Thomas J. Fuchs

74 papers A* 7A 1Journal 40Unranked 24

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	A Flexible Deep Learning Framework for Survival Analysis with Medical Data. MICCAI (15) Gabriele Campanella, Ida Häggström, Lucas Kook, Torsten Hothorn, Thomas J. Fuchs
2025	J	`jnl`	Domain-Specific Foundation Model Improves AI-Based Analysis of Neuropathology. CoRR Ruchika Verma, Shrishtee Kandoi, Robina Afzal, Shengjia Chen, Jannes Jegminat, Michael W. Karlovich, Melissa Umphlett, Timothy E. Richardson, Kevin Clare, Quazi Hossain, Jorge Samanamud, Phyllis L. Faust, Elan D. Louis, Ann C. McKee, Thor D. Stein, Jonathan D. Cherry, Jesse B. Mez, Anya C. McGoldrick, Dalilah D. Quintana Mora, Melissa J. Nirenberg, Ruth H. Walker, Yolfrankcis Mendez, Susan Morgello, Dennis W. Dickson, Melissa E. Murray, Carlos Cordon-Cardo, Nadejda M. Tsankova, Jamie M. Walker, Diana K. Dangoor, Stephanie McQuillan, Emma L. Thorn, Claudia De Sanctis, Shuying Li, Thomas J. Fuchs, Kurt Farrell, John F. Crary, Gabriele Campanella
2025	J	`jnl`	Keyword-optimized template insertion for clinical note classification via prompt-based learning. BMC Medical Informatics Decis. Mak. Eugenia Alleva, Isotta Landi, Leslee J. Shaw, Erwin P. Bottinger, Ipek Ensari, Thomas J. Fuchs
2025	J	`jnl`	PRISM2: Unlocking Multi-Modal General Pathology AI with Clinical Dialogue. CoRR George Shaikovski, Eugene Vorontsov, Adam Casson, Julian Viret, Eric Zimmermann, Neil A. Tenenholtz, Yi Kan Wang, Jan Bernhard, Ran A. Godrich, Juan Retamero, Razik Yousfi, Nicolò Fusi, Thomas J. Fuchs, Kristen Severson, Siqi Liu
2025	J	`jnl`	Predict Patient Self-reported Race from Skin Histological Images. CoRR Shengjia Chen, Ruchika Verma, Kevin Clare, Jannes Jegminat, Eugenia Alleva, Kuan-Lin Huang, Brandon Veremis, Thomas J. Fuchs, Gabriele Campanella
2025	—	`conf`	Predicting Patient Self-reported Race From Skin Histological Images with Deep Learning. FAIMI@MICCAI Shengjia Chen, Ruchika Verma, Kevin Clare, Jannes Jegminat, Eugenia Alleva, Kuan-Lin Huang, Brandon Veremis, Thomas J. Fuchs, Gabriele Campanella
2024	—	`conf`	Benchmarking Embedding Aggregation Methods in Computational Pathology: A Clinical Data Perspective. COMPAY@MICCAI Shengjia Chen, Gabriele Campanella, Abdulkadir Elmas, Aryeh Stock, Jennifer Zeng, Alexandros D. Polydorides, Adam J. Schoenfeld, Kuan-Lin Huang, Jane Houldsworth, Chad Vanderbilt, Thomas J. Fuchs
2024	J	`jnl`	Benchmarking Embedding Aggregation Methods in Computational Pathology: A Clinical Data Perspective. CoRR Shengjia Chen, Gabriele Campanella, Abdulkadir Elmas, Aryeh Stock, Jennifer Zeng, Alexandros D. Polydorides, Adam Schoenfeld, Kuan-Lin Huang, Jane Houldsworth, Chad M. Vanderbilt, Thomas J. Fuchs
2024	J	`jnl`	Beyond Multiple Instance Learning: Full Resolution All-In-Memory End-To-End Pathology Slide Modeling. CoRR Gabriele Campanella, Eugene Fluder, Jennifer Zeng, Chad M. Vanderbilt, Thomas J. Fuchs
