pushpak Pati; Valentin Anklin; Antonio Foncubierta; Maria Gabrani (COMPAY@MICCAI, 2021)

Quantifying Explainers of Graph Neural Networks in Computational Pathology. - Guillaume Jaume; Pushpak Pati; Behzad Bozorgtabar; Antonio Foncubierta; Anna Maria Anniciello; Florinda Feroce; Tilman Rau; Jean-Philippe Thiran; Maria Gabrani; Orcun Goksel (CVPR, 2021)

Learning Whole-Slide Segmentation from Inexact and Incomplete Labels Using Tissue Graphs. - Valentin Anklin; Pushpak Pati; Guillaume Jaume; Behzad Bozorgtabar; Antonio Foncubierta-Rodríguez; Jean-Philippe Thiran; Mathilde Sibony; Maria Gabrani; Orcun Goksel (MICCAI (2), 2021)

Hierarchical Cell-to-Tissue Graph Representations for Breast Cancer Subtyping in Digital Pathology. - Pushpak Pati; Guillaume Jaume; Antonio Foncubierta; Florinda Feroce; Anna Maria Anniciello; Giosuè Scognamiglio; Nadia Brancati; Maryse Fiche; Estelle Dubruc; Daniel Riccio; Maurizio Di Bonito; Giuseppe De Pietro; et al. (CoRR, 2021)

Reducing annotation effort in digital pathology: A Co-Representation learning framework for classification tasks. - Pushpak Pati; Antonio Foncubierta-Rodríguez; Orcun Goksel; Maria Gabrani (Medical Image Anal., 2021)

Differentiable Zooming for Multiple Instance Learning on Whole-Slide Images. - Kevin Thandiackal; Boqi Chen; Pushpak Pati; Guillaume Jaume; Drew F. K. Williamson; Maria Gabrani; Orcun Goksel (ECCV (21), 2022)

BRACS: A Dataset for BReAst Carcinoma Subtyping in H&E Histology Images. - Nadia Brancati; Anna Maria Anniciello; Pushpak Pati; Daniel Riccio; Giosuè Scognamiglio; Guillaume Jaume; Giuseppe De Pietro; Maurizio Di Bonito; Antonio Foncubierta; Gerardo Botti; Maria Gabrani; Florinda Feroce; et al. (Database J. Biol. Databases Curation, 2022)

Hierarchical graph representations in digital pathology. - Pushpak Pati; Guillaume Jaume; Antonio Foncubierta-Rodríguez; Florinda Feroce; Anna Maria Anniciello; Giosue Scognamiglio; Nadia Brancati; Maryse Fiche; Estelle Dubruc; Daniel Riccio; Maurizio Di Bonito; Giuseppe De Pietro; et al. (Medical Image Anal., 2022)

Deep Learning of Entity-Guided Representations in Digital Pathology. - Pushpak Pati (2022)

Multi-scale Feature Alignment for Continual Learning of Unlabeled Domains. - Kevin Thandiackal; Luigi Piccinelli; Pushpak Pati; Orcun Goksel (CoRR, 2023)

Matching single cells across modalities with contrastive learning and optimal transport. - Federico Gossi; Pushpak Pati; Panagiotis Chouvardas; Adriano Luca Martinelli; Marianna Kruithof-de Julio; Maria Anna Rapsomaniki (Briefings Bioinform., 2023)

Generative appearance replay for continual unsupervised domain adaptation. - Boqi Chen; Kevin Thandiackal; Pushpak Pati; Orcun Goksel (Medical Image Anal., 2023)

Weakly supervised joint whole-slide segmentation and classification in prostate cancer. - Pushpak Pati; Guillaume Jaume; Zeineb Ayadi; Kevin Thandiackal; Behzad Bozorgtabar; Maria Gabrani; Orcun Goksel (Medical Image Anal., 2023)

SI-MIL: Taming Deep MIL for Self-Interpretability in Gigapixel Histopathology. - Saarthak Kapse; Pushpak Pati; Srijan Das; Jingwei Zhang; Chao Chen 012; Maria Vakalopoulou; Joel H. Saltz; Dimitris Samaras; Rajarsi R. Gupta; Prateek Prasanna (CVPR, 2024)

Coca-Mil: Attention-Based Handcrafted-Deep Feature Fusion in Computational Pathology. - Paras Goel; Saarthak Kapse; Pushpak Pati; Prateek Prasanna (ISBI, 2024)

Ensemble of Prior-guided Expert Graph Models for Survival Prediction in Digital Pathology. - Vishwesh Ramanathan; Pushpak Pati; Matthew McNeil; Anne L. Martel (MICCAI (5), 2024)

Hybrid Quantum-Classical Graph Neural Networks for Tumor Classification in Digital Pathology. - Anupama Ray; Dhiraj Madan; Srushti Patil; Pushpak Pati; Maria Anna Rapsomaniki; Aviwe Kohlakala; Thembelihle Rose Dlamini; Stephanie Julia Muller; Kahn Rhrissorrakrai; Filippo Utro; Laxmi Parida (QCE, 2024)

Accelerating histopathology workflows with generative AI-based virtually multiplexed tumour profiling. - Pushpak Pati; Sofia Karkampouna; Francesco Bonollo; Eva Compérat; Martina Radic; Martin Spahn; Adriano Martinelli; Martin Wartenberg; Marianna Kruithof-de Julio; Maria Anna Rapsomaniki (Nat. Mac. Intell., 2024)

Efficient Parameter Optimisation for Quantum Kernel Alignment: A Sub-sampling Approach in Variational Training. - Mustafa Emre Sahin; Benjamin C. B. Symons; Pushpak Pati; Fayyaz Minhas; Declan Millar; Maria Gabrani; Stefano Mensa; Jan Lukas Robertus (Quantum, 2024)

Multi-Scale Feature Alignment for Continual Learning of Unlabeled Domains. - Kevin Thandiackal; Luigi Piccinelli; Rajarsi Gupta 001; Pushpak Pati; Orcun Goksel (IEEE Trans. Medical Imaging, 2024)

ModalTune: Fine-Tuning Slide-Level Foundation Models with Multi-Modal Information for Multi-task Learning in Digital Pathology. - Vishwesh Ramanathan; Tony Xu; Pushpak Pati; Faruk Ahmed; Maged Goubran; Anne L. Martel (CoRR, 2025)

GECKO: Gigapixel Vision-Concept Contrastive Pretraining in Histopathology. - Saarthak Kapse; Pushpak Pati; Srikar Yellapragada; Srijan Das; Rajarsi R. Gupta; Joel H. Saltz; Dimitris Samaras; Prateek Prasanna (CoRR, 2025)

BioLangFusion: Multimodal Fusion of DNA, mRNA, and Protein Language Models. - Amina Mollaysa; Artem Moskalev; Pushpak Pati; Tommaso Mansi; Mangal Prakash; Rui Liao (CoRR, 2025)