Welcome

I am a PhD student in the Machine Learning Laboratory headed by Prof. Joachim M. Buhmann, chair of Information Science and Engineering at ETH Zurich, Switzerland.

I am also a member of the Competence Center for Systems Physiology and Metabolic Diseases.

Research Interests

• Randomized Decision Forests
• Object Detection
• Survival Statistics
• Model Selection
• Machine Learning in Space Exploration

Research

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

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.

Publications

Peer-Reviewed Journal & Conference Publications

1. Thomas J. Fuchs and Joachim M. Buhmann, Computational Pathology: Challenges and Promises for Tissue Analysis, Journal of Computerized Medical Imaging and Graphics, Special Issue on Whole Slide Microscopic Image Processing, 2011 (in print)
2. Igor Cima, Ralph Schiess, Peter Wild, Martin Kaelin, Peter Schüffler, Vinzenz Lange, Paola Picotti, Reto Ossola, Arnoud Templeton, Olga Schubert, Thomas Fuchs, Thomas Leippold, Stephen Wyler, Jens Zehetner, Wolfram Jochum, Joachim Buhmann, Thomas Cerny, Holger Moch, Silke Gillessen, Ruedi Aebersold, and Wilhelm Krek, Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer, PNAS, February 7, 2011, doi:10.1073/pnas.1013699108
3. Johannes Haybaeck, Mathias Heikenwalder, Britta Klevenz, Petra Schwarz, Ilan Margalith, Claire Bridel, Kirsten Mertz, Elizabeta Zirdum, Benjamin Petsch, Thomas J. Fuchs, Lothar Stitz, Adriano Aguzzi, Aerosols Transmit Prions to Immunocompetent and Immunodeficient Mice, PLoS Pathog 7(1): e1001257. 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)
4. Sudhir Raman, Thomas J. Fuchs, Peter J. Wild , Edgar Dahl, Joachim M. Buhmann and Volker Roth, Infinite mixture-of-experts model for sparse survival regression with application to breast cancer, BMC Bioinformatics 2010
5. Peter J. Schuefler, Thomas J. Fuchs, Cheng Soon Ong, Joachim M. Buhmann, Computational TMA Analysis and Cell Nucleus Classification of Renal Cell Carcinoma, DAGM 2010
6. Kira Bettermann, Mihael Vucur, Johannes Haybaeck, Christiane Koppe, Jörn Janssen, Felix Heymann, Achim Weber, Ralf Weiskirchen, Christian Liedtke, Nikolaus Gassler, Michael Müller, Rita de Vos, Monika Julia Wolf, Yannick Boege, Gitta Maria Seleznik, Nicolas Zeller, Daniel Erny, Thomas Fuchs, Stefan Zoller, Stefano Cairo, Marie-Annick Buendia, Marco Prinz, Shizuo Akira, Frank Tacke, Mathias Heikenwalder, Christian Trautwein and Tom Luedde, TAK1 suppresses a NEMO-dependent, but NF-kB-independent pathway to liver cancer, Cancer CELL 17, 481-496, May 18, 2010
7. Verena Kaynig, Thomas J. Fuchs, Joachim M. Buhmann, Geometrical Consistent 3D Tracing of Neuronal Processes in ssTEM Data, MICCAI 2010
8. Julia E. Vogt, Sandhya Prabhakaran, Thomas J. Fuchs and Volker Roth, The Translation-invariant Wishart-Dirichlet Process for Clustering Distance Data, ICML 2010, runner-up Best Paper Award
9. Verena Kaynig, Thomas J. Fuchs, Joachim M. Buhmann, Neuron Geometry Extraction by Perceptual Grouping in ssTEM images, CVPR 2010
10. Stefan C. Saur, Hatem Alkadhi, Paul Stolzmann, Stephan Baumüller, Sebastian Leschka, Hans Scheffel, Lotus Desbiolles, Thomas J. Fuchs, Gábor Székely, Philippe C. Cattin, Effect of reader experience on variability, evaluation time and accuracy of coronary plaque detection with computed tomography coronary angiography, European Radiology, Volume 20, Number 7 / July, 2010