2024	J	`jnl`	PRISM: A Multi-Modal Generative Foundation Model for Slide-Level Histopathology. CoRR George Shaikovski, Adam Casson, Kristen Severson, Eric Zimmermann, Yi Kan Wang, Jeremy D. Kunz, Juan Retamero, Gerard Oakley, David S. Klimstra, Christopher Kanan, Matthew G. Hanna, Michal Zelechowski, Julian Viret, Neil A. Tenenholtz, James Brian Hall, Nicolò Fusi, Razik Yousfi, Peter Hamilton, William A. Moye, Eugene Vorontsov, Siqi Liu, Thomas J. Fuchs
2024	J	`jnl`	Screen Them All: High-Throughput Pan-Cancer Genetic and Phenotypic Biomarker Screening from H&E Whole Slide Images. CoRR Yi Kan Wang, Ludmila Tydlitatova, Jeremy D. Kunz, Gerard Oakley, Ran A. Godrich, Matthew C. H. Lee, Chad Vanderbilt, Razik Yousfi, Thomas J. Fuchs, David S. Klimstra, Siqi Liu
2024	J	`jnl`	Virchow2: Scaling Self-Supervised Mixed Magnification Models in Pathology. CoRR Eric Zimmermann, Eugene Vorontsov, Julian Viret, Adam Casson, Michal Zelechowski, George Shaikovski, Neil A. Tenenholtz, James Brian Hall, David S. Klimstra, Razik Yousfi, Thomas J. Fuchs, Nicoló Fusi, Siqi Liu, Kristen Severson
2023	J	`jnl`	Computational Pathology at Health System Scale - Self-Supervised Foundation Models from Three Billion Images. CoRR Gabriele Campanella, Ricky Kwan, Eugene Fluder, Jennifer Zeng, Aryeh Stock, Brandon Veremis, Alexandros D. Polydorides, Cyrus Hedvat, Adam Schoenfeld, Chad M. Vanderbilt, Patricia H. Kovatch, Carlos Cordon-Cardo, Thomas J. Fuchs
2023	—	`conf`	Joint Breast Neoplasm Detection and Subtyping using Multi-Resolution Network Trained on Large-Scale H&E Whole Slide Images with Weak Labels. MIDL Adam Casson, Siqi Liu, Ran A. Godrich, Hamed Aghdam, Brandon Rothrock, Kasper Malfroid, Christopher Kanan, Thomas J. Fuchs
2023	J	`jnl`	Keyword-optimized Template Insertion for Clinical Information Extraction via Prompt-based Learning. CoRR Eugenia Alleva, Isotta Landi, Leslee J. Shaw, Erwin P. Böttinger, Thomas J. Fuchs, Ipek Ensari
2023	J	`jnl`	Virchow: A Million-Slide Digital Pathology Foundation Model. CoRR Eugene Vorontsov, Alican Bozkurt, Adam Casson, George Shaikovski, Michal Zelechowski, Siqi Liu, Philippe Mathieu, Alexander van Eck, Donghun Lee, Julian Viret, Eric Robert, Yi Kan Wang, Jeremy D. Kunz, Matthew C. H. Lee, Jan Bernhard, Ran A. Godrich, Gerard Oakley, Ewan Millar, Matthew G. Hanna, Juan Retamero, William A. Moye, Razik Yousfi, Christopher Kanan, David S. Klimstra, Brandon Rothrock, Thomas J. Fuchs
2022	J	`jnl`	Deep Interactive Learning-based ovarian cancer segmentation of H&E-stained whole slide images to study morphological patterns of BRCA mutation. CoRR David Joon Ho, M. Herman Chui, Chad M. Vanderbilt, Ji Won Jung, Mark E. Robson, Chan-Sik Park, Jin Roh, Thomas J. Fuchs
2022	J	`jnl`	Deep Learning-Based Objective and Reproducible Osteosarcoma Chemotherapy Response Assessment and Outcome Prediction. CoRR David Joon Ho, Narasimhan P. Agaram, Marc-Henri Jean, Stephanie D. Suser, Cynthia Chu, Chad M. Vanderbilt, Paul A. Meyers, Leonard H. Wexler, John H. Healey, Thomas J. Fuchs, Meera R. Hameed
2022	J	`jnl`	Deep conditional transformation models for survival analysis. CoRR Gabriele Campanella, Lucas Kook, Ida Häggström, Torsten Hothorn, Thomas J. Fuchs
