Analysis and Validation of Image Search Engines in Histopathology

Searching for similar images in archives of histology and histopathology images is a crucial task that may aid in patient matching for various purposes, ranging from triaging and diagnosis to prognosis and prediction. Whole slide images (WSIs) are highly detailed digital representations of tissue specimens mounted on glass slides. Matching WSI to WSI can serve as the critical method for patient matching. In this paper, we report extensive analysis and validation of four search methods bag of visual words (BoVW), Yottixel, SISH, RetCCL, and some of their potential variants. We analyze their algorithms and structures and assess their performance. For this evaluation, we utilized four internal datasets ($1269$ patients) and three public datasets ($1207$ patients), totaling more than $200,000$ patches from $38$ different classes/subtypes across five primary sites. Certain search engines, for example, BoVW, exhibit notable efficiency and speed but suffer from low accuracy. Conversely, search engines like Yottixel demonstrate efficiency and speed, providing moderately accurate results. Recent proposals, including SISH, display inefficiency and yield inconsistent outcomes, while alternatives like RetCCL prove inadequate in both accuracy and efficiency. Further research is imperative to address the dual aspects of accuracy and minimal storage requirements in histopathological image search.

Selection of Distinct Morphologies to Divide & Conquer Gigapixel Pathology Images

Whole slide images (WSIs) are massive digital pathology files illustrating intricate tissue structures. Selecting a small, representative subset of patches from each WSI is essential yet challenging. Therefore, following the "Divide & Conquer" approach becomes essential to facilitate WSI analysis including the classification and the WSI matching in computational pathology. To this end, we propose a novel method termed "Selection of Distinct Morphologies" (SDM) to choose a subset of WSI patches. The aim is to encompass all inherent morphological variations within a given WSI while simultaneously minimizing the number of selected patches to represent these variations, ensuring a compact yet comprehensive set of patches. This systematically curated patch set forms what we term a "montage". We assess the representativeness of the SDM montage across various public and private histopathology datasets. This is conducted by using the leave-one-out WSI search and matching evaluation method, comparing it with the state-of-the-art Yottixel's mosaic. SDM demonstrates remarkable efficacy across all datasets during its evaluation. Furthermore, SDM eliminates the necessity for empirical parameterization, a crucial aspect of Yottixel's mosaic, by inherently optimizing the selection process to capture the distinct morphological features within the WSI.

Rotation-Agnostic Image Representation Learning for Digital Pathology

This paper addresses complex challenges in histopathological image analysis through three key contributions. Firstly, it introduces a fast patch selection method, FPS, for whole-slide image (WSI) analysis, significantly reducing computational cost while maintaining accuracy. Secondly, it presents PathDino, a lightweight histopathology feature extractor with a minimal configuration of five Transformer blocks and only 9 million parameters, markedly fewer than alternatives. Thirdly, it introduces a rotation-agnostic representation learning paradigm using self-supervised learning, effectively mitigating overfitting. We also show that our compact model outperforms existing state-of-the-art histopathology-specific vision transformers on 12 diverse datasets, including both internal datasets spanning four sites (breast, liver, skin, and colorectal) and seven public datasets (PANDA, CAMELYON16, BRACS, DigestPath, Kather, PanNuke, and WSSS4LUAD). Notably, even with a training dataset of 6 million histopathology patches from The Cancer Genome Atlas (TCGA), our approach demonstrates an average 8.5% improvement in patch-level majority vote performance. These contributions provide a robust framework for enhancing image analysis in digital pathology, rigorously validated through extensive evaluation. Project Page: https://rhazeslab.github.io/PathDino-Page/

When is a Foundation Model a Foundation Model

Recently, several studies have reported on the fine-tuning of foundation models for image-text modeling in the field of medicine, utilizing images from online data sources such as Twitter and PubMed. Foundation models are large, deep artificial neural networks capable of learning the context of a specific domain through training on exceptionally extensive datasets. Through validation, we have observed that the representations generated by such models exhibit inferior performance in retrieval tasks within digital pathology when compared to those generated by significantly smaller, conventional deep networks.

OSRE: Object-to-Spot Rotation Estimation for Bike Parking Assessment

Current deep models provide remarkable object detection in terms of object classification and localization. However, estimating object rotation with respect to other visual objects in the visual context of an input image still lacks deep studies due to the unavailability of object datasets with rotation annotations. This paper tackles these two challenges to solve the rotation estimation of a parked bike with respect to its parking area. First, we leverage the power of 3D graphics to build a camera-agnostic well-annotated Synthetic Bike Rotation Dataset (SynthBRSet). Then, we propose an object-to-spot rotation estimator (OSRE) by extending the object detection task to further regress the bike rotations in two axes. Since our model is purely trained on synthetic data, we adopt image smoothing techniques when deploying it on real-world images. The proposed OSRE is evaluated on synthetic and real-world data providing promising results. Our data and code are available at \href{https://github.com/saghiralfasly/OSRE-Project}{https://github.com/saghiralfasly/OSRE-Project}.

Learnable Irrelevant Modality Dropout for Multimodal Action Recognition on Modality-Specific Annotated Videos

With the assumption that a video dataset is multimodality annotated in which auditory and visual modalities both are labeled or class-relevant, current multimodal methods apply modality fusion or cross-modality attention. However, effectively leveraging the audio modality in vision-specific annotated videos for action recognition is of particular challenge. To tackle this challenge, we propose a novel audio-visual framework that effectively leverages the audio modality in any solely vision-specific annotated dataset. We adopt the language models (e.g., BERT) to build a semantic audio-video label dictionary (SAVLD) that maps each video label to its most K-relevant audio labels in which SAVLD serves as a bridge between audio and video datasets. Then, SAVLD along with a pretrained audio multi-label model are used to estimate the audio-visual modality relevance during the training phase. Accordingly, a novel learnable irrelevant modality dropout (IMD) is proposed to completely drop out the irrelevant audio modality and fuse only the relevant modalities. Moreover, we present a new two-stream video Transformer for efficiently modeling the visual modalities. Results on several vision-specific annotated datasets including Kinetics400 and UCF-101 validated our framework as it outperforms most relevant action recognition methods.