arXiv subjects

Wesley De Neve

Publications and source records attributed to Wesley De Neve.

At least 19 recordsLinked to original sources

arXiv2026

Region-Weighted Losses and Model Fusion for Cross-Modal PET Attenuation Correction

We describe our approach to the Big Cross-Modal Attenuation Correction (BIC-MAC) challenge, which asks for a pseudo-CT in Hounsfield Units to be synthesized from Non-Attenuation-Corrected PET (NAC-PET), DIXON MRI and a topogram, and scores both the pseudo-CT and the Attenuation-Corrected PET (AC-PET) reconstructed from it. Three ideas carried our improvements over the organizers' 3D U-Net baseline. The loss matters more than the architecture: we compute the $L_1$ error in the Carney attenuation-coefficient ($\mu$) space that the CT metric itself uses, weighted by anatomical region. Only once that loss was in place did the unregistered DIXON MRI work as extra input channels. A fixed convex combination of two independently trained models then beat both of its members on three of the four metrics and ranks first overall on the public validation leaderboard.

cs.CV↗

arXiv2025

When Tracking Fails: Analyzing Failure Modes of SAM2 for Point-Based Tracking in Surgical Videos

Video object segmentation (VOS) models such as SAM2 offer promising zero-shot tracking capabilities for surgical videos using minimal user input. Among the available input types, point-based tracking offers an efficient and low-cost alternative, yet its reliability and failure cases in complex surgical environments are not well understood. In this work, we systematically analyze the failure modes of point-based tracking in laparoscopic cholecystectomy videos. Focusing on three surgical targets, the gallbladder, grasper, and L-hook electrocautery, we compare the performance of point-based tracking with segmentation mask initialization. Our results show that point-based tracking is competitive for surgical tools but consistently underperforms for anatomical targets, where tissue similarity and ambiguous boundaries lead to failure. Through qualitative analysis, we reveal key factors influencing tracking outcomes and provide several actionable recommendations for selecting and placing tracking points to improve performance in surgical video analysis.

cs.CV↗

arXiv2025

SpurBreast: A Curated Dataset for Investigating Spurious Correlations in Real-world Breast MRI Classification

Deep neural networks (DNNs) have demonstrated remarkable success in medical imaging, yet their real-world deployment remains challenging due to spurious correlations, where models can learn non-clinical features instead of meaningful medical patterns. Existing medical imaging datasets are not designed to systematically study this issue, largely due to restrictive licensing and limited supplementary patient data. To address this gap, we introduce SpurBreast, a curated breast MRI dataset that intentionally incorporates spurious correlations to evaluate their impact on model performance. Analyzing over 100 features involving patient, device, and imaging protocol, we identify two dominant spurious signals: magnetic field strength (a global feature influencing the entire image) and image orientation (a local feature affecting spatial alignment). Through controlled dataset splits, we demonstrate that DNNs can exploit these non-clinical signals, achieving high validation accuracy while failing to generalize to unbiased test data. Alongside these two datasets containing spurious correlations, we also provide benchmark datasets without spurious correlations, allowing researchers to systematically investigate clinically relevant and irrelevant features, uncertainty estimation, adversarial robustness, and generalization strategies. Models and datasets are available at https://github.com/utkuozbulak/spurbreast.

eess.IV↗

arXiv2025

Token-Based Detection of Spurious Correlations in Vision Transformers

Due to their powerful feature association capabilities, neural network-based computer vision models have the ability to detect and exploit unintended patterns within the data, potentially leading to correct predictions based on incorrect or unintended but statistically relevant signals. These clues may vary from simple color aberrations to small pieces of text within the image. In situations where these unintended signals align with the predictive task, models can mistakenly link these features with the task and rely on them for making predictions. This phenomenon is referred to as spurious correlations, where patterns appear to be associated with the task but are actually coincidental. As a result, detection and mitigation of spurious correlations have become crucial tasks for building trustworthy, reliable, and generalizable machine learning models. In this work, we present a token-based diagnostic pipeline that applies leave-one-out token removal to detect spurious correlations in vision transformers. The proposed approach quantifies a model's reliance on non-core visual cues through complementary measures that capture both aggregate and localized spurious effects at the token level. Using both supervised and self-supervised trained models, we present large-scale experiments on the ImageNet dataset demonstrating the ability of the proposed method to identify spurious correlations. We also find that, even if the same architecture is used, the training methodology has a substantial impact on the model's reliance on spurious correlations. Furthermore, we show that for certain ImageNet classes, many images exhibit strong reliance on non-core visual cues across multiple models, and we discuss common sources of such signals (e.g., watermarks and background artifacts). Lastly, we present a case study investigating spurious signals in invasive breast mass classification.