2022	J	`jnl`	H&E-based Computational Biomarker Enables Universal EGFR Screening for Lung Adenocarcinoma. CoRR Gabriele Campanella, David Joon Ho, Ida Häggström, Anton S. Becker, Jason Chang, Chad M. Vanderbilt, Thomas J. Fuchs
2021	J	`jnl`	Deep Multi-Magnification Networks for multi-class breast cancer image segmentation. Comput. Medical Imaging Graph. David Joon Ho, Dig Vijay Kumar Yarlagadda, Timothy M. D'Alfonso, Matthew G. Hanna, Anne Grabenstetter, Peter Ntiamoah, Edi Brogi, Lee K. Tan, Thomas J. Fuchs
2021	J	`jnl`	EPIC-Survival: End-to-end Part Inferred Clustering for Survival Analysis, Featuring Prognostic Stratification Boosting. CoRR Hassan Muhammad, Chensu Xie, Carlie S. Sigel, Michael Doukas, Lindsay Alpert, Thomas J. Fuchs
2021	—	`conf`	EPIC-Survival: End-to-end Part Inferred Clustering for Survival Analysis, with Prognostic Stratification Boosting. MIDL Hassan Muhammad, Chensu Xie, Carlie S. Sigel, Michael Doukas, Lindsay Alpert, Amber Lea Simpson, Thomas J. Fuchs
2021	J	`jnl`	Integrated digital pathology at scale: A solution for clinical diagnostics and cancer research at a large academic medical center. J. Am. Medical Informatics Assoc. Peter J. Schüffler, Luke Geneslaw, Dig Vijay Kumar Yarlagadda, Matthew G. Hanna, Jennifer Samboy, Evangelos Stamelos, Chad M. Vanderbilt, John Philip, Marc-Henri Jean, Lorraine Corsale, Allyne Manzo, Neeraj H. G. Paramasivam, John S. Ziegler, Jianjiong Gao, Juan C. Perin, Young Suk Kim, Umeshkumar K. Bhanot, Michael H. A. Roehrl, Orly Ardon, Sarah Chiang, Dilip D. Giri, Carlie S. Sigel, Lee K. Tan, Melissa Murray, Christina Virgo, Christine England, Yukako Yagi, S. Joseph Sirintrapun, David S. Klimstra, Meera R. Hameed, Victor E. Reuter, Thomas J. Fuchs
2021	—	`conf`	Nuc2Vec: Learning Representations of Nuclei in Histopathology Images with Contrastive Loss. MIDL Chao Feng, Chad M. Vanderbilt, Thomas J. Fuchs
2020	—	`conf`	Beyond Classification: Whole Slide Tissue Histopathology Analysis By End-To-End Part Learning. MIDL Chensu Xie, Hassan Muhammad, Chad M. Vanderbilt, Raul Caso, Dig Vijay Kumar Yarlagadda, Gabriele Campanella, Thomas J. Fuchs
2020	—	`conf`	Deep Interactive Learning: An Efficient Labeling Approach for Deep Learning-Based Osteosarcoma Treatment Response Assessment. MICCAI (5) David Joon Ho, Narasimhan P. Agaram, Peter J. Schüffler, Chad M. Vanderbilt, Marc-Henri Jean, Meera R. Hameed, Thomas J. Fuchs
2020	J	`jnl`	Deep Interactive Learning: An Efficient Labeling Approach for Deep Learning-Based Osteosarcoma Treatment Response Assessment. CoRR David Joon Ho, Narasimhan P. Agaram, Peter J. Schüffler, Chad M. Vanderbilt, Marc-Henri Jean, Meera R. Hameed, Thomas J. Fuchs
2019	J	`jnl`	Deep Multi-Magnification Networks for Multi-Class Breast Cancer Image Segmentation. CoRR David Joon Ho, Dig Vijay Kumar Yarlagadda, Timothy M. D'Alfonso, Matthew G. Hanna, Anne Grabenstetter, Peter Ntiamoah, Edi Brogi, Lee K. Tan, Thomas J. Fuchs
