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5. Metrics reloaded: recommendations for image analysis validation

Author

Maier-Hein, L., Reinke, A., Godau, P., Tizabi, M.D., Buettner, F., Christodoulou, E., Glocker, B., Isensee, F., Kleesiek, J., Kozubek, M., Reyes, M., Riegler, M.A., Wiesenfarth, M., Kavur, A.E., Sudre, C.H., Baumgartner, M., Eisenmann, M., Heckmann-Notzel, D., Radsch, T., Acion, L., Antonelli, M., Arbel, T., Bakas, S., Benis, A., Blaschko, M.B., Cardoso, M.J., Cheplygina, V., Cimini, B.A., Collins, G.S., Farahani, K., Ferrer, L., Galdran, A., Ginneken, B. van, Haase, R., Hashimoto, D.A., Hoffman, M.M., Huisman, M., Jannin, P., Kahn, C.E., Kainmueller, D., Kainz, B., Karargyris, A., Karthikesalingam, A., Kofler, F., Kopp-Schneider, A., Kreshuk, A., Kurc, T., Landman, B.A., Litjens, G.J., Madani, A., Maier-Hein, K., Martel, A.L., Mattson, P., Meijering, E., Menze, B., Moons, K.G., Muller, H., Nichyporuk, B., Nickel, F., Petersen, J., Rajpoot, N., Rieke, N., Saez-Rodriguez, J., Sanchez, C.I., Shetty, S., Smeden, M. van, Summers, R.M., Taha, A.A., Tiulpin, A., Tsaftaris, S.A., Calster, B. van, Varoquaux, G., Jager, P.F., Maier-Hein, L., Reinke, A., Godau, P., Tizabi, M.D., Buettner, F., Christodoulou, E., Glocker, B., Isensee, F., Kleesiek, J., Kozubek, M., Reyes, M., Riegler, M.A., Wiesenfarth, M., Kavur, A.E., Sudre, C.H., Baumgartner, M., Eisenmann, M., Heckmann-Notzel, D., Radsch, T., Acion, L., Antonelli, M., Arbel, T., Bakas, S., Benis, A., Blaschko, M.B., Cardoso, M.J., Cheplygina, V., Cimini, B.A., Collins, G.S., Farahani, K., Ferrer, L., Galdran, A., Ginneken, B. van, Haase, R., Hashimoto, D.A., Hoffman, M.M., Huisman, M., Jannin, P., Kahn, C.E., Kainmueller, D., Kainz, B., Karargyris, A., Karthikesalingam, A., Kofler, F., Kopp-Schneider, A., Kreshuk, A., Kurc, T., Landman, B.A., Litjens, G.J., Madani, A., Maier-Hein, K., Martel, A.L., Mattson, P., Meijering, E., Menze, B., Moons, K.G., Muller, H., Nichyporuk, B., Nickel, F., Petersen, J., Rajpoot, N., Rieke, N., Saez-Rodriguez, J., Sanchez, C.I., Shetty, S., Smeden, M. van, Summers, R.M., Taha, A.A., Tiulpin, A., Tsaftaris, S.A., Calster, B. van, Varoquaux, G., and Jager, P.F.

Abstract

Contains fulltext : 305368.pdf (Publisher’s version ) (Closed access), Increasing evidence shows that flaws in machine learning (ML) algorithm validation are an underestimated global problem. In biomedical image analysis, chosen performance metrics often do not reflect the domain interest, and thus fail to adequately measure scientific progress and hinder translation of ML techniques into practice. To overcome this, we created Metrics Reloaded, a comprehensive framework guiding researchers in the problem-aware selection of metrics. Developed by a large international consortium in a multistage Delphi process, it 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), dataset and algorithm output. On the basis of the problem fingerprint, users are guided through the process of choosing and applying appropriate validation metrics while being made aware of potential pitfalls. Metrics Reloaded targets image analysis problems that can be interpreted as classification tasks at image, object or pixel level, namely image-level classification, object detection, semantic segmentation and instance segmentation tasks. To improve the user experience, we implemented the framework in the Metrics Reloaded online tool. Following the convergence of ML methodology across application domains, Metrics Reloaded fosters the convergence of validation methodology. Its applicability is demonstrated for various biomedical use cases.

