Ke Yuan

Adalberto Claudio Quiros, Nicolas Coudray, Anna Yeaton et al.

Definitive cancer diagnosis and management depend upon the extraction of information from microscopy images by pathologists. These images contain complex information requiring time-consuming expert human interpretation that is prone to human bias. Supervised deep learning approaches have proven powerful for classification tasks, but they are inherently limited by the cost and quality of annotations used for training these models. To address this limitation of supervised methods, we developed Histomorphological Phenotype Learning (HPL), a fully blue{self-}supervised methodology that requires no expert labels or annotations and operates via the automatic discovery of discriminatory image features in small image tiles. Tiles are grouped into morphologically similar clusters which constitute a library of histomorphological phenotypes, revealing trajectories from benign to malignant tissue via inflammatory and reactive phenotypes. These clusters have distinct features which can be identified using orthogonal methods, linking histologic, molecular and clinical phenotypes. Applied to lung cancer tissues, we show that they align closely with patient survival, with histopathologically recognised tumor types and growth patterns, and with transcriptomic measures of immunophenotype. We then demonstrate that these properties are maintained in a multi-cancer study. These results show the clusters represent recurrent host responses and modes of tumor growth emerging under natural selection. Code, pre-trained models, learned embeddings, and documentation are available to the community at https://github.com/AdalbertoCq/Histomorphological-Phenotype-Learning

Zhengqi Xu, Ke Yuan, Huiqiong Wang et al.

Recently, model merging techniques have surfaced as a solution to combine multiple single-talent models into a single multi-talent model. However, previous endeavors in this field have either necessitated additional training or fine-tuning processes, or require that the models possess the same pre-trained initialization. In this work, we identify a common drawback in prior works w.r.t. the inconsistency of unit similarity in the weight space and the activation space. To address this inconsistency, we propose an innovative model merging framework, coined as merging under dual-space constraints (MuDSC). Specifically, instead of solely maximizing the objective of a single space, we advocate for the exploration of permutation matrices situated in a region with a unified high similarity in the dual space, achieved through the linear combination of activation and weight similarity matrices. In order to enhance usability, we have also incorporated adaptations for group structure, including Multi-Head Attention and Group Normalization. Comprehensive experimental comparisons demonstrate that MuDSC can significantly boost the performance of merged models with various task combinations and architectures. Furthermore, the visualization of the merged model within the multi-task loss landscape reveals that MuDSC enables the merged model to reside in the overlapping segment, featuring a unified lower loss for each task. Our code is publicly available at https://github.com/zju-vipa/training_free_model_merging.

Lucas Farndale, Robert Insall, Ke Yuan

Medical imaging technologies are generating increasingly large amounts of high-quality, information-dense data. Despite the progress, practical use of advanced imaging technologies for research and diagnosis remains limited by cost and availability, so information-sparse data such as H&E stains are relied on in practice. The study of diseased tissue requires methods which can leverage these information-dense data to extract more value from routine, information-sparse data. Using self-supervised deep learning, we demonstrate that it is possible to distil knowledge during training from information-dense data into models which only require information-sparse data for inference. This improves downstream classification accuracy on information-sparse data, making it comparable with the fully-supervised baseline. We find substantial effects on the learned representations, and this training process identifies subtle features which otherwise go undetected. This approach enables the design of models which require only routine images, but contain insights from state-of-the-art data, allowing better use of the available resources.