2019	J	`jnl`	DeepPET: A deep encoder-decoder network for directly solving the PET image reconstruction inverse problem. Medical Image Anal. Ida Häggström, Charles Ross Schmidtlein, Gabriele Campanella, Thomas J. Fuchs
2019	J	`jnl`	Towards Unsupervised Cancer Subtyping: Predicting Prognosis Using A Histologic Visual Dictionary. CoRR Hassan Muhammad, Carlie S. Sigel, Gabriele Campanella, Thomas Börner, Linda M. Pak, Stefan Büttner, Jan N. M. IJzermans, Bas Groot Koerkamp, Michael Doukas, William R. Jarnagin, Amber L. Simpson, Thomas J. Fuchs
2019	—	`conf`	Unsupervised Subtyping of Cholangiocarcinoma Using a Deep Clustering Convolutional Autoencoder. MICCAI (1) Hassan Muhammad, Carlie S. Sigel, Gabriele Campanella, Thomas Börner, Linda M. Pak, Stefan Büttner, Jan N. M. IJzermans, Bas Groot Koerkamp, Michael Doukas, William R. Jarnagin, Amber L. Simpson, Thomas J. Fuchs
2019	—	`conf`	VOCA: Cell Nuclei Detection In Histopathology Images By Vector Oriented Confidence Accumulation. MIDL Chensu Xie, Chad M. Vanderbilt, Anne Grabenstetter, Thomas J. Fuchs
2018	J	`jnl`	DeepRec: A deep encoder-decoder network for directly solving the PET reconstruction inverse problem. CoRR Ida Haeggstroem, Charles Ross Schmidtlein, Gabriele Campanella, Thomas J. Fuchs
2018	—	`conf`	Survival Modeling of Pancreatic Cancer with Radiology Using Convolutional Neural Networks. POCUS/BIVPCS/CuRIOUS/CPM@MICCAI Hassan Muhammad, Ida Häggström, David S. Klimstra, Thomas J. Fuchs
2018	J	`jnl`	Terabyte-scale Deep Multiple Instance Learning for Classification and Localization in Pathology. CoRR Gabriele Campanella, Vitor Werneck Krauss Silva, Thomas J. Fuchs
2018	J	`jnl`	Towards machine learned quality control: A benchmark for sharpness quantification in digital pathology. Comput. Medical Imaging Graph. Gabriele Campanella, Arjun R. Rajanna, Lorraine Corsale, Peter J. Schüffler, Yukako Yagi, Thomas J. Fuchs
2016	J	`jnl`	Autonomous Terrain Classification With Co- and Self-Training Approach. IEEE Robotics Autom. Lett. Kyohei Otsu, Masahiro Ono, Thomas J. Fuchs, Ian Baldwin, Takashi Kubota
2016	J	`jnl`	Computational Pathology: Challenges and Promises for Tissue Analysis. CoRR Thomas J. Fuchs, Joachim M. Buhmann
2016	—	`conf`	DeepScope: Nonintrusive Whole Slide Saliency Annotation and Prediction from Pathologists at the Microscope. CIBB Andrew J. Schaumberg, S. Joseph Sirintrapun, Hikmat A. Al-Ahmadie, Peter J. Schüffler, Thomas J. Fuchs
2016	—	`conf`	Mitochondria-based Renal Cell Carcinoma Subtyping: Learning from Deep vs. Flat Feature Representations. MLHC Peter J. Schüffler, Judy Sarungbam, Hassan Muhammad, Ed Reznik, Satish K. Tickoo, Thomas J. Fuchs
2016	J	`jnl`	Mitochondria-based Renal Cell Carcinoma Subtyping: Learning from Deep vs. Flat Feature Representations. CoRR Peter J. Schüffler, Judy Sarungbam, Hassan Muhammad, Ed Reznik, Satish K. Tickoo, Thomas J. Fuchs
2016	J	`jnl`	Multi-Organ Cancer Classification and Survival Analysis. CoRR Stefan Bauer, Nicolas Carion, Peter J. Schüffler, Thomas J. Fuchs, Peter J. Wild, Joachim M. Buhmann
