RESUMEN

Single-cell multi-omics integration enables joint analysis at the single-cell level of resolution to provide more accurate understanding of complex biological systems, while spatial multi-omics integration is benefit to the exploration of cell spatial heterogeneity to facilitate more comprehensive downstream analyses. Existing methods are mainly designed for single-cell multi-omics data with little consideration of spatial information and still have room for performance improvement. A reliable multi-omics integration method designed for both single-cell and spatially resolved data is necessary and significant. We propose a multi-omics integration method based on dual-path graph attention auto-encoder (SSGATE). It can construct the neighborhood graphs based on single-cell expression profiles or spatial coordinates, enabling it to process single-cell data and utilize spatial information from spatially resolved data. It can also perform self-supervised learning for integration through the graph attention auto-encoders from two paths. SSGATE is applied to integration of transcriptomics and proteomics, including single-cell and spatially resolved data of various tissues from different sequencing technologies. SSGATE shows better performance and stronger robustness than competitive methods and facilitates downstream analysis.

Asunto(s)

Análisis de la Célula Individual , Análisis de la Célula Individual/métodos , Biología Computacional/métodos , Humanos , Proteómica/métodos , Algoritmos , Transcriptoma , Multiómica

RESUMEN

BACKGROUND: The emergence of high-resolved spatial transcriptomics (ST) has facilitated the research of novel methods to investigate biological development, organism growth, and other complex biological processes. However, high-resolved and whole transcriptomics ST datasets require customized imputation methods to improve the signal-to-noise ratio and the data quality. FINDINGS: We propose an efficient and adaptive Gaussian smoothing (EAGS) imputation method for high-resolved ST. The adaptive 2-factor smoothing of EAGS creates patterns based on the spatial and expression information of the cells, creates adaptive weights for the smoothing of cells in the same pattern, and then utilizes the weights to restore the gene expression profiles. We assessed the performance and efficiency of EAGS using simulated and high-resolved ST datasets of mouse brain and olfactory bulb. CONCLUSIONS: Compared with other competitive methods, EAGS shows higher clustering accuracy, better biological interpretations, and significantly reduced computational consumption.

Asunto(s)

Imagen por Resonancia Magnética , Transcriptoma , Animales , Ratones , Imagen por Resonancia Magnética/métodos , Perfilación de la Expresión Génica , Distribución Normal , Relación Señal-Ruido

RESUMEN

Multi-sensor data fusion plays an irreplaceable role in actual production and application. Dempster-Shafer theory (DST) is widely used in numerous fields of information modeling and information fusion due to the flexibility and effectiveness of processing uncertain information and dealing with uncertain information without prior probabilities. However, when highly contradictory evidence is combined, it may produce results that are inconsistent with human intuition. In order to solve this problem, a hybrid method for combining belief functions based on soft likelihood functions (SLFs) and ordered weighted averaging (OWA) operators is proposed. More specifically, a soft likelihood function based on OWA operators is used to provide the possibility to fuse uncertain information compatible with each other. It can characterize the degree to which the probability information of compatible propositions in the collected evidence is affected by unknown uncertain factors. This makes the results of using the Dempster's combination rule to fuse uncertain information from multiple sources more comprehensive and credible. Experimental results manifest that this method is reliable. Example and application show that this method has obvious advantages in solving the problem of conflict evidence fusion in multi-sensor. In particular, in target recognition, when three pieces of evidence are fused, the target recognition rate is 96.92%, etc.