no code implementations • 11 Mar 2024 • Ricardo Omar Ramirez Flores, Philipp Sven Lars Schäfer, Leonie Küchenhoff, Julio Saez-Rodriguez
The application of single-cell molecular profiling coupled with spatial technologies has enabled charting cellular heterogeneity in reference tissues and in disease.
1 code implementation • 17 Jan 2024 • Sebastian Lobentanzer, Pablo Rodriguez-Mier, Stefan Bauer, Julio Saez-Rodriguez
Correlation is not causation.
no code implementations • 8 Dec 2023 • Gustavo Stolovitzky, Julio Saez-Rodriguez, Julie Bletz, Jacob Albrecht, Gaia Andreoletti, James C. Costello, Paul Boutros
Data Science research is undergoing a revolution fueled by the transformative power of technology, the Internet, and an ever increasing computational capacity.
no code implementations • 24 May 2023 • Andreas Maier, Michael Hartung, Mark Abovsky, Klaudia Adamowicz, Gary D. Bader, Sylvie Baier, David B. Blumenthal, Jing Chen, Maria L. Elkjaer, Carlos Garcia-Hernandez, Mohamed Helmy, Markus Hoffmann, Igor Jurisica, Max Kotlyar, Olga Lazareva, Hagai Levi, Markus List, Sebastian Lobentanzer, Joseph Loscalzo, Noel Malod-Dognin, Quirin Manz, Julian Matschinske, Miles Mee, Mhaned Oubounyt, Alexander R. Pico, Rudolf T. Pillich, Julian M. Poschenrieder, Dexter Pratt, Nataša Pržulj, Sepideh Sadegh, Julio Saez-Rodriguez, Suryadipto Sarkar, Gideon Shaked, Ron Shamir, Nico Trummer, Ugur Turhan, Ruisheng Wang, Olga Zolotareva, Jan Baumbach
In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood.
3 code implementations • 10 May 2023 • Sebastian Lobentanzer, Shaohong Feng, The BioChatter Consortium, Andreas Maier, Cankun Wang, Jan Baumbach, Nils Krehl, Qin Ma, Julio Saez-Rodriguez
Current-generation Large Language Models (LLMs) have stirred enormous interest in recent months, yielding great potential for accessibility and automation, while simultaneously posing significant challenges and risk of misuse.
no code implementations • 3 Feb 2023 • Annika Reinke, Minu D. Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A. Emre Kavur, Tim Rädsch, Carole H. Sudre, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew Blaschko, Florian Buettner, M. Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A. Cimini, Gary S. Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Robert Haase, Daniel A. Hashimoto, Michael M. Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Hannes Kenngott, Jens Kleesiek, Florian Kofler, Thijs Kooi, Annette Kopp-Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L. Martel, Peter Mattson, Erik Meijering, Bjoern Menze, Karel G. M. Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M. Rafelski, Nasir Rajpoot, Mauricio Reyes, Michael A. Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I. Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M. Summers, Abdel A. Taha, Aleksei Tiulpin, Sotirios A. Tsaftaris, Ben van Calster, Gaël Varoquaux, Manuel Wiesenfarth, Ziv R. Yaniv, Paul F. Jäger, Lena Maier-Hein
Validation metrics are key for the reliable tracking of scientific progress and for bridging the current chasm between artificial intelligence (AI) research and its translation into practice.
no code implementations • 27 Dec 2022 • Sebastian Lobentanzer, Patrick Aloy, Jan Baumbach, Balazs Bohar, Pornpimol Charoentong, Katharina Danhauser, Tunca Doğan, Johann Dreo, Ian Dunham, Adrià Fernandez-Torras, Benjamin M. Gyori, Michael Hartung, Charles Tapley Hoyt, Christoph Klein, Tamas Korcsmaros, Andreas Maier, Matthias Mann, David Ochoa, Elena Pareja-Lorente, Ferdinand Popp, Martin Preusse, Niklas Probul, Benno Schwikowski, Bünyamin Sen, Maximilian T. Strauss, Denes Turei, Erva Ulusoy, Judith Andrea Heidrun Wodke, Julio Saez-Rodriguez
Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods.
