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  1. AU="Sznitman, Raphael"
  2. AU="Philippe Ciais"
  3. AU="Suprasert, Prapaporn"
  4. AU="Chang, Yinshui"
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  1. Article ; Online: A reinforcement learning approach for VQA validation: An application to diabetic macular edema grading.

    Fountoukidou, Tatiana / Sznitman, Raphael

    Medical image analysis

    2023  Volume 87, Page(s) 102822

    Abstract: Recent advances in machine learning models have greatly increased the performance of automated methods in medical image analysis. However, the internal functioning of such models is largely hidden, which hinders their integration in clinical practice. ... ...

    Abstract Recent advances in machine learning models have greatly increased the performance of automated methods in medical image analysis. However, the internal functioning of such models is largely hidden, which hinders their integration in clinical practice. Explainability and trust are viewed as important aspects of modern methods, for the latter's widespread use in clinical communities. As such, validation of machine learning models represents an important aspect and yet, most methods are only validated in a limited way. In this work, we focus on providing a richer and more appropriate validation approach for highly powerful Visual Question Answering (VQA) algorithms. To better understand the performance of these methods, which answer arbitrary questions related to images, this work focuses on an automatic visual Turing test (VTT). That is, we propose an automatic adaptive questioning method, that aims to expose the reasoning behavior of a VQA algorithm. Specifically, we introduce a reinforcement learning (RL) agent that observes the history of previously asked questions, and uses it to select the next question to pose. We demonstrate our approach in the context of evaluating algorithms that automatically answer questions related to diabetic macular edema (DME) grading. The experiments show that such an agent has similar behavior to a clinician, whereby asking questions that are relevant to key clinical concepts.
    MeSH term(s) Humans ; Diabetic Retinopathy/diagnostic imaging ; Macular Edema/diagnostic imaging ; Algorithms ; Machine Learning ; Diabetes Mellitus
    Language English
    Publishing date 2023-04-26
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1356436-5
    ISSN 1361-8423 ; 1361-8431 ; 1361-8415
    ISSN (online) 1361-8423 ; 1361-8431
    ISSN 1361-8415
    DOI 10.1016/j.media.2023.102822
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book ; Conference proceedings: CURAC 2016 - Tagungsband

    Ansó, Juan / Gerber, Kate / Gerber, Nicolas / Schwalbe, Marius / Sznitman, Raphael / Weber, Stefan / Williamson, Tom / Wimmer, William / Nabavi, Arya

    15. Jahrestagung der Deutschen Gesellschaft für Computer- und Roboterassistierte Chirurgie e.V. : 29.09. – 01.10.2016, Bern

    2016  

    Event/congress Deutsche Gesellschaft für Computer- und Roboterassistierte Chirurgie (15., 2016, Bern, Jahrestagung)
    Author's details Juan Ansó, Kate Gerber, Nicolas Gerber, Marius Schwalbe, Raphael Sznitman, Stefan WEber, Tom Williamson, Wilhelm Wimmer, Arya Nabavi
    Keywords Computerassistierte Chirurgie
    Subject Navigationschirurgie ; Roboterchirurgie ; Roboterassistierte Chirurgie ; Computer-assistierte Navigationschirurgie ; Computer-assistierte Chirurgie ; computer aided surgery ; CAS ; CANS ; Computergestützte Chirurgie ; Computergestützte Intervention ; Bild geführte Chirurgie ; Chirurgische Navigation
    Subject code 610
    Language German ; English
    Size xviii, 306 Seiten, Illustrationen
    Publisher Der Andere Verlag
    Publishing place Uelvesbüll
    Publishing country Germany
    Document type Book ; Conference proceedings
    Note Beiträge teils in deutscher, teils in englischer Sprache
    HBZ-ID HT019481322
    ISBN 978-3-86247-595-7 ; 3-86247-595-6
    Database Catalogue ZB MED Medicine, Health

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  3. Article ; Online: RF-ULM: Ultrasound Localization Microscopy Learned from Radio-Frequency Wavefronts.

    Hahne, Christopher / Chabouh, Georges / Chavignon, Arthur / Couture, Olivier / Sznitman, Raphael

    IEEE transactions on medical imaging

    2024  Volume PP

    Abstract: In Ultrasound Localization Microscopy (ULM), achieving high-resolution images relies on the precise localization of contrast agent particles across a series of beamformed frames. However, our study uncovers an enormous potential: The process of delay-and- ...