cs.CV↗

arXiv2025

Improved Sub-Visible Particle Classification in Flow Imaging Microscopy via Generative AI-Based Image Synthesis

Sub-visible particle analysis using flow imaging microscopy combined with deep learning has proven effective in identifying particle types, enabling the distinction of harmless components such as silicone oil from protein particles. However, the scarcity of available data and severe imbalance between particle types within datasets remain substantial hurdles when applying multi-class classifiers to such problems, often forcing researchers to rely on less effective methods. The aforementioned issue is particularly challenging for particle types that appear unintentionally and in lower numbers, such as silicone oil and air bubbles, as opposed to protein particles, where obtaining large numbers of images through controlled settings is comparatively straightforward. In this work, we develop a state-of-the-art diffusion model to address data imbalance by generating high-fidelity images that can augment training datasets, enabling the effective training of multi-class deep neural networks. We validate this approach by demonstrating that the generated samples closely resemble real particle images in terms of visual quality and structure. To assess the effectiveness of using diffusion-generated images in training datasets, we conduct large-scale experiments on a validation dataset comprising 500,000 protein particle images and demonstrate that this approach improves classification performance with no negligible downside. Finally, to promote open research and reproducibility, we publicly release both our diffusion models and the trained multi-class deep neural network classifiers, along with a straightforward interface for easy integration into future studies, at https://github.com/utkuozbulak/svp-generative-ai.

cs.CV↗

arXiv2025

Toward Using Machine Learning as a Shape Quality Metric for Liver Point Cloud Generation

While 3D medical shape generative models such as diffusion models have shown promise in synthesizing diverse and anatomically plausible structures, the absence of ground truth makes quality evaluation challenging. Existing evaluation metrics commonly measure distributional distances between training and generated sets, while the medical field requires assessing quality at the individual level for each generated shape, which demands labor-intensive expert review. In this paper, we investigate the use of classical machine learning (ML) methods and PointNet as an alternative, interpretable approach for assessing the quality of generated liver shapes. We sample point clouds from the surfaces of the generated liver shapes, extract handcrafted geometric features, and train a group of supervised ML and PointNet models to classify liver shapes as good or bad. These trained models are then used as proxy discriminators to assess the quality of synthetic liver shapes produced by generative models. Our results show that ML-based shape classifiers provide not only interpretable feedback but also complementary insights compared to expert evaluation. This suggests that ML classifiers can serve as lightweight, task-relevant quality metrics in 3D organ shape generation, supporting more transparent and clinically aligned evaluation protocols in medical shape modeling.

cs.LG↗

arXiv2025

Revisiting the Evaluation Bias Introduced by Frame Sampling Strategies in Surgical Video Segmentation Using SAM2

Real-time video segmentation is a promising opportunity for AI-assisted surgery, offering intraoperative guidance by identifying tools and anatomical structures. Despite growing interest in surgical video segmentation, annotation protocols vary widely across datasets -- some provide dense, frame-by-frame labels, while others rely on sparse annotations sampled at low frame rates such as 1 FPS. In this study, we investigate how such inconsistencies in annotation density and frame rate sampling influence the evaluation of zero-shot segmentation models, using SAM2 as a case study for cholecystectomy procedures. Surprisingly, we find that under conventional sparse evaluation settings, lower frame rates can appear to outperform higher ones due to a smoothing effect that conceals temporal inconsistencies. However, when assessed under real-time streaming conditions, higher frame rates yield superior segmentation stability, particularly for dynamic objects like surgical graspers. To understand how these differences align with human perception, we conducted a survey among surgeons, nurses, and machine learning engineers and found that participants consistently preferred high-FPS segmentation overlays, reinforcing the importance of evaluating every frame in real-time applications rather than relying on sparse sampling strategies. Our findings highlight the risk of evaluation bias that is introduced by inconsistent dataset protocols and bring attention to the need for temporally fair benchmarking in surgical video AI.

cs.CV↗

arXiv2025

FedRef: Bayesian Fine-Tuning using a Reference Model to Mitigate Catastrophic Forgetting for Heterogeneous Federated Learning

