在空间转录学数据上的基准绘图方法
bioRxiv : the preprint server for biology
|September 5, 2025
概括
高通量空间转录学 (ST) 的智能子采样或草图可以引入偏差. 空间平滑的杆分数提供了一个平衡的方法,保留组织结构并捕获罕见的细胞状态以进行公正的分析.
科学领域:
- 计算生物学
- 基因组学
- 生物信息学
背景情况:
- 高通量空间转录学 (ST) 产生了大量的数据集,为分析带来了计算挑战.
- 目前的子采样方法 (草图) 往往优先考虑基因表达,忽视物理位置并引入空间偏差.
- 现有的方法可能会通过过多采样高度变化的区域和不足采样均区域来扭曲组织结构.
研究的目的:
- 系统地对现有的空间转录学绘制方法进行比较.
- 评估不同数据表示 (PCA嵌入,空间坐标,光滑嵌入) 对采样准确性的影响.
- 开发和验证一种新的草图方法,以平衡转录组表示与空间完整性.
主要方法:
- 在各种ST数据集 (老鼠卵巢,MERFISH大脑,人类乳腺癌,肺部) 和模拟中进行统一采样,杆评分采样,Geosketch和scSampler的基准测试.
- 输入表示包括PCA嵌入,空间坐标和空间光滑嵌入.
- 从空间平滑的随机SVD基础上使用杆分数的空间意识方法的开发.
主要成果:
- 只有表达式的草图可以捕捉到整体异质性,但会扭曲组织结构.
- 只有坐标采样保留了组织覆盖面,但错过了转录极端.
- 在维护组织覆盖,恢复罕见细胞状态和避免边缘效应方面,空间平滑的杆得分表现优异,在多个指标 (豪斯多夫距离,ARI,PCA负载漂移,MSE) 上表现优于替代品.
结论:
- 标准的ST绘图方法容易产生空间偏差.
- 一种使用平滑杆分数的新,空间意识的草图方法有效地平衡了转录和空间信息.
- 这种方法能够快速,公正地分析大规模的空间转录组数据,同时保持细胞异质性和组织结构.
相关概念视频
Vector Algebra: Graphical Method
13.7K
Vectors can be multiplied by scalars, added to other vectors, or subtracted from other vectors. The vector sum of two (or more) vectors is called the resultant vector or, for short, the resultant.
We use the laws of geometry to construct resultant vectors, followed by trigonometry to find vector magnitudes and directions. For a geometric construction of the sum of two vectors in a plane, we follow the parallelogram rule. Suppose two vectors are at arbitrary positions. Translate either one of...
We use the laws of geometry to construct resultant vectors, followed by trigonometry to find vector magnitudes and directions. For a geometric construction of the sum of two vectors in a plane, we follow the parallelogram rule. Suppose two vectors are at arbitrary positions. Translate either one of...
13.7K
Relative Velocity in Two Dimensions
7.0K
Relative velocity is the velocity of an object as observed from a particular reference frame, or the velocity of one reference frame with respect to another reference frame. The concept of relative velocity can be used to describe motion in two dimensions. Consider a particle P and two reference frames S and S′. The position of the origin of S′ as measured in S is , the position of P as measured in S′ is , and the position of P as measured in S is , which can be evaluated by...
7.0K
Relative Motion Analysis using Rotating Axes
1.0K
Consider a component AB undergoing a linear motion. Along with a linear motion, point B also rotates around point A. To comprehend this complex movement, position vectors for both points A and B are established using a stationary reference frame.
However, to express the relative position of point B relative to point A, an additional frame of reference, denoted as x'y', is necessary. This additional frame not only translates but also rotates relative to the fixed frame, making it...
However, to express the relative position of point B relative to point A, an additional frame of reference, denoted as x'y', is necessary. This additional frame not only translates but also rotates relative to the fixed frame, making it...
1.0K
Topographic Surveying and Contours
1.6K
Topographic surveying is critical for documenting the Earth's surface, focusing on capturing elevations, slopes, and natural and man-made features. It is essential in construction planning, water resource management, and land-use analysis. The primary outcome of such surveys is a topographic map, which uses contour lines to visually represent the shape and slope of the terrain, providing valuable insights into the landscape's characteristics.Contour lines are fundamental to understanding the...
1.6K
Plotting of Topographic Maps
855
Topographic maps represent the Earth's surface features using contour lines, which connect points of equal elevation to create a two-dimensional representation of three-dimensional terrain. Creating a topographic map requires a systematic approach.Begin by plotting a scaled grid and marking intersections corresponding to the survey's elevation data points. Assign elevation values at these intersections to build the base map. Next, determine contour levels using a consistent contour interval,...
855
Methods of Obtaining Topography
550
Topography involves measuring and mapping land elevations, natural features, and artificial structures to create accurate representations of the terrain. Topographic surveying relies on traditional and modern methods, each with distinct advantages and limitations.Traditional Surveying Methods:Transit stadia surveys and plane table surveys were widely used traditional surveying methods. These techniques relied on instruments like theodolites and stadia rods for measuring distances and angles,...
550