    Abstract In Ultrasound Localization Microscopy (ULM), achieving high-resolution images relies on the precise localization of contrast agent particles across a series of beamformed frames. However, our study uncovers an enormous potential: The process of delay-and-sum beamforming leads to an irreversible reduction of Radio-Frequency (RF) channel data, while its implications for localization remain largely unexplored. The rich contextual information embedded within RF wavefronts, including their hyperbolic shape and phase, offers great promise for guiding Deep Neural Networks (DNNs) in challenging localization scenarios. To fully exploit this data, we propose to directly localize scatterers in RF channel data. Our approach involves a custom super-resolution DNN using learned feature channel shuffling, non-maximum suppression, and a semi-global convolutional block for reliable and accurate wavefront localization. Additionally, we introduce a geometric point transformation that facilitates seamless mapping to the B-mode coordinate space. To understand the impact of beamforming on ULM, we validate the effectiveness of our method by conducting an extensive comparison with State-Of-The-Art (SOTA) techniques. We present the inaugural in vivo results from a wavefront-localizing DNN, highlighting its real-world practicality. Our findings show that RF-ULM bridges the domain shift between synthetic and real datasets, offering a considerable advantage in terms of precision and complexity. To enable the broader research community to benefit from our findings, our code and the associated SOTA methods are made available at https://github.com/hahnec/rf-ulm.
    Language English
    Publishing date 2024-04-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 622531-7
    ISSN 1558-254X ; 0278-0062
    ISSN (online) 1558-254X
    ISSN 0278-0062
    DOI 10.1109/TMI.2024.3391297
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Machine learning for predicting Plasmodium liver stage development in vitro using microscopy imaging.

    Otesteanu, Corin F / Caldelari, Reto / Heussler, Volker / Sznitman, Raphael

    Computational and structural biotechnology journal

    2024  Volume 24, Page(s) 334–342

    Abstract: Malaria, a significant global health challenge, is caused ... ...

    Abstract Malaria, a significant global health challenge, is caused by
    Language English
    Publishing date 2024-04-18
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2024.04.029
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: DeepPyramid+: medical image segmentation using Pyramid View Fusion and Deformable Pyramid Reception.

    Ghamsarian, Negin / Wolf, Sebastian / Zinkernagel, Martin / Schoeffmann, Klaus / Sznitman, Raphael

    International journal of computer assisted radiology and surgery

    2024  Volume 19, Issue 5, Page(s) 851–859

    Abstract: Purpose: Semantic segmentation plays a pivotal role in many applications related to medical image and video analysis. However, designing a neural network architecture for medical image and surgical video segmentation is challenging due to the diverse ... ...

    Abstract Purpose: Semantic segmentation plays a pivotal role in many applications related to medical image and video analysis. However, designing a neural network architecture for medical image and surgical video segmentation is challenging due to the diverse features of relevant classes, including heterogeneity, deformability, transparency, blunt boundaries, and various distortions. We propose a network architecture, DeepPyramid+, which addresses diverse challenges encountered in medical image and surgical video segmentation.
    Methods: The proposed DeepPyramid+ incorporates two major modules, namely "Pyramid View Fusion" (PVF) and "Deformable Pyramid Reception" (DPR), to address the outlined challenges. PVF replicates a deduction process within the neural network, aligning with the human visual system, thereby enhancing the representation of relative information at each pixel position. Complementarily, DPR introduces shape- and scale-adaptive feature extraction techniques using dilated deformable convolutions, enhancing accuracy and robustness in handling heterogeneous classes and deformable shapes.
    Results: Extensive experiments conducted on diverse datasets, including endometriosis videos, MRI images, OCT scans, and cataract and laparoscopy videos, demonstrate the effectiveness of DeepPyramid+ in handling various challenges such as shape and scale variation, reflection, and blur degradation. DeepPyramid+ demonstrates significant improvements in segmentation performance, achieving up to a 3.65% increase in Dice coefficient for intra-domain segmentation and up to a 17% increase in Dice coefficient for cross-domain segmentation.
    Conclusions: DeepPyramid+ consistently outperforms state-of-the-art networks across diverse modalities considering different backbone networks, showcasing its versatility. Accordingly, DeepPyramid+ emerges as a robust and effective solution, successfully overcoming the intricate challenges associated with relevant content segmentation in medical images and surgical videos. Its consistent performance and adaptability indicate its potential to enhance precision in computerized medical image and surgical video analysis applications.
    MeSH term(s) Humans ; Neural Networks, Computer ; Image Processing, Computer-Assisted/methods ; Video Recording ; Magnetic Resonance Imaging/methods ; Tomography, Optical Coherence/methods ; Female ; Laparoscopy/methods ; Algorithms
    Language English
    Publishing date 2024-01-08
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2365628-1
    ISSN 1861-6429 ; 1861-6410
    ISSN (online) 1861-6429
    ISSN 1861-6410
    DOI 10.1007/s11548-023-03046-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Book ; Online: A reinforcement learning approach for VQA validation

