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I have the enormous privilege to work at the only institution on earth with
a working rover on another planet:
NASA's Jet Propulsion Laboratory in Pasadena. I am intrigued by making sense out of vast amounts of data and the best way to do that is machine learning. Hence my research focuses on developing new statistical learning algorithms and on their application in computer vision, computational pathology and robotics. As a research scientist in JPL's robotics group I naturally hope that these techniques will make the next generation of autonomous spacecrafts even smarter and their scientific insights even more thrilling. In addition I have a visitor appointment at the California Institute of Technology where I occasionally give guest lectures and organize the Machine Learning Seminar. My postdoctoral research was focused on Approximate Bayesian Computation and its application in Martian terrain classification, likelihood-free parameter estimation and medical imaging. This work was conducted at the Computational Vision lab of Pietro Perona at Caltech and the Surface System Perception group of Larry Matthies at JPL. In 2010 I received my PhD (Dr.Sc.) from ETH Zurich for my work in the Machine Learning Laboratory of Joachim Buhmann. During this time I was also a member of the CC-SPMD. I received my MSc degree (Dipl.-Ing.) from TU Graz where I majored in technical mathematics with a minor in computer science. Most of the work for my master thesis on Bayesian networks was conducted at SCR in Princeton. |
 
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Publications
I also try to keep my Google Scholar profile up to date.Peer Reviwed Articles
| [1] | , Structure Preserving Embedding of Dissimilarity Data, Advances in Computer Vision and Pattern Recognition, Springer, 2012 @InCollection {roth_structure_2012, author = "Volker Roth and Thomas J. Fuchs and Julia E. Vogt and Sandhya Prabhakaran and Joachim M. Buhmann", title = "Structure Preserving Embedding of Dissimilarity Data", booktitle = "Advances in Computer Vision and Pattern Recognition", publisher = "Springer", year = "2012", } | BibTeX |
| [2] | , Automated Analysis of Tissue Micro-Array Images on the example of Renal Cell Carcinoma, Advances in Computer Vision and Pattern Recognition, Springer, 2012 @InCollection {schuffler_automated_2012, author = "Peter J. Schueffler and Thomas J. Fuchs and Cheng Soon Ong and Julia E. Vogt and Sandhya Prabhakaran and Volker Roth and Joachim M. Buhmann", title = "Automated Analysis of Tissue Micro-Array Images on the example of Renal Cell Carcinoma", booktitle = "Advances in Computer Vision and Pattern Recognition", publisher = "Springer", year = "2012", } | BibTeX |
| [3] | , A Seven-Marker Signature and Clinical Outcome in Malignant Melanoma: A Large-Scale Tissue-Microarray Study with Two Independent Patient Cohorts, PLoS ONE, 7, 6, e38222, Public Library of Science, 2012 @article {meyer_seven-marker_2012, author = "Stefanie Meyer* and Thomas J. Fuchs * and Anja Bosserhoff and Ferdinand Hofstaedter and Armin Pauer and Volker Roth and Joachim Buhmann and Ingrid Moll and Nikos Anagnostou and Johanna Brandner and Kristian Ikenberg and Holger Moch and Michael Landthaler and Thomas Vogt and Peter Wild", journal = "PLoS ONE", publisher = "Public Library of Science", title = "A Seven-Marker Signature and Clinical Outcome in Malignant Melanoma: A Large-Scale Tissue-Microarray Study with Two Independent Patient Cohorts", year = "2012", month = "06", volume = "7", url = "http://dx.doi.org/10.1371%2Fjournal.pone.0038222", pages = "e38222", number = "6", doi = "10.1371/journal.pone.0038222", } | PDF BibTeX |
