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Abstract: The study presented in this paper evaluated gene expression profiles from The Cancer Genome Atlas (TCGA). To reduce complexity, we focused on genes in the cGAS–STING pathway, crucial for cytosolic DNA detection and immune response. The study analyzes three clinical variables: disease-specific survival (DSS), overall survival (OS), and tumor stage. To effectively utilize the high-dimensional gene expression data, we needed to find a way to project these data meaningfully. Since gene pathways can be represented as graphs, a novel method of presenting genomics data using graph data structure was employed, rather than the conventional tabular format. To leverage the gene expression data represented as graphs, we utilized a graph convolutional network (GCN) machine learning model in conjunction with the genetic algorithm optimization technique. This allowed for obtaining an optimal graph representation topology and capturing important activations within the pathway for each use case, enabling a more insightful analysis of the cGAS–STING pathway and its activations across different cancer types and clinical variables. To tackle the problem of unexplainable AI, graph visualization alongside the integrated gradients method was employed to explain the GCN model’s decision-making process, identifying key nodes (genes) in the cGAS–STING pathway. This approach revealed distinct molecular mechanisms, enhancing interpretability. This study demonstrates the potential of GCNs combined with explainable AI to analyze gene expression, providing insights into cancer progression. Further research with more data is needed to validate these findings.
Keywords: cGAS–STING, graph-convolutional-network, graphs, cancer, pan-cancer, machine learning, NGS
Published in DiRROS: 09.09.2025; Views: 634; Downloads: 341
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Abstract: This paper is an attempt to consider an alternative pluralist pantheism (Mary Jane Rubenstein) as the next step in the evolution of interpersonal, interspecies, and God–human–nature relationships and its possible realisation in (post-)Christian ecofeminism and its epistemology. It follows the methodology and epistemology of theological ecofeminism, which assumes that the oppression of women and the exploitation of nature stem from the same constellation of phenomena: patriarchal domination, dualistic anthropologies, and global hypercapitalism. Recognising that pantheism is a very complex phenomenon and should not be viewed as a single codified viewpoint, but rather as a diverse family of different doctrines, this paper understands pantheism primarily as the paradigm that asserts that everything is part of a divine unity consisting of an all-encompassing, manifested deity or God/Goddess. The paper first explains the pan-en-theistic turn in Christian ecofeminism as a tool for deconstructing the dominant Cartesian dualistic binaries and their symbolism and metanarratives, and as the first “safe” phase of transition from Christian anthropocentrism. From this standpoint, Grace M. Jantzen’s defense of pantheism as an alternative to transcendental theism is further explored as she argues that divinity is found “in” the physical and material world and nowhere else. The paper then moves to the second phase, proposed in the final part of the paper, on the possibility of the theoretical adoption of pluralist pantheism in (post-)Christian ecofeminist ecotheology. Here, the question of the “fear and horror of pantheism” in Western thought is discussed.
Keywords: ecofeminist theology, nature, pan-en-theism, pluralistic pantheism
Published in DiRROS: 05.01.2024; Views: 1693; Downloads: 1118
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