    Fountoukidou, Tatiana / Sznitman, Raphael

    an application to diabetic macular edema grading

    2023  

    Abstract: Recent advances in machine learning models have greatly increased the performance of automated methods in medical image analysis. However, the internal functioning of such models is largely hidden, which hinders their integration in clinical practice. ... ...

    Abstract Recent advances in machine learning models have greatly increased the performance of automated methods in medical image analysis. However, the internal functioning of such models is largely hidden, which hinders their integration in clinical practice. Explainability and trust are viewed as important aspects of modern methods, for the latter's widespread use in clinical communities. As such, validation of machine learning models represents an important aspect and yet, most methods are only validated in a limited way. In this work, we focus on providing a richer and more appropriate validation approach for highly powerful Visual Question Answering (VQA) algorithms. To better understand the performance of these methods, which answer arbitrary questions related to images, this work focuses on an automatic visual Turing test (VTT). That is, we propose an automatic adaptive questioning method, that aims to expose the reasoning behavior of a VQA algorithm. Specifically, we introduce a reinforcement learning (RL) agent that observes the history of previously asked questions, and uses it to select the next question to pose. We demonstrate our approach in the context of evaluating algorithms that automatically answer questions related to diabetic macular edema (DME) grading. The experiments show that such an agent has similar behavior to a clinician, whereby asking questions that are relevant to key clinical concepts.

    Comment: 16 pages (+ 23 pages supplementary material)
    Keywords Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Artificial Intelligence
    Subject code 006
    Publishing date 2023-07-19
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Book ; Online: Geometric Ultrasound Localization Microscopy

    Hahne, Christopher / Sznitman, Raphael

    2023  

    Abstract: Contrast-Enhanced Ultra-Sound (CEUS) has become a viable method for non-invasive, dynamic visualization in medical diagnostics, yet Ultrasound Localization Microscopy (ULM) has enabled a revolutionary breakthrough by offering ten times higher resolution. ...

    Abstract Contrast-Enhanced Ultra-Sound (CEUS) has become a viable method for non-invasive, dynamic visualization in medical diagnostics, yet Ultrasound Localization Microscopy (ULM) has enabled a revolutionary breakthrough by offering ten times higher resolution. To date, Delay-And-Sum (DAS) beamformers are used to render ULM frames, ultimately determining the image resolution capability. To take full advantage of ULM, this study questions whether beamforming is the most effective processing step for ULM, suggesting an alternative approach that relies solely on Time-Difference-of-Arrival (TDoA) information. To this end, a novel geometric framework for micro bubble localization via ellipse intersections is proposed to overcome existing beamforming limitations. We present a benchmark comparison based on a public dataset for which our geometric ULM outperforms existing baseline methods in terms of accuracy and robustness while only utilizing a portion of the available transducer data.

    Comment: Pre-print accepted for MICCAI 2023
    Keywords Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Machine Learning
    Subject code 006
    Publishing date 2023-06-27
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: A positive/unlabeled approach for the segmentation of medical sequences using point-wise supervision.

    Lejeune, Laurent / Sznitman, Raphael

    Medical image analysis

    2021  Volume 73, Page(s) 102185

    Abstract: The ability to quickly annotate medical imaging data plays a critical role in training deep learning frameworks for segmentation. Doing so for image volumes or video sequences is even more pressing as annotating these is particularly burdensome. To ... ...