Federated learning (FL) enables collaborative model training across distributed clients while preserving data privacy. However, data and system heterogeneity often cause catastrophic forgetting and unbounded drift in model updates, leading to degraded predictive performance and increased client-side computation. To address these challenges, we propose FedRef, a Bayesian fine-tuning method that leverages a reference model constructed from previous global models. FedRef integrates a MAP-based regularization term that calibrates global model updates toward a temporally aggregated reference model, thereby mitigating catastrophic forgetting and improving update stability. Unlike prior approaches, FedRef performs all fine-tuning operations on the server side, reducing client-side computational overhead while maintaining effective global optimization. Experiments on image classification (FEMNIST, CINIC-10) and medical image segmentation (FeTS2022) demonstrate that FedRef achieves superior predictive performance and faster convergence under heterogeneous, non-IID settings, while significantly lowering client-side computation compared with existing methods. These results highlight FedRef as an efficient and robust optimization framework for real-world FL scenarios.

cs.LG↗

arXiv2025

The Impact of the Single-Label Assumption in Image Recognition Benchmarking

Deep neural networks (DNNs) are typically evaluated under the assumption that each image has a single correct label. However, many images in benchmarks like ImageNet contain multiple valid labels, creating a mismatch between evaluation protocols and the actual complexity of visual data. This mismatch can penalize DNNs for predicting correct but unannotated labels, which may partly explain reported accuracy drops, such as the widely cited 11 to 14 percent top-1 accuracy decline on ImageNetV2, a replication test set for ImageNet. This raises the question: do such drops reflect genuine generalization failures or artifacts of restrictive evaluation metrics? We rigorously assess the impact of multi-label characteristics on reported accuracy gaps. To evaluate the multi-label prediction capability (MLPC) of single-label-trained models, we introduce a variable top-$k$ evaluation, where $k$ matches the number of valid labels per image. Applied to 315 ImageNet-trained models, our analyses demonstrate that conventional top-1 accuracy disproportionately penalizes valid but secondary predictions. We also propose Aggregate Subgroup Model Accuracy (ASMA) to better capture multi-label performance across model subgroups. Our results reveal wide variability in MLPC, with some models consistently ranking multiple correct labels higher. Under this evaluation, the perceived gap between ImageNet and ImageNetV2 narrows substantially. To further isolate multi-label recognition performance from contextual cues, we introduce PatchML, a synthetic dataset containing systematically combined object patches. PatchML demonstrates that many models trained with single-label supervision nonetheless recognize multiple objects. Altogether, these findings highlight limitations in single-label evaluation and reveal that modern DNNs have stronger multi-label capabilities than standard metrics suggest.

cs.CV↗

arXiv2025

Towards Improved Cervical Cancer Screening: Vision Transformer-Based Classification and Interpretability

We propose a novel approach to cervical cell image classification for cervical cancer screening using the EVA-02 transformer model. We developed a four-step pipeline: fine-tuning EVA-02, feature extraction, selecting important features through multiple machine learning models, and training a new artificial neural network with optional loss weighting for improved generalization. With this design, our best model achieved an F1-score of 0.85227, outperforming the baseline EVA-02 model (0.84878). We also utilized Kernel SHAP analysis and identified key features correlating with cell morphology and staining characteristics, providing interpretable insights into the decision-making process of the fine-tuned model. Our code is available at https://github.com/Khoa-NT/isbi2025_ps3c.

cs.CV↗

arXiv2025

Boosting 3D Liver Shape Datasets with Diffusion Models and Implicit Neural Representations

While the availability of open 3D medical shape datasets is increasing, offering substantial benefits to the research community, we have found that many of these datasets are, unfortunately, disorganized and contain artifacts. These issues limit the development and training of robust models, particularly for accurate 3D reconstruction tasks. In this paper, we examine the current state of available 3D liver shape datasets and propose a solution using diffusion models combined with implicit neural representations (INRs) to augment and expand existing datasets. Our approach utilizes the generative capabilities of diffusion models to create realistic, diverse 3D liver shapes, capturing a wide range of anatomical variations and addressing the problem of data scarcity. Experimental results indicate that our method enhances dataset diversity, providing a scalable solution to improve the accuracy and reliability of 3D liver reconstruction and generation in medical applications. Finally, we suggest that diffusion models can also be applied to other downstream tasks in 3D medical imaging.

