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Phythesis: Physics-Guided Evolutionary Scene Synthesis for Energy-Efficient Data Center Design via LLMs

arXiv:2512.10611v1 Announce Type: new Abstract: Data center (DC) infrastructure serves as the backbone to support the escalating demand for computing capacity. Traditional design methodologies that blend human expertise with specialized simulation tools scale poorly with the increasing system complexity. Recent studies adopt generative artificial intelligence to design plausible human-centric indoor layouts. However, they do not consider the underlying physics, making them unsuitable for the DC design that sets quantifiable operational objectives and strict physical constraints. To bridge the gap, we propose Phythesis, a novel framework that synergizes large language models (LLMs) and physics-guided evolutionary optimization to automate simulation-ready (SimReady) scene synthesis for energy-efficient DC design. Phythesis employs an iterative bi-level optimization architecture, where (i) the LLM-driven optimization level generates physically plausible three-dimensional layouts and self-criticizes them to refine the scene topology, and (ii) the physics-informed optimization level identifies the optimal asset parameters and selects the best asset combination. Experiments on three generation scales show that Phythesis achieves 57.3% generation success rate increase and 11.5% power usage effectiveness (PUE) improvement, compared with the vanilla LLM-based solution.

Single-cell multi-omics analysis reveals cancer regulatory elements of transcriptional programs and clinical implications

Cell Death Dis. 2025 Oct 21;16(1):746. doi: 10.1038/s41419-025-08060-7.

ABSTRACT

The regulatory mechanisms governing transcriptional programs in the cancer genome remain elusive, particularly those concerning cell-type specificity. We carefully curated single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) and single-cell RNA sequencing (scRNA-seq) data from eight distinct carcinoma tissues, including breast, skin, colon, endometrium, lung, ovary, liver, and kidney. Using single-cell multi-omics analysis, we identified extensive open chromatin regions and constructed peak-gene link networks, which can reveal distinct cancer gene regulation and genetic risks. We further explored conserved epigenetic regulation across cell types within cancer and elucidated their functional implications. Moreover, we identified cell-type-associated transcription factors (TFs) that regulate key cellular functions, such as the TEAD family of TFs, which widely control cancer-related signaling pathways in tumor cells. In colon cancer, we further identified tumor-specific TFs that are more highly activated in tumor cells than in normal epithelial cells, including CEBPG, LEF1, SOX4, TCF7, and TEAD4, which are pivotal in driving malignant transcriptional programs and represent potential therapeutic targets, as corroborated by single-cell sequencing data from multiple sources and in vitro experiments. Our findings provide a comprehensive understanding of the regulatory dynamics underlying carcinomas and offer valuable insights into potential therapeutic interventions.

PMID:41120274 | PMC:PMC12541060 | DOI:10.1038/s41419-025-08060-7

Epigenetically regulated gene expression profiles decipher four molecular subtypes with prognostic and therapeutic implications in gastric cancer

Gastric cancer (GC) is one of the most common malignant tumors of the digestive tract which seriously endangers the health of human beings worldwide. Transcriptomic deregulation by epigenetic mechanisms plays ...
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