Publications

Publications developed during the course of the project in reverse order of publication (latest first).

AuthorsTitleVenueYearLinks
Niccoló Marini, Sebastian Otálora, Manfredo Atzori, Henning MüllerSemi-supervised training of deep convolutional neural networks with heterogeneous data and few local annotations: An experiment on prostate histopathology image classificationMedical Image Analysis2021


Fabio Giachelle, Dennis Dosso and Gianmaria SilvelloNanoWeb: Search, Access and Explore Life Science Nanopublications on the Web (Extended Abstract).Proc. 29th Italian Symposium on Advanced Database Systems (SEBD 2021)2021


Giorgio Maria Di Nunzio, Alessandro Fabris, Gianmaria Silvello and Gian Antonio SustoIncentives for Item Duplication under Fair Ranking PoliciesIn Proc. of the 2nd International Workshop on Algorithmic Bias in Search and Recommendation (BIAS@ECIR2021)2021


Ornella Irrera and Gianmaria SilvelloBackground Linking: Joining Entity Linking with Learning to Rank ModelsProc. of the 17th Italian Research Conference on Digital Libraries (IRCDL 2021)2021


Sebastian Otálora, Niccolo Marini, Henning Müller, and Manfredo Atzori.Combining weakly and strongly supervised learning improves strong supervision in Gleason pattern classificationBMC Medical Imaging2021


Mart van Rijthoven, Maschenka Balkenhol, Karina Silina, Jeroen van der Laak, Francesco CiompiHookNet: Multi-resolution convolutional neural networks for semantic segmentation in histopathology whole-slide imagesMedical Image Anal. Journal2021


Dennis Dosso and Gianmaria SilvelloData Credit Distribution through LineageProc. of the 17th Italian Research Conference on Digital Libraries (IRCDL 2021)2021PDF




Fabio Giachelle, Dennis Dosso, Gianmaria SilvelloSearch, access, and explore nanopublications on the WebPeerJ Computer Science2021Open Access paper




Witali Aswolinskiy, David Tellez, Gabriel Raya, Lieke van der Woude, Monika Looijen-Salamon, Jeroen van der Laak, Katrien Grünberg, Francesco CiompiNeural image compression for non-small cell lung cancer subtype classification in H&E stained whole-slide imagesSPIE Medical Imaging2021PDF

Conference Link




Mart van Rijthoven, Maschenka Balkenhol, Manfredo Atzori, Peter Bult, Jeroen van der Laak, and Francesco Ciompi Few-shot weakly supervised detection and retrieval in histopathology whole-slide imagesSPIE Medical Imaging2021PDF

Conference Link




Niccolo Marini, Sebastian Otalora, Henning Muller, and Manfredo AtzoriSemi-supervised learning with a teacher-student paradigm for histopathology classification: a resource to face data heterogeneity and lack of local annotationsInternational Workshop on Artificial Intelligence for Digital Pathology, International Conference on Pattern Recognition (ICPR)2021website





Anjani Dhrangadhariya, Sebastian Otalora, Manfredo Atzori, and Henning MullerClassification of noisy free-text prostate cancer pathology reports using natural language processingInternational Workshop on Artificial Intelligence for Digital Pathology, International Conference on Pattern Recognition (ICPR)2021website





Stefano MarchesinDeveloping Unsupervised Knowledge-Enhanced Models to Reduce the Semantic Gap in Information RetrievalPh.D. Thesis at the University of Padua2020


Maristella Agosti, Stefano Marchesin and Gianmaria SilvelloLearning Unsupervised Knowledge-Enhanced Representations to Reduce the Semantic Gap in Information RetrievalACM Transactions on Information Systems (TOIS)2020PDF





Dennis Dosso, Gianmaria SilvelloData Credit Distribution: A New Method to Estimate Databases ImpactJournal of Informetrics2020PDF