| [4] | , A high-throughput metabolomics method to predict high concentration cytotoxicity of drugs from low concentration profiles, Metabolomics, 8, 433-443, Springer Boston, 2012 @article {heux_high-throughput_2012, author = "Stephanie Heux and Thomas J. Fuchs and Joachim Buhmann and Nicola Zamboni and Uwe Sauer", title = "A high-throughput metabolomics method to predict high concentration cytotoxicity of drugs from low concentration profiles", journal = "Metabolomics", publisher = "Springer Boston", issn = "1573-3882", keyword = "Biomedical and Life Sciences", pages = "433-443", volume = "8", issue = "3", url = "http://dx.doi.org/10.1007/s11306-011-0386-0", note = "10.1007/s11306-011-0386-0", year = "2012", } | PDF BibTeX |
| [5] | , p53 suppresses type II endometrial carcinomas in mice and governs endometrial tumour aggressiveness in humans, EMBO Molecular Medicine, Wiley Inc., 2012 @article {wild_p53_2012, author = "Peter J. Wild and Kristian Ikenberg and Thomas J. Fuchs and Strahil Georgiev and Aurelia Noske and Matthias Roessle and Rosmarie Caduff and Athanassios Dellas and Daniel Fink and Holger Moch and Wilhelm Krek and Ian J. Frew", title = "p53 suppresses type II endometrial carcinomas in mice and governs endometrial tumour aggressiveness in humans", journal = "EMBO Molecular Medicine", publisher = "Wiley Inc.", issn = "1757-4684", url = "http://dx.doi.org/10.1002/emmm.201101063", doi = "10.1002/emmm.201101063", year = "2012", } | PDF BibTeX |
| [6] | , End-to-End Dexterous Manipulation with Deliberate Interactive Estimation, International Conference on Robotics and Automation (ICRA) (accepted), 2012, Finalist - Best Manipulation Paper Award @article {hudson_end-to-end_2012, author = "Nicolas H. Hudson and Tom Howard and Jeremy Ma and Abhinandan Jain and Max Bajracharya and Steven Myint and Larry Matthies and Paul Backes and Paul Hebert and Thomas J. Fuchs and Joel Burdick", title = "End-to-End Dexterous Manipulation with Deliberate Interactive Estimation", journal = "International Conference on Robotics and Automation (ICRA) (accepted)", year = "2012", url = "http://robotics.caltech.edu/wiki/images/d/de/DARPAICRA12.pdf", } | PDF BibTeX |
| [7] | , Combined Shape, Appearance and Silhouette for Simultaneous Manipulator and Object Tracking, International Conference on Robotics and Automation (ICRA) (accepted), 2012 @article {hebert_combined_2012, title = "Combined Shape, Appearance and Silhouette for Simultaneous Manipulator and Object Tracking", author = "Paul Hebert and Nicolas Hudson and Jeremy Ma and Thomas Howard and Thomas J. Fuchs and Max Bajracharya and Joel Burdick", journal = "International Conference on Robotics and Automation (ICRA) (accepted)", year = "2012", url = "http://robotics.caltech.edu/wiki/images/d/d3/HebertICRA12.pdf", } | PDF BibTeX |
| [8] | , Computational pathology: Challenges and promises for tissue analysis, Journal of Computerized Medical Imaging and Graphics, 35, 7, 515-530, 2011, Top 25 Hottest Articles 2011 @article {fuchs_computational_2011, title = "Computational pathology: Challenges and promises for tissue analysis", journal = "Journal of Computerized Medical Imaging and Graphics", volume = "35", number = "7", day = "8", month = "April", year = "2011", pages = "515-530", note = "", issn = "0895-6111", doi = "DOI: 10.1016/j.compmedimag.2011.02.006", url = "http://www.sciencedirect.com/science/article/pii/S0895611111000383", author = "Thomas J. Fuchs and Joachim M. Buhmann", } | PDF BibTeX |
| [9] | , Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer, Proceedings of the National Academy of Sciences, 108, 8, 3342-3347, 2011 @article {cima_cancer_2011, author = "Cima, Igor and Schiess, Ralph and Wild, Peter and Kaelin, Martin and Schueffler, Peter and Lange, Vinzenz and Picotti, Paola and Ossola, Reto and Templeton, Arnoud and Schubert, Olga and Thomas J. Fuchs and Leippold, Thomas and Wyler, Stephen and Zehetner, Jens and Jochum, Wolfram and Buhmann, Joachim and Cerny, Thomas and Moch, Holger and Gillessen, Silke and Aebersold, Ruedi and Krek, Wilhelm", title = "Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer", volume = "108", number = "8", pages = "3342-3347", year = "2011", doi = "10.1073/pnas.1013699108", url = "http://www.pnas.org/content/108/8/3342.abstract", eprint = "http://www.pnas.org/content/108/8/3342.full.pdf+html", journal = "Proceedings of the National Academy of Sciences", } | PDF BibTeX |
