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	<title>foundation model &#8211; Science</title>
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	<title>foundation model &#8211; Science</title>
	<link>https://scienmag.com</link>
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		<title>Global AI Model WeedNet Identifies 1,593 Weed Species With Record Accuracy</title>
		<link>https://scienmag.com/global-ai-model-weednet-identifies-1593-weed-species-with-record-accuracy/</link>
		
		<dc:creator><![CDATA[Blake Davidson]]></dc:creator>
		<pubDate>Thu, 08 Oct 2026 21:41:43 +0000</pubDate>
				<category><![CDATA[Technology and Engineering]]></category>
		<category><![CDATA[agricultural robotics]]></category>
		<category><![CDATA[AI in sustainable farming]]></category>
		<category><![CDATA[AI-powered weed management]]></category>
		<category><![CDATA[computer vision]]></category>
		<category><![CDATA[fine-tuning]]></category>
		<category><![CDATA[foundation model]]></category>
		<category><![CDATA[global weed species recognition]]></category>
		<category><![CDATA[interdisciplinary research in weed identification]]></category>
		<category><![CDATA[Invasive Species]]></category>
		<category><![CDATA[invasive weed identification technology]]></category>
		<category><![CDATA[Iowa State University]]></category>
		<category><![CDATA[large-scale weed species database]]></category>
		<category><![CDATA[Machine learning]]></category>
		<category><![CDATA[machine learning for crop protection]]></category>
		<category><![CDATA[Nature Communications.]]></category>
		<category><![CDATA[plant growth stage identification using AI]]></category>
		<category><![CDATA[plant species classification with artificial intelligence]]></category>
		<category><![CDATA[precision agriculture]]></category>
		<category><![CDATA[precision agriculture weed control]]></category>
		<category><![CDATA[self-supervised learning]]></category>
		<category><![CDATA[weed identification]]></category>
		<category><![CDATA[weed identification AI]]></category>
		<category><![CDATA[WeedNet]]></category>
		<category><![CDATA[WeedNet weed detection system]]></category>
		<guid isPermaLink="false">https://scienmag.com/?p=249745</guid>

					<description><![CDATA[A foundation model-based AI system called WeedNet identifies 1,593 weed species with 91.02 percent accuracy and reaches 97.38 percent accuracy for Iowa weeds after regional fine-tuning.]]></description>
										<content:encoded><![CDATA[<p>Weeds are among the most persistent threats to global agriculture, stealing water, nutrients, and sunlight from crops while demanding enormous labor and chemical inputs to control. The stakes of getting weed management right are enormous: misidentify a weed at a critical growth stage, and a farmer may apply the wrong herbicide, miss the optimal window for mechanical control, or allow an invasive species to gain a foothold in a field. Yet identifying weeds accurately is surprisingly difficult, even for trained eyes. Many species look nearly identical to one another, and the same plant can change dramatically in appearance between seedling, vegetative, flowering, and senescent stages. A new study published in Nature Communications presents an artificial intelligence system designed to tackle exactly this challenge at a planetary scale.</p>
<p>The system, called WeedNet, was developed by a large interdisciplinary team led by Yanben Shen and Timilehin T. Ayanlade, with corresponding authors Soumik Sarkar and Arti Singh, bringing together researchers at Iowa State University and the University of Arizona. Their goal was ambitious: build a single AI model capable of recognizing an extensive set of weed species from around the world, and then adapt that global knowledge to the specific weed communities of individual regions. The work addresses a bottleneck that has long frustrated agricultural AI. Computer vision models need vast amounts of expert-verified training data, but curated, labeled images of weeds are scarce, expensive to produce, and highly variable in quality. Morphological similarity between species compounds the problem, causing even sophisticated deep learning systems to confuse close relatives.</p>
<p>Technically, WeedNet is an end-to-end identification pipeline built on a foundation model architecture, the same class of large, general-purpose neural networks that has transformed fields from language processing to medical imaging. Rather than training from scratch on limited weed photographs, the researchers employed self-supervised learning, a technique in which the model learns visual representations from unlabeled imagery by solving pretext tasks, such as predicting hidden portions of images or distinguishing between different views of the same plant. This pretraining allows the network to internalize the general statistical structure of plant imagery, capturing features like leaf venation, stem architecture, inflorescence shape, and texture, before it is ever asked to make a species-level judgment. Fine-tuning on labeled weed data then specializes these general representations for the taxonomy at hand.</p>
<p>The reported performance is striking. Across 1,593 weed species, WeedNet achieved 91.02 percent overall identification accuracy. Even more remarkable, 41 percent of the species in the evaluation were identified with perfect accuracy, meaning the model correctly classified every test image for those taxa. For a task where many species differ only subtly, in the hairiness of a leaf margin or the arrangement of florets, this level of performance suggests the foundation model approach captures discriminative features that earlier, smaller-scale systems missed. The team then demonstrated the second half of their global-to-local strategy by fine-tuning the model for a specific region. The resulting local Iowa WeedNet model reached 97.38 percent overall accuracy across 84 weed species relevant to Iowa agriculture, a substantial gain over the global model and a demonstration that regional adaptation is both feasible and effective.</p>
