FPL+: Filtered Pseudo Label-based Unsupervised Cross-Modality Adaptation for 3D Medical Image Segmentation

Adapting a medical image segmentation model to a new domain is important for improving its cross-domain transferability, and due to the expensive annotation process, Unsupervised Domain Adaptation (UDA) is appealing where only unlabeled images are needed for the adaptation. Existing UDA methods are mainly based on image or feature alignment with adversarial training for regularization, and they are limited by insufficient supervision in the target domain. In this paper, we propose an enhanced Filtered Pseudo Label (FPL+)-based UDA method for 3D medical image segmentation. It first uses cross-domain data augmentation to translate labeled images in the source domain to a dual-domain training set consisting of a pseudo source-domain set and a pseudo target-domain set. To leverage the dual-domain augmented images to train a pseudo label generator, domain-specific batch normalization layers are used to deal with the domain shift while learning the domain-invariant structure features, generating high-quality pseudo labels for target-domain images. We then combine labeled source-domain images and target-domain images with pseudo labels to train a final segmentor, where image-level weighting based on uncertainty estimation and pixel-level weighting based on dual-domain consensus are proposed to mitigate the adverse effect of noisy pseudo labels. Experiments on three public multi-modal datasets for Vestibular Schwannoma, brain tumor and whole heart segmentation show that our method surpassed ten state-of-the-art UDA methods, and it even achieved better results than fully supervised learning in the target domain in some cases.

OpenMEDLab: An Open-source Platform for Multi-modality Foundation Models in Medicine

The emerging trend of advancing generalist artificial intelligence, such as GPTv4 and Gemini, has reshaped the landscape of research (academia and industry) in machine learning and many other research areas. However, domain-specific applications of such foundation models (e.g., in medicine) remain untouched or often at their very early stages. It will require an individual set of transfer learning and model adaptation techniques by further expanding and injecting these models with domain knowledge and data. The development of such technologies could be largely accelerated if the bundle of data, algorithms, and pre-trained foundation models were gathered together and open-sourced in an organized manner. In this work, we present OpenMEDLab, an open-source platform for multi-modality foundation models. It encapsulates not only solutions of pioneering attempts in prompting and fine-tuning large language and vision models for frontline clinical and bioinformatic applications but also building domain-specific foundation models with large-scale multi-modal medical data. Importantly, it opens access to a group of pre-trained foundation models for various medical image modalities, clinical text, protein engineering, etc. Inspiring and competitive results are also demonstrated for each collected approach and model in a variety of benchmarks for downstream tasks. We welcome researchers in the field of medical artificial intelligence to continuously contribute cutting-edge methods and models to OpenMEDLab, which can be accessed via https://github.com/openmedlab.

Increasing SAM Zero-Shot Performance on Multimodal Medical Images Using GPT-4 Generated Descriptive Prompts Without Human Annotation

This study develops and evaluates a novel multimodal medical image zero-shot segmentation algorithm named Text-Visual-Prompt SAM (TV-SAM) without any manual annotations. TV-SAM incorporates and integrates large language model GPT-4, Vision Language Model GLIP, and Segment Anything Model (SAM), to autonomously generate descriptive text prompts and visual bounding box prompts from medical images, thereby enhancing SAM for zero-shot segmentation. Comprehensive evaluations are implemented on seven public datasets encompassing eight imaging modalities to demonstrate that TV-SAM can effectively segment unseen targets across various modalities without additional training, significantly outperforming SAM AUTO and GSAM, closely matching the performance of SAM BBOX with gold standard bounding box prompts, and surpassing the state-of-the-art on specific datasets like ISIC and WBC. The study indicates that TV-SAM serves as an effective multimodal medical image zero-shot segmentation algorithm, highlighting the significant contribution of GPT-4 to zero-shot segmentation. By integrating foundational models such as GPT-4, GLIP, and SAM, it could enhance the capability to address complex problems in specialized domains. The code is available at: https://github.com/JZK00/TV-SAM.

Memory-Efficient Prompt Tuning for Incremental Histopathology Classification

Recent studies have made remarkable progress in histopathology classification. Based on current successes, contemporary works proposed to further upgrade the model towards a more generalizable and robust direction through incrementally learning from the sequentially delivered domains. Unlike previous parameter isolation based approaches that usually demand massive computation resources during model updating, we present a memory-efficient prompt tuning framework to cultivate model generalization potential in economical memory cost. For each incoming domain, we reuse the existing parameters of the initial classification model and attach lightweight trainable prompts into it for customized tuning. Considering the domain heterogeneity, we perform decoupled prompt tuning, where we adopt a domain-specific prompt for each domain to independently investigate its distinctive characteristics, and one domain-invariant prompt shared across all domains to continually explore the common content embedding throughout time. All domain-specific prompts will be appended to the prompt bank and isolated from further changes to prevent forgetting the distinctive features of early-seen domains. While the domain-invariant prompt will be passed on and iteratively evolve by style-augmented prompt refining to improve model generalization capability over time. In specific, we construct a graph with existing prompts and build a style-augmented graph attention network to guide the domain-invariant prompt exploring the overlapped latent embedding among all delivered domains for more domain generic representations. We have extensively evaluated our framework with two histopathology tasks, i.e., breast cancer metastasis classification and epithelium-stroma tissue classification, where our approach yielded superior performance and memory efficiency over the competing methods.