| [10] | , Aerosols Transmit Prions to Immunocompetent and Immunodeficient Mice, PLoS Pathog, 7, 1, e1001257, Public Library of Science, 2011, In the news: WIRED, ORF, NZZ, Spiegel, Die Welt, Die Zeit, Focus, Bild, 20 Minuten, Salzburger Nachrichten, N24,n-tv, Handelsblatt, SF, Tagesspiegel, Spektrum, NewScientist, Risc Science, Deutsche Welle, USZ, Daily Mail, The Times od India, Scientific American, more ... Video Schweizer Fernsehen (german) @article {haybaeck_aerosols_2011, author = "Haybaeck, Johannes and Heikenwalder, Mathias and Klevenz, Britta and Schwarz, Petra and Margalith, Ilan and Bridel, Claire and Mertz, Kirsten and Zirdum, Elizabeta and Petsch, Benjamin and Thomas J. Fuchs and Stitz, Lothar and Aguzzi, Adriano", journal = "PLoS Pathog", publisher = "Public Library of Science", title = "Aerosols Transmit Prions to Immunocompetent and Immunodeficient Mice", year = "2011", month = "01", volume = "7", url = "http://dx.doi.org/10.1371%2Fjournal.ppat.1001257", pages = "e1001257", number = "1", doi = "10.1371/journal.ppat.1001257", } | PDF BibTeX |
| [11] | , Infinite mixture-of-experts model for sparse survival regression with application to breast cancer, BMC Bioinformatics, 11, Suppl 8, S8, 2010 @Article {raman_infinite_2010, author = "Raman, Sudhir and Thomas J. Fuchs and Wild, Peter and Dahl, Edgar and Buhmann, Joachim and Roth, Volker", title = "Infinite mixture-of-experts model for sparse survival regression with application to breast cancer", journal = "BMC Bioinformatics", volume = "11", year = "2010", number = "Suppl 8", pages = "S8", url = "http://www.biomedcentral.com/1471-2105/11/S8/S8", doi = "10.1186/1471-2105-11-S8-S8", pubmedid = "21034433", issn = "1471-2105", } | PDF BibTeX |
| [12] | , Computational TMA analysis and cell nucleus classification of renal cell carcinoma, Proceedings of the 32nd DAGM conference on Pattern recognition, 202--211, Springer, 2010 @inproceedings {schuffler_computational_2010, author = "Schueffler, Peter J. and Thomas J. Fuchs and Ong, Cheng Soon and Roth, Volker and Buhmann, Joachim M.", title = "Computational TMA analysis and cell nucleus classification of renal cell carcinoma", booktitle = "Proceedings of the 32nd DAGM conference on Pattern recognition", year = "2010", isbn = "3-642-15985-0, 978-3-642-15985-5", location = "Darmstadt, Germany", pages = "202--211", numpages = "10", url = "http://portal.acm.org/citation.cfm?id=1926258.1926281", acmid = "1926281", publisher = "Springer", address = "Berlin, Heidelberg", } | PDF BibTeX |
| [13] | , TAK1 suppresses a NEMO-dependent but NF-kappaB-independent pathway to liver cancer, Cancer Cell, 17, 5, 481--496, 2010 @Article {bettermann_tak1_2010, title = "TAK1 suppresses a NEMO-dependent but NF-kappaB-independent pathway to liver cancer", volume = "17", url = "http://www.ncbi.nlm.nih.gov/pubmed/20478530", number = "5", journal = "Cancer Cell", author = "Bettermann, Kira and Vucur, Mihael and Haybaeck, Johannes and Koppe, Christiane and Janssen, Joern and Heymann, Felix and Weber, Achim and Weiskirchen, Ralf and Liedtke, Christian and Gassler, Nikolaus and Mueller, Michael and de Vos, Rita and Wolf, Monika Julia and Boege, Yannick and Seleznik, Gitta Maria and Zeller, Nicolas and Erny, Daniel and Thomas J. Fuchs and Zoller, Stefan and Cairo, Stefano and Buendia, Marie-Annick and Prinz, Marco and Akira, Shizuo and Tacke, Frank and Heikenwaelder, Mathias and Trautwein, Christian and Luedde, Tom", year = "2010", pages = "481--496", } | PDF BibTeX |