Sebastian Otálora, Niccolò Marini, Manfredo Atzori, and Henning MüllerSemi-Weakly Supervised Learning for Prostate Cancer Image Classification with Teacher-Student Deep Convolutional Networks The 5th MICCAI Workshop on Large-scale Annotation of Biomedical data and Expert Label Synthesis LABELS 20202020PDF



Federica Vezzani, Giorgio Maria Di NunzioMethodology for the standardization of terminological resources: the design of the TriMED database for supporting multi-register medical communicationTerminology2020

Juan S. Lara, Victor H. Contreras O., Sebastián Otálora, Henning Müller, Fabio A. González Multimodal Latent Semantic Alignment for Automated Prostate Tissue Classification and RetrievalMedical Image Computing and Computer Assisted Intervention – MICCAI 20202020PDF



Dennis Dosso, Susan Davidson, Gianmaria SilvelloData Provenance for Attributes: Attribute LineageProc. of ProvWeek 2020, 12th Workshop on Theory and Practice of Provenance (TaPP 2020)2020PDF



Federica Vezzani, Giorgio Maria Di NunzioOn the Formal Standardization of Terminology Resources: The Case Study of TriMEDProceedings of The 12th Language Resources and Evaluation Conference (LREC 2020)2020PDF



David Tellez, Diederik Hoppener, Cornelis Verhoef, Dirk Grunhagen, Pieter Nierop, Michal Drozdzal, Jeroen van der Laak, Francesco CiompiExtending Unsupervised Neural Image Compression With Supervised Multitask LearningMedical Imaging with Deep Learning (MIDL)2020Link to OpenReview





Maristella Agosti, Giorgio Maria Di Nunzio, Stefano MarchesinA Post-Analysis of Query Reformulation Methods for Clinical Trials Retrieval (discussion paper)28th Symposium on Advanced Database Systems (SEBD 2020)2020PDF




Dennis Dosso, Gianmaria SilvelloA Document-based RDF Keyword Search System: Query-by-Query Analysis28th Symposium on Advanced Database Systems2020PDF




Sebastian Otálora, Oscar Jimenez-del-Toro, Manfredo Atzori, Amjad Khan, Vincent Andrearczyk, Henning MüllerA systematic comparison of deep learning strategies for weakly supervised Gleason grading.SPIE Digital Pathology2020PDF




Anjani K. Dhrangadhariya, Oscar Jimenez-del-Toro, Vincent Andrearczyk, Manfredo Atzori and Henning MüllerExploiting the biomedical literature to mine out a large multimodal dataset of rare cancer studiesSPIE Digital Pathology2020SPIE digital library



Amjad Khan, Manfredo Atzori, Sebastian Otálora, Vincent Andrearczyk and Henning MüllerGeneralizing convolution neural networks on stain color heterogeneous data for computational pathologySPIE Digital Pathology2020ACNP Full Text




Henning Müller, Vincent Andrearczyk, Oscar Jimenez-del-Toro, Anjani Dhrangadhariya, Roger Schaer and Manfredo AtzoriStudying Publicly Available Medical Images from the Open Access Literature and Social Networks for Model Training and Knowledge ExtractionMultimedia Modeling (MMM 2020), Seoul, Korea2020PDF




Dennis Dosso ; Gianmaria Silvello Search Text to Retrieve Graphs: A Scalable RDF Keyword-Based Search SystemIEEE Access Journal2020Journal Page



Giorgio Maria Di Nunzio, Stefano Marchesin, Maristella AgostiExploring how to Combine Query Reformulations for Precision MedicinePrecision Medicine Track, The Text Retrieval Conference (TREC 2019), NIST, Gaithersburg, Md. USA, 13-15 November 20192019PDF




Stefano Marchesin, Alberto Purpura and Gianmaria SilvelloFocal Elements of Neural Information Retrieval Models. An Outlook through a Reproducibility StudyInformation Processing & Management, 20192019PDF





D. Tellez, G. Litjens, P. Bandi, W. Bulten, J. Bokhorst, F. Ciompi and J. van der LaakQuantifying the effects of data augmentation and stain color normalization in convolutional neural networks for computational pathologyMedical Image Analysis2019PDF