<p>One of the most scientifically valuable contributions of the study is its analysis of what drives performance. The researchers systematically tested the model under conditions of intra-species dissimilarity, where images of the same species look very different from one another, and inter-species similarity, where images of different species look nearly alike. These are precisely the failure modes that plague weed identification. Their findings indicate that diversity in the collected images, spanning all growth stages and the distinguishable plant characteristics that experts actually use in the field, is crucial to model performance. In other words, the model is only as good as the ecological breadth of its training data. A dataset heavy on flowering specimens will fail on seedlings; a dataset from one continent will stumble on weeds photographed under different lighting, soils, and backgrounds elsewhere.</p>
<p>The implications for precision agriculture are considerable. Modern weed control increasingly relies on targeted interventions: spot spraying, mechanical hoeing, and laser weeding systems that act on individual plants rather than blanketing entire fields with herbicide. All of these depend on fast, reliable in-field species identification. To test whether WeedNet could serve as the perceptual brain of such machinery, the team validated the model on images captured by drones and ground rovers, platforms that introduce motion blur, unusual viewing angles, variable illumination, and occlusion by crop canopy. The successful performance on these imagery sources highlights the model&#8217;s potential for integration into robotic platforms, moving it from a laboratory benchmark toward a working component of autonomous field equipment.</p>
<p>Beyond robotics, the researchers explored a conversational dimension. By integrating WeedNet with artificial intelligence systems capable of natural language interaction, they created intelligent consulting tools that can serve farmers, researchers, and government agencies. A farmer could photograph an unfamiliar plant and receive not just a species name but contextual guidance relevant to that identification, while an ecological conservation agency could use the same underlying model to monitor invasive weed spread across diverse landscapes. This fusion of visual identification with conversational AI reflects a broader trend in agricultural technology, where standalone perception models are becoming front ends to richer decision-support systems that translate a classification into actionable management advice.</p>
<p>The global-to-local design also carries lessons for how foundation models should be deployed in domain sciences generally. A single monolithic model trained on globally averaged data will inevitably be mediocre everywhere, because weed floras differ radically between regions, and local species that dominate Midwestern cornfields may be absent from Asian rice paddies and vice versa. WeedNet&#8217;s architecture treats the global model as a shared foundation, a reservoir of general plant visual knowledge, from which targeted regional models can be efficiently derived through fine-tuning. This mirrors strategies now standard in natural language processing, where large pretrained models are adapted to specialized vocabularies and tasks, and suggests a template for other biodiversity applications, from crop disease diagnosis to pollinator monitoring, where global data exists but local expertise is the scarce resource.</p>
<p>The scale of the collaboration itself is noteworthy. The author team spans agronomy, mechanical engineering, computer science, plant pathology, and a data science institute, reflecting the reality that modern agricultural AI cannot be built by any single discipline. Agronomists supplied the taxonomic and phenological expertise needed to curate and verify species labels; machine learning researchers designed the self-supervised and fine-tuning pipelines; and roboticists and extension specialists grounded the work in the practical constraints of fields and farms. The project received support from the U.S. National Science Foundation and the U.S. Department of Agriculture, including the AI Institute for Resilient Agriculture, and drew on iNaturalist as a data source, underscoring how citizen-science platforms are becoming indispensable infrastructure for biodiversity AI.</p>
<p>Challenges remain before systems like WeedNet become ubiquitous in the world&#8217;s fields. Model accuracy, however high, is not perfect, and the consequences of a wrong identification, an unnecessary herbicide application or a missed invasive incursion, mean that trustworthiness strategies and uncertainty communication will need to accompany any deployment. The authors emphasize enhanced trustworthiness as a core component of their pipeline, an acknowledgment that agricultural users need to know when a model is confident and when it should defer to human expertise. Continued expansion of training data, particularly for underrepresented regions, growth stages, and rare species, will further improve robustness. Still, the trajectory is clear. A model that can identify more than 1,500 weed species with over 91 percent accuracy, adapt to local floras with near-perfect regional performance, and run on drones and rovers represents a genuine step change in how the oldest of agricultural chores, knowing your enemy, can be automated for the sustainable farms of the coming decade.</p>
<p><strong>Subject of Research:</strong> AI-based global weed species identification and classification using foundation models</p>
<p><strong>Article Title:</strong> WeedNet: a foundation model-based global-to-local AI approach for weed species identification and classification</p>
<p><strong>Article References:</strong> Shen, Y., Ayanlade, T. T., Boddepalli, V. N., Saadati, M., Rairdin, A., Deng, Z. K., Arshad, M. A., Chiranjeevi, S., Balu, A., Mueller, D., Singh, A. K., Everman, W., Merchant, N., Ganapathysubramanian, B., Anderson, M., Sarkar, S., &amp; Singh, A. (2026). WeedNet: a foundation model-based global-to-local AI approach for weed species identification and classification. <em>Nature Communications</em>. <a href="https://doi.org/10.1038/s41467-026-78044-4" rel="noopener noreferrer">https://doi.org/10.1038/s41467-026-78044-4</a></p>
