Rahi Navelkar, Andrea Cosolo, Iago Maceda Porto, Bogdan Bintu, Yubao Cheng, Vincent Gardeux, Silvia Gutnik, Taihei Fujimori 等 40 位作者
In recent years, multiplexed Fluorescence In Situ Hybridization (FISH) or FISH-omics methods have rapidly expanded, enabling the quantification of chromatin organization in single cells, often in conjunction with measurements of RNAs and proteins. These approaches have deepened our understanding of how 3D chromosome architecture relates to transcriptional activity and cell states in health and disease. Despite these advances, results from Chromatin Tracing FISH-omics experiments remain challenging to share, reuse, and analyze due to the absence of standardized data exchange specifications. Building on the release of microscopy metadata standards, we introduce the FISH Omics Format-Chromatin Tracing (FOF-CT), a community-developed standard for processed results from diverse imaging modalities. We describe the FOF-CT file format and present a curated collection of datasets deposited in the 4D Nucleome Data Portal and the OME Image Data Resource (IDR). We also highlight their potential for reuse, integration, and modeling by outlining example analysis pipelines and illustrating biological insights enabled by standardized, FAIR-compliant Chromatin Tracing datasets. FOF-CT natively represents both ball-and-stick and volumetric Chromatin Tracing data, unifying the two modalities within a single, modular table-based architecture (FOF-bas-CT and FOF-vol-CT, respectively).
Md Zubair, Hao Zheng, Grayson W. Armstrong, Lucy Q. Shen, Gabriela Wilson, Yu Tian, Xingquan Zhu, Min Shi
Medical decision systems increasingly rely on data from multiple sources to ensure reliable and unbiased diagnosis. However, existing multimodal learning models fail to achieve this goal because they often overlook two critical challenges. First, various data modalities may learn unevenly, thereby converging to a model biased towards certain modalities. Second, the model may emphasize learning on certain demographic groups causing unfair performances. The two aspects can influence each other, as different data modalities may favor respective groups during optimization, leading to both imbalanced and unfair multimodal learning. This paper proposes a novel approach called MultiFair for multimodal medical classification, which addresses these challenges with a dual-level gradient modulation process. MultiFair dynamically modulates training gradients regarding the optimization direction and magnitude at both data modality and group levels. We evaluate MultiFair on three real-world medical classification datasets with diverse demographic attributes,including multiclass classification and missing-modality settings. Experimental results demonstrate its effectiveness.