| [14] | , Geometrical consistent 3D tracing of neuronal processes in ssTEM data, Proceedings of the 13th international conference on Medical image computing and computer-assisted intervention: Part II, MICCAI'10, 209--216, Springer-Verlag, 2010 @inproceedings {kaynig_geometrical_2010, author = "Kaynig, Verena and Thomas J. Fuchs and Buhmann, Joachim M.", title = "Geometrical consistent 3D tracing of neuronal processes in ssTEM data", booktitle = "Proceedings of the 13th international conference on Medical image computing and computer-assisted intervention: Part II", series = "MICCAI'10", year = "2010", isbn = "3-642-15744-0, 978-3-642-15744-8", location = "Beijing, China", pages = "209--216", numpages = "8", url = "http://portal.acm.org/citation.cfm?id=1928047.1928075", acmid = "1928075", publisher = "Springer-Verlag", address = "Berlin, Heidelberg", } | PDF BibTeX |
| [15] | , The Translation-invariant Wishart-Dirichlet Process for Clustering Distance Data, Proceedings of the 27th International Conference on Machine Learning, ICML'10, 1111-1118, 2010, Runner-up - Best Paper Award @inproceedings {vogt_translation-invariant_2010, author = "Julia E. Vogt and Sandhya Prabhakaran and Thomas J. Fuchs and Volker Roth", title = "The Translation-invariant Wishart-Dirichlet Process for Clustering Distance Data", booktitle = "Proceedings of the 27th International Conference on Machine Learning", series = "ICML'10", year = "2010", pages = "1111-1118", url = "http://www.icml2010.org/papers/248.pdf", } | PDF BibTeX |
| [16] | , Neuron geometry extraction by perceptual grouping in ssTEM images, Computer Vision and Pattern Recognition, IEEE Computer Society Conference on, 0, 2902-2909, IEEE Computer Society, 2010 @article {kaynig_neuron_2010, author = "Verena Kaynig and Thomas J. Fuchs and Joachim M. Buhmann", title = "Neuron geometry extraction by perceptual grouping in ssTEM images", journal = "Computer Vision and Pattern Recognition, IEEE Computer Society Conference on", volume = "0", isbn = "978-1-4244-6984-0", year = "2010", pages = "2902-2909", doi = "http://doi.ieeecomputersociety.org/10.1109/CVPR.2010.5540029", url = "http://www.computer.org/portal/web/csdl/doi/10.1109/CVPR.2010.5540029", publisher = "IEEE Computer Society", address = "Los Alamitos, CA, USA", } | PDF BibTeX |
| [17] | , Effect of reader experience on variability, evaluation time and accuracy of coronary plaque detection with computed tomography coronary angiography, European Radiology, 20, 1599-1606, Springer-Verlag, 2010 @article {saur_effect_2010, author = "Saur, Stefan and Alkadhi, Hatem and Stolzmann, Paul and Baumueller, Stephan and Leschka, Sebastian and Scheffel, Hans and Desbiolles, Lotus and Thomas J. Fuchs and Szekely, Gabor and Cattin, Philippe", affiliation = "Computer Vision Laboratory, ETH Zurich, Zurich, Switzerland", title = "Effect of reader experience on variability, evaluation time and accuracy of coronary plaque detection with computed tomography coronary angiography", journal = "European Radiology", publisher = "Springer-Verlag", address = "Berlin, Heidelberg", issn = "0938-7994", keyword = "Medicine", pages = "1599-1606", volume = "20", issue = "7", url = "http://dx.doi.org/10.1007/s00330-009-1709-7", note = "10.1007/s00330-009-1709-7", year = "2010", } | PDF BibTeX |