Evaluating and Enhancing Large Language Models Performance in Domain-specific Medicine: Osteoarthritis Management with DocOA

The efficacy of large language models (LLMs) in domain-specific medicine, particularly for managing complex diseases such as osteoarthritis (OA), remains largely unexplored. This study focused on evaluating and enhancing the clinical capabilities of LLMs in specific domains, using osteoarthritis (OA) management as a case study. A domain specific benchmark framework was developed, which evaluate LLMs across a spectrum from domain-specific knowledge to clinical applications in real-world clinical scenarios. DocOA, a specialized LLM tailored for OA management that integrates retrieval-augmented generation (RAG) and instruction prompts, was developed. The study compared the performance of GPT-3.5, GPT-4, and a specialized assistant, DocOA, using objective and human evaluations. Results showed that general LLMs like GPT-3.5 and GPT-4 were less effective in the specialized domain of OA management, particularly in providing personalized treatment recommendations. However, DocOA showed significant improvements. This study introduces a novel benchmark framework which assesses the domain-specific abilities of LLMs in multiple aspects, highlights the limitations of generalized LLMs in clinical contexts, and demonstrates the potential of tailored approaches for developing domain-specific medical LLMs.

Amplifying robotics capacities with a human touch: An immersive low-latency panoramic remote system

AI and robotics technologies have witnessed remarkable advancements in the past decade, revolutionizing work patterns and opportunities in various domains. The application of these technologies has propelled society towards an era of symbiosis between humans and machines. To facilitate efficient communication between humans and intelligent robots, we propose the "Avatar" system, an immersive low-latency panoramic human-robot interaction platform. We have designed and tested a prototype of a rugged mobile platform integrated with edge computing units, panoramic video capture devices, power batteries, robot arms, and network communication equipment. Under favorable network conditions, we achieved a low-latency high-definition panoramic visual experience with a delay of 357ms. Operators can utilize VR headsets and controllers for real-time immersive control of robots and devices. The system enables remote control over vast physical distances, spanning campuses, provinces, countries, and even continents (New York to Shenzhen). Additionally, the system incorporates visual SLAM technology for map and trajectory recording, providing autonomous navigation capabilities. We believe that this intuitive system platform can enhance efficiency and situational experience in human-robot collaboration, and with further advancements in related technologies, it will become a versatile tool for efficient and symbiotic cooperation between AI and humans.

Large language models in bioinformatics: applications and perspectives

Large language models (LLMs) are a class of artificial intelligence models based on deep learning, which have great performance in various tasks, especially in natural language processing (NLP). Large language models typically consist of artificial neural networks with numerous parameters, trained on large amounts of unlabeled input using self-supervised or semi-supervised learning. However, their potential for solving bioinformatics problems may even exceed their proficiency in modeling human language. In this review, we will present a summary of the prominent large language models used in natural language processing, such as BERT and GPT, and focus on exploring the applications of large language models at different omics levels in bioinformatics, mainly including applications of large language models in genomics, transcriptomics, proteomics, drug discovery and single cell analysis. Finally, this review summarizes the potential and prospects of large language models in solving bioinformatic problems.

A Comprehensive Overview of Fish-Eye Camera Distortion Correction Methods

The fisheye camera, with its unique wide field of view and other characteristics, has found extensive applications in various fields. However, the fisheye camera suffers from significant distortion compared to pinhole cameras, resulting in distorted images of captured objects. Fish-eye camera distortion is a common issue in digital image processing, requiring effective correction techniques to enhance image quality. This review provides a comprehensive overview of various methods used for fish-eye camera distortion correction. The article explores the polynomial distortion model, which utilizes polynomial functions to model and correct radial distortions. Additionally, alternative approaches such as panorama mapping, grid mapping, direct methods, and deep learning-based methods are discussed. The review highlights the advantages, limitations, and recent advancements of each method, enabling readers to make informed decisions based on their specific needs.

PointMoment:Mixed-Moment-based Self-Supervised Representation Learning for 3D Point Clouds

Large and rich data is a prerequisite for effective training of deep neural networks. However, the irregularity of point cloud data makes manual annotation time-consuming and laborious. Self-supervised representation learning, which leverages the intrinsic structure of large-scale unlabelled data to learn meaningful feature representations, has attracted increasing attention in the field of point cloud research. However, self-supervised representation learning often suffers from model collapse, resulting in reduced information and diversity of the learned representation, and consequently degrading the performance of downstream tasks. To address this problem, we propose PointMoment, a novel framework for point cloud self-supervised representation learning that utilizes a high-order mixed moment loss function rather than the conventional contrastive loss function. Moreover, our framework does not require any special techniques such as asymmetric network architectures, gradient stopping, etc. Specifically, we calculate the high-order mixed moment of the feature variables and force them to decompose into products of their individual moment, thereby making multiple variables more independent and minimizing the feature redundancy. We also incorporate a contrastive learning approach to maximize the feature invariance under different data augmentations of the same point cloud. Experimental results show that our approach outperforms previous unsupervised learning methods on the downstream task of 3D point cloud classification and segmentation.