1 code implementation • 3 Jun 2022 • Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D. Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A. Riegler, Manuel Wiesenfarth, A. Emre Kavur, Carole H. Sudre, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Tim Rädsch, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew Blaschko, M. Jorge Cardoso, Veronika Cheplygina, Beth A. Cimini, Gary S. Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Robert Haase, Daniel A. Hashimoto, Michael M. Hoffman, Merel Huisman, Pierre Jannin, Charles E. Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Hannes Kenngott, Florian Kofler, Annette Kopp-Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L. Martel, Peter Mattson, Erik Meijering, Bjoern Menze, Karel G. M. Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I. Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M. Summers, Abdel A. Taha, Aleksei Tiulpin, Sotirios A. Tsaftaris, Ben van Calster, Gaël Varoquaux, Paul F. Jäger
The framework was developed in a multi-stage Delphi process and is based on the novel concept of a problem fingerprint - a structured representation of the given problem that captures all aspects that are relevant for metric selection, from the domain interest to the properties of the target structure(s), data set and algorithm output.
1 code implementation • 13 Sep 2021 • Rosa Hernansaiz-Ballesteros, Christian H. Holland, Aurelien Dugourd, Julio Saez-Rodriguez
Motivation: Omics data, such as transcriptomics or phosphoproteomics, are broadly used to get a snap-shot of the molecular status of cells.
1 code implementation • 12 Apr 2021 • Annika Reinke, Minu D. Tizabi, Carole H. Sudre, Matthias Eisenmann, Tim Rädsch, Michael Baumgartner, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Peter Bankhead, Arriel Benis, Matthew Blaschko, Florian Buettner, M. Jorge Cardoso, Jianxu Chen, Veronika Cheplygina, Evangelia Christodoulou, Beth Cimini, Gary S. Collins, Sandy Engelhardt, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Robert Haase, Fred Hamprecht, Daniel A. Hashimoto, Doreen Heckmann-Nötzel, Peter Hirsch, Michael M. Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, A. Emre Kavur, Hannes Kenngott, Jens Kleesiek, Andreas Kleppe, Sven Kohler, Florian Kofler, Annette Kopp-Schneider, Thijs Kooi, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L. Martel, Peter Mattson, Erik Meijering, Bjoern Menze, David Moher, Karel G. M. Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, M. Alican Noyan, Jens Petersen, Gorkem Polat, Susanne M. Rafelski, Nasir Rajpoot, Mauricio Reyes, Nicola Rieke, Michael Riegler, Hassan Rivaz, Julio Saez-Rodriguez, Clara I. Sánchez, Julien Schroeter, Anindo Saha, M. Alper Selver, Lalith Sharan, Shravya Shetty, Maarten van Smeden, Bram Stieltjes, Ronald M. Summers, Abdel A. Taha, Aleksei Tiulpin, Sotirios A. Tsaftaris, Ben van Calster, Gaël Varoquaux, Manuel Wiesenfarth, Ziv R. Yaniv, Paul Jäger, Lena Maier-Hein
While the importance of automatic image analysis is continuously increasing, recent meta-research revealed major flaws with respect to algorithm validation.
no code implementations • 9 Oct 2019 • Lena Maier-Hein, Annika Reinke, Michal Kozubek, Anne L. Martel, Tal Arbel, Matthias Eisenmann, Allan Hanbuary, Pierre Jannin, Henning Müller, Sinan Onogur, Julio Saez-Rodriguez, Bram van Ginneken, Annette Kopp-Schneider, Bennett Landman
The number of biomedical image analysis challenges organized per year is steadily increasing.
1 code implementation • 19 Dec 2014 • Thomas Cokelaer, Julio Saez-Rodriguez
Systems biology is an inter-disciplinary field that studies systems of biological components at different scales, which may be molecules, cells or entire organism.
Computational Engineering, Finance, and Science Molecular Networks