David Tellez, Geert Litjens, Jeroen van der Laak, Francesco CiompiNeural Image Compression for Gigapixel Histopathology Image AnalysisIEEE Transactions on Pattern Analysis and Machine Intelligence, 2019, DOI: 10.1109/TPAMI.2019.29368412019PDF




G. Litjens, F. Ciompi, J. Wolterink, B. de Vos, T. Leiner, J. Teuwen and I. IsgumState-of-the-Art Deep Learning in Cardiovascular Image AnalysisJACC Cardiovascular Imaging2019PDF



Zaneta Swiderska-Chadaj
et al.
Hans Pinckaers, Mart van Rijthoven, Maschenka Balkenhol, Margarita Melnikova, Oscar Geessink, Quirine Manson, Mark Sherman, António Polónia, Jeremy Parry, Mustapha Abubakar, Geert J. S. Litjens, Jeroen van der Laak, Francesco Ciompi
Learning to detect lymphocytes in immunohistochemistry with deep learningMedical Image Analysis, 20192019Elsevier Page





John-Melle Bokhorst
et al.
Hans Pinckaers, Peter van Zwam, Iris Nagtegaal, Jeroen van der Laak, Francesco Ciompi
Learning from sparsely annotated data for semantic segmentation in histopathology imagesMedical Imaging with Deep Learning, 20192019PDF




Alberto Purpura, Marco Maggipinto, Gianmaria Silvello, Gian Antonio SustoProbabilistic Word Embeddings in Neural IR: A Promising Model That Does Not Work as Expected (For Now)The 5th ACM SIGIR International Conference on the Theory of Information Retrieval (ICTIR 2019)2019PDF





Erika Fabris, Tobias Kuhn, Gianmaria SilvelloA Framework for Citing Nanopublications23rd International Conference on Theory and Practice of Digital Libraries (TPDL 2019)2019PDF





Dennis DossoA Keyword Search and Citation System for RDF GraphsBCS-IRSG Symposium: Future Directions in Information Access - BCS-IRSG FDIA 20192019PDF





Dennis Dosso, Gianmaria SilvelloA Scalable Virtual Document-Based Keyword Search System for RDF DatasetsProceedings of the 42nd International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR2019), July 21-25, 2019, Paris, France2019PDF




Maristella Agosti, Giorgio Maria Di Nunzio, Stefano MarchesinAn Analysis of Query Reformulation Techniques for Precision Medicine Proceedings of the 42nd International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR2019), July 21-25, 2019, Paris, France2019PDF





Maristella Agosti, Giorgio Maria Di Nunzio, Stefano Marchesin, Gianmaria SilvelloMedical Retrieval using Structured Information Extracted from Knowledge Bases Proceedings of the 27th Italian Symposium on Advanced Database Systems (SEBD 2019), June 16-19, 2019, Castiglione della Pescaia, Italy2019PDF




Roger Schaer, Sebastian Otálora, Oscar Jimenez del Toro, Manfredo Atzori and Henning MüllerDeep learning based retrieval system for gigapixel histopathology cases and open access literatureJournal of pathology informatics, 20192019Journal Page, PDF




Stefano MarchesinKnowledge Enhanced Representations to Reduce the Semantic Gap in Clinical Decision Support9th PhD Symposium on Future Directions in Information Access (FDIA 2019), 20192019PDF




Stefano Marchesin and Maristella AgostiKnowledge Enhanced Representations for Clinical Decision SupportProceedings of the 10th Italian Information Retrieval Workshop, CEUR Workshop Proceedings, Vol. 2441, pages 17-182019PDF




Sebastian Otálora, Manfredo Atzori, Vincent Andrearczyk, Amjad Khan and Henning MüllerStaining invariant features for improving generalization of deep convolutional neural networks in computational pathologyFrontiers in Bioengineering and Biotechnology-Bioinformatics and Computational Biology2019HTML