| [18] | , Randomized Tree Ensembles for Object Detection in Computational Pathology, Proceedings of the 5th International Symposium on Advances in Visual Computing: Part I, ISVC '09, 367--378, Springer-Verlag, 2009 @inproceedings {fuchs_randomized_2009, author = "Thomas J. Fuchs and Haybaeck, Johannes and Wild, Peter J. and Heikenwalder, Mathias and Moch, Holger and Aguzzi, Adriano and Buhmann, Joachim M.", title = "Randomized Tree Ensembles for Object Detection in Computational Pathology", booktitle = "Proceedings of the 5th International Symposium on Advances in Visual Computing: Part I", series = "ISVC '09", year = "2009", isbn = "978-3-642-10330-8", location = "Las Vegas, Nevada", pages = "367--378", numpages = "12", url = "http://dx.doi.org/10.1007/978-3-642-10331-5_35", doi = "http://dx.doi.org/10.1007/978-3-642-10331-5_35", acmid = "1696162", publisher = "Springer-Verlag", address = "Berlin, Heidelberg", } | PDF BibTeX |
| [19] | , Inter-active learning of randomized tree ensembles for object detection, Computer Vision Workshops (ICCV Workshops), 2009 IEEE 12th International Conference on Computer Vision, 1370--1377, 2009 @inproceedings {fuchs_inter-active_2009, author = "Thomas J. Fuchs and Joachim M. Buhmann", title = "Inter-active learning of randomized tree ensembles for object detection", booktitle = "Computer Vision Workshops (ICCV Workshops), 2009 IEEE 12th International Conference on Computer Vision", year = "2009", pages = "1370--1377", isbn = "978-1-4244-4442-7", doi = "http://dx.doi.org/10.1109/ICCVW.2009.5457452", url = "http://dx.doi.org/10.1109/ICCVW.2009.5457452", } | PDF BibTeX |
| [20] | , Detection of Urothelial Bladder Cancer Cells in Voided Urine Can Be Improved by a Combination of Cytology and Standardized Microsatellite Analysis, Cancer Epidemiol Biomarkers Prev, 18, 6, 1798-1806, 2009 @article {wild_detection_2009, author = "Peter J. Wild and Thomas J. Fuchs and Robert Stoehr and Dieter Zimmermann and Simona Frigerio and Barbara Padberg and Inbal Steiner and Ellen C. Zwarthoff and Maximilian Burger and Stefan Denzinger and Ferdinand Hofstaedter and Glen Kristiansen and Thomas Hermanns and Hans-Helge Seifert and Maurizio Provenzano and Tullio Sulser and Volker Roth and Joachim M. Buhmann and Holger Moch and Arndt Hartmann", title = "Detection of Urothelial Bladder Cancer Cells in Voided Urine Can Be Improved by a Combination of Cytology and Standardized Microsatellite Analysis", journal = "Cancer Epidemiol Biomarkers Prev", volume = "18", number = "6", pages = "1798-1806", doi = "10.1158/1055-9965.EPI-09-0099", year = "2009", url = "http://cebp.aacrjournals.org/cgi/content/abstract/18/6/1798", eprint = "http://cebp.aacrjournals.org/cgi/reprint/18/6/1798.pdf", } | PDF BibTeX |
| [21] | , Prognostic relevance of Wnt-inhibitory factor-1 (WIF1) and Dickkopf-3 (DKK3) promoter methylation in human breast cancer, BMC Cancer, 9, 1, 217, 2009 @Article {veeck_prognostic_2009, author = "Jurgen Veeck and Peter Wild and Thomas J. Fuchs and Peter Schueffler and Arndt Hartmann and Ruth Knuchel and Edgar Dahl", title = "Prognostic relevance of Wnt-inhibitory factor-1 (WIF1) and Dickkopf-3 (DKK3) promoter methylation in human breast cancer", journal = "BMC Cancer", volume = "9", year = "2009", number = "1", pages = "217", url = "http://www.biomedcentral.com/1471-2407/9/217", doi = "10.1186/1471-2407-9-217", pubmedid = "19570204", issn = "1471-2407", } | PDF BibTeX |
| [22] | , Graph-Based Pancreatic Islet Segmentation for Early Type 2 Diabetes Mellitus on Histopathological Tissue, MICCAI (1), 633-640, 2009 @inproceedings {floros_graph-based_2009, author = "Xenofon E. Floros and Thomas J. Fuchs and Markus P. Rechsteiner and Giatgen Spinas and Holger Moch and Joachim M. Buhmann", title = "Graph-Based Pancreatic Islet Segmentation for Early Type 2 Diabetes Mellitus on Histopathological Tissue", booktitle = "MICCAI (1)", year = "2009", pages = "633-640", ee = "http://dx.doi.org/10.1007/978-3-642-04271-3_77", url = "http://www.springerlink.com/index/2PG4628N77772L77.pdf", } | PDF BibTeX |