2016	J	`jnl`	Real-Time Data Mining of Massive Data Streams from Synoptic Sky Surveys. CoRR S. George Djorgovski, Matthew J. Graham, Ciro Donalek, Ashish Mahabal, Andrew J. Drake, Michael J. Turmon, Thomas J. Fuchs
2016	J	`jnl`	Real-time data mining of massive data streams from synoptic sky surveys. Future Gener. Comput. Syst. S. George Djorgovski, Matthew J. Graham, Ciro Donalek, Ashish Mahabal, Andrew J. Drake, Michael J. Turmon, Thomas J. Fuchs
2015	J	`jnl`	Boosting Convolutional Features for Robust Object Proposals. CoRR Nikolaos Karianakis, Thomas J. Fuchs, Stefano Soatto
2015	J	`jnl`	Machine learning approaches to analyze histological images of tissues from radical prostatectomies. Comput. Medical Imaging Graph. Arkadiusz Gertych, Nathan Ing, Zhaoxuan Ma, Thomas J. Fuchs, Sadri Salman, Sambit Mohanty, Sanica Bhele, Adriana Velásquez-Vacca, Mahul B. Amin, Beatrice S. Knudsen
2015	A*	`conf`	Robot-Centric Activity Prediction from First-Person Videos: What Will They Do to Me'. HRI Michael S. Ryoo, Thomas J. Fuchs, Lu Xia, Jake K. Aggarwal, Larry H. Matthies
2015	J	`jnl`	Understanding Neural Networks Through Deep Visualization. CoRR Jason Yosinski, Jeff Clune, Anh Mai Nguyen, Thomas J. Fuchs, Hod Lipson
2014	—	`conf`	Automated Real-Time Classification and Decision Making in Massive Data Streams from Synoptic Sky Surveys. eScience S. George Djorgovski, Ashish Mahabal, Ciro Donalek, Matthew J. Graham, Andrew J. Drake, Michael J. Turmon, Thomas J. Fuchs
2014	J	`jnl`	Early Recognition of Human Activities from First-Person Videos Using Onset Representations. CoRR Michael S. Ryoo, Thomas J. Fuchs, Lu Xia, J. K. Aggarwal, Larry H. Matthies
2014	A*	`conf`	Sparse meta-Gaussian information bottleneck. ICML Mélanie Rey, Volker Roth, Thomas J. Fuchs
2013	—	`ch.`	Automated Analysis of Tissue Micro-Array Images on the Example of Renal Cell Carcinoma. Similarity-Based Pattern Analysis and Recognition Peter J. Schüffler, Thomas J. Fuchs, Cheng Soon Ong, Volker Roth, Joachim M. Buhmann
2013	J	`jnl`	Feature Selection Strategies for Classifying High Dimensional Astronomical Data Sets. CoRR Ciro Donalek, Arun Kumar A., S. George Djorgovski, Ashish Mahabal, Matthew J. Graham, Thomas J. Fuchs, Michael J. Turmon, N. Sajeeth Philip, Michael Ting-Chang Yang, Giuseppe Longo
2013	—	`conf`	Feature selection strategies for classifying high dimensional astronomical data sets. IEEE BigData Ciro Donalek, S. George Djorgovski, Ashish Mahabal, Matthew J. Graham, Andrew J. Drake, Arun Kumar A., N. Sajeeth Philip, Thomas J. Fuchs, Michael J. Turmon, Michael Ting-Chang Yang, Giuseppe Longo
2013	—	`conf`	Quickly Boosting Decision Trees - Pruning Underachieving Features Early. ICML (3) Ron Appel, Thomas J. Fuchs, Piotr Dollár, Pietro Perona
2013	A	`conf`	Recognizing Humans in Motion: Trajectory-based Aerial Video Analysis. BMVC Yumi Iwashita, Michael S. Ryoo, Thomas J. Fuchs, Curtis Padgett
2013	—	`ch.`	Structure Preserving Embedding of Dissimilarity Data. Similarity-Based Pattern Analysis and Recognition Volker Roth, Thomas J. Fuchs, Julia E. Vogt, Sandhya Prabhakaran, Joachim M. Buhmann
