ImageCLEF 2013: The vision, the data and the open challenges

This paper presents an overview of the ImageCLEF 2013 lab. Since its first edition in 2003, ImageCLEF has become one of the key initiatives promoting the benchmark evaluation of algorithms for the cross-language annotation and retrieval of images in various domains, such as public and personal images, to data acquired by mobile robot platforms and botanic collections. Over the years, by providing new data collections and challenging tasks to the community of interest, the ImageCLEF lab has achieved an unique position in the multi lingual image annotation and retrieval research landscape. The 2013 edition consisted of three tasks: the photo annotation and retrieval task, the plant identification task and the robot vision task. Furthermore, the medical annotation task, that traditionally has been under the ImageCLEF umbrella and that this year celebrates its tenth anniversary, has been organized in conjunction with AMIA for the first time. The paper describes the tasks and the 2013 competition, giving an unifying perspective of the present activities of the lab while discussion the future challenges and opportunities.This work has been partially supported by the Halser Foundation (B. C.),by the LiMoSINe FP7 project under grant # 288024 (B. T.), by the Khresmoi (grant# 257528) and PROMISE ( grant # 258191) FP 7 projects (H.M.) and by the tranScriptorium FP7 project under grant # 600707 (M. V., R. P.)Caputo ., B.; Muller ., H.; Thomee ., B.; Villegas, M.; Paredes Palacios, R.; Zellhofer ., D.; Goeau ., H.... (2013). ImageCLEF 2013: The vision, the data and the open challenges. En Information Access Evaluation. Multilinguality, Multimodality, and Visualization. Springer Verlag (Germany). 8138:250-268. https://doi.org/10.1007/978-3-642-40802-1_26S2502688138Muller, H., Clough, P., Deselaers, T., Caputo, B.: ImageCLEF: experimental evaluation in visual information retrieval. Springer (2010)Tsikrika, T., Seco de Herrera, A.G., Müller, H.: Assessing the scholarly impact of imageCLEF. In: Forner, P., Gonzalo, J., Kekäläinen, J., Lalmas, M., de Rijke, M. (eds.) CLEF 2011. LNCS, vol. 6941, pp. 95–106. Springer, Heidelberg (2011)Huiskes, M., Lew, M.: The MIR Flickr retrieval evaluation. In: Proceedings of the 10th ACM Conference on Multimedia Information Retrieval, Vancouver, BC, Canada, pp. 39–43 (2008)Huiskes, M., Thomee, B., Lew, M.: New trends and ideas in visual concept detection. In: Proceedings of the 11th ACM Conference on Multimedia Information Retrieval, Philadelphia, PA, USA, pp. 527–536 (2010)Villegas, M., Paredes, R.: Overview of the ImageCLEF 2012 Scalable Web Image Annotation Task. In: CLEF 2012 Evaluation Labs and Workshop, Online Working Notes, Rome, Italy (2012)Zellhöfer, D.: Overview of the Personal Photo Retrieval Pilot Task at ImageCLEF 2012. In: CLEF 2012 Evaluation Labs and Workshop, Online Working Notes, Rome, Italy (2012)Villegas, M., Paredes, R., Thomee, B.: Overview of the ImageCLEF 2013 Scalable Concept Image Annotation Subtask. In: CLEF 2013 Evaluation Labs and Workshop, Online Working Notes, Valencia, Spain (2013)Zellhöfer, D.: Overview of the ImageCLEF 2013 Personal Photo Retrieval Subtask. In: CLEF 2013 Evaluation Labs and Workshop, Online Working Notes, Valencia, Spain (2013)Leafsnap (2011)Plantnet (2013)Mobile flora (2013)Folia (2012)Goëau, H., Bonnet, P., Joly, A., Bakic, V., Boujemaa, N., Barthelemy, D., Molino, J.F.: The imageclef 2013 plant identification task. In: ImageCLEF 2013 Working Notes (2013)Pronobis, A., Xing, L., Caputo, B.: Overview of the CLEF 2009 robot vision track. In: Peters, C., Caputo, B., Gonzalo, J., Jones, G.J.F., Kalpathy-Cramer, J., Müller, H., Tsikrika, T. (eds.) CLEF 2009. LNCS, vol. 6242, pp. 110–119. Springer, Heidelberg (2010)Pronobis, A., Caputo, B.: The robot vision task. In: Muller, H., Clough, P., Deselaers, T., Caputo, B. (eds.) ImageCLEF. The Information Retrieval Series, vol. 32, pp. 185–198. Springer, Heidelberg (2010)Pronobis, A., Christensen, H.I., Caputo, B.: Overview of the imageCLEF@ICPR 2010 robot vision track. In: Ünay, D., Çataltepe, Z., Aksoy, S. (eds.) ICPR 2010. LNCS, vol. 6388, pp. 171–179. Springer, Heidelberg (2010)Martinez-Gomez, J., Garcia-Varea, I., Caputo, B.: Overview of the imageclef 2012 robot vision task. In: CLEF 2012 Working Notes (2012)Rusu, R., Cousins, S.: 3d is here: Point cloud library (pcl). In: 2011 IEEE International Conference on Robotics and Automation (ICRA), pp. 1–4. IEEE (2011)Bosch, A., Zisserman, A., Munoz, X.: Image classification using random forests and ferns. In: International Conference on Computer Vision, pp. 1–8. Citeseer (2007)Dalal, N., Triggs, B.: Histograms of oriented gradients for human detection. 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In: Peters, C., Clough, P., Gonzalo, J., Jones, G.J.F., Kluck, M., Magnini, B. (eds.) CLEF 2004. LNCS, vol. 3491, pp. 597–613. Springer, Heidelberg (2005)Clough, P., Müller, H., Deselaers, T., Grubinger, M., Lehmann, T.M., Jensen, J., Hersh, W.: The CLEF 2005 cross–language image retrieval track. In: Peters, C., Gey, F.C., Gonzalo, J., Müller, H., Jones, G.J.F., Kluck, M., Magnini, B., de Rijke, M., Giampiccolo, D. (eds.) CLEF 2005. LNCS, vol. 4022, pp. 535–557. Springer, Heidelberg (2006)Müller, H., Deselaers, T., Deserno, T., Clough, P., Kim, E., Hersh, W.: Overview of the imageCLEFmed 2006 medical retrieval and medical annotation tasks. In: Peters, C., Clough, P., Gey, F.C., Karlgren, J., Magnini, B., Oard, D.W., de Rijke, M., Stempfhuber, M. (eds.) CLEF 2006. LNCS, vol. 4730, pp. 595–608. Springer, Heidelberg (2007)Müller, H., Deselaers, T., Deserno, T., Kalpathy–Cramer, J., Kim, E., Hersh, W.: Overview of the imageCLEFmed 2007 medical retrieval and medical annotation tasks. 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The Springer International Series on Information Retrieval, vol. 32. Springer, Heidelberg (2010)Kalpathy-Cramer, J., Müller, H., Bedrick, S., Eggel, I., García Seco de Herrera, A., Tsikrika, T.: The CLEF 2011 medical image retrieval and classification tasks. In: Working Notes of CLEF 2011 (Cross Language Evaluation Forum) (2011)Müller, H., García Seco de Herrera, A., Kalpathy-Cramer, J., Demner Fushman, D., Antani, S., Eggel, I.: Overview of the ImageCLEF 2012 medical image retrieval and classification tasks. In: Working Notes of CLEF 2012 (Cross Language Evaluation Forum) (2012)García Seco de Herrera, A., Kalpathy-Cramer, J., Demner Fushman, D., Antani, S., Müller, H.: Overview of the ImageCLEF 2013 medical tasks. In: Working Notes of CLEF 2013 (Cross Language Evaluation Forum) (2013