    Abstract The ability to quickly annotate medical imaging data plays a critical role in training deep learning frameworks for segmentation. Doing so for image volumes or video sequences is even more pressing as annotating these is particularly burdensome. To alleviate this problem, this work proposes a new method to efficiently segment medical imaging volumes or videos using point-wise annotations only. This allows annotations to be collected extremely quickly and remains applicable to numerous segmentation tasks. Our approach trains a deep learning model using an appropriate Positive/Unlabeled objective function using sparse point-wise annotations. While most methods of this kind assume that the proportion of positive samples in the data is known a-priori, we introduce a novel self-supervised method to estimate this prior efficiently by combining a Bayesian estimation framework and new stopping criteria. Our method iteratively estimates appropriate class priors and yields high segmentation quality for a variety of object types and imaging modalities. In addition, by leveraging a spatio-temporal tracking framework, we regularize our predictions by leveraging the complete data volume. We show experimentally that our approach outperforms state-of-the-art methods tailored to the same problem.
    MeSH term(s) Bayes Theorem ; Humans ; Supervised Machine Learning
    Language English
    Publishing date 2021-07-31
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1356436-5
    ISSN 1361-8423 ; 1361-8431 ; 1361-8415
    ISSN (online) 1361-8423 ; 1361-8431
    ISSN 1361-8415
    DOI 10.1016/j.media.2021.102185
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Prediction of chronic central serous chorioretinopathy through combined manual annotation and AI-assisted volume measurement of flat irregular pigment epithelium.

    Desideri, Lorenzo Ferro / Scandella, Davide / Berger, Lieselotte / Sznitman, Raphael / Zinkernagel, Martin / Anguita, Rodrigo

    Ophthalmologica. Journal international d'ophtalmologie. International journal of ophthalmology. Zeitschrift fur Augenheilkunde

    2024  

    Abstract: Introduction: The aim of this study is to investigate the role of an artificial intelligence (AI)-developed OCT program to predict the clinical course of central serous chorioretinopathy (CSC ) based on baseline pigment epithelium detachment (PED) ... ...

    Abstract Introduction: The aim of this study is to investigate the role of an artificial intelligence (AI)-developed OCT program to predict the clinical course of central serous chorioretinopathy (CSC ) based on baseline pigment epithelium detachment (PED) features.
    Methods: Single-center, observational study with a retrospective design. Treatment-naïve patients with acute CSC and chronic CSC were recruited and OCTs were analyzed by an AI-developed platform (Discovery OCT Fluid and Biomarker Detector, RetinAI AG, Switzerland), providing automatic detection and volumetric quantification of PEDs. Flat irregular PED presence was annotated manually and afterwards measured by the AI program automatically.
    Results: 115 eyes of 101 patients with CSC were included, of which 70 were diagnosed with chronic CSC and 45 with acute CSC. It was found that patients with baseline presence of foveal flat PEDs and multiple flat foveal and extrafoveal PEDs had a higher chance of developing chronic form. AI-based volumetric analysis revealed no significant differences between the groups.
    Conclusions: While more evidence is needed to confirm the effectiveness of AI-based PED quantitative analysis, this study highlights the significance of identifying flat irregular PEDs at the earliest stage possible in patients with CSC, to optimize patient management and long-term visual outcomes.
    Language English
    Publishing date 2024-03-29
    Publishing country Switzerland
    Document type News
    ZDB-ID 209735-7
    ISSN 1423-0267 ; 0030-3755
    ISSN (online) 1423-0267
    ISSN 0030-3755
    DOI 10.1159/000538543
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Book ; Online: Logical Implications for Visual Question Answering Consistency

    Tascon-Morales, Sergio / Márquez-Neila, Pablo / Sznitman, Raphael

    2023  

    Abstract: Despite considerable recent progress in Visual Question Answering (VQA) models, inconsistent or contradictory answers continue to cast doubt on their true reasoning capabilities. However, most proposed methods use indirect strategies or strong ... ...

    Abstract Despite considerable recent progress in Visual Question Answering (VQA) models, inconsistent or contradictory answers continue to cast doubt on their true reasoning capabilities. However, most proposed methods use indirect strategies or strong assumptions on pairs of questions and answers to enforce model consistency. Instead, we propose a novel strategy intended to improve model performance by directly reducing logical inconsistencies. To do this, we introduce a new consistency loss term that can be used by a wide range of the VQA models and which relies on knowing the logical relation between pairs of questions and answers. While such information is typically not available in VQA datasets, we propose to infer these logical relations using a dedicated language model and use these in our proposed consistency loss function. We conduct extensive experiments on the VQA Introspect and DME datasets and show that our method brings improvements to state-of-the-art VQA models, while being robust across different architectures and settings.
    Keywords Computer Science - Computer Vision and Pattern Recognition
    Subject code 006
    Publishing date 2023-03-16
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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