Large AI Models in Health Informatics: Applications, Challenges, and the Future

Large AI models, or foundation models, are models recently emerging with massive scales both parameter-wise and data-wise, the magnitudes of which often reach beyond billions. Once pretrained, large AI models demonstrate impressive performance in various downstream tasks. A concrete example is the recent debut of ChatGPT, whose capability has compelled people's imagination about the far-reaching influence that large AI models can have and their potential to transform different domains of our life. In health informatics, the advent of large AI models has brought new paradigms for the design of methodologies. The scale of multimodality data in the biomedical and health domain has been ever-expanding especially since the community embraced the era of deep learning, which provides the ground to develop, validate, and advance large AI models for breakthroughs in health-related areas. This article presents an up-to-date comprehensive review of large AI models, from background to their applications. We identify seven key sectors that large AI models are applicable and might have substantial influence, including 1) molecular biology and drug discovery; 2) medical diagnosis and decision-making; 3) medical imaging and vision; 4) medical informatics; 5) medical education; 6) public health; and 7) medical robotics. We examine their challenges in health informatics, followed by a critical discussion about potential future directions and pitfalls of large AI models in transforming the field of health informatics.

Conflict-Based Cross-View Consistency for Semi-Supervised Semantic Segmentation

Semi-supervised semantic segmentation has recently gained increasing research interest as it can reduce the requirement for large-scale fully-annotated training data by effectively exploiting large amounts of unlabelled data. The current methods often suffer from the confirmation bias from the pseudo-labelling process, which can be alleviated by the co-training framework. The current co-training-based semi-supervised semantic segmentation methods rely on hand-crafted perturbations to prevent the different sub-nets from collapsing into each other, but these artificial perturbations cannot lead to the optimal solution. In this work, we propose a new conflict-based cross-view consistency (CCVC) method based on a two-branch co-training framework for semi-supervised semantic segmentation. Our work aims at enforcing the two sub-nets to learn informative features from irrelevant views. In particular, we first propose a new cross-view consistency (CVC) strategy that encourages the two sub-nets to learn distinct features from the same input by introducing a feature discrepancy loss, while these distinct features are expected to generate consistent prediction scores of the input. The CVC strategy helps to prevent the two sub-nets from stepping into the collapse. In addition, we further propose a conflict-based pseudo-labelling (CPL) method to guarantee the model will learn more useful information from conflicting predictions, which will lead to a stable training process. We validate our new semi-supervised semantic segmentation approach on the widely used benchmark datasets PASCAL VOC 2012 and Cityscapes, where our method achieves new state-of-the-art performance.

Bridging Synthetic and Real Images: a Transferable and Multiple Consistency aided Fundus Image Enhancement Framework

Deep learning based image enhancement models have largely improved the readability of fundus images in order to decrease the uncertainty of clinical observations and the risk of misdiagnosis. However, due to the difficulty of acquiring paired real fundus images at different qualities, most existing methods have to adopt synthetic image pairs as training data. The domain shift between the synthetic and the real images inevitably hinders the generalization of such models on clinical data. In this work, we propose an end-to-end optimized teacher-student framework to simultaneously conduct image enhancement and domain adaptation. The student network uses synthetic pairs for supervised enhancement, and regularizes the enhancement model to reduce domain-shift by enforcing teacher-student prediction consistency on the real fundus images without relying on enhanced ground-truth. Moreover, we also propose a novel multi-stage multi-attention guided enhancement network (MAGE-Net) as the backbones of our teacher and student network. Our MAGE-Net utilizes multi-stage enhancement module and retinal structure preservation module to progressively integrate the multi-scale features and simultaneously preserve the retinal structures for better fundus image quality enhancement. Comprehensive experiments on both real and synthetic datasets demonstrate that our framework outperforms the baseline approaches. Moreover, our method also benefits the downstream clinical tasks.

Diffusion Models in Bioinformatics: A New Wave of Deep Learning Revolution in Action

Denoising diffusion models have emerged as one of the most powerful generative models in recent years. They have achieved remarkable success in many fields, such as computer vision, natural language processing (NLP), and bioinformatics. Although there are a few excellent reviews on diffusion models and their applications in computer vision and NLP, there is a lack of an overview of their applications in bioinformatics. This review aims to provide a rather thorough overview of the applications of diffusion models in bioinformatics to aid their further development in bioinformatics and computational biology. We start with an introduction of the key concepts and theoretical foundations of three cornerstone diffusion modeling frameworks (denoising diffusion probabilistic models, noise-conditioned scoring networks, and stochastic differential equations), followed by a comprehensive description of diffusion models employed in the different domains of bioinformatics, including cryo-EM data enhancement, single-cell data analysis, protein design and generation, drug and small molecule design, and protein-ligand interaction. The review is concluded with a summary of the potential new development and applications of diffusion models in bioinformatics.