ImageCLEF 2014: Overview and analysis of the results

This paper presents an overview of the ImageCLEF 2014 evaluation lab. Since its first edition in 2003, ImageCLEF has become one of the key initiatives promoting the benchmark evaluation of algorithms for the annotation and retrieval of images in various domains, such as public and personal images, to data acquired by mobile robot platforms and medical archives. Over the years, by providing new data collections and challenging tasks to the community of interest, the ImageCLEF lab has achieved an unique position in the image annotation and retrieval research landscape. The 2014 edition consists of four tasks: domain adaptation, scalable concept image annotation, liver CT image annotation and robot vision. This paper describes the tasks and the 2014 competition, giving a unifying perspective of the present activities of the lab while discussing future challenges and opportunities.This work has been partially supported by the tranScriptorium FP7 project under grant #600707 (M. V., R. P.).Caputo, B.; Müller, H.; Martinez-Gomez, J.; Villegas Santamaría, M.; Acar, B.; Patricia, N.; Marvasti, N.... (2014). ImageCLEF 2014: Overview and analysis of the results. En Information Access Evaluation. Multilinguality, Multimodality, and Interaction: 5th International Conference of the CLEF Initiative, CLEF 2014, Sheffield, UK, September 15-18, 2014. Proceedings. Springer Verlag (Germany). 192-211. https://doi.org/10.1007/978-3-319-11382-1_18S192211Bosch, A., Zisserman, A.: Image classification using random forests and ferns. In: Proc. CVPR (2007)Caputo, B., Müller, H., Martinez-Gomez, J., Villegas, M., Acar, B., Patricia, N., Marvasti, N., Üsküdarlı, S., Paredes, R., Cazorla, M., Garcia-Varea, I., Morell, V.: ImageCLEF 2014: Overview and analysis of the results. In: Kanoulas, E., et al. (eds.) CLEF 2014. LNCS, vol. 8685, Springer, Heidelberg (2014)Caputo, B., Patricia, N.: Overview of the ImageCLEF 2014 Domain Adaptation Task. 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Convolutional Sparse Kernel Network for Unsupervised Medical Image Analysis

The availability of large-scale annotated image datasets and recent advances in supervised deep learning methods enable the end-to-end derivation of representative image features that can impact a variety of image analysis problems. Such supervised approaches, however, are difficult to implement in the medical domain where large volumes of labelled data are difficult to obtain due to the complexity of manual annotation and inter- and intra-observer variability in label assignment. We propose a new convolutional sparse kernel network (CSKN), which is a hierarchical unsupervised feature learning framework that addresses the challenge of learning representative visual features in medical image analysis domains where there is a lack of annotated training data. Our framework has three contributions: (i) We extend kernel learning to identify and represent invariant features across image sub-patches in an unsupervised manner. (ii) We initialise our kernel learning with a layer-wise pre-training scheme that leverages the sparsity inherent in medical images to extract initial discriminative features. (iii) We adapt a multi-scale spatial pyramid pooling (SPP) framework to capture subtle geometric differences between learned visual features. We evaluated our framework in medical image retrieval and classification on three public datasets. Our results show that our CSKN had better accuracy when compared to other conventional unsupervised methods and comparable accuracy to methods that used state-of-the-art supervised convolutional neural networks (CNNs). Our findings indicate that our unsupervised CSKN provides an opportunity to leverage unannotated big data in medical imaging repositories.Comment: Accepted by Medical Image Analysis (with a new title 'Convolutional Sparse Kernel Network for Unsupervised Medical Image Analysis'). The manuscript is available from following link (https://doi.org/10.1016/j.media.2019.06.005

Experiences from the ImageCLEF Medical Retrieval and Annotation Tasks

The medical tasks in ImageCLEF have been run every year from 2004-2018 and many different tasks and data sets have been used over these years. The created resources are being used by many researchers well beyond the actual evaluation campaigns and are allowing to compare the performance of many techniques on the same grounds and in a reproducible way. Many of the larger data sets are from the medical literature, as such images are easier to obtain and to share than clinical data, which was used in a few smaller ImageCLEF challenges that are specifically marked with the disease type and anatomic region. This chapter describes the main results of the various tasks over the years, including data, participants, types of tasks evaluated and also the lessons learned in organizing such tasks for the scientific community

