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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.
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Algoritmos , Processamento de Imagem Assistida por Computador , Aprendizado de Máquina , SemânticaRESUMO
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.
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Inteligência ArtificialRESUMO
Photoacoustic imaging potentially allows for the real-time visualization of functional human tissue parameters such as oxygenation but is subject to a challenging underlying quantification problem. While in silico studies have revealed the great potential of deep learning (DL) methodology in solving this problem, the inherent lack of an efficient gold standard method for model training and validation remains a grand challenge. This work investigates whether DL can be leveraged to accurately and efficiently simulate photon propagation in biological tissue, enabling photoacoustic image synthesis. Our approach is based on estimating the initial pressure distribution of the photoacoustic waves from the underlying optical properties using a back-propagatable neural network trained on synthetic data. In proof-of-concept studies, we validated the performance of two complementary neural network architectures, namely a conventional U-Net-like model and a Fourier Neural Operator (FNO) network. Our in silico validation on multispectral human forearm images shows that DL methods can speed up image generation by a factor of 100 when compared to Monte Carlo simulations with 5×108 photons. While the FNO is slightly more accurate than the U-Net, when compared to Monte Carlo simulations performed with a reduced number of photons (5×106), both neural network architectures achieve equivalent accuracy. In contrast to Monte Carlo simulations, the proposed DL models can be used as inherently differentiable surrogate models in the photoacoustic image synthesis pipeline, allowing for back-propagation of the synthesis error and gradient-based optimization over the entire pipeline. Due to their efficiency, they have the potential to enable large-scale training data generation that can expedite the clinical application of photoacoustic imaging.
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Aprendizado Profundo , Humanos , Análise Espectral , Antebraço , Método de Monte Carlo , Redes Neurais de ComputaçãoRESUMO
Advances in mammography have sparked an exponential increase in the detection of early-stage breast lesions, most commonly ductal carcinoma in situ (DCIS). More than 50% of DCIS lesions are benign and will remain indolent, never progressing to invasive cancers. However, the factors that promote DCIS invasion remain poorly understood. Here, we show that SMARCE1 is required for the invasive progression of DCIS and other early-stage tumors. We show that SMARCE1 drives invasion by regulating the expression of secreted proteases that degrade basement membrane, an ECM barrier surrounding all epithelial tissues. In functional studies, SMARCE1 promotes invasion of in situ cancers growing within primary human mammary tissues and is also required for metastasis in vivo. Mechanistically, SMARCE1 drives invasion by forming a SWI/SNF-independent complex with the transcription factor ILF3. In patients diagnosed with early-stage cancers, SMARCE1 expression is a strong predictor of eventual relapse and metastasis. Collectively, these findings establish SMARCE1 as a key driver of invasive progression in early-stage tumors.
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Neoplasias da Mama/patologia , Carcinoma Ductal de Mama/patologia , Carcinoma Intraductal não Infiltrante/patologia , Movimento Celular , Proteínas Cromossômicas não Histona/metabolismo , Proteínas de Ligação a DNA/metabolismo , Recidiva Local de Neoplasia/patologia , Animais , Apoptose , Neoplasias da Mama/metabolismo , Carcinoma Ductal de Mama/metabolismo , Carcinoma Intraductal não Infiltrante/metabolismo , Proliferação de Células , Progressão da Doença , Feminino , Humanos , Camundongos , Camundongos Endogâmicos NOD , Camundongos SCID , Invasividade Neoplásica , Recidiva Local de Neoplasia/metabolismo , Prognóstico , Taxa de Sobrevida , Células Tumorais Cultivadas , Ensaios Antitumorais Modelo de XenoenxertoRESUMO
Spectral imaging has the potential to become a key technique in interventional medicine as it unveils much richer optical information compared to conventional RBG (red, green, and blue)-based imaging. Thus allowing for high-resolution functional tissue analysis in real time. Its higher information density particularly shows promise for the development of powerful perfusion monitoring methods for clinical use. However, even though in vivo validation of such methods is crucial for their clinical translation, the biomedical field suffers from a lack of publicly available datasets for this purpose. Closing this gap, we generated the SPECTRAL Perfusion Arm Clamping dAtaset (SPECTRALPACA). It comprises ten spectral videos (â¼20 Hz, approx. 20,000 frames each) systematically recorded of the hands of ten healthy human participants in different functional states. We paired each spectral video with concisely tracked regions of interest, and corresponding diffuse reflectance measurements recorded with a spectrometer. Providing the first openly accessible in human spectral video dataset for perfusion monitoring, our work facilitates the development and validation of new functional imaging methods.