<p><strong>Image Credits:</strong> AI Generated</p>
<p><strong>DOI:</strong> <a href="https://doi.org/10.1038/s41467-026-78044-4" rel="noopener noreferrer">10.1038/s41467-026-78044-4</a></p>
<p><strong>Keywords:</strong> WeedNet, weed identification, foundation model, self-supervised learning, precision agriculture, computer vision, fine-tuning, Iowa State University, agricultural robotics, invasive species, Nature Communications, machine learning</p>
]]></content:encoded>
					
		
		
		<post-id xmlns="com-wordpress:feed-additions:1">249745</post-id>	</item>
		<item>
		<title>AI Learns a Patient&#8217;s Anatomy in Five Minutes to Align X-rays with 3D Scans</title>
		<link>https://scienmag.com/ai-learns-a-patients-anatomy-in-five-minutes-to-align-x-rays-with-3d-scans/</link>
		
		<dc:creator><![CDATA[Ophelia Keating]]></dc:creator>
		<pubDate>Sat, 26 Sep 2026 01:52:41 +0000</pubDate>
				<category><![CDATA[Medicine]]></category>
		<category><![CDATA[Technology and Engineering]]></category>
		<category><![CDATA[2D/3D registration]]></category>
		<category><![CDATA[advancements in surgical robotics]]></category>
		<category><![CDATA[AI-driven 2D/3D medical image registration]]></category>
		<category><![CDATA[CT and MRI to X-ray registration]]></category>
		<category><![CDATA[differentiable rendering]]></category>
		<category><![CDATA[fast neural network adaptation for medical imaging]]></category>
		<category><![CDATA[foundation model]]></category>
		<category><![CDATA[image analysis in minimally invasive procedures]]></category>
		<category><![CDATA[image-guided surgery]]></category>
		<category><![CDATA[image-guided surgery technology]]></category>
		<category><![CDATA[interventional radiology]]></category>
		<category><![CDATA[intraoperative imaging integration]]></category>
		<category><![CDATA[Medical Imaging]]></category>
		<category><![CDATA[medical imaging computational framework]]></category>
		<category><![CDATA[neural network for patient-specific anatomy]]></category>
		<category><![CDATA[neural networks]]></category>
		<category><![CDATA[open-source software]]></category>
		<category><![CDATA[patient-specific adaptation]]></category>
		<category><![CDATA[personalized surgical planning]]></category>
		<category><![CDATA[rapid alignment of X-ray and 3D scans]]></category>
		<category><![CDATA[real-time surgical navigation]]></category>
		<category><![CDATA[self-supervised learning]]></category>
		<category><![CDATA[surgical navigation]]></category>
		<category><![CDATA[X-ray fluoroscopy]]></category>
		<guid isPermaLink="false">https://scienmag.com/?p=216027</guid>

					<description><![CDATA[Researchers have unveiled xvr, a self-supervised AI framework that adapts a pretrained neural network to any patient's anatomy in about five minutes and registers X-ray images to 3D scans in seconds with an order-of-magnitude accuracy improvement over existing methods.]]></description>
										<content:encoded><![CDATA[<p>Surgeons and interventional radiologists rely on a deceptively simple question every time they guide a needle, a screw, or a catheter through the body: given a live X-ray image on the monitor and a detailed three-dimensional scan taken before the operation, exactly where is the patient&#8217;s anatomy in relation to the imaging beam? Answering that question — a computational problem known as 2D/3D registration — has long been a bottleneck for image-guided surgery and surgical robotics. A team led by researchers at the Massachusetts Institute of Technology and Harvard Medical School now reports in Nature a framework called xvr that solves it with unprecedented speed, generality, and accuracy, adapting a neural network to any individual patient in roughly five minutes and then registering X-rays to their three-dimensional scans in seconds.</p>
<p>The technical challenge is fundamentally one of bridging two very different kinds of images. Before an operation, patients typically receive a computed tomography (CT) or magnetic resonance imaging (MR) scan: a rich three-dimensional volume showing bones, vessels, and soft tissue in exquisite detail. During the operation, however, clinicians work with two-dimensional X-ray fluoroscopy — fast, low-dose, live images that look nothing like the slices of a CT volume. Registration is the task of finding the precise six-degree-of-freedom pose of the imaging system, essentially the position and orientation of a virtual camera, that would make a simulated X-ray of the preoperative scan match the real X-ray on the table. Get that pose right, and the surgeon can overlay the patient&#8217;s three-dimensional anatomy onto the live fluoroscopic view, guiding instruments with confidence.</p>
<p>Existing approaches have split into two camps, each with crippling limitations. Intensity-based optimization methods simulate X-rays from the 3D volume at candidate poses and iteratively adjust the pose until the simulated image best matches the real one. These methods are flexible in principle, but their similarity metrics and optimizer settings must be painstakingly tuned for each individual case, and the authors note that this per-individual hyperparameter tuning has prevented them from generalizing across the broad spectrum of fluoroscopy-guided procedures. Deep-learning approaches, meanwhile, promise fast inference but demand enormous manually labelled training datasets — pairs of X-rays and ground-truth poses that are expensive and often impossible to collect — and the resulting networks remain confined to the specific anatomy on which they were trained. A network trained on pelvic X-rays cannot simply be pointed at a spine or a skull.</p>
<p>The xvr framework, developed by Vivek Gopalakrishnan, Neel Dey, Polina Golland and colleagues across MIT, Harvard Medical School, Massachusetts General Hospital, Saint Luke&#8217;s Marion Bloch Neuroscience Institute, and Boston Children&#8217;s Hospital, sidesteps both traps with a self-supervised strategy. The key insight is that a patient&#8217;s own preoperative scan can serve as an unlimited source of training data. Using physics-based, differentiable X-ray rendering — implemented through ray-tracing algorithms including trilinear interpolation and Siddon&#8217;s exact radiological path method, with attenuation governed by the Beer–Lambert law — the system synthesizes realistic X-ray images from the patient&#8217;s CT or MR volume at randomly chosen virtual camera poses. Because the renderer is differentiable with respect to the camera pose, gradients can flow from an image-similarity loss all the way back to the pose parameters, enabling gradient-based optimization of registration. No manual annotation of the real X-rays is ever required.</p>