Published
2024

6. Understanding metric-related pitfalls in image analysis validation

Author

Reinke, A., Tizabi, M.D., Baumgartner, M., Eisenmann, M., Heckmann-Notzel, D., Kavur, A.E., Radsch, T., Sudre, C.H., Acion, L., Antonelli, M., Arbel, T., Bakas, S., Benis, A., Buettner, F., Cardoso, M.J., Cheplygina, V., Chen, J., Christodoulou, E., Cimini, B.A., Farahani, K., Ferrer, L., Galdran, A., Ginneken, B. van, Glocker, B., Godau, P., Hashimoto, D.A., Hoffman, M.M., Huisman, M., Isensee, F., Jannin, P., Kahn, C.E., Kainmueller, D., Kainz, B., Karargyris, A., Kleesiek, J., Kofler, F., Kooi, T., Kopp-Schneider, A., Kozubek, M., Kreshuk, A., Kurc, T., Landman, B.A., Litjens, G.J., Madani, A., Maier-Hein, K., Martel, A.L., Meijering, E., Menze, B., Moons, K.G., Muller, H., Nichyporuk, B., Nickel, F., Petersen, J., Rafelski, S.M., Rajpoot, N., Reyes, M., Riegler, M.A., Rieke, N., Saez-Rodriguez, J., Sanchez, C.I., Shetty, S., Summers, R.M., Taha, A.A., Tiulpin, A., Tsaftaris, S.A., Calster, B. van, Varoquaux, G., Yaniv, Z.R., Jager, P.F., Maier-Hein, L., Reinke, A., Tizabi, M.D., Baumgartner, M., Eisenmann, M., Heckmann-Notzel, D., Kavur, A.E., Radsch, T., Sudre, C.H., Acion, L., Antonelli, M., Arbel, T., Bakas, S., Benis, A., Buettner, F., Cardoso, M.J., Cheplygina, V., Chen, J., Christodoulou, E., Cimini, B.A., Farahani, K., Ferrer, L., Galdran, A., Ginneken, B. van, Glocker, B., Godau, P., Hashimoto, D.A., Hoffman, M.M., Huisman, M., Isensee, F., Jannin, P., Kahn, C.E., Kainmueller, D., Kainz, B., Karargyris, A., Kleesiek, J., Kofler, F., Kooi, T., Kopp-Schneider, A., Kozubek, M., Kreshuk, A., Kurc, T., Landman, B.A., Litjens, G.J., Madani, A., Maier-Hein, K., Martel, A.L., Meijering, E., Menze, B., Moons, K.G., Muller, H., Nichyporuk, B., Nickel, F., Petersen, J., Rafelski, S.M., Rajpoot, N., Reyes, M., Riegler, M.A., Rieke, N., Saez-Rodriguez, J., Sanchez, C.I., Shetty, S., Summers, R.M., Taha, A.A., Tiulpin, A., Tsaftaris, S.A., Calster, B. van, Varoquaux, G., Yaniv, Z.R., Jager, P.F., and Maier-Hein, L.

Abstract

Contains fulltext : 305370.pdf (Publisher’s version ) (Closed access), Validation metrics are key for tracking scientific progress and bridging the current chasm between artificial intelligence research and its translation into practice. However, increasing evidence shows that, particularly in image analysis, metrics are often chosen inadequately. Although taking into account the individual strengths, weaknesses and limitations of validation metrics is a critical prerequisite to making educated choices, the relevant knowledge is currently scattered and poorly accessible to individual researchers. Based on a multistage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides a reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. Although focused on biomedical image analysis, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. The work serves to enhance global comprehension of a key topic in image analysis validation.

Published
2024

14. Density theorems for complete minimal surfaces in R^3

Author

Alarcon, A., Ferrer, L., and Martin, F.