| [23] | , Nuclear detection of Y-box protein-1 (YB-1) closely associates with progesterone receptor negativity and is a strong adverse survival factor in human breast cancer, BMC Cancer, 9, 1, 410, 2009 @Article {dahl_nuclear_2009, author = "Edgar Dahl and Abdelaziz En-Nia and Frank Wiesmann and Renate Krings and Sonja Djudjaj and Elisabeth Breuer and Thomas J. Fuchs and Peter Wild and Arndt Hartmann and Sandra Dunn and Peter Mertens", title = "Nuclear detection of Y-box protein-1 (YB-1) closely associates with progesterone receptor negativity and is a strong adverse survival factor in human breast cancer", journal = "BMC Cancer", volume = "9", year = "2009", number = "1", pages = "410", url = "http://www.biomedcentral.com/1471-2407/9/410", doi = "10.1186/1471-2407-9-410", pubmedid = "19930682", issn = "1471-2407", } | PDF BibTeX |
| [24] | , Prediction rules for the detection of coronary artery plaques: evidence from cardiac CT, Investigative Radiology, 44, 8, 483-490, 2009 @Article {saur_predictive_2009, author = "Stefan C. Saur and Philippe C. Cattin and Lotus Desbiolles and Thomas J. Fuchs and Gabor Szekely and Hatem Alkadhi", title = "Prediction rules for the detection of coronary artery plaques: evidence from cardiac CT", journal = "Investigative Radiology", year = "2009", volume = "44", pages = "483-490", number = "8", month = "August", doi = "http://dx.doi.org/10.1097/RLI.0b013e3181a8afc4", url = "http://journals.lww.com/investigativeradiology/Abstract/2009/08000/Prediction_Rules_for_the_Detection_of_Coronary.8.aspx", } | PDF BibTeX |
| [25] | , The Bayesian group-Lasso for analyzing contingency tables, Proceedings of the 26th Annual International Conference on Machine Learning, ICML '09, 881--888, ACM, 2009 @inproceedings {raman_bayesian_2009, author = "Sudhir Raman and Thomas J. Fuchs and Peter J. Wild and Edgar Dahl and Volker Roth", title = "The Bayesian group-Lasso for analyzing contingency tables", booktitle = "Proceedings of the 26th Annual International Conference on Machine Learning", series = "ICML '09", year = "2009", isbn = "978-1-60558-516-1", location = "Montreal, Quebec, Canada", pages = "881--888", numpages = "8", url = "http://doi.acm.org/10.1145/1553374.1553487", doi = "10.1145/1553374.1553487", acmid = "1553487", publisher = "ACM", address = "New York, NY, USA", } | PDF BibTeX |
| [26] | , Guided review by frequent itemset mining: additional evidence for plaque detection, International Journal of Computer Assisted Radiology and Surgery, 4, 3, 263--271, 2009 @Article {saur_guided_2009, author = "Stefan C. Saur and Hatem Alkadhi and Lotus Desbiolles and Thomas J. Fuchs and Gabor Szekely and Philippe C. Cattin", title = "Guided review by frequent itemset mining: additional evidence for plaque detection", journal = "International Journal of Computer Assisted Radiology and Surgery", year = "2009", volume = "4", pages = "263--271", number = "3", month = "May", url = "http://dx.doi.org/10.1007/s11548-009-0290-5", } | PDF BibTeX |
| [27] | , Computational Pathology Analysis of Tissue Microarrays Predicts Survival of Renal Clear Cell Carcinoma Patients, Medical Image Computing and Computer-Assisted Intervention - MICCAI 2008, Lecture Notes in Computer Science, 5242, 1-8, Springer-Verlag, 2008 @incollection {fuchs_computational_2008, author = "Thomas J. Fuchs and Peter J. Wild and Holger Moch and Joachim M. Buhmann", title = "Computational Pathology Analysis of Tissue Microarrays Predicts Survival of Renal Clear Cell Carcinoma Patients", booktitle = "Medical Image Computing and Computer-Assisted Intervention - MICCAI 2008", series = "Lecture Notes in Computer Science", editor = "Metaxas, Dimitris and Axel, Leon and Fichtinger, Gabor and Szekely, Gabor", publisher = "Springer-Verlag", address = "Berlin, Heidelberg", isbn = "978-3-540-85989-5", keyword = "Computer Science", pages = "1-8", volume = "5242", url = "http://dx.doi.org/10.1007/978-3-540-85990-1_1", doi = "10.1007/978-3-540-85990-1_1", year = "2008", } | PDF BibTeX |