<p>On top of this self-supervised recipe, the team built a foundation model: a single neural network pretrained on thousands of whole-body volumetric scans drawn from public datasets including TotalSegmentator, CTPelvic1K, an MR angiography atlas, and whole-body PET/CT data. During pretraining, the network learns a general competence in the inverse problem of pose estimation — inferring from a synthetic X-ray where the virtual camera must have been. The crucial trick is patient-specific fine-tuning. When a new patient arrives, xvr renders synthetic X-rays from that patient&#8217;s scan, applies heavy data augmentation such as Gaussian noise, local contrast enhancement, random masking, and simulated collimation to mimic real fluoroscopy, and adapts the foundation model to this specific anatomy in about five minutes. The network thereby inherits broad anatomical knowledge from pretraining while becoming a bespoke expert on the individual on the operating table.</p>
<p>Handling the bewildering variety of real clinical imaging hardware demanded further engineering. X-ray machines differ in detector size, pixel spacing, principal point, and source-to-detector distance, and a naive network would falter when these intrinsic parameters change. xvr solves this with a resampling strategy that warps any incoming X-ray to a set of canonical intrinsics matching the network&#8217;s training data, so the same adapted network works regardless of the machine. Rotation representations — a notorious source of instability in pose regression — are handled with care, drawing on recent results on continuous rotation parameterizations. After the network produces its initial pose guess, a refinement stage applies iterative gradient-based optimization, blending two similarity measures: multiscale normalized cross-correlation, whose loss landscape is smooth and forgiving far from the true pose, and gradient normalized cross-correlation, which pinpoints the optimum sharply but only nearby. Averaging the two achieves millimetre-accurate registration, and the refinement corrects the network&#8217;s weakest axis — depth, or source-to-object distance, where initial errors of around fifteen millimetres are squeezed down within one to ten seconds.</p>
<p>The scale of the evaluation sets the work apart. According to the authors, this is, to their knowledge, the largest assessment of 2D/3D registration on real fluoroscopy conducted to date, spanning diverse anatomical structures, volumetric imaging modalities, and multiple hospitals. Public benchmarks included DeepFluoro, a femur dataset, and the Ljubljana cerebral angiography gold standard, while additional clinical evaluation drew on CTA and digital subtraction angiography data from Brigham and Women&#8217;s-affiliated collections and MRA/DSA data from Boston Children&#8217;s Hospital, governed by institutional review board approvals. Across this breadth, xvr achieved high accuracy in seconds and improved on the accuracy of existing methods by an order of magnitude — a striking margin in a field where incremental gains are the norm. Error metrics reported as median target registration error and submillimetre success rates showed the system ranking first across the benchmark datasets.</p>
<p>The clinical implications reach well beyond a single procedure. Image-guided interventions and surgical robotics — from spine surgery, where wrong-level errors remain a documented patient-safety concern, to orthopaedic trauma reconstruction, to neurovascular procedures such as treating vein of Galen malformations in children — all depend on knowing where preoperative three-dimensional anatomy sits relative to the live X-ray beam. Radiation oncology, telerobotic and magnetic-navigation neurovascular interventions, and intraoperative device reconstruction similarly stand to benefit. Because xvr performs rigid registration pan-anatomically, a single tool could serve orthopaedic surgeons, neurosurgeons, interventional radiologists, and radiation therapists alike, and its differentiable rendering engine opens a path toward the harder problem of deformable registration, in which anatomy moves and deforms during the procedure.</p>
<p>Equally significant is the decision to release everything openly. The Python package and command-line interface for xvr, built on the team&#8217;s DiffDRR library and PyTorch, are available on GitHub along with scripts to replicate every experiment in the paper. The team has also remixed the public benchmark datasets into standardized formats and released them to the community through a public repository, with permission from the original dataset authors. In a field where reproducibility has been a persistent headache and where proprietary, anatomy-specific systems dominate commercial deployments, an open-source, anatomy-agnostic, annotation-free registration engine could lower the barrier to entry for research groups and hospitals worldwide.</p>
<p>Caveats remain, as they do for any technology crossing from bench to bedside. The framework addresses rigid registration — treating the anatomy as a fixed body — whereas breathing, soft-tissue deformation, and surgical manipulation introduce motion that rigid models cannot capture, though the group&#8217;s associated work on polyrigid deformable registration suggests this frontier is next. Clinical datasets used for real-world evaluation cannot be released publicly for privacy reasons, and prospective validation inside live surgical workflows will be the decisive test. Still, the combination of five-minute patient adaptation, second-scale registration, order-of-magnitude accuracy gains across anatomy and hospitals, and fully open software marks a genuine inflection point. Registration, long the quiet obstacle between preoperative planning and intraoperative guidance, may finally be becoming a solved problem — and with it, the vision of routinely available, fluoroscopy-anchored surgical navigation moves measurably closer to the operating theatre.</p>