Subjects
Mathematics - Differential Geometry, 53A10, 49Q05
Abstract

In this paper we have proved several approximation theorems for the family of minimal surfaces in R^3 that imply, among other things, that complete minimal surfaces are dense in the space of all minimal surfaces endowed with the topology of C^k convergence on compact sets, for any k. As a consequence of the above density result, we have been able to produce the first example of a complete proper minimal surface in R^3 with uncountably many ends., Comment: 32 pages, 8 figures. To appear in G.A.F.A

Published
2006

15. A uniqueness theorem for the singly periodic genus-one helicoid

Author

Alarcon, A., Ferrer, L., and Martin, F.

Subjects
Mathematics - Differential Geometry, Primary 53A10, Secondary 53C42
Abstract

The singly periodic genus-one helicoid was in the origin of the discovery of the first example of a complete minimal surface with finite topology but infinite total curvature, the celebrated Hoffman-Karcher-Wei's genus one helicoid. The objective of this paper is to give a uniqueness theorem for the singly periodic genus-one helicoid provided the existence of one symmetry., Comment: 12 pages, 6 figures

Published
2005

17. Early detection of HIV infection and of asymptomatic sexually transmitted infections among men who have sex with men

Author

Brander, C., Clotet, B., Coll, J., Bravo, I., Chamorro, A., García-Cuyas, F., Ornelas, A., Piñol, M., Revollo, B., Sirera, G., Videla, S., Blanco, J.L., Fernández, E., García, F., Gatell, J.M., Leal, L., Leon, A., Carrillo, A., Ditzel, E., Meulbroek, M., Pujol, F., Saz, J., Taboada, H., Casabona, J., Ferrer, L., and González, V.

Published
2018
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18. GATE : a simulation toolkit for PET and SPECT

Author

Jan, S., Santin, G., Strul, D., Staelens, S., Assie, K., Autret, D., Avner, S., Barbier, R., Bardies, M., Bloomfield, P. M., Brasse, D., Breton, V., Bruyndonckx, P., Buvat, I., Chatziioannou, A. F., Choi, Y., Chung, Y. H., Comtat, C., Donnarieix, D., Ferrer, L., Glick, S. J., Groiselle, C. J., Guez, D., Honore, P. -F., Kerhoas-Cavata, S., Kirov, A. S., Kohli, V., Koole, M., Krieguer, M., van der Laan, D. J., Lamare, F., Largeron, G., Lartizien, C., Lazaro, D., Maas, M. C., Maigne, L., Mayet, F., Melot, F., Merheb, C., Pennacchio, E., Perez, J., Pietrzyk, U., Rannou, F. R., Rey, M., Schaart, D. R., Schmidtlein, C. R., Simon, L., Song, T. Y., Vieira, J. -M., Visvikis, D., Van de Walle, R., Wieers, E., and Morel, C.

Subjects
Physics - Medical Physics, Physics - Biological Physics
Abstract

Monte Carlo simulation is an essential tool in emission tomography that can assist in the design of new medical imaging devices, the optimization of acquisition protocols, and the development or assessment of image reconstruction algorithms and correction techniques. GATE, the Geant4 Application for Tomographic Emission, encapsulates the Geant4 libraries to achieve a modular, versatile, scripted simulation toolkit adapted to the field of nuclear medicine. In particular, GATE allows the description of time-dependent phenomena such as source or detector movement, and source decay kinetics. This feature makes it possible to simulate time curves under realistic acquisition conditions and to test dynamic reconstruction algorithms. A public release of GATE licensed under the GNU Lesser General Public License can be downloaded at the address http://www-lphe.epfl.ch/GATE/.

Published
2004
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23. Interaction among health workers and trans men: Findings from a qualitative study in Chile.

Author

Bernales, M., Cordón, P., Gonzalez, S., Pedrero, V., and Ferrer, L.

