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arXiv 2024年

作者： Li, Haopeng Deng, Andong Liu, Jun Rahmani, Hossein Guo, Yulan Schiele, Bernt Bennamoun, Mohammed Ke, Qiuhong School of Computing and Information Systems University of Melbourne Australia Center for Research in Computer Vision University of Central Florida United States Pillar Singapore University of Technology and Design Singapore School of Computing and Communications Lancaster University United Kingdom School of Electronics and Communication Engineering Sun Yat-sen University China Department of Computer Vision and Machine Learning Max Planck Institute for Informatics Saarland Informatics Campus Germany School of Physics Maths and Computing University of Western Australia Australia Department of Data Science & AI Monash University Australia

Reasoning over sports videos for question answering is an important task with numerous applications, such as player training and information retrieval. However, this task has not been explored due to the lack of relevant datasets and the challenging nature it presents. Most datasets for video question answering (VideoQA) focus mainly on general and coarse-grained understanding of daily-life videos, which is not applicable to sports scenarios requiring professional action understanding and fine-grained motion analysis. In this paper, we introduce the first dataset, named Sports-QA, specifically designed for the sports VideoQA task. The Sports-QA dataset includes various types of questions, such as descriptions, chronologies, causalities, and counterfactual conditions, covering multiple sports. Furthermore, to address the characteristics of the sports VideoQA task, we propose a new Auto-Focus Transformer (AFT) capable of automatically focusing on particular scales of temporal information for question answering. We conduct extensive experiments on Sports-QA, including baseline studies and the evaluation of different methods. The results demonstrate that our AFT achieves state-of-the-art performance. Copyright © 2024, The Authors. All rights reserved.

关键词： Question answering

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Florid – a Nationwide Identification Service for Plants from Photos and Habitat Information

SSRN

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SSRN 2024年

作者： Brun, Philipp de Witte, Lucienne Popp, Manuel Richard Zurell, Damaris Karger, Dirk Nikolaus Descombes, Patrice de Lutio, Riccardo Wegner, Jan Dirk Bornand, Christophe Eggenberg, Stefan Olevski, Tasko Zimmermann, Niklaus E. Swiss Federal Research Institute WSL Birmensdorf8903 Switzerland Musée et jardins botaniques cantonaux Lausanne1007 Switzerland Institute of Biochemistry and Biology University of Potsdam Potsdam14469 Germany EcoVision Lab Photogrammetry and Remote Sensing ETH Zurich Zürich8092 Switzerland Department of Mathematical Modeling and Machine Learning University of Zurich Zürich8057 Switzerland InfoFlora Switzerland Bern3013 Switzerland Swiss Data Science Center ETH Zurich Zürich8092 Switzerland University of Basel Switzerland

Citizen science has become key to biodiversity monitoring but critically depends on accurate quality control that is scalable and tailored to the focal region. We developed FlorID, a free-to-use identification service for all native and many non-native plants of Switzerland. FlorID can identify >3000 species, using vision transformers trained on 1.5M photos, and ecological predictions from multilayer perceptrons, trained on 6.7M occurrence observations and 20 high-resolution environmental variables. Embedded in a free-to-use application programming interface, FlorID can be accessed directly, via webservice, and via FlorApp smartphone application. If multiple images and spatiotemporal location are available, FlorID correctly identifies 93% of field observations and has a top-5 accuracy of 99%. Ecological predictions boost identification success especially for native species with distinct distributions. By evaluating information on appearance and fine-grained ecology, FlorID is a blueprint for similar solutions targeting different taxa or regions, and a basis for developments like automated community inventories. © 2024, The Authors. All rights reserved.