<p><strong>Subject of Research:</strong> Self-supervised patient-specific neural networks for 2D/3D X-ray to volumetric image registration in image-guided interventions</p>
<p><strong>Article Title:</strong> Rapid patient-specific neural networks for X-ray to volume registration</p>
<p><strong>Article References:</strong> Gopalakrishnan, V., Chlorogiannis, D.-D., Abumoussa, A., Larson, A. M., Haouchine, N., Orbach, D. B., Frisken, S., Dey, N., &amp; Golland, P. (2026). Rapid patient-specific neural networks for X-ray to volume registration. <em>Nature</em>. <a href="https://doi.org/10.1038/s41586-026-11045-x" rel="noopener noreferrer">https://doi.org/10.1038/s41586-026-11045-x</a></p>
<p><strong>Image Credits:</strong> AI Generated</p>
<p><strong>DOI:</strong> <a href="https://doi.org/10.1038/s41586-026-11045-x" rel="noopener noreferrer">10.1038/s41586-026-11045-x</a></p>
<p><strong>Keywords:</strong> 2D/3D registration, X-ray fluoroscopy, neural networks, image-guided surgery, self-supervised learning, foundation model, differentiable rendering, surgical navigation, medical imaging, patient-specific adaptation, interventional radiology, open-source software</p>
]]></content:encoded>
					
		
		
		<post-id xmlns="com-wordpress:feed-additions:1">216027</post-id>	</item>
		<item>
		<title>Foundation Model Spots Hidden Flaws in Digital Cancer Slides with Near-Perfect Accuracy</title>
		<link>https://scienmag.com/foundation-model-spots-hidden-flaws-in-digital-cancer-slides-with-near-perfect-accuracy/</link>
		
		<dc:creator><![CDATA[Blake Davidson]]></dc:creator>
		<pubDate>Thu, 24 Sep 2026 22:29:24 +0000</pubDate>
				<category><![CDATA[Technology and Engineering]]></category>
		<category><![CDATA[AI in pathology quality assurance]]></category>
		<category><![CDATA[AI-based digital slide validation]]></category>
		<category><![CDATA[artifact detection]]></category>
		<category><![CDATA[AUROC]]></category>
		<category><![CDATA[Cancer diagnostics]]></category>
		<category><![CDATA[cancer diagnostics image reliability]]></category>
		<category><![CDATA[deep learning for histopathology]]></category>
		<category><![CDATA[digital cancer slide analysis]]></category>
		<category><![CDATA[digital pathology]]></category>
		<category><![CDATA[FDA digital pathology tools]]></category>
		<category><![CDATA[foundation model]]></category>
		<category><![CDATA[hidden flaws in digital pathology]]></category>
		<category><![CDATA[HistoART artifact detection system]]></category>
		<category><![CDATA[histopathology]]></category>
		<category><![CDATA[image analysis]]></category>
		<category><![CDATA[Machine learning]]></category>
		<category><![CDATA[medical image quality assessment]]></category>
		<category><![CDATA[microscopy image quality control]]></category>
		<category><![CDATA[quality control]]></category>
		<category><![CDATA[ResNet50]]></category>
		<category><![CDATA[tissue imaging artifact identification]]></category>
		<category><![CDATA[UNI]]></category>
		<category><![CDATA[whole slide imaging artifact detection]]></category>
		<category><![CDATA[whole-slide imaging]]></category>
		<guid isPermaLink="false">https://scienmag.com/?p=212751</guid>

					<description><![CDATA[FDA researchers have built HistoART, a system that uses a fine-tuned pathology foundation model to detect six common artifact types in whole slide images with an AUROC of 0.995, outperforming both a ResNet50 deep learning model and a handcrafted feature approach across more than 50,000 image patches from multiple scanners.]]></description>
										<content:encoded><![CDATA[<p>Every day, pathologists in hospitals around the world peer into digital images of human tissue, hunting for the subtle cellular signatures of cancer. The technology that makes this possible, known as whole slide imaging, converts an entire glass microscope slide into a gigapixel digital file that can be stored, shared, and analyzed by algorithms. But the digitization process is far from flawless. Tissue folds, air bubbles, out-of-focus regions, blood contamination, marker traces, and damaged tissue can all creep into these images during slide preparation and scanning. These artifacts are more than cosmetic blemishes; they can silently corrupt the performance of the artificial intelligence systems increasingly used to assist in cancer diagnosis, leading to unreliable or even misleading results.</p>
<p>Now, a team of researchers at the U.S. Food and Drug Administration&#8217;s Division of Imaging, Diagnostics, and Software Reliability has developed a new tool designed to catch these flaws before they can do damage. The system, called HistoART, is described in a study published in the journal Neural Computing and Applications. Led by Seyed Kahaki, with contributions from Alexander Webber, Ghada Zamzmi, Adarsh Subbaswamy, Rucha Deshpande, and Aldo Badano, the work compares three fundamentally different strategies for detecting artifacts in whole slide images, and finds that a large foundation model originally trained for general pathology tasks outperforms both a conventional deep learning network and a classical, hand-engineered approach.</p>
<p>The stakes are higher than they might first appear. As hospitals adopt digital pathology workflows, the reliability of downstream image analysis tasks, from tumor detection to grading, depends on the quality of the images feeding into them. An algorithm trained to recognize cancer cells may misinterpret a tissue fold as a suspicious structure, or an air bubble as a region of lost tissue. Previous studies have documented how quality control, or the lack of it, directly affects the accuracy of computational pathology systems. Yet many existing quality control tools rely on fixed rules and handcrafted measurements that may not generalize across the wide variety of scanners, staining protocols, and tissue types encountered in real-world laboratories.</p>