Subjects
HEALTH services accessibility, SOCIAL support, RESEARCH evaluation, ATTITUDES of medical personnel, RESEARCH methodology, MEDICAL care, INTERVIEWING, PATIENT-centered care, VIDEOCONFERENCING, EXPERIENCE, QUALITATIVE research, ETHNOLOGY research, GENDER identity, GENDER transition, INTELLECT, RESEARCH funding, DESCRIPTIVE statistics, TRANS men, THEMATIC analysis, DATA analysis software, EMOTIONS, SOCIODEMOGRAPHIC factors, CONTENT analysis, GROUP dynamics
Abstract

Purpose: To explore trans men's access and use of healthcare services in Chile, based on the experiences of the trans men themselves, as well as of healthcare professionals. Methods: A qualitative study with an ethnographic approach was carried out with 30 participants: 14 trans men and 16 healthcare professionals. Semi‐structured one‐on‐one interviews with open‐ended questions were used to collect the data. A thematic analysis was carried out with the NVivo Software. Results: Three main themes were identified: (1) failures in the recognition of trans identity, (2) challenges with patient‐centered care, and (3) use of other ("non‐trans") health services. Conclusions: The results suggest that not all transition processes are the same, individuals seek different ways; therefore, it is necessary to consider different body types and identities when planning programs and care for men in transition. Moreover, the accompaniment provided during the gender transition process should contemplate emotional and mental support. Clinical Relevance: The study outlines the need for all healthcare professionals to have training and knowledge about the transgender population, regardless of whether they are part of the teams supporting gender transition processes. The role of nurses and the contributions that can be made from nursing discipline in this research field are fundamental. [ABSTRACT FROM AUTHOR]

Published
2024
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25. An Analytical Solution for Friction Stir Welding of an AISI 1018 Steel

Author

Ferrer L., V. H., Hernández C., C. A., Vargas Aguilar, R. O., Allan, Rod, Series editor, Förstner, Ulrich, Series editor, Salomons, Wim, Series editor, Klapp, Jaime, editor, Ruíz Chavarría, Gerardo, editor, Medina Ovando, Abraham, editor, López Villa, Abel, editor, and Sigalotti, Leonardo Di G., editor

Published
2015
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32. Small Ruminant Lentivirus: A practical approach.

Author

Jacob-Ferreira, J., Pires, I., Alegria, N., Coelho, A. C., Garcês, A., Ferrer, L. M., Lacasta, D., and Quintas, H.

Subjects
RUMINANTS, LENTIVIRUSES, RETROVIRUSES, CHRONIC diseases, DISEASE progression, MILK yield
Abstract

Copyright of Veterinarska Stanica is the property of Croatian Veterinary Institute and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2023
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44. 1325P TRIDENT: Machine learning (ML) multimodal signatures to identify patients that would benefit most from tremelimumab (T) addition to durvalumab (D) + chemotherapy (CT) with data from the POSEIDON trial

Author

Skoulidis, F., Jabbour, S., Garon, E.B., Iyengar, P., Scagliotti, G., Ferrer, L., Etchepare, G., Gallinato, O., Faure, J., Bernard, P., Colin, T., Menu, P., Lin, Y., Cai, L., Faria, J., Remorino, A., Luciani-Silverman, L., Miller, K.P., Dellamonica, D., and Zhang, Y.

Published
2024
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46. New Trends and Applications in Oceanographic Numerical Modelling

Author

Ferrer, L., Uriarte, Ad., González, M., Bock, Hans-Georg, editor, de Hoog, Frank, editor, Friedman, Avner, editor, Gupta, Arvind, editor, Neunzert, Helmut, editor, Pulleyblank, William R., editor, Rusten, Torgeir, editor, Santosa, Fadil, editor, Tornberg, Anna-Karin, editor, Capasso, Vincenzo, editor, Mattheij, Robert, editor, Scherzer, Otmar, editor, Bonilla, Luis L., editor, Moscoso, Miguel, editor, Platero, Gloria, editor, and Vega, Jose M., editor

Published
2008
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