关键词： Blueprints

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Capsule Vision 2024 Challenge: Multi-Class Abnormality Classification for Video Capsule Endoscopy

arXiv

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arXiv 2024年

作者： Handa, Palak Mahbod, Amirreza Schwarzhans, Florian Woitek, Ramona Goel, Nidhi Dhir, Manas Chhabra, Deepti Jha, Shreshtha Sharma, Pallavi Thakur, Vijay Chawla, Simarpreet Singh Gunjan, Deepak Kakarla, Jagadeesh Raman, Balasubramanian Research Center for Medical Image Analysis and Artificial Intelligence Department of Medicine Danube Private University Krems Austria Department of Electronics and Communication Engineering Indira Gandhi Delhi Technical University for Women Delhi India Department of Artificial Intelligence and Data Sciences Indira Gandhi Delhi Technical University for Women Delhi India Department of Artificial Intelligence and Machine Learning University School of Automation and Robotics Guru Gobind Singh Indraprastha University Delhi India Department of Electronics and Communication Engineering Delhi Technological University Delhi India Columbia University New YorkNY United States Department of Gastroenterology and HNU All India Institute of Medical Sciences Delhi India Chennai Kancheepuram India Department of Computer Science and Engineering Indian Institute of Technology Roorkee India

We present the Capsule Vision 2024 Challenge: Multi-Class Abnormality Classification for Video Capsule Endoscopy. It was virtually organized by the research center for Medical Image analysis and Artificial Intelligence (MIAAI), Department of Medicine, Danube Private University, Krems, Austria in collaboration with the 9th International Conference on Computer Vision & Image Processing (CVIP 2024) being organized by the Indian Institute of Information Technology, Design and Manufacturing (IIITDM) Kancheepuram, Chennai, India. This document provides an overview of the challenge, including the registration process, rules, submission format, description of the datasets used, qualified team rankings, all team descriptions, and the benchmarking results reported by the organizers. © 2024, CC BY.

关键词： Endoscopy

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Unlocking the Potential of Digital Pathology: Novel Baselines for Compression

arXiv

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arXiv 2024年

作者： Fischer, Maximilian Neher, Peter Schuffler, Peter Ziegler, Sebastian Xiao, Shuhan Peretzke, Robin Clunie, David Ulrich, Constantin Baumgartner, Michael Muckenhuber, Alexander Almeida, Silvia Dias Gotz, Michael Kleesiek, Jens Nolden, Marco Braren, Rickmer Maier-Hein, Klaus Heidelberg Germany Partner site Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Medical Faculty Heidelberg University Heidelberg Germany Clinic of Diagnostics and Interventional Radiology Section Experimental Radiology Ulm University Medical Centre Ulm Germany Institute of Pathology TUM School of Medicine and Health Technical University of Munich Munich Germany Department of Diagnostic and Interventional Radiology Faculty of Medicine Technical University of Munich Munich Germany University Medicine Essen Essen Germany Partner site Essen Germany Pattern Analysis and Learning Group Department of Radiation Oncology Heidelberg University Hospital Heidelberg Germany NCT Heidelberg a partnership between DKFZ University Medical Center Heidelberg Germany Research Campus M2OLIE Mannheim Germany PixelMed Publishing BangorPA United States Munich Center for Machine Learning Munich Germany Helmholtz Imaging German Cancer Research Center Germany

Digital pathology offers a groundbreaking opportunity to transform clinical practice in histopathological image analysis, yet faces a significant hurdle: the substantial file sizes of pathological Whole Slide Images (WSI). While current digital pathology solutions rely on lossy JPEG compression to address this issue, lossy compression can introduce color and texture disparities, potentially impacting clinical decision-making. While prior research addresses perceptual image quality and downstream performance independently of each other, we jointly evaluate compression schemes for perceptual and downstream task quality on four different datasets. In addition, we collect an initially uncompressed dataset for an unbiased perceptual evaluation of compression schemes. Our results show that deep learning models fine-tuned for perceptual quality outperform conventional compression schemes like JPEG-XL or WebP for further compression of WSI. However, they exhibit a significant bias towards the compression artifacts present in the training data and struggle to generalize across various compression schemes. We introduce a novel evaluation metric based on feature similarity between original files and compressed files that aligns very well with the actual downstream performance on the compressed WSI. Our metric allows for a general and standardized evaluation of lossy compression schemes and mitigates the requirement to independently assess different downstream tasks. Our study provides novel insights for the assessment of lossy compression schemes for WSI and encourages a unified evaluation of lossy compression schemes to accelerate the clinical uptake of digital pathology. © 2024, CC BY-NC-SA.