cs.CV↗

arXiv2025

One Patient's Annotation is Another One's Initialization: Towards Zero-Shot Surgical Video Segmentation with Cross-Patient Initialization

Video object segmentation is an emerging technology that is well-suited for real-time surgical video segmentation, offering valuable clinical assistance in the operating room by ensuring consistent frame tracking. However, its adoption is limited by the need for manual intervention to select the tracked object, making it impractical in surgical settings. In this work, we tackle this challenge with an innovative solution: using previously annotated frames from other patients as the tracking frames. We find that this unconventional approach can match or even surpass the performance of using patients' own tracking frames, enabling more autonomous and efficient AI-assisted surgical workflows. Furthermore, we analyze the benefits and limitations of this approach, highlighting its potential to enhance segmentation accuracy while reducing the need for manual input. Our findings provide insights into key factors influencing performance, offering a foundation for future research on optimizing cross-patient frame selection for real-time surgical video analysis.

cs.CV↗

arXiv2025

Exploring Patient Data Requirements in Training Effective AI Models for MRI-based Breast Cancer Classification

The past decade has witnessed a substantial increase in the number of startups and companies offering AI-based solutions for clinical decision support in medical institutions. However, the critical nature of medical decision-making raises several concerns about relying on external software. Key issues include potential variations in image modalities and the medical devices used to obtain these images, potential legal issues, and adversarial attacks. Fortunately, the open-source nature of machine learning research has made foundation models publicly available and straightforward to use for medical applications. This accessibility allows medical institutions to train their own AI-based models, thereby mitigating the aforementioned concerns. Given this context, an important question arises: how much data do medical institutions need to train effective AI models? In this study, we explore this question in relation to breast cancer detection, a particularly contested area due to the prevalence of this disease, which affects approximately 1 in every 8 women. Through large-scale experiments on various patient sizes in the training set, we show that medical institutions do not need a decade's worth of MRI images to train an AI model that performs competitively with the state-of-the-art, provided the model leverages foundation models. Furthermore, we observe that for patient counts greater than 50, the number of patients in the training set has a negligible impact on the performance of models and that simple ensembles further improve the results without additional complexity.

eess.IV↗

arXiv2025

Color Flow Imaging Microscopy Improves Identification of Stress Sources of Protein Aggregates in Biopharmaceuticals

Protein-based therapeutics play a pivotal role in modern medicine targeting various diseases. Despite their therapeutic importance, these products can aggregate and form subvisible particles (SvPs), which can compromise their efficacy and trigger immunological responses, emphasizing the critical need for robust monitoring techniques. Flow Imaging Microscopy (FIM) has been a significant advancement in detecting SvPs, evolving from monochrome to more recently incorporating color imaging. Complementing SvP images obtained via FIM, deep learning techniques have recently been employed successfully for stress source identification of monochrome SvPs. In this study, we explore the potential of color FIM to enhance the characterization of stress sources in SvPs. To achieve this, we curate a new dataset comprising 16,000 SvPs from eight commercial monoclonal antibodies subjected to heat and mechanical stress. Using both supervised and self-supervised convolutional neural networks, as well as vision transformers in large-scale experiments, we demonstrate that deep learning with color FIM images consistently outperforms monochrome images, thus highlighting the potential of color FIM in stress source classification compared to its monochrome counterparts.

cs.CV↗

arXiv2025

Self-supervised Benchmark Lottery on ImageNet: Do Marginal Improvements Translate to Improvements on Similar Datasets?

Machine learning (ML) research strongly relies on benchmarks in order to determine the relative effectiveness of newly proposed models. Recently, a number of prominent research effort argued that a number of models that improve the state-of-the-art by a small margin tend to do so by winning what they call a "benchmark lottery". An important benchmark in the field of machine learning and computer vision is the ImageNet where newly proposed models are often showcased based on their performance on this dataset. Given the large number of self-supervised learning (SSL) frameworks that has been proposed in the past couple of years each coming with marginal improvements on the ImageNet dataset, in this work, we evaluate whether those marginal improvements on ImageNet translate to improvements on similar datasets or not. To do so, we investigate twelve popular SSL frameworks on five ImageNet variants and discover that models that seem to perform well on ImageNet may experience significant performance declines on similar datasets. Specifically, state-of-the-art frameworks such as DINO and Swav, which are praised for their performance, exhibit substantial drops in performance while MoCo and Barlow Twins displays comparatively good results. As a result, we argue that otherwise good and desirable properties of models remain hidden when benchmarking is only performed on the ImageNet validation set, making us call for more adequate benchmarking. To avoid the "benchmark lottery" on ImageNet and to ensure a fair benchmarking process, we investigate the usage of a unified metric that takes into account the performance of models on other ImageNet variant datasets.