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Pele , Humanos , Pele/irrigação sanguínea , Pele/diagnóstico por imagem , Gravação em Vídeo , Mãos/irrigação sanguínea , Braço/irrigação sanguínea , Braço/diagnóstico por imagemRESUMO
Intelligent systems in interventional healthcare depend on the reliable perception of the environment. In this context, photoacoustic tomography (PAT) has emerged as a non-invasive, functional imaging modality with great clinical potential. Current research focuses on converting the high-dimensional, not human-interpretable spectral data into the underlying functional information, specifically the blood oxygenation. One of the largely unexplored issues stalling clinical advances is the fact that the quantification problem is ambiguous, i.e. that radically different tissue parameter configurations could lead to almost identical photoacoustic spectra. In the present work, we tackle this problem with conditional Invertible Neural Networks (cINNs). Going beyond traditional point estimates, our network is used to compute an approximation of the conditional posterior density of tissue parameters given the measurement. To this end, an automatic mode detection algorithm extracts the plausible solution from the sample-based posterior. According to a comprehensive validation study based on both synthetic and real images, our approach is well-suited for exploring ambiguity in quantitative PAT.
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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. However, increasing evidence shows that particularly in image analysis, metrics are often chosen inadequately in relation to the underlying research problem. This could be attributed to a lack of accessibility of metric-related knowledge: While 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 multi-stage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides the first reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. Focusing on biomedical image analysis but with the potential of transfer to other fields, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. To facilitate comprehension, illustrations and specific examples accompany each pitfall. As a structured body of information accessible to researchers of all levels of expertise, this work enhances global comprehension of a key topic in image analysis validation.
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Laparoscopic surgery has evolved as a key technique for cancer diagnosis and therapy. While characterization of the tissue perfusion is crucial in various procedures, such as partial nephrectomy, doing so by means of visual inspection remains highly challenging. We developed a laparoscopic real-time multispectral imaging system featuring a compact and lightweight multispectral camera and the possibility to complement the conventional surgical view of the patient with functional information at a video rate of 25 Hz. To enable contrast agent-free ischemia monitoring during laparoscopic partial nephrectomy, we phrase the problem of ischemia detection as an out-of-distribution detection problem that does not rely on data from any other patient and uses an ensemble of invertible neural networks at its core. An in-human trial demonstrates the feasibility of our approach and highlights the potential of spectral imaging combined with advanced deep learning-based analysis tools for fast, efficient, reliable, and safe functional laparoscopic imaging.
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Meios de Contraste , Laparoscopia , Humanos , Nefrectomia/métodos , Redes Neurais de Computação , Laparoscopia/métodos , IsquemiaRESUMO
Photoacoustic tomography (PAT) has the potential to recover morphological and functional tissue properties with high spatial resolution. However, previous attempts to solve the optical inverse problem with supervised machine learning were hampered by the absence of labeled reference data. While this bottleneck has been tackled by simulating training data, the domain gap between real and simulated images remains an unsolved challenge. We propose a novel approach to PAT image synthesis that involves subdividing the challenge of generating plausible simulations into two disjoint problems: (1) Probabilistic generation of realistic tissue morphology, and (2) pixel-wise assignment of corresponding optical and acoustic properties. The former is achieved with Generative Adversarial Networks (GANs) trained on semantically annotated medical imaging data. According to a validation study on a downstream task our approach yields more realistic synthetic images than the traditional model-based approach and could therefore become a fundamental step for deep learning-based quantitative PAT (qPAT).
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Photoacoustic (PA) imaging has the potential to revolutionize functional medical imaging in healthcare due to the valuable information on tissue physiology contained in multispectral photoacoustic measurements. Clinical translation of the technology requires conversion of the high-dimensional acquired data into clinically relevant and interpretable information. In this work, we present a deep learning-based approach to semantic segmentation of multispectral photoacoustic images to facilitate image interpretability. Manually annotated photoacoustic and ultrasound imaging data are used as reference and enable the training of a deep learning-based segmentation algorithm in a supervised manner. Based on a validation study with experimentally acquired data from 16 healthy human volunteers, we show that automatic tissue segmentation can be used to create powerful analyses and visualizations of multispectral photoacoustic images. Due to the intuitive representation of high-dimensional information, such a preprocessing algorithm could be a valuable means to facilitate the clinical translation of photoacoustic imaging.
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Semantic image segmentation is an important prerequisite for context-awareness and autonomous robotics in surgery. The state of the art has focused on conventional RGB video data acquired during minimally invasive surgery, but full-scene semantic segmentation based on spectral imaging data and obtained during open surgery has received almost no attention to date. To address this gap in the literature, we are investigating the following research questions based on hyperspectral imaging (HSI) data of pigs acquired in an open surgery setting: (1) What is an adequate representation of HSI data for neural network-based fully automated organ segmentation, especially with respect to the spatial granularity of the data (pixels vs. superpixels vs. patches vs. full images)? (2) Is there a benefit of using HSI data compared to other modalities, namely RGB data and processed HSI data (e.g. tissue parameters like oxygenation), when performing semantic organ segmentation? According to a comprehensive validation study based on 506 HSI images from 20 pigs, annotated with a total of 19 classes, deep learning-based segmentation performance increases - consistently across modalities - with the spatial context of the input data. Unprocessed HSI data offers an advantage over RGB data or processed data from the camera provider, with the advantage increasing with decreasing size of the input to the neural network. Maximum performance (HSI applied to whole images) yielded a mean DSC of 0.90 ((standard deviation (SD)) 0.04), which is in the range of the inter-rater variability (DSC of 0.89 ((standard deviation (SD)) 0.07)). We conclude that HSI could become a powerful image modality for fully-automatic surgical scene understanding with many advantages over traditional imaging, including the ability to recover additional functional tissue information. Our code and pre-trained models are available at https://github.com/IMSY-DKFZ/htc.