关键词： Image compression

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Astrocytes mediate analogous memory in a multi-layer neuron-astrocytic network

arXiv

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arXiv 2021年

作者： Tsybina, Yuliya Kastalskiy, Innokentiy Krivonosov, Mikhail Zaikin, Alexey Kazantsev, Victor Gorban, Alexander Gordleeva, Susanna Scientific and Educational Mathematical Center 'Mathematics of Future Technology' Lobachevsky State University of Nizhny Novgorod Nizhny Novgorod Russia Laboratory of Autowave Processes Institute of Applied Physics Russian Academy of Sciences Nizhny Novgorod Russia Neuroscience and Cognitive Technology Laboratory Center for Technologies in Robotics and Mechatronics Components Innopolis University Innopolis Russia Center for Neurotechnology and Machine Learning Immanuel Kant Baltic Federal University Kaliningrad Russia Neuroscience Research Institute Samara State Medical University Samara Russia Dept of Mathematics Leicester University Leicester United Kingdom Centre for Analysis of Complex Systems Sechenov First Moscow State Medical University Sechenov University Moscow Russia Institute for Women's Health and Department of Mathematics University College London London United Kingdom

Modeling the neuronal processes underlying short-term working memory remains the focus of many theoretical studies in neuroscience. Here we propose a mathematical model of spiking neuron network (SNN) demonstrating how a piece of information can be maintained as a robust activity pattern for several seconds then completely disappear if no other stimuli come. Such short-term memory traces are preserved due to the activation of astrocytes accompanying the SNN. The astrocytes exhibit calcium transients at a time scale of seconds. These transients further modulate the efficiency of synaptic transmission and, hence, the firing rate of neighboring neurons at diverse timescales through gliotransmitter release. We show how such transients continuously encode frequencies of neuronal discharges and provide robust short-term storage of analogous information. This kind of short-term memory can keep operative information for seconds, then completely forget it to avoid overlapping with forthcoming patterns. The SNN is inter-connected with the astrocytic layer by local inter-cellular diffusive connections. The astrocytes are activated only when the neighboring neurons fire quite synchronously, e.g. when an information pattern is loaded. For illustration, we took greyscale photos of people's faces where the grey level encoded the level of applied current stimulating the neurons. The astrocyte feedback modulates (facilitates) synaptic transmission by varying the frequency of neuronal firing. We show how arbitrary patterns can be loaded, then stored for a certain interval of time, and retrieved if the appropriate clue pattern is applied to the input. © 2021, CC BY.

关键词： Image recognition

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Skeleton Recall Loss for Connectivity Conserving and Resource Efficient Segmentation of Thin Tubular Structures

arXiv

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arXiv 2024年

作者： Kirchhoff, Yannick Rokuss, Maximilian R. Roy, Saikat Kovacs, Balint Ulrich, Constantin Wald, Tassilo Zenk, Maximilian Vollmuth, Philipp Kleesiek, Jens Isensee, Fabian Maier-Hein, Klaus Heidelberg Division of Medical Image Computing Germany Faculty of Mathematics and Computer Science Heidelberg University Germany HIDSS4Health - Helmholtz Information and Data Science School for Health Heidelberg Karlsruhe Germany Medical Faculty Heidelberg Heidelberg University Heidelberg Germany Helmholtz Imaging German Cancer Research Center Heidelberg Germany Clinic for Neuroradiology University Hospital Bonn Bonn Germany Medical Faculty Bonn University of Bonn Bonn Germany University Hospital Essen Essen Germany West German Cancer Center Essen University Hospital Essen Essen Germany Pattern Analysis and Learning Group Department of Radiation Oncology Heidelberg University Hospital Germany

