The integration of multimodal data including pathology images and gene profiles is widely applied in precise survival prediction. Despite recent advances in multimodal survival models, collecting complete modalities for multi-modal fusion still poses a significant challenge, hindering their application in clinical settings. Current approaches tackling incomplete modalities often fall short, as they typically compensate for only a limited part of the knowledge of missing modalities. To address this issue, we propose a Distilled Prompt Learning framework (DisPro) to utilize the strong robustness of Large Language Models (LLMs) to missing modalities, which employs two-stage prompting for compensation of comprehensive information for missing modalities. In the first stage, Unimodal Prompting (UniPro) distills the knowledge distribution of each modality, preparing for supplementing modality-specific knowledge of the missing modality in the subsequent stage. In the second stage, Multimodal Prompting (MultiPro) leverages available modalities as prompts for LLMs to infer the missing modality, which provides modality-common information. Simultaneously, the unimodal knowledge acquired in the first stage is injected into multimodal inference to compensate for the modality-specific knowledge of the missing modality. Extensive experiments covering various missing scenarios demonstrated the superiority of the proposed method. The code is available at https://github.com/Innse/DisPro.

Histo-genomic multi-modal methods have emerged as a powerful paradigm, demonstrating significant potential for cancer prognosis. However, genome sequencing, unlike histopathology imaging, is still not widely accessible in underdeveloped regions, limiting the application of these multi-modal approaches in clinical settings. To address this, we propose a novel Genome-informed Hyper-Attention Network, termed G-HANet, which is capable of effectively learning the histo-genomic associations during training to elevate uni-modal whole slide image (WSI)-based inference for the first time. Compared with the potential knowledge distillation strategy for this setting (i.e., distilling a multi-modal network to a uni-modal network), our end-to-end model is superior in training efficiency and learning cross-modal interactions. Specifically, the network comprises cross-modal associating branch (CAB) and hyper-attention survival branch (HSB). Through the genomic data reconstruction from WSIs, CAB effectively distills the associations between functional genotypes and morphological phenotypes and offers insights into the gene expression profiles in the feature space. Subsequently, HSB leverages the distilled histo-genomic associations as well as the generated morphology-based weights to achieve the hyper-attention modeling of the patients from both histopathology and genomic perspectives to improve cancer prognosis. Extensive experiments are conducted on five TCGA benchmarking datasets and the results demonstrate that G-HANet significantly outperforms the state-of-the-art WSI-based methods and achieves competitive performance with genome-based and multi-modal methods. G-HANet is expected to be explored as a useful tool by the research community to address the current bottleneck of insufficient histo-genomic data pairing in the context of cancer prognosis and precision oncology. The code is available at https://github.com/ZacharyWang-007/G-HANet.

Multimodal learning significantly benefits cancer survival prediction, especially the integration of pathological images and genomic data. Despite advantages of multimodal learning for cancer survival prediction, massive redundancy in multimodal data prevents it from extracting discriminative and compact information: (1) An extensive amount of intra-modal task-unrelated information blurs discriminability, especially for gigapixel whole slide images (WSIs) with many patches in pathology and thousands of pathways in genomic data, leading to an "intra-modal redundancy" issue. (2) Duplicated information among modalities dominates the representation of multimodal data, which makes modality-specific information prone to being ignored, resulting in an "inter-modal redundancy" issue. To address these, we propose a new framework, Prototypical Information Bottlenecking and Disentangling (PIBD), consisting of Prototypical Information Bottleneck (PIB) module for intra-modal redundancy and Prototypical Information Disentanglement (PID) module for inter-modal redundancy. Specifically, a variant of information bottleneck, PIB, is proposed to model prototypes approximating a bunch of instances for different risk levels, which can be used for selection of discriminative instances within modality. PID module decouples entangled multimodal data into compact distinct components: modality-common and modality-specific knowledge, under the guidance of the joint prototypical distribution. Extensive experiments on five cancer benchmark datasets demonstrated our superiority over other methods. The code is released.

Unsupervised domain adaptation (UDA) aims to estimate a transferable model for unlabeled target domains by exploiting labeled source data. Optimal Transport (OT) based methods have recently been proven to be a promising solution for UDA with a solid theoretical foundation and competitive performance. However, most of these methods solely focus on domain-level OT alignment by leveraging the geometry of domains for domain-invariant features based on the global embeddings of images. However, global representations of images may destroy image structure, leading to the loss of local details that offer category-discriminative information. This study proposes an end-to-end Deep Hierarchical Optimal Transport method (DeepHOT), which aims to learn both domain-invariant and category-discriminative representations by mining hierarchical structural relations among domains. The main idea is to incorporate a domain-level OT and image-level OT into a unified OT framework, hierarchical optimal transport, to model the underlying geometry in both domain space and image space. In DeepHOT framework, an image-level OT serves as the ground distance metric for the domain-level OT, leading to the hierarchical structural distance. Compared with the ground distance of the conventional domain-level OT, the image-level OT captures structural associations among local regions of images that are beneficial to classification. In this way, DeepHOT, a unified OT framework, not only aligns domains by domain-level OT, but also enhances the discriminative power through image-level OT. Moreover, to overcome the limitation of high computational complexity, we propose a robust and efficient implementation of DeepHOT by approximating origin OT with sliced Wasserstein distance in image-level OT and accomplishing the mini-batch unbalanced domain-level OT. Extensive experiments show the superiority of DeepHOT in several benchmark datasets. The code will be released on GitHub.