<p>HistoART tackles the problem with a three-way comparison. The first approach, the foundation model-based approach, fine-tunes UNI, a general-purpose foundation model for computational pathology that has been trained on massive collections of pathology images. Foundation models of this kind learn rich, general-purpose visual representations that can be adapted to many downstream tasks with relatively little additional training. The second approach, the deep learning approach, is built on a ResNet50 backbone, a widely used convolutional neural network architecture originally developed for general image recognition. The third, the knowledge-based approach, dispenses with learned representations altogether and instead relies on handcrafted features derived from texture, color, and frequency-based metrics, drawing on decades of classical image analysis research.</p>
<p>All three approaches were trained and evaluated to detect six of the most prevalent artifact types in whole slide images: tissue folds, out-of-focus regions, air bubbles, tissue damage, marker traces, and blood contamination. Each of these artifacts arises at a different stage of the workflow. Tissue folds occur when sections of tissue wrinkle during mounting on the slide. Out-of-focus regions result from imperfect autofocus during scanning. Air bubbles become trapped under the coverslip, marker traces are left by pens used to label slides, and blood contamination can obscure underlying tissue architecture. Detecting such a heterogeneous set of defects demands a system capable of recognizing very different visual patterns, from the sharp linear creases of a fold to the diffuse haze of an out-of-focus patch.</p>
<p>The evaluation was deliberately broad. The researchers assembled a dataset of more than 50,000 image patches sourced from diverse whole slide imaging scanners, including instruments from Hamamatsu, Philips, and Leica Aperio AT2, and drawn from multiple imaging sites. This diversity matters because artifacts can look different depending on the scanner that produced the image, and a detection system that works well on one manufacturer&#8217;s output may fail on another&#8217;s. By testing across scanners and sites, the team aimed to assess how well each approach would generalize beyond a single laboratory environment, a persistent weakness of many published machine learning studies in pathology.</p>
<p>The results were striking. The foundation model-based approach achieved a patch-wise area under the receiver operating characteristic curve, or AUROC, of 0.995, with a 95 percent confidence interval of 0.994 to 0.995, a level of performance that approaches the theoretical ceiling of a perfect classifier. The ResNet50-based deep learning approach reached an AUROC of 0.977, with a confidence interval of 0.977 to 0.978, while the knowledge-based approach, built on handcrafted features, trailed at 0.940, with a confidence interval of 0.933 to 0.946. The AUROC metric measures a classifier&#8217;s ability to distinguish between positive and negative cases across all possible decision thresholds, so the gap between 0.995 and 0.940 represents a substantial difference in real-world reliability, particularly for the subtle or ambiguous artifacts that matter most in clinical practice.</p>
<p>Why would a foundation model so decisively outperform a purpose-built convolutional network? The likely answer lies in the breadth of its pretraining. UNI was trained on enormous and varied collections of pathology imagery, meaning it has already encountered an extraordinary range of tissue appearances, staining variations, and imaging conditions before any artifact-specific fine-tuning begins. When subsequently adapted to the artifact detection task, it brings that prior knowledge to bear, allowing it to distinguish, say, a genuine tissue fold from a naturally occurring tissue edge with greater confidence than a network learning visual features from scratch. The handcrafted approach, meanwhile, is limited by the imagination of its designers: texture descriptors, color statistics, and frequency-domain measures capture certain artifact signatures well but may miss patterns that do not fit predefined mathematical descriptions.</p>
<p>Detection alone, however, is not enough. A laboratory needs to know what to do with the information. To bridge the gap between detection and actionable conclusions, the team developed a quality report scorecard that quantifies the number of high-quality image patches in a dataset and visualizes the distribution of artifact subgroups. This reporting layer transforms raw per-patch predictions into a summary that laboratory staff and algorithm developers can act upon: a slide riddled with folds can be rescanned or excluded, a scanner producing systematic out-of-focus regions can be serviced, and a dataset destined for training a diagnostic model can be filtered to remove compromised patches. In this way, HistoART functions not merely as a classifier but as a quality assurance pipeline for the entire digital pathology workflow.</p>
<p>The researchers describe the resulting system as a multi-branch pipeline that may enhance the reliability of whole slide image analysis by providing a scalable and interpretable approach for improving digital pathology workflows. Interpretability is a key selling point of the scorecard design, since regulators and clinicians are often wary of black-box systems that flag images without explaining why. By visualizing which artifact types dominate a slide or dataset, the tool offers a transparent window into the failure modes of the imaging process. Consistent with the team&#8217;s commitment to open science, all the data and methods from the work are available for download on GitHub, allowing other laboratories to adopt, scrutinize, and extend the system. As whole slide imaging continues its march toward becoming the default medium of diagnostic pathology, tools like HistoART suggest that the quality of the digital slide, long treated as an afterthought, is finally being engineered with the same rigor as the diagnoses that depend on it.</p>
<p><strong>Subject of Research:</strong> Artifact detection in whole slide histopathology images using foundation models, deep learning, and handcrafted features</p>