Accurately segmenting thin tubular structures, such as vessels, nerves, roads or concrete cracks, is a crucial task in computer vision. Standard deep learning-based segmentation loss functions, such as Dice or Cross-Entropy, focus on volumetric overlap, often at the expense of preserving structural connectivity or topology. This can lead to segmentation errors that adversely affect downstream tasks, including flow calculation, navigation, and structural inspection. Although current topology-focused losses mark an improvement, they introduce significant computational and memory overheads. This is particularly relevant for 3D data, rendering these losses infeasible for larger volumes as well as increasingly important multi-class segmentation problems. To mitigate this, we propose a novel Skeleton Recall Loss, which effectively addresses these challenges by circumventing intensive GPU-based calculations with inexpensive CPU operations. It demonstrates overall superior performance to current state-of-the-art approaches on five public datasets for topology-preserving segmentation, while substantially reducing computational overheads by more than 90%. In doing so, we introduce the first multi-class capable loss function for thin structure segmentation, excelling in both efficiency and efficacy for topology-preservation. Our code is available to the community, providing a foundation for further advancements, at: https://***/MIC-DKFZ/Skeleton-Recall. © 2024, CC BY.

关键词： Topology

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A Self-Supervised Image Registration Approach for Measuring Local Response Patterns in Metastatic Ovarian Cancer

arXiv

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arXiv 2024年

作者： Machado, Inês P. Reithmeir, Anna Kogl, Fryderyk Rundo, Leonardo Funingana, Gabriel Reinius, Marika Mungmeeprued, Gift Gao, Zeyu McCague, Cathal Kerfoot, Eric Woitek, Ramona Sala, Evis Ou, Yangming Brenton, James Schnabel, Julia Crispin, Mireia Department of Oncology University of Cambridge United Kingdom Cancer Research UK Cambridge Institute University of Cambridge United Kingdom Early Cancer Institute University of Cambridge United Kingdom School of Computation Information & Technology Technical University of Munich Germany Institute of Machine Learning in Biomedical Imaging Helmholtz Munich Germany Department of Information and Electrical Engineering University of Salerno Italy School of Biomedical Engineering & Imaging Sciences King’s College London United Kingdom Research Center for Medical Image Analysis and AI Danube University Austria Department of Radiologic Sciences Università Cattolica del Sacro Cuore Italy Department of Radiology Boston Children’s Hospital Harvard Medical School United States

High-grade serous ovarian carcinoma (HGSOC) is characterised by significant spatial and temporal heterogeneity, typically manifesting at an advanced metastatic stage. A major challenge in treating advanced HGSOC is effectively monitoring localised change in tumour burden across multiple sites during neoadjuvant chemotherapy (NACT) and predicting long-term pathological response and overall patient survival. In this work, we propose a self-supervised deformable image registration algorithm that utilises a general-purpose image encoder for image feature extraction to co-register contrast-enhanced computerised tomography scan images acquired before and after neoadjuvant chemotherapy. This approach addresses challenges posed by highly complex tumour deformations and longitudinal lesion matching during treatment. Localised tumour changes are calculated using the Jacobian determinant maps of the registration deformation at multiple disease sites and their macroscopic areas, including hypo-dense (i.e., cystic/necrotic), hyper-dense (i.e., calcified), and intermediate density (i.e., soft tissue) portions. A series of experiments is conducted to understand the role of a general-purpose image encoder and its application in quantifying change in tumour burden during neoadjuvant chemotherapy in HGSOC. This work is the first to demonstrate the feasibility of a self-supervised image registration approach in quantifying NACT-induced localised tumour changes across the whole disease burden of patients with complex multisite HGSOC, which could be used as a potential marker for ovarian cancer patient’s long-term pathological response and survival. © 2024, CC BY.

