scFusionTTT: Single-cell transcriptomics and proteomics fusion with Test-Time Training layers

Single-cell multi-omics (scMulti-omics) refers to the paired multimodal data, such as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), where the regulation of each cell was measured from different modalities, i.e. genes and proteins. scMulti-omics can reveal heterogeneity inside tumors and understand the distinct genetic properties of diverse cell types, which is crucial to targeted therapy. Currently, deep learning methods based on attention structures in the bioinformatics area face two challenges. The first challenge is the vast number of genes in a single cell. Traditional attention-based modules struggled to effectively leverage all gene information due to their limited capacity for long-context learning and high-complexity computing. The second challenge is that genes in the human genome are ordered and influence each other's expression. Most of the methods ignored this sequential information. The recently introduced Test-Time Training (TTT) layer is a novel sequence modeling approach, particularly suitable for handling long contexts like genomics data because TTT layer is a linear complexity sequence modeling structure and is better suited to data with sequential relationships. In this paper, we propose scFusionTTT, a novel method for Single-Cell multimodal omics Fusion with TTT-based masked autoencoder. Of note, we combine the order information of genes and proteins in the human genome with the TTT layer, fuse multimodal omics, and enhance unimodal omics analysis. Finally, the model employs a three-stage training strategy, which yielded the best performance across most metrics in four multimodal omics datasets and four unimodal omics datasets, demonstrating the superior performance of our model. The dataset and code will be available on https://github.com/DM0815/scFusionTTT.

Learn from Balance: Rectifying Knowledge Transfer for Long-Tailed Scenarios

Knowledge Distillation (KD) transfers knowledge from a large pre-trained teacher network to a compact and efficient student network, making it suitable for deployment on resource-limited media terminals. However, traditional KD methods require balanced data to ensure robust training, which is often unavailable in practical applications. In such scenarios, a few head categories occupy a substantial proportion of examples. This imbalance biases the trained teacher network towards the head categories, resulting in severe performance degradation on the less represented tail categories for both the teacher and student networks. In this paper, we propose a novel framework called Knowledge Rectification Distillation (KRDistill) to address the imbalanced knowledge inherited in the teacher network through the incorporation of the balanced category priors. Furthermore, we rectify the biased predictions produced by the teacher network, particularly focusing on the tail categories. Consequently, the teacher network can provide balanced and accurate knowledge to train a reliable student network. Intensive experiments conducted on various long-tailed datasets demonstrate that our KRDistill can effectively train reliable student networks in realistic scenarios of data imbalance.