<p><strong>Article Title:</strong> HistoART: Histopathology artifact detection based on large foundation model</p>
<p><strong>Article References:</strong> Kahaki, S., Webber, A., Zamzmi, G., Subbaswamy, A., Deshpande, R., &amp; Badano, A. (2026). HistoART: Histopathology artifact detection based on large foundation model. <em>Neural Computing and Applications, 38</em>(18), Article 753. <a href="https://doi.org/10.1007/s00521-026-12454-9" rel="noopener noreferrer">https://doi.org/10.1007/s00521-026-12454-9</a></p>
<p><strong>Image Credits:</strong> AI Generated</p>
<p><strong>DOI:</strong> <a href="https://doi.org/10.1007/s00521-026-12454-9" rel="noopener noreferrer">10.1007/s00521-026-12454-9</a></p>
<p><strong>Keywords:</strong> histopathology, whole slide imaging, artifact detection, foundation model, UNI, ResNet50, digital pathology, quality control, machine learning, AUROC, cancer diagnostics, image analysis</p>
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		<post-id xmlns="com-wordpress:feed-additions:1">212751</post-id>	</item>
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		<title>CROWN AI Model Masters More Than 200 Cytology Tasks With Expert-Level Accuracy</title>
		<link>https://scienmag.com/crown-ai-model-masters-more-than-200-cytology-tasks-with-expert-level-accuracy/</link>
		
		<dc:creator><![CDATA[Blake Davidson]]></dc:creator>
		<pubDate>Sun, 20 Sep 2026 19:13:25 +0000</pubDate>
				<category><![CDATA[Cancer]]></category>
		<category><![CDATA[AI-assisted cytopathology]]></category>
		<category><![CDATA[cancer detection automation]]></category>
		<category><![CDATA[cancer diagnosis]]></category>
		<category><![CDATA[cervical and thyroid cancer screening AI]]></category>
		<category><![CDATA[cervical cancer screening]]></category>
		<category><![CDATA[computational pathology advancements]]></category>
		<category><![CDATA[cytology AI model]]></category>
		<category><![CDATA[cytopathology]]></category>
		<category><![CDATA[deep learning]]></category>
		<category><![CDATA[deep learning in cancer screening]]></category>
		<category><![CDATA[digital pathology]]></category>
		<category><![CDATA[DINOv2]]></category>
		<category><![CDATA[foundation model]]></category>
		<category><![CDATA[foundation models in pathology]]></category>
		<category><![CDATA[high-accuracy cytology tasks]]></category>
		<category><![CDATA[image retrieval]]></category>
		<category><![CDATA[machine learning for cytology]]></category>
		<category><![CDATA[medical imaging AI]]></category>
		<category><![CDATA[self-supervised learning]]></category>
		<category><![CDATA[self-supervised learning in medical imaging]]></category>
		<category><![CDATA[Sun Yat-sen University Cancer Center research]]></category>
		<category><![CDATA[universal visual foundation model]]></category>
		<category><![CDATA[vision transformer]]></category>
		<category><![CDATA[weakly supervised learning]]></category>
		<guid isPermaLink="false">https://scienmag.com/?p=201612</guid>

					<description><![CDATA[Researchers have developed CROWN, a self-supervised visual foundation model pretrained on more than ten million cytology images that achieved top performance across 202 diagnostic task settings, with classification accuracy exceeding 95 percent in 48 evaluations.]]></description>
										<content:encoded><![CDATA[<p>Cytopathology sits at the front line of cancer detection. Every day, pathologists around the world scrutinize Pap smears, fine-needle aspirates, effusion preparations and blood films under the microscope, hunting for the subtle cellular anomalies that signal malignancy. The work is meticulous, expertise-hungry and increasingly strained by screening volumes that continue to climb as organized cervical cancer and thyroid nodule programs expand. A team of researchers led by investigators at Sun Yat-sen University Cancer Center in Guangzhou, China, now reports a step change in how machine intelligence can shoulder that burden. In a technical report published in Nature Cancer, the group unveils CROWN, short for Cytology visual foundation netwoRk Optimized With self-supervised learNing, a universal visual foundation model designed to serve as a general-purpose backbone for virtually any computational cytology task.</p>
<p>The central idea behind CROWN is borrowed from one of the most consequential trends in modern artificial intelligence: the foundation model. Rather than training a bespoke neural network for each individual diagnostic problem, a foundation model is pretrained once on an enormous, unlabeled corpus and then adapted cheaply to many downstream applications. Foundation models have already transformed natural-language processing and, more recently, computational pathology of tissue sections. Cytology, however, has lagged behind. Cytological preparations differ fundamentally from histology: they consist of sparsely distributed, individually preserved cells on cluttered, often stain-inconsistent backgrounds rather than dense tissue architecture. Prior cytology-specific models have tended to be narrow, task-specific classifiers that generalize poorly across staining protocols, scanners and anatomical sites.</p>
<p>To build CROWN, the team assembled a pretraining corpus of more than ten million cytology image patches drawn from multiple institutions and anatomical sites. Crucially, the model was trained with a DINOv2-based self-supervised framework, a strategy that requires no manual annotations whatsoever during pretraining. In self-supervised learning, the network learns by solving pretext problems on the raw images themselves, for example by learning to recognize that differently cropped or augmented views of the same image patch should map to similar internal representations. This forces the model to discover the visual grammar of cytology on its own: nuclear contours, chromatin texture, cytoplasmic staining, cell-to-cell arrangements and the characteristic appearance of malignant, benign and reactive cells, all without a single pathologist-supplied label.</p>