关键词： Tumors

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sbi reloaded: a toolkit for simulation-based inference workflows

arXiv

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arXiv 2024年

作者： Boelts, Jan Deistler, Michael Gloeckler, Manuel Tejero-Cantero, Álvaro Lueckmann, Jan-Matthis Moss, Guy Steinbach, Peter Moreau, Thomas Muratore, Fabio Linhart, Julia Durkan, Conor Vetter, Julius Miller, Benjamin Kurt Herold, Maternus Ziaeemehr, Abolfazl Pals, Matthijs Gruner, Theo Bischoff, Sebastian Krouglova, Anastasia N. Gao, Richard Lappalainen, Janne K. Mucsányi, Bálint Pei, Felix Schulz, Auguste Stefanidi, Zinovia Rodrigues, Pedro L.C. Schröder, Cornelius Zaid, Faried Abu Beck, Jonas Kapoor, Jaivardhan Greenberg, David S. Gonçalves, Pedro J. Macke, Jakob H. Machine Learning in Science University of Tübingen Germany Tübingen AI Center Germany TransferLab AppliedAI Institute for Europe Germany ML Colab Cluster ML in Science University of Tübingen Germany Google Research United States Helmholtz-Zentrum Dresden-Rossendorf Germany Université Paris-Saclay INRIA CEA Palaiseau France Robert Bosch GmbH Germany School of Informatics University of Edinburgh United Kingdom University of Amsterdam Netherlands Research and Innovation Center BMW Group Germany Institute for Applied Mathematics and Scientific Computing University of the Bundeswehr Munich Germany Aix Marseille INSERM INS France TU Darmstadt Hessian.AI Germany University Hospital Tübingen M3 Research Center Germany Faculty of Science KU Leuven B-3000 Belgium Imec Belgium Methods of Machine Learning University of Tübingen Germany Neuroscience Institute Carnegie Mellon University United States Université Grenoble Alpes INRIA CNRS Grenoble INP LJK France Hertie Institute for AI in Brain Health University of Tübingen Germany Institute of Coastal Systems - Analysis and Modeling Helmholtz AI Germany Departments of Computer Science Electrical Engineering KU Leuven Belgium Department Empirical Inference Max Planck Institute for Intelligent Systems Tübingen Germany

Scientists and engineers use simulators to model empirically observed phenomena. However, tuning the parameters of a simulator to ensure its outputs match observed data presents a significant challenge. Simulation-based inference (SBI) addresses this by enabling Bayesian inference for simulators, identifying parameters that match observed data and align with prior knowledge. Unlike traditional Bayesian inference, SBI only needs access to simulations from the model and does not require evaluations of the likelihood-function. In addition, SBI algorithms do not require gradients through the simulator, allow for massive parallelization of simulations, and can perform inference for different observations without further simulations or training, thereby amortizing inference. Over the past years, we have developed, maintained, and extended sbi, a PyTorch-based package4 that implements Bayesian SBI algorithms based on neural networks. The sbi toolkit implements a wide range of inference methods, neural network architectures, sampling methods, and diagnostic tools. In addition, it provides well-tested default settings but also offers flexibility to fully customize every step of the simulation-based inference workflow. Taken together, the sbi toolkit enables scientists and engineers to apply state-of-the-art SBI methods to black-box simulators, opening up new possibilities for aligning simulations with empirically observed data. © 2024, CC BY-SA.