| [28] | , Weakly Supervised Cell Nuclei Detection and Segmentation on Tissue Microarrays of Renal Cell Carcinoma, Pattern Recognition. DAGM 2008, Lecture Notes in Computer Science, 5096, 173--182, Springer-Verlag, 2008 @InProceedings {fuchs_weakly_2008, author = "Thomas J. Fuchs and Tilman Lange and Peter J. Wild and Holger Moch and Joachim M. Buhmann", title = "Weakly Supervised Cell Nuclei Detection and Segmentation on Tissue Microarrays of Renal Cell Carcinoma", booktitle = "Pattern Recognition. DAGM 2008", volume = "5096", publisher = "Springer-Verlag", address = "Berlin, Heidelberg", pages = "173--182", series = "Lecture Notes in Computer Science", year = "2008", isbn = "978-3-540-69320-8", issn = "0302-9743 (Print) 1611-3349 (Online)", doi = "10.1007/978-3-540-69321-", url = "http://www.springerlink.com/index/L380G56T1V230715.pdf", } | PDF BibTeX |
| [29] | , Automatic and Robust Forearm Segmentation using Graph Cuts, 5th IEEE International Symposium on Biomedical Imaging. ISBI 2008, 77--80, IEEE, 2008 @InProceedings {fuernstahl_automatic_2008, author = "Philipp Fuernstahl and Thomas J. Fuchs and Andreas Schweizer and Ladislav Nagy and Gabor Szekely and Matthias Harders", title = "Automatic and Robust Forearm Segmentation using Graph Cuts", booktitle = "5th IEEE International Symposium on Biomedical Imaging. ISBI 2008", publisher = "IEEE", address = "Paris, France", year = "2008", pages = "77--80", url = "http://dx.doi.org/10.1109/ISBI.2008.4540936", doi = "10.1109/ISBI.2008.4540936", isbn = "978-1-4244-2002-5", } | PDF BibTeX |
| [30] | , Nuclear karyopherin alpha2 expression predicts poor survival in patients with advanced breast cancer irrespective of treatment intensity, International Journal of Cancer, 123/6, IF 4,693, 1433--1438, Wiley Inc., 2008 @article {gluz_nuclear_2008, author = "Gluz, Oleg and Wild, Peter and Meiler, Robert and Diallo-Danebrock, Raihana and Ting, Evelyn and Mohrmann, Svjetlana and Schuett, Gerhart and Dahl, Edgar and Thomas J. Fuchs and Herr, Alexander and Gaumann, Andreas and Frick, Markus and Poremba, Christopher and Nitz, Ulrike Anneliese and Hartmann, Arndt", title = "Nuclear karyopherin alpha2 expression predicts poor survival in patients with advanced breast cancer irrespective of treatment intensity", journal = "International Journal of Cancer", volume = "123/6", number = "IF 4,693", publisher = "Wiley Inc.", issn = "1097-0215", url = "http://onlinelibrary.wiley.com/doi/10.1002/ijc.23628/full", doi = "10.1002/ijc.23628", pages = "1433--1438", year = "2008", } | PDF BibTeX |
| [31] | , The acute coronary syndrome -- pre-hospital diagnostic quality, Resuscitation, 66, 3, 323 - 330, 2005 @article {gemes_acute_2005, title = "The acute coronary syndrome -- pre-hospital diagnostic quality", journal = "Resuscitation", volume = "66", number = "3", pages = "323 - 330", year = "2005", issn = "0300-9572", doi = "DOI: 10.1016/j.resuscitation.2005.04.006", url = "http://www.sciencedirect.com/science/article/B6T19-4GV9846-3/2/bcd3755266ba68b84536b39803426401", author = "Geza Gemes and Thomas J. Fuchs and Gernot Wildner and Freyja-Maria Smolle-Juettner and Josef Smolle and Kurt Stoschitzky and Gerhard Prause", } | PDF BibTeX |
Theses
- Thomas J. Fuchs, Computational Pathology: A Machine Learning Approach, PhD Thesis, ETH Zurich, 2010
- Thomas J. Fuchs, Bayesian Networks Classification in Bioinformatics and Medical Decision Support, Master Thesis, Technical University Graz, 2005
Patents
- Thomas J. Fuchs, Wachmann B., Cheng J., Wehrwein B., Recursive d-separation Determination in Bayesian Networks, International Patent
- Thomas J. Fuchs, Wachmann B., Neubauer C., Cheng J., Semiautomated Lymph Node Classification, Invention Disclosure
Other Publications
- Thomas J. Fuchs, et al., Chronik der Steiermark. Eine interaktive Geschichte der Steiermark., Multimedia CD-ROM, Archiv Verlag Wien, 2003