Evaluating performance of biomedical image retrieval systems - an overview of the medical image retrieval task at ImageCLEF 2004-2013

Medical image retrieval and classification have been extremely active research topics over the past 15 years. Within the ImageCLEF benchmark in medical image retrieval and classification, a standard test bed was created that allows researchers to compare their approaches and ideas on increasingly large and varied data sets including generated ground truth. This article describes the lessons learned in ten evaluation campaigns. A detailed analysis of the data also highlights the value of the resources created

Test collections for medical information retrieval evaluation

The web has rapidly become one of the main resources for medical information for many people: patients, clinicians, medical doctors, etc. Measuring the effectiveness with which information can be retrieved from web resources for these users is crucial: it brings better information to professionals for better diagnosis, treatment, patient care; and helps patients and relatives get informed on their condition. Several existing information retrieval (IR) evaluation campaigns have been developed to assess and improve medical IR methods, for example the TREC Medical Record Track [11] and TREC Genomics Track [10]. These campaigns only target certain type of users, mainly clinicians and some medical professionals: queries are mainly centered on cohorts of records describing a specific patient cases or on biomedical reports. Evaluating search effectiveness over the many heterogeneous online medical information sources now available, which are increasingly used by a diverse range of medical professionals and, very importantly, the general public, is vital to the understanding and development of medical IR. We describe the development of two benchmarks for medical IR evaluation from the Khresmoi project. The first of these has been developed using existing medical query logs for internal research within the Khresmoi project and targets both medical professionals and general public; the second has been created in the framework of a new CLEFeHealth evaluation campaign and is designed to evaluate patient search in context

Analysis of biomedical and health queries: Lessons learned from TREC and CLEF evaluation benchmarks

International audienceBACKGROUND:Inherited ichthyoses represent a group of rare skin disorders characterized by scaling, hyperkeratosis and inconstant erythema, involving most of the tegument. Epidemiology remains poorly described. This study aims to evaluate the prevalence of inherited ichthyosis (excluding very mild forms) and its different clinical forms in France.METHODS:Capture - recapture method was used for this study. According to statistical requirements, 3 different lists (reference/competence centres, French association of patients with ichthyosis and internet network) were used to record such patients. The study was conducted in 5 areas during a closed period.RESULTS:The prevalence was estimated at 13.3 per million people (/M) (CI95\%, [10.9 - 17.6]). With regard to autosomal recessive congenital ichthyosis, the prevalence was estimated at 7/M (CI 95\% [5.7 - 9.2]), with a prevalence of lamellar ichthyosis and congenital ichthyosiform erythroderma of 4.5/M (CI 95\% [3.7 - 5.9]) and 1.9/M (CI 95\% [1.6 - 2.6]), respectively. Prevalence of keratinopathic forms was estimated at 1.1/M (CI 95\% [0.9 - 1.5]). Prevalence of syndromic forms (all clinical forms together) was estimated at 1.9/M (CI 95\% [1.6 - 2.6]).CONCLUSIONS:Our results constitute a crucial basis to properly size the necessary health measures that are required to improve patient care and design further clinical studies

Use Case Oriented Medical Visual Information Retrieval & System Evaluation

Large amounts of medical visual data are produced daily in hospitals, while new imaging techniques continue to emerge. In addition, many images are made available continuously via publications in the scientific literature and can also be valuable for clinical routine, research and education. Information retrieval systems are useful tools to provide access to the biomedical literature and fulfil the information needs of medical professionals. The tools developed in this thesis can potentially help clinicians make decisions about difficult diagnoses via a case-based retrieval system based on a use case associated with a specific evaluation task. This system retrieves articles from the biomedical literature when querying with a case description and attached images. This thesis proposes a multimodal approach for medical case-based retrieval with focus on the integration of visual information connected to text. Furthermore, the ImageCLEFmed evaluation campaign was organised during this thesis promoting medical retrieval system evaluation