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Aprendizado Profundo , Processamento de Imagem Assistida por Computador , Animais , Processamento de Imagem Assistida por Computador/métodos , Redes Neurais de Computação , Semântica , SuínosRESUMO
Recent developments in data science in general and machine learning in particular have transformed the way experts envision the future of surgery. Surgical Data Science (SDS) is a new research field that aims to improve the quality of interventional healthcare through the capture, organization, analysis and modeling of data. While an increasing number of data-driven approaches and clinical applications have been studied in the fields of radiological and clinical data science, translational success stories are still lacking in surgery. In this publication, we shed light on the underlying reasons and provide a roadmap for future advances in the field. Based on an international workshop involving leading researchers in the field of SDS, we review current practice, key achievements and initiatives as well as available standards and tools for a number of topics relevant to the field, namely (1) infrastructure for data acquisition, storage and access in the presence of regulatory constraints, (2) data annotation and sharing and (3) data analytics. We further complement this technical perspective with (4) a review of currently available SDS products and the translational progress from academia and (5) a roadmap for faster clinical translation and exploitation of the full potential of SDS, based on an international multi-round Delphi process.
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Ciência de Dados , Aprendizado de Máquina , HumanosRESUMO
With the impact of artificial intelligence (AI) algorithms on medical research on the rise, the importance of competitions for comparative validation of algorithms, so-called challenges, has been steadily increasing, to a point at which challenges can be considered major drivers of research, particularly in the biomedical image analysis domain. Given their importance, high quality, transparency, and interpretability of challenges is essential for good scientific practice and meaningful validation of AI algorithms, for instance towards clinical translation. This mini-review presents several issues related to the design, execution, and interpretation of challenges in the biomedical domain and provides best-practice recommendations. PATIENT SUMMARY: This paper presents recommendations on how to reliably compare the usefulness of new artificial intelligence methods for analysis of medical images.
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Inteligência Artificial , Pesquisa Biomédica , Algoritmos , HumanosRESUMO
PURPOSE: Photoacoustic tomography (PAT) is a novel imaging technique that can spatially resolve both morphological and functional tissue properties, such as vessel topology and tissue oxygenation. While this capacity makes PAT a promising modality for the diagnosis, treatment, and follow-up of various diseases, a current drawback is the limited field of view provided by the conventionally applied 2D probes. METHODS: In this paper, we present a novel approach to 3D reconstruction of PAT data (Tattoo tomography) that does not require an external tracking system and can smoothly be integrated into clinical workflows. It is based on an optical pattern placed on the region of interest prior to image acquisition. This pattern is designed in a way that a single tomographic image of it enables the recovery of the probe pose relative to the coordinate system of the pattern, which serves as a global coordinate system for image compounding. RESULTS: To investigate the feasibility of Tattoo tomography, we assessed the quality of 3D image reconstruction with experimental phantom data and in vivo forearm data. The results obtained with our prototype indicate that the Tattoo method enables the accurate and precise 3D reconstruction of PAT data and may be better suited for this task than the baseline method using optical tracking. CONCLUSIONS: In contrast to previous approaches to 3D ultrasound (US) or PAT reconstruction, the Tattoo approach neither requires complex external hardware nor training data acquired for a specific application. It could thus become a valuable tool for clinical freehand PAT.
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Imageamento Tridimensional/métodos , Imagens de Fantasmas , Tatuagem/métodos , Tomografia Computadorizada por Raios X/métodos , Ultrassonografia/métodos , HumanosRESUMO
Image-based tracking of medical instruments is an integral part of surgical data science applications. Previous research has addressed the tasks of detecting, segmenting and tracking medical instruments based on laparoscopic video data. However, the proposed methods still tend to fail when applied to challenging images and do not generalize well to data they have not been trained on. This paper introduces the Heidelberg Colorectal (HeiCo) data set - the first publicly available data set enabling comprehensive benchmarking of medical instrument detection and segmentation algorithms with a specific emphasis on method robustness and generalization capabilities. Our data set comprises 30 laparoscopic videos and corresponding sensor data from medical devices in the operating room for three different types of laparoscopic surgery. Annotations include surgical phase labels for all video frames as well as information on instrument presence and corresponding instance-wise segmentation masks for surgical instruments (if any) in more than 10,000 individual frames. The data has successfully been used to organize international competitions within the Endoscopic Vision Challenges 2017 and 2019.