关键词： Neural networks

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Longitudinal Segmentation of MS Lesions via Temporal Difference Weighting

arXiv

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arXiv 2024年

作者： Rokuss, Maximilian R. Kirchhoff, Yannick Roy, Saikat Kovacs, Balint Ulrich, Constantin Wald, Tassilo Zenk, Maximilian Denner, Stefan Isensee, Fabian Vollmuth, Philipp Kleesiek, Jens Maier-Hein, Klaus Heidelberg Division of Medical Image Computing Germany Faculty of Mathematics and Computer Science Heidelberg University Germany HIDSS4Health - Helmholtz Information and Data Science School for Health Karlsruhe Heidelberg Germany Medical Faculty Heidelberg Heidelberg University Heidelberg Germany Helmholtz Imaging German Cancer Research Center Heidelberg Germany Department of Neuroradiology Heidelberg University Hospital Heidelberg Germany Division for Computational Neuroimaging Department of Neuroradiology Heidelberg University Hospital Heidelberg Germany University Hospital Essen Essen Germany West German Cancer Center Essen University Hospital Essen Essen Germany Pattern Analysis and Learning Group Department of Radiation Oncology Heidelberg University Hospital Germany

Accurate segmentation of Multiple Sclerosis (MS) lesions in longitudinal MRI scans is crucial for monitoring disease progression and treatment efficacy. Although changes across time are taken into account when assessing images in clinical practice, most existing deep learning methods treat scans from different timepoints separately. Among studies utilizing longitudinal images, a simple channel-wise concatenation is the primary albeit suboptimal method employed to integrate timepoints. We introduce a novel approach that explicitly incorporates temporal differences between baseline and follow-up scans through a unique architectural inductive bias called Difference Weighting Block. It merges features from two timepoints, emphasizing changes between scans. We achieve superior scores in lesion segmentation (Dice Score, Hausdorff distance) as well as lesion detection (lesion-level F1 score) as compared to state-of-the-art longitudinal and single timepoint models across two datasets. Our code is made publicly available at: ***/MIC-DKFZ/ Longitudinal-Difference-Weighting. © 2024, CC BY.

关键词： Image segmentation

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AstroPhot: Fitting Everything Everywhere All at Once in Astronomical Images

arXiv

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arXiv 2023年

作者： Stone, Connor J. Courteau, Stéphane Cuillandre, Jean-Charles Hezaveh, Yashar Perreault-Levasseur, Laurence Arora, Nikhil Department of Physics Université de Montréal MontréalQC Canada Mila - Québec Artificial Intelligence Institute MontréalQC Canada Ciela - Montréal Institute for Astrophysical Data Analysis and Machine Learning MontréalQC Canada Department of Physics Engineering Physics & Astronomy Queen’s University KingstonON Canada AIM CEA CNRS Université Paris-Saclay Université de Paris Gif-sur-YvetteF-91191 France Center for Computational Astrophysics Flatiron Institute 162 5th Avenue New YorkNY10010 United States New York University Abu Dhabi PO Box 129188 Abu Dhabi United Arab Emirates New York University Abu Dhabi United Arab Emirates

We present ASTROPHOT, a fast, powerful, and user-friendly Python based astronomical image photometry solver. ASTROPHOT incorporates automatic differentiation and GPU (or parallel CPU) acceleration, powered by the machine learning library PYTORCH. Everything: ASTROPHOT can fit models for sky, stars, galaxies, PSFs, and more in a principled X2 forward optimization, recovering Bayesian posterior information and covariance of all parameters. Everywhere: ASTROPHOT can optimize forward models on CPU or GPU;across images that are large, multiband, multi-epoch, rotated, dithered, and more. All at once: The models are optimized together, thus handling overlapping objects and including the covariance between parameters (including PSF and galaxy parameters). A number of optimization algorithms are available including Levenberg-Marquardt, Gradient descent, and No-U-Turn MCMC sampling. With an object-oriented user interface, ASTROPHOT makes it easy to quickly extract detailed information from complex astronomical data for individual images or large survey programs. This paper outlines novel features of the ASTROPHOT code and compares it to other popular astronomical image modeling software. ASTROPHOT is open-source, fully Python based, and freely accessible here: https://***/Autostronomy/AstroPhot © 2023, CC BY.

关键词： Python

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