Survival prediction is a complicated ordinal regression task that aims to predict the ranking risk of death, which generally benefits from the integration of histology and genomic data. Despite the progress in joint learning from pathology and genomics, existing methods still suffer from challenging issues: 1) Due to the large size of pathological images, it is difficult to effectively represent the gigapixel whole slide images (WSIs). 2) Interactions within tumor microenvironment (TME) in histology are essential for survival analysis. Although current approaches attempt to model these interactions via co-attention between histology and genomic data, they focus on only dense local similarity across modalities, which fails to capture global consistency between potential structures, i.e. TME-related interactions of histology and co-expression of genomic data. To address these challenges, we propose a Multimodal Optimal Transport-based Co-Attention Transformer framework with global structure consistency, in which optimal transport (OT) is applied to match patches of a WSI and genes embeddings for selecting informative patches to represent the gigapixel WSI. More importantly, OT-based co-attention provides a global awareness to effectively capture structural interactions within TME for survival prediction. To overcome high computational complexity of OT, we propose a robust and efficient implementation over micro-batch of WSI patches by approximating the original OT with unbalanced mini-batch OT. Extensive experiments show the superiority of our method on five benchmark datasets compared to the state-of-the-art methods. The code is released1.

Physical signs of patients indicate crucial evidence for diagnosing both location and nature of the disease, where there is a sequential relationship between the two tasks. Thus their joint learning can utilize intrinsic association by transferring related knowledge across relevant tasks. Choosing the right time to transfer is a critical problem for joint learning. However, how to dynamically adjust when tasks interact to capture the right time for transferring related knowledge is still an open issue. To this end, we propose a Task-Coupling Elastic Learning (TCEL) framework to model the task relatedness for classifying disease-location and disease-nature based on physical sign images. The main idea is to dynamically transfer relevant knowledge by progressively shifting task-coupling from loose to tight during the multi-stage training. In the early stage of training, we relax the constraints of modeling relations to focus more in learning the generic task-common features. In the later stage, the semantic guidance will be strengthened to learn the task-specific features. Specifically, a dynamic sequential module (DSM) is proposed to explicitly model the sequential relationship and enable multi-stage training. Moreover, to address the side effect of DSM, a new loss regularization is proposed. The extensive experiments on these two clinical datasets show the superiority of the proposed method over the baselines, and demonstrate the effectiveness of the proposed task-coupling elastic mechanism.

Zero-shot learning uses semantic attributes to connect the search space of unseen objects. In recent years, although the deep convolutional network brings powerful visual modeling capabilities to the ZSL task, its visual features have severe pattern inertia and lack of representation of semantic relationships, which leads to severe bias and ambiguity. In response to this, we propose the Graph-based Visual-Semantic Entanglement Network to conduct graph modeling of visual features, which is mapped to semantic attributes by using a knowledge graph, it contains several novel designs: 1. it establishes a multi-path entangled network with the convolutional neural network (CNN) and the graph convolutional network (GCN), which input the visual features from CNN to GCN to model the implicit semantic relations, then GCN feedback the graph modeled information to CNN features; 2. it uses attribute word vectors as the target for the graph semantic modeling of GCN, which forms a self-consistent regression for graph modeling and supervise GCN to learn more personalized attribute relations; 3. it fuses and supplements the hierarchical visual-semantic features refined by graph modeling into visual embedding. Our method outperforms state-of-the-art approaches on multiple representative ZSL datasets: AwA2, CUB, and SUN by promoting the semantic linkage modelling of visual features.

Food recognition plays a much critical role in various health-care applications. However, it poses many challenges to current approaches due to the diverse appearances of food dishes and the non-uniform composition of ingredients for the foods in the same category. Current methods primarily focus on the appearance of foods without considering their semantic information, easily finding the wrong attention areas of food images. Second, these methods lack the dynamic weighting of multiple semantic features in the modeling process. Thus this paper proposes a novel Multi-View Attention Network within the multi-task learning framework that incorporates multiple semantic features into the food recognition task from both ingredient recognition and recipe modeling. It also utilizes the multi-view attention mechanism to automatically adjust the weights of different semantic features and enables different tasks to interact with each other so as to obtain a more comprehensive feature representation. The experiments conducted on both ChineseFoodNet and VIREO Food-172 benchmark databases validate the proposed method with the obvious improvement of the performance and the lower parameter size.