cs.CV↗

arXiv2024

Leveraging Human-Machine Interactions for Computer Vision Dataset Quality Enhancement

Large-scale datasets for single-label multi-class classification, such as \emph{ImageNet-1k}, have been instrumental in advancing deep learning and computer vision. However, a critical and often understudied aspect is the comprehensive quality assessment of these datasets, especially regarding potential multi-label annotation errors. In this paper, we introduce a lightweight, user-friendly, and scalable framework that synergizes human and machine intelligence for efficient dataset validation and quality enhancement. We term this novel framework \emph{Multilabelfy}. Central to Multilabelfy is an adaptable web-based platform that systematically guides annotators through the re-evaluation process, effectively leveraging human-machine interactions to enhance dataset quality. By using Multilabelfy on the ImageNetV2 dataset, we found that approximately $47.88\%$ of the images contained at least two labels, underscoring the need for more rigorous assessments of such influential datasets. Furthermore, our analysis showed a negative correlation between the number of potential labels per image and model top-1 accuracy, illuminating a crucial factor in model evaluation and selection. Our open-source framework, Multilabelfy, offers a convenient, lightweight solution for dataset enhancement, emphasizing multi-label proportions. This study tackles major challenges in dataset integrity and provides key insights into model performance evaluation. Moreover, it underscores the advantages of integrating human expertise with machine capabilities to produce more robust models and trustworthy data development. The source code for Multilabelfy will be available at https://github.com/esla/Multilabelfy. \keywords{Computer Vision \and Dataset Quality Enhancement \and Dataset Validation \and Human-Computer Interaction \and Multi-label Annotation.}

cs.CV↗

arXiv2023

Towards Abdominal 3-D Scene Rendering from Laparoscopy Surgical Videos using NeRFs

Given that a conventional laparoscope only provides a two-dimensional (2-D) view, the detection and diagnosis of medical ailments can be challenging. To overcome the visual constraints associated with laparoscopy, the use of laparoscopic images and videos to reconstruct the three-dimensional (3-D) anatomical structure of the abdomen has proven to be a promising approach. Neural Radiance Fields (NeRFs) have recently gained attention thanks to their ability to generate photorealistic images from a 3-D static scene, thus facilitating a more comprehensive exploration of the abdomen through the synthesis of new views. This distinguishes NeRFs from alternative methods such as Simultaneous Localization and Mapping (SLAM) and depth estimation. In this paper, we present a comprehensive examination of NeRFs in the context of laparoscopy surgical videos, with the goal of rendering abdominal scenes in 3-D. Although our experimental results are promising, the proposed approach encounters substantial challenges, which require further exploration in future research.

cs.CV↗

arXiv2023

Know Your Self-supervised Learning: A Survey on Image-based Generative and Discriminative Training

Although supervised learning has been highly successful in improving the state-of-the-art in the domain of image-based computer vision in the past, the margin of improvement has diminished significantly in recent years, indicating that a plateau is in sight. Meanwhile, the use of self-supervised learning (SSL) for the purpose of natural language processing (NLP) has seen tremendous successes during the past couple of years, with this new learning paradigm yielding powerful language models. Inspired by the excellent results obtained in the field of NLP, self-supervised methods that rely on clustering, contrastive learning, distillation, and information-maximization, which all fall under the banner of discriminative SSL, have experienced a swift uptake in the area of computer vision. Shortly afterwards, generative SSL frameworks that are mostly based on masked image modeling, complemented and surpassed the results obtained with discriminative SSL. Consequently, within a span of three years, over $100$ unique general-purpose frameworks for generative and discriminative SSL, with a focus on imaging, were proposed. In this survey, we review a plethora of research efforts conducted on image-oriented SSL, providing a historic view and paying attention to best practices as well as useful software packages. While doing so, we discuss pretext tasks for image-based SSL, as well as techniques that are commonly used in image-based SSL. Lastly, to aid researchers who aim at contributing to image-focused SSL, we outline a number of promising research directions.

cs.CV↗