Hyperspectral images (HSIs) offer great potential for computational pathology. But, limited by the lack of adequate annotated data and the high spectral redundancy of HSIs, traditional supervised learning techniques are usually bottlenecked. To exploit the structural properties of HSIs and learn representations with good transferability, we propose Separated Self-Supervised Spectral Regression (S4R). Concretely, we find one spectral band can be represented by a linear combination of the remaining bands. Regressing the distribution of the linear coefficients learns the inherent properties of HSIs and pathological information about the tissue. Besides, reconstructing the missing band, especially the tissue boundaries makes the model learn pathology details that are critical to downstream tasks. Coupling these two pretext tasks makes the self-supervised model understand spectral structures of HSIs w.r.t. pathological semantics and spatial micro details. Furthermore, we design two brand-new architectures to avoid the interference of extraneous signal based on S4R: S4R-CLS and S4R-SEG for HSI classification and segmentation, respectively. Two downstream tasks are incorporated into a unified framework, which first encodes different bands from HSIs via a depthwise separable encoder, and then selectively aggregates band features to generate final predictions. In S4R-SEG, we propose to pick the best matching bands with the guidance of a classification paradigm. Extensive experiments show S4R performs much better than competitors on both tasks. Theoretical analysis and clinical discussion also indicate the great potential for further medical applications. The code and pre-trained checkpoints are available at https://github.com/DeepMed-Lab-ECNU/S4R.

Histology analysis of the tumor micro-environment integrated with genomic assays is widely regarded as the cornerstone for cancer analysis and survival prediction. This paper jointly incorporates genomics and Whole Slide Images (WSIs), and focuses on addressing the primary challenges involved in multi-modality prognosis analysis: 1) the high-order relevance is difficult to be modeled from dimensional imbalanced gigapixel WSIs and tens of thousands of genetic sequences, and 2) the lack of medical expertise and clinical knowledge hampers the effectiveness of prognosis-oriented multi-modal fusion. Due to the nature of the prognosis task, statistical priors and clinical knowledge are essential factors to provide the likelihood of survival over time, which, however, has been under-studied. To this end, we propose a prognosis-oriented image-omics fusion framework, dubbed Clinical Stage Prompt induced Multimodal Prognosis (CiMP). Concretely, we leverage the capabilities of the advanced LLM to generate descriptions derived from structured clinical records and utilize the generated clinical staging prompts to inquire critical prognosis-related information from each modality intentionally. In addition, we propose a Group Multi-Head Self-Attention module to capture structured group-specific features within cohorts of genomic data. Experimental results on five TCGA datasets show the superiority of our proposed method, achieving state-of-the-art performance compared to previous multi-modal prognostic models. Furthermore, the clinical interpretability and discussion also highlight the immense potential for further medical applications. Our code will be released at https://github.com/DeepMed-Lab-ECNU/CiMP/.

Hyperspectral images (HSIs) offer great potential for computational pathology. However, limited by the spectral redundancy and the lack of spectral prior in popular 2D networks, previous HSI based techniques do not perform well. To address these problems, we propose to segment HSIs from a deformable perspective, which processes different spectral bands independently and fuses spatiospectral features of interest via deformable attention mechanisms. In addition, we propose Deformable Self-Supervised Spectral Regression (DF-S3R), which introduces two self-supervised pre-text tasks based on the low rank prior of HSIs enabling the network learning with spectrum-related features. During pre-training, DF-S3R learns both spectral structures and spatial morphology, and the jointly pre-trained architectures help alleviate the transfer risk to downstream fine-tuning. Compared to previous works, experiments show that our deformable architecture and pre-training method perform much better than other competitive methods on pathological semantic segmentation tasks, and the visualizations indicate that our method can trace the critical spectral characteristics from subtle spectral disparities. Code will be released at https://github.com/Ayakax/DFS3R.

RGB images and medical hyperspectral images (MHSIs) are two widely-used modalities in computational pathology. The former is cheap, easy and fast to obtain while lacking pathological information such as physiochemical state. The latter is an emerging modality which captures electromagnetic radiation matter interaction but suffers from problems such as high time cost and low spatial resolution. In this paper, we bring forward a unified dual-task multi-modality self-supervised learning (SSL) framework, called Uni-Dual, which takes the most use of both paired and unpaired RGB-MHSIs. Concretely, we design a unified SSL paradigm for RGB images and MHSIs. Two tasks are proposed: (1) a discrimination learning task which learns high-level semantics via mining the cross-correlation across unpaired RGB-MHSIs, (2) a reconstruction learning task which models low-level stochastic variations via furthering the interaction across RGB-MHSI pairs. Our Uni-Dual enjoys the following benefits: (1) A unified model which can be easily transferred to different downstream tasks on various modality combinations. (2) We consider multi-constituent and structured information learning from MHSIs and RGB images for low-cost high-precision clinical purposes. Experiments conducted on various downstream tasks with different modalities show the proposed Uni-Dual substantially outperforms other competitive SSL methods.