11. Thomas J. Fuchs, Johannes Haybaeck, Peter Wild, Mathias Heikenwalder, Holger Moch, Adriano Aguzzi, Joachim M. Buhmann, Randomized Tree Ensembles for Object Detection in Computational Pathology, ISVC 2009
12. Thomas J. Fuchs and Joachim M. Buhmann, Inter-Active Learning of Randomized Tree Ensembles for Object Detection, Workshop on On-line Learning for Computer Vision, ICCV 2009
13. Wild PJ, Fuchs TJ, Stoehr R, Zimmermann D, Frigerio S, Padberg B, Steiner I, Zwarthoff EC, Burger M, Denzinger S, Hofstaedter F, Kristiansen G, Hermanns T, Seifert HH, Provenzano M, Sulser T, Roth V, Buhmann JM, Moch H, Hartmann A., 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. 2009 Jun;18(6):1798-806. Epub 2009 May 19.
14. Juergen Veeck, Peter J. Wild, Thomas J. Fuchs, Peter J. Schueffler, Arndt Hartmann, Ruth Knüchel, Edgar Dahl, Prognostic relevance of Wnt-inhibitory factor-1 (WIF1) and Dickkopf-3 (DKK3) promoter methylation in human breast cancer, BMC Cancer 2009, 9:217
15. Floros X., Fuchs T.J., Rechsteiner M., Spinas G., Moch H., Buhmann J.M., Graph-Based Pancreatic Islet Segmentation for Early Type 2 Diabetes Mellitus on Histopathological Tissue, Medical Image Computing and Computer-Assisted Intervention, MICCAI 2009
16. Edgar Dahl, Abdelaziz En-Nia, Frank Wiesmann, Renate Krings, Sonja Djudjaj, Elisabeth Breuer, Thomas J Fuchs, Peter J Wild, Arndt Hartmann, Sandra E Dunn and Peter R Mertens, 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 2009, 9:410
17. Stefan C. Saur, Philippe C. Cattin, Lotus Desbiolles, Thomas J. Fuchs, Gábor Székely, Hatem Alkadhi, Prediction Rules for the Detection of Coronary Artery Plaques: Evidence From Cardiac CT, Journal of Investigative Radiology, 2009, vol. 44, no8, pp. 483-490
18. Sudhir Raman, Thomas J. Fuchs, Peter J. Wild, Edgar Dahl, Volker Roth, The Bayesian Group-Lasso for Analyzing Contingency Tables, Proceedings of the 26th International Conference on Machine Learning, Montreal, Canada, ICML 2009.
19. Stefan C. Saur, Hatem Alkadhi, Lotus Desbiolles, Thomas J. Fuchs, Gábor Székely and Philippe C. Cattin, Guided review by frequent itemset mining: additional evidence for plaque detection, International Journal of Computer Assisted Radiology and Surgery, 2009
20. Fuchs TJ, Wild P, Moch H, Buhmannm J, Computational Pathology Analysis of Tissue Microarrays Predicts Survival of Renal Clear Cell Carcinoma Patients", Medical Image Computing and Computer-Assisted Intervention, MICCAI 2008.
21. Fuchs TJ, Lange T, Wild P, Moch H, Buhmann J, Weakly Supervised Cell Nuclei Detection and Segmentation on Tissue Microarrays of Renal Cell Carcinoma, DAGM 2008.
22. Volker Roth, Thomas Fuchs, Sudhir Raman, Peter Wild, Edgar Dahl and Joachim Buhmann. Full Bayesian Survival Models for Analyzing Human Breast Tumors., MLCB - Machine Learning in Computational Biology Workshop @ NIPS 2008
23. Fuernstahl P, Fuchs TJ, Schweizer A, Nagy L, Székely G, Harders M, Automatic and Robust Forearm Segmentation using Graph Cuts, Biomedical Imaging: From Nano to Macro, ISBI 2008.
24. Gluz O, Wild P, Meiler R, Diallo-Danebrock R, Ting E, Mohrmann S, Schuett G, Dahl E, Fuchs TJ, Herr A, Gaumann A, Frick M, Poremba C, Nitz UA, Hartmann A., Nuclear Karyopherin 2 expression predicts poor survival in patients with advanced breast cancer irrespective of treatment intensity., International Journal of Cancer 2008 Sep 15;123(6):1433-8.
25. Gemes G, Fuchs TJ, Wildner G, Smolle-Juttner FM, Smolle J, Stoschitzky K, Prause G, The Acute Coronary Syndrome - Prehospital diagnostic quality, Resuscitation. 2005 Sep;66(3):323-30.