- Renate Basch-Ritter, Thomas J. Fuchs, et al., Die k.u.k. Riviera. Reisen durch Historie und Gegenwart, Multimedia CD-ROM, www.kuk-riviera.at, ISBN 3-9500977-1-6, 2002
- Renate Basch-Ritter, Thomas J. Fuchs, et al., Österreich auf allen Meeren. Geschichte der k.(u.)k. Marine von 1382 bis 1918, Multimedia CD-ROM, www.kuk-marine.at, ISBN 3-9500977-0-8, 2001
- Renate Basch-Ritter, Thomas J. Fuchs, et al., 1000 Jahre Österreich, Multimedia CD-ROM (awards on national and European level), 1996
Research
Research interests:- Approximate Bayesian Computation
- Randomized Decision Forests
- Object Detection
- Survival Statistics
- Model Selection
Favorite areas of application:
- Computational Pathology: www.computational-pathology.org
- Space Exploration and Astronomy
Computer Vision
Left: MIB-1 stained nuclei of hepatocytes in murine liver tissue. (0.23μm/pixel) Right: SAR images from Venus, taken by the Magellan space probe. (75m/pixel)
Machine Learning
Left: Learning of randomized detection forests (RDF).
Right: Graphical Model of a Bayesian mixture of survival experts.
Computational Pathology
www.computational-pathology.org The great success of histology in general and tissue microarrays (TMA) in particular is closely related to experimental techniques which yield localized protein expression values in tissue. High resolution scanning technologies in recent years renders an automated analysis of histological slices feasible both for medical research and for practical clinical work. This project aims at the development of a data processing pipeline which models the complete pathological workflow from the microscopic inspection of tissue samples to the diagnostic analysis of survival curves.
The workflow is subdivided into three main parts:
(i.) Generating a gold standard: The absence of an objective ground truth requires us to generate a gold standard by combining the knowledge of several pathologists. The inference of a gold standard has to be performed for cell nuclei detection in tissue, for benign/cancerous classification of cells and for quantification of stainings. These labels are indispensable for the training of classifiers and for their validation.
(ii.) Machine learning and pattern recognition: We are developing a data processing system which is able to detect cell nuclei, to segment their shapes, to classify them as tumor or non-tumor cells and to estimate protein expression values. This system uses algorithm technology from computer vision and statistical learning.
(iii.) Validation of the results: The automatic tissue classification is validated w.r.t. the gold standard and external targets such as the survival time of patients or the development of metastasis.
The proof of concept will be demonstrated by an operational workflow to automate and thus to objectify the analysis of histological tissues and, thereby, promote biomedical and clinical research.
Teaching
Master Students
- Georg Troxler: "Automated estimation of immunohistochemical staining on tissue microarrays of clear cell renal cell carcinoma"
- Sara Abbasabadi: "Automated Micrometastases Detection on Immunohistochemically Stained Lymph Nodes"
Lectures & Exercises
- [2012] Caltech Machine Learning Seminar, more ...
- [2010] Computational Intelligence Lab, more ...
- [2009] Advanced Topics in Pattern Recognition, more ...
- [2008] CIMST Summerschool
- [2007] CIMST Summerschool
- [2007] C# Programming (Languages in Depth series), more ...
- [2006] Introductions to Computational Science
- [2006] Informatik I
Software
Computer Vision - Experiment Manager
CompPath Application Suite
- TMA Annotator
- TMA Estimator
- TMA Classifier
- Node Annotator
Computational Pathology Online - Web Application
Metabolomics Studio - R Package
PRR: Prediction Relevance Ranking - R Package
