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.

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.

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.

Less is More? Revisiting the Importance of Frame Rate in Real-Time Zero-Shot Surgical Video Segmentation

Real-time video segmentation is a promising feature for AI-assisted surgery, providing intraoperative guidance by identifying surgical tools and anatomical structures. However, deploying state-of-the-art segmentation models, such as SAM2, in real-time settings is computationally demanding, which makes it essential to balance frame rate and segmentation performance. In this study, we investigate the impact of frame rate on zero-shot surgical video segmentation, evaluating SAM2's effectiveness across multiple frame sampling rates for cholecystectomy procedures. Surprisingly, our findings indicate that in conventional evaluation settings, frame rates as low as a single frame per second can outperform 25 FPS, as fewer frames smooth out segmentation inconsistencies. However, when assessed in a real-time streaming scenario, higher frame rates yield superior temporal coherence and stability, particularly for dynamic objects such as surgical graspers. Finally, we investigate human perception of real-time surgical video segmentation among professionals who work closely with such data and find that respondents consistently prefer high FPS segmentation mask overlays, reinforcing the importance of real-time evaluation in AI-assisted surgery.

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.

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.

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.

Re-assessing ImageNet: How aligned is its single-label assumption with its multi-label nature?

ImageNet, an influential dataset in computer vision, is traditionally evaluated using single-label classification, which assumes that an image can be adequately described by a single concept or label. However, this approach may not fully capture the complex semantics within the images available in ImageNet, potentially hindering the development of models that effectively learn these intricacies. This study critically examines the prevalent single-label benchmarking approach and advocates for a shift to multi-label benchmarking for ImageNet. This shift would enable a more comprehensive assessment of the capabilities of deep neural network (DNN) models. We analyze the effectiveness of pre-trained state-of-the-art DNNs on ImageNet and one of its variants, ImageNetV2. Studies in the literature have reported unexpected accuracy drops of 11% to 14% on ImageNetV2. Our findings show that these reported declines are largely attributable to a characteristic of the dataset that has not received sufficient attention -- the proportion of images with multiple labels. Taking this characteristic into account, the results of our experiments provide evidence that there is no substantial degradation in effectiveness on ImageNetV2. Furthermore, we acknowledge that ImageNet pre-trained models exhibit some capability at capturing the multi-label nature of the dataset even though they were trained under the single-label assumption. Consequently, we propose a new evaluation approach to augment existing approaches that assess this capability. Our findings highlight the importance of considering the multi-label nature of the ImageNet dataset during benchmarking. Failing to do so could lead to incorrect conclusions regarding the effectiveness of DNNs and divert research efforts from addressing other substantial challenges related to the reliability and robustness of these models.

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.}

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.