2012	A*	`conf`	Combined shape, appearance and silhouette for simultaneous manipulator and object tracking. ICRA Paul Hebert, Nicolas Hudson, Jeremy Ma, Thomas Howard, Thomas J. Fuchs, Max Bajracharya, Joel W. Burdick
2012	A*	`conf`	End-to-end dexterous manipulation with deliberate interactive estimation. ICRA Nicolas Hudson, Thomas Howard, Jeremy Ma, Abhinandan Jain, Max Bajracharya, Steven Myint, Calvin Kuo, Larry H. Matthies, Paul Backes, Paul Hebert, Thomas J. Fuchs, Joel W. Burdick
2011	J	`jnl`	Computational pathology: Challenges and promises for tissue analysis. Comput. Medical Imaging Graph. Thomas J. Fuchs, Joachim M. Buhmann
2010	—	`conf`	Computational TMA Analysis and Cell Nucleus Classification of Renal Cell Carcinoma. DAGM-Symposium Peter J. Schüffler, Thomas J. Fuchs, Cheng Soon Ong, Volker Roth, Joachim M. Buhmann
2010	—	`conf`	Geometrical Consistent 3D Tracing of Neuronal Processes in ssTEM Data. MICCAI (2) Verena Kaynig, Thomas J. Fuchs, Joachim M. Buhmann
2010	J	`jnl`	Infinite mixture-of-experts model for sparse survival regression with application to breast cancer. BMC Bioinform. Sudhir Raman, Thomas J. Fuchs, Peter J. Wild, Edgar Dahl, Joachim M. Buhmann, Volker Roth
2010	A*	`conf`	Neuron geometry extraction by perceptual grouping in ssTEM images. CVPR Verena Kaynig, Thomas J. Fuchs, Joachim M. Buhmann
2010	A*	`conf`	The Translation-invariant Wishart-Dirichlet Process for Clustering Distance Data. ICML Julia E. Vogt, Sandhya Prabhakaran, Thomas J. Fuchs, Volker Roth
2009	—	`conf`	Graph-Based Pancreatic Islet Segmentation for Early Type 2 Diabetes Mellitus on Histopathological Tissue. MICCAI (1) Xenofon E. Floros, Thomas J. Fuchs, Markus P. Rechsteiner, Giatgen Spinas, Holger Moch, Joachim M. Buhmann
2009	J	`jnl`	Guided review by frequent itemset mining: additional evidence for plaque detection. Int. J. Comput. Assist. Radiol. Surg. Stefan C. Saur, Hatem Alkadhi, Lotus Desbiolles, Thomas J. Fuchs, Gábor Székely, Philippe C. Cattin
2009	—	`conf`	Inter-active learning of randomized tree ensembles for object detection. ICCV Workshops Thomas J. Fuchs, Joachim M. Buhmann
2009	—	`conf`	Randomized Tree Ensembles for Object Detection in Computational Pathology. ISVC (1) Thomas J. Fuchs, Johannes Haybaeck, Peter J. Wild, Mathias Heikenwalder, Holger Moch, Adriano Aguzzi, Joachim M. Buhmann
2009	A*	`conf`	The Bayesian group-Lasso for analyzing contingency tables. ICML Sudhir Raman, Thomas J. Fuchs, Peter J. Wild, Edgar Dahl, Volker Roth
2008	—	`conf`	Automatic and robust forearm segmentation using graph cuts. ISBI Philipp Fürnstahl, Thomas J. Fuchs, Andreas Schweizer, Ladislav Nagy, Gábor Székely, Matthias Harders
2008	—	`conf`	Computational Pathology Analysis of Tissue Microarrays Predicts Survival of Renal Clear Cell Carcinoma Patients. MICCAI (2) Thomas J. Fuchs, Peter J. Wild, Holger Moch, Joachim M. Buhmann
2008	—	`conf`	Weakly Supervised Cell Nuclei Detection and Segmentation on Tissue Microarrays of Renal Clear Cell Carcinoma. DAGM-Symposium Thomas J. Fuchs, Tilman Lange, Peter J. Wild, Holger Moch, Joachim M. Buhmann