Digital pathology has transformed the traditional pathology practice of analyzing tissue under a microscope into a computer vision workflow. Whole slide imaging allows pathologists to view and analyze microscopic images on a computer monitor, enabling computational pathology. By leveraging artificial intelligence (AI) and machine learning (ML), computational pathology has emerged as a promising field in recent years. Recently, task-specific AI/ML (e.g., convolutional neural networks) has risen to the forefront, achieving above-human performance in many image processing and computer vision tasks. The performance of task-specific AI/ML models depends on the availability of many annotated training datasets, which presents a rate-limiting factor for AI/ML development in pathology. Tasks-specific AI/ML models cannot benefit from multimodal data and lack generalization, e.g., the AI models often struggle to generalize to new datasets or unseen variations in image acquisition, staining techniques, or tissue types. The 2020s are witnessing the rise of foundation models and generative AI. A foundation model is a large AI model trained using sizeable data, which is later adapted (or fine-tuned) to perform different tasks using a modest amount of task-specific annotated data. These AI models provide in-context learning, can self-correct mistakes, and promptly adjust to user feedback. In this review, we briefly overview recent advances in computational pathology enabled by task-specific AI, their challenges, and limitations, and then introduce various foundation models. We propose to create a pathology-specific generative AI based on multimodal foundation models and present its potentially transformative role in digital pathology. We describe different use cases, delineating how it could serve as an expert companion of pathologists and help them efficiently and objectively perform routine laboratory tasks, including quantifying image analysis, generating pathology reports, diagnosis, and prognosis. We also outline the potential role that foundation models and generative AI can play in standardizing the pathology laboratory workflow, education, and training.

Revolutionizing Digital Pathology with the Power of Generative Artificial Intelligence and Foundation Models.

As it is empirically observed that Vision Transformers (ViTs) are quite insensitive to the order of input tokens, the need for an appropriate self-supervised pretext task that enhances the location awareness of ViTs is becoming evident. To address this, we present DropPos, a novel pretext task designed to reconstruct Dropped Positions. The formulation of DropPos is simple: we first drop a large random subset of positional embeddings and then the model classifies the actual position for each non-overlapping patch among all possible positions solely based on their visual appearance. To avoid trivial solutions, we increase the difficulty of this task by keeping only a subset of patches visible. Additionally, considering there may be different patches with similar visual appearances, we propose position smoothing and attentive reconstruction strategies to relax this classification problem, since it is not necessary to reconstruct their exact positions in these cases. Empirical evaluations of DropPos show strong capabilities. DropPos outperforms supervised pre-training and achieves competitive results compared with state-of-the-art self-supervised alternatives on a wide range of downstream benchmarks. This suggests that explicitly encouraging spatial reasoning abilities, as DropPos does, indeed contributes to the improved location awareness of ViTs. The code is publicly available at https://github.com/Haochen-Wang409/DropPos.

DropPos: Pre-Training Vision Transformers by Reconstructing Dropped Positions

With the significant advancements of Large Language Models (LLMs) in the field of Natural Language Processing (NLP), the development of image-text multimodal models has garnered widespread attention. Current surveys on image-text multimodal models mainly focus on representative models or application domains, but lack a review on how general technical models influence the development of domain-specific models, which is crucial for domain researchers. Based on this, this paper first reviews the technological evolution of image-text multimodal models, from early explorations of feature space to visual language encoding structures, and then to the latest large model architectures. Next, from the perspective of technological evolution, we explain how the development of general image-text multimodal technologies promotes the progress of multimodal technologies in the biomedical field, as well as the importance and complexity of specific datasets in the biomedical domain. Then, centered on the tasks of image-text multimodal models, we analyze their common components and challenges. After that, we summarize the architecture, components, and data of general image-text multimodal models, and introduce the applications and improvements of image-text multimodal models in the biomedical field. Finally, we categorize the challenges faced in the development and application of general models into external factors and intrinsic factors, further refining them into 2 external factors and 5 intrinsic factors, and propose targeted solutions, providing guidance for future research directions. For more details and data, please visit our GitHub page: https://github.com/i2vec/A-survey-on-image-text-multimodal-models. 

A survey on advancements in image-text multimodal models: From general techniques to biomedical implementations

Time series classification (TSC) has emerged as a critical task in various domains, and deep neural models have shown superior performance in TSC tasks. However, these models are vulnerable to adversarial attacks, where subtle perturbations can significantly impact the prediction results. Existing adversarial methods often suffer from over-parameterization or random logit perturbation, hindering their effectiveness. Additionally, increasing the attack success rate (ASR) typically involves generating more noise, making the attack more easily detectable. To address these limitations, we propose SWAP, a novel attacking method for TSC models. SWAP focuses on enhancing the confidence of the second-ranked logits while minimizing the manipulation of other logits. This is achieved by minimizing the Kullback-Leibler divergence between the target logit distribution and the predictive logit distribution. Experimental results demonstrate that SWAP achieves state-of-the-art performance, with an ASR exceeding 50% and an 18% increase compared to existing methods.

pdf/swap-exploiting-second-ranked-logits-for-adversarial-attacks-28fckdb2tq.pdf

SWAP: Exploiting Second-Ranked Logits for Adversarial Attacks on Time Series

Pretraining has proven to be a powerful technique in natural language processing (NLP), exhibiting remarkable success in various NLP downstream tasks. However, in the medical domain, existing pretrained models on electronic health records (EHR) fail to capture the hierarchical nature of EHR data, limiting their generalization capability across diverse downstream tasks using a single pretrained model. To tackle this challenge, this paper introduces a novel, general, and unified pretraining framework called MEDHMP, specifically designed for hierarchically multimodal EHR data. The effectiveness of the proposed MEDHMP is demonstrated through experimental results on eight downstream tasks spanning three levels. Comparisons against eighteen baselines further highlight the efficacy of our approach.

pdf/hierarchical-pretraining-on-multimodal-electronic-health-2u3vpcq5k9.pdf

Hierarchical Pretraining on Multimodal Electronic Health Records

Abstract Medical data refers to health-related information associated with regular patient care or as part of a clinical trial program. There are many categories of such data, such as clinical imaging data, bio-signal data, electronic health records (EHR), and multi-modality medical data. With the development of deep neural networks in the last decade, the emerging pre-training paradigm has become dominant in that it has significantly improved machine learning methods′ performance in a data-limited scenario. In recent years, studies of pre-training in the medical domain have achieved significant progress. To summarize these technology advancements, this work provides a comprehensive survey of recent advances for pre-training on several major types of medical data. In this survey, we summarize a large number of related publications and the existing benchmarking in the medical domain. Especially, the survey briefly describes how some pre-training methods are applied to or developed for medical data. From a data-driven perspective, we examine the extensive use of pre-training in many medical scenarios. Moreover, based on the summary of recent pre-training studies, we identify several challenges in this field to provide insights for future studies. 

/pdf/pre-training-in-medical-data-a-survey-2ic9t0ps.pdf

Pre-training in Medical Data: A Survey

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Pre-training in Medical Data: A Survey