Zelin Zang
Publications
BioM-JEPA: joint-embedding prediction of graph-connected gene blocks in single cells
Single-cell transcriptomes are sparse observations of coordinated biological programmes, yet most self-supervised models learn by reconstructing individual genes. Here we present BioM-JEPA, a joint-embedding predictive architecture that instead predicts aggregate representations of graph-connected gene blocks defined by protein-association and corpus-derived coexpression evidence. A student network infers each target-block representation from the remaining genes in a cell, while a slowly updated teacher supplies the corresponding target from the full observed gene set. Under the reported extraction procedure, block-level prediction produced embeddings with higher effective rank and weaker association with detected-gene depth in the tested diagnostics than token-prediction, random-block and reconstruction controls. Across CellBench tasks, frozen BioM-JEPA embeddings retained expression, pathway and neighbourhood information and achieved the lowest aggregate perturbation-response error among the evaluated models. Representation diagnostics were also consistent with canonical pancreatic programmes and compositional relationships between genetic perturbations. Linear attention avoids constructing a quadratic gene-by-gene attention matrix; in a matched one-epoch hPancreas experiment at batch size 8, BioM-JEPA provided 5.75-fold higher fine-tuning throughput and 3.76-fold higher held-out embedding throughput than scFoundation. Together, these results support graph-connected gene blocks as useful prediction units for JEPA-style representation learning in single-cell biology.
Revisiting Cross-Attention Mechanisms: Leveraging Beneficial Noise for Domain-Adaptive Learning
Unsupervised Domain Adaptation (UDA) seeks to transfer knowledge from a labeled source domain to an unlabeled target domain but often suffers from severe domain and scale gaps that degrade performance. Existing cross-attention-based transformers can align features across domains, yet they struggle to preserve content semantics under large appearance and scale variations. To explicitly address these challenges, we introduce the concept of beneficial noise, which regularizes cross-attention by injecting controlled perturbations, encouraging the model to ignore style distractions and focus on content. We propose the Domain-Adaptive Cross-Scale Matching (DACSM) framework, which consists of a Domain-Adaptive Transformer (DAT) for disentangling domain-shared content from domain-specific style, and a Cross-Scale Matching (CSM) module that adaptively aligns features across multiple resolutions. DAT incorporates beneficial noise into cross-attention, enabling progressive domain translation with enhanced robustness, yielding content-consistent and style-invariant representations. Meanwhile, CSM ensures semantic consistency under scale changes. Extensive experiments on VisDA-2017, Office-Home, and DomainNet demonstrate that DACSM achieves state-of-the-art performance, with up to +2.3% improvement over CDTrans on VisDA-2017. Notably, DACSM achieves a +5.9% gain on the challenging "truck" class of VisDA, evidencing the strength of beneficial noise in handling scale discrepancies. These results highlight the effectiveness of combining domain translation, beneficial-noise-enhanced attention, and scale-aware alignment for robust cross-domain representation learning.