MoME: Mixture of Multimodal Experts for Cancer Survival Prediction

Survival analysis, as a challenging task, requires integrating Whole Slide Images (WSIs) and genomic data for comprehensive decision-making. There are two main challenges in this task: significant heterogeneity and complex inter- and intra-modal interactions between the two modalities. Previous approaches utilize co-attention methods, which fuse features from both modalities only once after separate encoding. However, these approaches are insufficient for modeling the complex task due to the heterogeneous nature between the modalities. To address these issues, we propose a Biased Progressive Encoding (BPE) paradigm, performing encoding and fusion simultaneously. This paradigm uses one modality as a reference when encoding the other. It enables deep fusion of the modalities through multiple alternating iterations, progressively reducing the cross-modal disparities and facilitating complementary interactions. Besides modality heterogeneity, survival analysis involves various biomarkers from WSIs, genomics, and their combinations. The critical biomarkers may exist in different modalities under individual variations, necessitating flexible adaptation of the models to specific scenarios. Therefore, we further propose a Mixture of Multimodal Experts (MoME) layer to dynamically selects tailored experts in each stage of the BPE paradigm. Experts incorporate reference information from another modality to varying degrees, enabling a balanced or biased focus on different modalities during the encoding process. Extensive experimental results demonstrate the superior performance of our method on various datasets, including TCGA-BLCA, TCGA-UCEC and TCGA-LUAD. Codes are available at https://github.com/BearCleverProud/MoME.

Knowledge Transfer via Multi-Head Feature Adaptation for Whole Slide Image Classification

Transferring prior knowledge from a source domain to the same or similar target domain can greatly enhance the performance of models on the target domain. However, it is challenging to directly leverage the knowledge from the source domain due to task discrepancy and domain shift. To bridge the gaps between different tasks and domains, we propose a Multi-Head Feature Adaptation module, which projects features in the source feature space to a new space that is more similar to the target space. Knowledge transfer is particularly important in Whole Slide Image (WSI) classification since the number of WSIs in one dataset might be too small to achieve satisfactory performance. Therefore, WSI classification is an ideal testbed for our method, and we adapt multiple knowledge transfer methods for WSI classification. The experimental results show that models with knowledge transfer outperform models that are trained from scratch by a large margin regardless of the number of WSIs in the datasets, and our method achieves state-of-the-art performances among other knowledge transfer methods on multiple datasets, including TCGA-RCC, TCGA-NSCLC, and Camelyon16 datasets.

Diagnose Like a Pathologist: Transformer-Enabled Hierarchical Attention-Guided Multiple Instance Learning for Whole Slide Image Classification

Multiple Instance Learning (MIL) and transformers are increasingly popular in histopathology Whole Slide Image (WSI) classification. However, unlike human pathologists who selectively observe specific regions of histopathology tissues under different magnifications, most methods do not incorporate multiple resolutions of the WSIs, hierarchically and attentively, thereby leading to a loss of focus on the WSIs and information from other resolutions. To resolve this issue, we propose the Hierarchical Attention-Guided Multiple Instance Learning framework to fully exploit the WSIs, which can dynamically and attentively discover the discriminative regions across multiple resolutions of the WSIs. Within this framework, to further enhance the performance of the transformer and obtain a more holistic WSI (bag) representation, we propose an Integrated Attention Transformer, consisting of multiple Integrated Attention Modules, which is the combination of a transformer layer and an aggregation module that produces a bag representation based on every instance representation in that bag. The results of the experiments show that our method achieved state-of-the-art performances on multiple datasets, including Camelyon16, TCGA-RCC, TCGA-NSCLC, and our in-house IMGC dataset.

Embedding-Enhanced Giza++: Improving Alignment in Low- and High- Resource Scenarios Using Embedding Space Geometry

A popular natural language processing task decades ago, word alignment has been dominated until recently by GIZA++, a statistical method based on the 30-year-old IBM models. Though recent years have finally seen Giza++ performance bested, the new methods primarily rely on large machine translation models, massively multilingual language models, or supervision from Giza++ alignments itself. We introduce Embedding-Enhanced Giza++, and outperform Giza++ without any of the aforementioned factors. Taking advantage of monolingual embedding space geometry of the source and target language only, we exceed Giza++'s performance in every tested scenario for three languages. In the lowest-resource scenario of only 500 lines of bitext, we improve performance over Giza++ by 10.9 AER. Our method scales monotonically outperforming Giza++ for all tested scenarios between 500 and 1.9 million lines of bitext. Our code will be made publicly available.