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  • βœ‡cs.AI, q-bio.NC updates on arXiv.org
  • Learning to Align Human Code Preferences Xin Yin Β· Chao Ni Β· Xiaohu Yang
    arXiv:2507.20109v2 Announce Type: replace-cross Abstract: Large Language Models (LLMs) have demonstrated remarkable potential in automating software development tasks. While recent advances leverage Supervised Fine-Tuning (SFT) and Direct Preference Optimization (DPO) to align models with human preferences, the optimal training strategy remains unclear across diverse code preference scenarios. This paper systematically investigates the roles of SFT and DPO in aligning LLMs with different code p
     

Learning to Align Human Code Preferences

9 December 2025 at 13:00
arXiv:2507.20109v2 Announce Type: replace-cross Abstract: Large Language Models (LLMs) have demonstrated remarkable potential in automating software development tasks. While recent advances leverage Supervised Fine-Tuning (SFT) and Direct Preference Optimization (DPO) to align models with human preferences, the optimal training strategy remains unclear across diverse code preference scenarios. This paper systematically investigates the roles of SFT and DPO in aligning LLMs with different code preferences. Through both theoretical analysis and empirical observation, we hypothesize that SFT excels in scenarios with objectively verifiable optimal solutions, while applying SFT followed by DPO (S&D) enables models to explore superior solutions in scenarios without objectively verifiable optimal solutions. Based on the analysis and experimental evidence, we propose Adaptive Preference Optimization (APO), a dynamic integration approach that adaptively amplifies preferred responses, suppresses dispreferred ones, and encourages exploration of potentially superior solutions during training. Extensive experiments across six representative code preference tasks validate our theoretical hypotheses and demonstrate that APO consistently matches or surpasses the performance of existing SFT and S&D strategies. Our work provides both theoretical foundations and practical guidance for selecting appropriate training strategies in different code preference alignment scenarios.

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

21 October 2025 at 18:00

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

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