<p>Architecturally, CROWN follows the vision transformer paradigm that has become the standard for large-scale visual representation learning, in which an image is divided into small patches that are processed through attention mechanisms so that every patch can influence every other. The authors pretrained the network at scale and then evaluated its frozen features across an unusually broad benchmark suite: 202 task-setting combinations spanning patch-level classification, cell segmentation, object detection, image retrieval and slide-level prediction. The evaluation cohorts included private institutional collections, among them cohorts containing lymph node metastasis samples and cervical screening specimens, alongside a battery of public datasets covering cervical cytology, thyroid aspirates, effusion cytology and hematology preparations. The benchmark data supporting the analyses have been made publicly available, a transparency measure the researchers argue is essential for credible comparison of future cytology encoders.</p>
<p>The headline results are striking. Across the diverse benchmark settings, CROWN achieved the best overall performance among established pretrained encoders. In 48 patch-level classification evaluations the model exceeded 95 percent accuracy, and in 22 of those evaluations accuracy surpassed 98 percent. Zero-shot evaluations, in which the model classifies images it has never seen labeled examples of, and linear probing evaluations, in which only a simple linear classifier is fitted on top of the frozen features, both demonstrated that the representations learned during unsupervised pretraining capture diagnostically meaningful information without task-specific fine-tuning of the backbone.</p>
<p>The versatility of the learned features extended well beyond classification. On public thyroid and cervical segmentation datasets, CROWN-based models delivered strong DICE scores at both the single-cell and whole-image levels, indicating that the encoder preserves fine-grained spatial information needed to trace individual cell boundaries. On blood-cell object detection benchmarks, CROWN features supported competitive average precision, and on image retrieval tasks spanning more than a dozen anatomical sites and fine-grained subtypes across the two institutional cohorts, the model retrieved diagnostically relevant neighbor images with high mean-average accuracy, a capability with potential value in case-based decision support and digital consultation.</p>
<p>Perhaps most consequential for real-world screening are the slide-level experiments. Whole cytology slides contain thousands of cells, and labeling them individually is prohibitively expensive. CROWN was evaluated in weakly supervised and few-shot settings, in which the model must classify an entire slide from slide-level labels alone or from only a handful of labeled examples. Using prototype-based classification, in which query slides are assigned to the class whose representative feature prototype lies nearest in the learned embedding space, CROWN maintained strong accuracy even with minimal supervision. Grad-CAM visualizations showed that the model concentrates its attention on diagnostically relevant regions, offering pathologists a window into why a prediction was made, an interpretability feature considered essential for clinical acceptance of artificial intelligence in pathology.</p>
<p>The study also compared CROWN directly against publicly released task-specific models on representative public cytology datasets, as well as against a family of established pretrained encoders including general-purpose vision models and histology-oriented foundation models. CROWN outperformed or matched these alternatives across most benchmark combinations, reinforcing the authors&#8217; argument that a single, cytology-specialized visual backbone can displace fragmented collections of narrow models. The benchmark itself, with 202 distinct task-setting combinations evaluated under five-fold cross-validation and reported with standard error measurements, ranks among the most comprehensive evaluations ever assembled for computational cytology and sets a reference point that subsequent work will be measured against.</p>
<p>The code and model weights for CROWN have been released for academic research purposes on GitHub and the Hugging Face model hub, lowering the barrier for laboratories worldwide to adapt the model to local datasets and staining protocols. The researchers are candid about limitations: the pretraining data contain patient-derived material and remain restricted by institutional ethics regulations and privacy requirements, so the pretraining corpus itself is not publicly available. The team also cautions that prospective clinical validation will be needed before CROWN can support real diagnostic workflows. Nevertheless, the message is clear. By demonstrating that self-supervised pretraining at scale can yield a single visual backbone that generalizes across organs, preparations, scanners and task types, CROWN establishes a credible template for universal computational cytology, a field in which the demand for expert eyes far outstrips the supply. If follow-up clinical studies bear out its benchmark performance, models of this kind could help triage slides, flag suspicious cells and extend expert-level screening to regions where cytologists are scarce.</p>
<p><strong>Subject of Research:</strong> A self-supervised visual foundation model for universal computational cytopathology</p>
<p><strong>Article Title:</strong> A universal visual foundation model for computational cytopathology</p>
<p><strong>Article References:</strong> A universal visual foundation model for computational cytopathology. (n.d.). <a href="https://doi.org/10.1038/s43018-026-01240-0" rel="noopener noreferrer">https://doi.org/10.1038/s43018-026-01240-0</a></p>
<p><strong>Image Credits:</strong> AI Generated</p>
<p><strong>DOI:</strong> <a href="https://doi.org/10.1038/s43018-026-01240-0" rel="noopener noreferrer">10.1038/s43018-026-01240-0</a></p>
<p><strong>Keywords:</strong> cytopathology, foundation model, self-supervised learning, DINOv2, vision transformer, cervical cancer screening, digital pathology, deep learning, cancer diagnosis, medical imaging AI, image retrieval, weakly supervised learning</p>
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