Theses & Technical Reports

1. Thomas J. Fuchs, Computational Pathology: A Machine Learning Approach, PhD Thesis, ETH Zurich, 2010
2. Thomas J. Fuchs, Bayesian Networks Classification in Bioinformatics and Medical Decision Support, Master Thesis, Technical University Graz, 2005

Patents & Invention Disclosures

1. Fuchs Th.J., Wachmann B., Cheng J., Wehrwein B., Recursive d-separation Determination in Bayesian Networks, International Patent
2. Fuchs Th.J., Wachmann B., Neubauer C., Cheng J., Semiautomated Lymph Node Classification, Invention Disclosure

Workshop Papers & Posters

1. Wey N., Fuchs Th., Bieri M., Wild P., Abbasabadi S., Wethmar A., Aguzzi A., Buhmann J., Moch H., Computer based measurement of morphologic features on virtual histological slides, 11th Annual MipTec Conference, 2008
2. T.J. Fuchs, P.J. Wild, N. Wey, T. Lange, P. Fürnstahl, W. Einhäuser, H. Moch, J. Buhmann, Automated analysis of immunohistochemical staining of clear cell renal cell carcinoma tissue microarrays, Tagung der Deutschen Gesellschaft für Pathologie, DGP 2008.
3. P.J. Wild, T. Fuchs, I. Steiner, S. Frigerio, D.R. Zimmermann, B. Padberg, E.C. Zwarthoff, R. Stoehr, F. Hofstaedter, G.O. Kristiansen, S. Denzinger, M. Provenzano, T. Hermanns, H.H. Seifert, T. Sulser, V. Roth1, J.M. Buhmann, H. Moch, A. Hartmann, Combined analysis of FGFR3 status and UroVysion test exactly defines high-grade and high-stage urothelial bladder tumors, Tagung der Deutschen Gesellschaft für Pathologie, DGP 2008.
4. T. Fuchs, P.J. Wild, P. Fürnstahl, N. Wey, W. Einhäuser, H. Moch, J. Buhmann, Automated quantification of immunohistochemical staining of clear cell renal cell carcinoma tissue microarrays, CIMST Workshop 2008
5. Corinne Dahinden, Thomas Fuchs, Volker Roth, Peter Wild, Peter Schraml, Joachim Buhmann, Peter Bühlmann, and Holger Moch, Variable Selection and Interaction Analysis for Survival Time Prediction from Tissue Microarray Data, CC-SPMD Retreat Ittingen, 2008.
6. Stéphanie Heux, Jennifer C. Ewald, Thomas J. Fuchs, Joachim M. Buhmann, Uwe Sauer, Functional elucidation of drug targets in metabolism and drug toxicity in yeast with metabolomics and fluxomics, CC-SPMD Retreat Ittingen, 2008.
7. T. Fuchs, V. Roth, P.J. Wild, J.W.F. Catto, A. Hartmann, H. Moch, J. Buhmann, Group-wise Interaction Analysis of Molecular Markers in Urothelial Cancer Progression, Statistics for Biomolecular Data Intergration and Modeling, Wokrshop, Ascona 2007,
8. Corinne Dahinden, Thomas Fuchs, Tilman Lange, Peter Bühlmann, Joachim Buhmann, Peter Schraml, Peter Wild and Holger Moch, Automated Quantification of Protein Expression on Tissue Microarrays from Human Renal Cell Carcinoma and Modelling of Molecular Pathways, CC-SPMD Retreat Ittingen, 2007.
9. Sarah-Maria Fendt, Thomas Fuchs, Silvia Boller, Joachim Buhmann and Uwe Sauer, Functional mapping of regulation in metabolism, CC-SPMD Retreat Ittingen, 2007.
10. Unal G., Fuchs Th.J., Wachmann B., Fang T., Slabaugh G., Krieg R., Schultz Ch., Seethamraju R., Harisinghani M., Weissleder R., A System for Lymph Node Segmentation and Classification Using LN-MRI
11. Hartler, J.; Thallinger, G.; Stocker, G.; Sturn, A.; Burkard, T.; Körner, E.; Fuchs, T.; Mechtler, K.; Trajanoski, Z.: MASPECTRAS:Web-based System for Storage, Retrieval, Quantification and Analysis of Proteomic LC MS/MS Data, Third International Symposium of the Austrian Proteomics Platform, Seefeld 2006
12. Hartler, J.; Thallinger, G.; Stocker, G.; Sturn, A.; Burkard, T.; Körner, E.; Fuchs, T.; Mechtler, K.; Trajanoski, Z.: MASPECTRAS:Web-based System for Storage, Retrieval, and Analysis of Proteomic LC MS/MS Data, HUPO 4th Annual World Congress. Munich 2005
13. Hartler, J.; Thallinger, G.; Sturn, A.; Burkard, T.; Körner, E.; Fuchs, T.; Mechtler, K.; Trajanoski, Z.: MASPECTRAS. - in: Web-basiertes Datenbanksystem zur Verwaltung von Proteomik-Daten, Österreichische Akademie der Wissenschaften. 2005
14. Hartler, J.; Fuchs, T.; Thallinger, G.; Morandell, S.; Huber, L.; Mechtler, K.; Trajanoski, Z.: Development of a web based mass spectrometry analysis system, ÖGBMT Symposium 2004

Other Publications

1. Th.J. Fuchs et al., Chronik der Steiermark. Eine interaktive Geschichte der Steiermark., Multimedia CD-ROM, Archiv Verlag Wien, 2003
2. R. Basch-Ritter, Th.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
3. R. Basch-Ritter, Th.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
4. R. Basch-Ritter, Th.J. Fuchs, et al., 1000 Jahre Österreich, Multimedia CD-ROM (awards on national and European level), 1996

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

• [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

http://comp-path.inf.ethz.ch

Metabolomics Studio - R Package

PRR: Prediction Relevance Ranking - R Package

Random Detection Forests

C# Library, coming soon

Links

• mloss: machine learning open source software
• Machine Learning Laboratory @ ETH
• Department of Computer Science @ ETH
• ETH Zurich
• University Hospital Zurich
• Competence Center of Systems Physiology and Metabolic Diseases