SurvConvMixer:基于ConvMixer的可靠和可解释的癌症生存预测,使用途径级基因表达图像
Shuo Wang1,2, Yuanning Liu3,4, Hao Zhang3,4
1College of Computer Science and Technology, Jilin University, Qianjin Street, Changchun, 130012, Jilin, China. shuowang0114@163.com.
BMC bioinformatics
|March 28, 2024
概括
我们开发了SurvConvMixer,这是用于癌症存活率预测的强大且可解释的模型. 这种方法使用基因表达数据来预测患者的结果,增强精准医学策略.
科学领域:
- 计算生物学是一种计算生物学.
- 生物信息学是一种生物信息学.
- 癌症研究 癌症研究
背景情况:
- 癌症仍然是全球主要的死亡原因,需要在个性化医学的患者生存分析和预测方面取得进展.
- 稳定性和可解释性对于生存预测模型至关重要,确保可靠的知识获取和对模型决策的透明见解.
研究的目的:
- 推出SurvConvMixer,这是一种新型模型,旨在对短期,中期和长期癌症患者的生存预测进行可靠和可解释的预测.
- 为了利用定制的基因表达图像和ConvMixer架构进行路径特定的表示学习.
主要方法:
- 使用ConvMixer来从特定路径的基因表达图像中学习表示.
- 通过对外部,未经训练的数据集进行验证来评估模型的稳定性.
- 采用梯度加权类激活映射 (Grad-Cam) 来实现模型可解释性,生成路径级激活热图.
- 进行了威尔科克森等级和测试,以确定影响模型预测的统计学上显著途径.
主要成果:
- SurvConvMixer在预测肺腺癌,肺状细胞癌和皮肤皮肤黑色素瘤的短期,中期和长期整体存活率方面表现显著.
- 外部验证证实了该模型的稳定性和对未见的数据集的概括性.
- 格拉德-卡姆分析与统计测试相结合,确定了对模型预测至关重要的关键生存相关途径.
结论:
- SurvConvMixer为癌症生存预测提供了强大的和可解释的解决方案,显著推进了精准医学应用.
- 该模型能够概括和识别关键的生物通路,这突显了其临床实用性的潜力.
- 对已识别的途径进行进一步的研究可以为癌症进展和生存提供更深入的生物学见解.
相关概念视频
01:21Cancer Survival Analysis
345
Cancer survival analysis focuses on quantifying and interpreting the time from a key starting point, such as diagnosis or the initiation of treatment, to a specific endpoint, such as remission or death. This analysis provides critical insights into treatment effectiveness and factors that influence patient outcomes, helping to shape clinical decisions and guide prognostic evaluations. A cornerstone of oncology research, survival analysis tackles the challenges of skewed, non-normally...
345
01:05Cancer-Critical Genes II: Tumor Suppressor Genes
7.4K
Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
7.4K
02:43Mouse Models of Cancer Study
5.5K
Mice have long served as models for studying human biology and pathology because of their phylogenetic and physiological similarity with humans. They are also easy to maintain and breed in the laboratory, and hence, many inbred strains are now available for research. Studies on mice have contributed immeasurably to our understanding of cancer biology.
The development of transgenic, knockout, and knock-in mice has led to an exponential increase in their use as model organisms in research,...
The development of transgenic, knockout, and knock-in mice has led to an exponential increase in their use as model organisms in research,...
5.5K
02:53Adaptive Mechanisms in Cancer Cells
5.7K
Cancer cells accumulate genetic changes at an abnormally rapid rate due to the defects in the DNA repair mechanisms. From an evolutionary perspective, such genetic instability is advantageous for cancer development. Mutant cell lines accumulate a series of beneficial mutations that contribute to their progression into cancer.
Some of the advantages that cancer cells have on normal cells include - enhanced ability to divide without terminally differentiating, induce new blood vessel formation,...
Some of the advantages that cancer cells have on normal cells include - enhanced ability to divide without terminally differentiating, induce new blood vessel formation,...
5.7K
02:07Tumor Progression
6.3K
Tumor progression is a phenomenon where the pre-formed tumor acquires successive mutations to become clinically more aggressive and malignant. In the 1950s, Foulds first described the stepwise progression of cancer cells through successive stages.
Colon cancer is one of the best-documented examples of tumor progression. Early mutation in the APC gene in colon cells causes a small growth on the colon wall called a polyp. With time, this polyp grows into a benign, pre-cancerous tumor. Further...
Colon cancer is one of the best-documented examples of tumor progression. Early mutation in the APC gene in colon cells causes a small growth on the colon wall called a polyp. With time, this polyp grows into a benign, pre-cancerous tumor. Further...
6.3K
01:24Kaplan-Meier Approach
136
The Kaplan-Meier estimator is a non-parametric method used to estimate the survival function from time-to-event data. In medical research, it is frequently employed to measure the proportion of patients surviving for a certain period after treatment. This estimator is fundamental in analyzing time-to-event data, making it indispensable in clinical trials, epidemiological studies, and reliability engineering. By estimating survival probabilities, researchers can evaluate treatment effectiveness,...
136