Content Adaptive Latents and Decoder for Neural Image Compression

In recent years, neural image compression (NIC) algorithms have shown powerful coding performance. However, most of them are not adaptive to the image content. Although several content adaptive methods have been proposed by updating the encoder-side components, the adaptability of both latents and the decoder is not well exploited. In this work, we propose a new NIC framework that improves the content adaptability on both latents and the decoder. Specifically, to remove redundancy in the latents, our content adaptive channel dropping (CACD) method automatically selects the optimal quality levels for the latents spatially and drops the redundant channels. Additionally, we propose the content adaptive feature transformation (CAFT) method to improve decoder-side content adaptability by extracting the characteristic information of the image content, which is then used to transform the features in the decoder side. Experimental results demonstrate that our proposed methods with the encoder-side updating algorithm achieve the state-of-the-art performance.

Slow Motion Matters: A Slow Motion Enhanced Network for Weakly Supervised Temporal Action Localization

Weakly supervised temporal action localization (WTAL) aims to localize actions in untrimmed videos with only weak supervision information (e.g. video-level labels). Most existing models handle all input videos with a fixed temporal scale. However, such models are not sensitive to actions whose pace of the movements is different from the ``normal" speed, especially slow-motion action instances, which complete the movements with a much slower speed than their counterparts with a normal speed. Here arises the slow-motion blurred issue: It is hard to explore salient slow-motion information from videos at ``normal" speed. In this paper, we propose a novel framework termed Slow Motion Enhanced Network (SMEN) to improve the ability of a WTAL network by compensating its sensitivity on slow-motion action segments. The proposed SMEN comprises a Mining module and a Localization module. The mining module generates mask to mine slow-motion-related features by utilizing the relationships between the normal motion and slow motion; while the localization module leverages the mined slow-motion features as complementary information to improve the temporal action localization results. Our proposed framework can be easily adapted by existing WTAL networks and enable them be more sensitive to slow-motion actions. Extensive experiments on three benchmarks are conducted, which demonstrate the high performance of our proposed framework.

Towards Explainable 3D Grounded Visual Question Answering: A New Benchmark and Strong Baseline

Recently, 3D vision-and-language tasks have attracted increasing research interest. Compared to other vision-and-language tasks, the 3D visual question answering (VQA) task is less exploited and is more susceptible to language priors and co-reference ambiguity. Meanwhile, a couple of recently proposed 3D VQA datasets do not well support 3D VQA task due to their limited scale and annotation methods. In this work, we formally define and address a 3D grounded VQA task by collecting a new 3D VQA dataset, referred to as FE-3DGQA, with diverse and relatively free-form question-answer pairs, as well as dense and completely grounded bounding box annotations. To achieve more explainable answers, we labelled the objects appeared in the complex QA pairs with different semantic types, including answer-grounded objects (both appeared and not appeared in the questions), and contextual objects for answer-grounded objects. We also propose a new 3D VQA framework to effectively predict the completely visually grounded and explainable answer. Extensive experiments verify that our newly collected benchmark datasets can be effectively used to evaluate various 3D VQA methods from different aspects and our newly proposed framework also achieves state-of-the-art performance on the new benchmark dataset. Both the newly collected dataset and our codes will be publicly available at http://github.com/zlccccc/3DGQA.

Improving RGB-D Point Cloud Registration by Learning Multi-scale Local Linear Transformation

Point cloud registration aims at estimating the geometric transformation between two point cloud scans, in which point-wise correspondence estimation is the key to its success. In addition to previous methods that seek correspondences by hand-crafted or learnt geometric features, recent point cloud registration methods have tried to apply RGB-D data to achieve more accurate correspondence. However, it is not trivial to effectively fuse the geometric and visual information from these two distinctive modalities, especially for the registration problem. In this work, we propose a new Geometry-Aware Visual Feature Extractor (GAVE) that employs multi-scale local linear transformation to progressively fuse these two modalities, where the geometric features from the depth data act as the geometry-dependent convolution kernels to transform the visual features from the RGB data. The resultant visual-geometric features are in canonical feature spaces with alleviated visual dissimilarity caused by geometric changes, by which more reliable correspondence can be achieved. The proposed GAVE module can be readily plugged into recent RGB-D point cloud registration framework. Extensive experiments on 3D Match and ScanNet demonstrate that our method outperforms the state-of-the-art point cloud registration methods even without correspondence or pose supervision. The code is available at: https://github.com/514DNA/LLT.

SketchSampler: Sketch-based 3D Reconstruction via View-dependent Depth Sampling

Reconstructing a 3D shape based on a single sketch image is challenging due to the large domain gap between a sparse, irregular sketch and a regular, dense 3D shape. Existing works try to employ the global feature extracted from sketch to directly predict the 3D coordinates, but they usually suffer from losing fine details that are not faithful to the input sketch. Through analyzing the 3D-to-2D projection process, we notice that the density map that characterizes the distribution of 2D point clouds (i.e., the probability of points projected at each location of the projection plane) can be used as a proxy to facilitate the reconstruction process. To this end, we first translate a sketch via an image translation network to a more informative 2D representation that can be used to generate a density map. Next, a 3D point cloud is reconstructed via a two-stage probabilistic sampling process: first recovering the 2D points (i.e., the x and y coordinates) by sampling the density map; and then predicting the depth (i.e., the z coordinate) by sampling the depth values at the ray determined by each 2D point. Extensive experiments are conducted, and both quantitative and qualitative results show that our proposed approach significantly outperforms other baseline methods.