arXiv subjects

Kerui Huang

Publications and source records attributed to Kerui Huang.

6 recordsLinked to original sources

arXiv2026

The Cathaya argyrophylla Genome Reveals the Evolutionary Trade-offs of a Living Fossil

Cathaya argyrophylla is an endangered paleoendemic gymnosperm characterized by restricted ecological adaptability and high pathogen susceptibility. To elucidate its genomic architecture and evolutionary history, a de novo chromosome-level genome assembly was constructed using PacBio High-Fidelity long reads and Hi-C scaffolding. The resulting 22.73 Gb assembly resolves into 12 pseudochromosomes, demonstrating genome gigantism driven primarily by a 72.92 percent repeat sequence content and extensive intron expansion. Phylogenomic analysis using single-copy orthologs identifies C. argyrophylla as a sister lineage to the Pinus clade, with an estimated divergence time of 102.8 million years ago. Analysis of gene family dynamics reveals significant expansions in pathways related to membrane lipid metabolism, transmembrane transport, and translation machinery, indicating specific molecular adaptations for cellular homeostasis in resource-limited environments. Conversely, the genome exhibits massive contractions in endogenous defense networks, including plant-pathogen interactions, brassinosteroid signaling, and DNA repair mechanisms. This distinct genomic reduction correlates directly with the slow growth rate and weak innate immunity observed in the species, while the expanded transmembrane transport networks suggest an obligate physiological reliance on symbiotic microbiomes for survival. Ultimately, this reference genome establishes a critical molecular resource for future conservation and breeding programs.

q-bio.GN↗

arXiv2026

Synonymous Codon Usage Bias Overrides Phylogeny to Reflect Convergent Frond Architecture in a Rapidly Radiating Fern Family Thelypteridaceae

Convergent evolution provides powerful evidence for natural selection, yet its molecular basis is typically sought in protein-coding amino acid substitutions. Whether adaptive pressures can drive the convergent evolution of synonymous codon usage bias (CUB) to override phylogenetic history remains a fundamental question. Here, we investigate this within the rapidly radiating fern family Thelypteridaceae by establishing a comparative framework that integrates chloroplast phylogenomics with dimensionality reduction of codon usage, morphological data, and divergence time estimation. Our results reveal that chloroplast CUB patterns are strikingly incongruent with the phylogeny of this family. Instead, they partition species into distinct clusters that strongly correlate with a convergently evolved morphological trait, lamina base architecture, a key adaptation whose radiation we date to the early Neogene. This convergent molecular signal is driven by a specific subset of photosynthesis-related genes (ndhJ, psaA, and psbD), which exhibit a high density of type-specific, third-position codon substitutions. These findings demonstrate that CUB can serve as a powerful, quantifiable indicator of adaptive history, revealing a cryptic layer of molecular convergence linked to the regulation of protein synthesis. Our work providing a new framework for uncovering adaptive histories obscured by complex evolutionary processes.

q-bio.PE↗

arXiv2025

Reasoning Efficiently Through Adaptive Chain-of-Thought Compression: A Self-Optimizing Framework

Chain-of-Thought (CoT) reasoning enhances Large Language Models (LLMs) by prompting intermediate steps, improving accuracy and robustness in arithmetic, logic, and commonsense tasks. However, this benefit comes with high computational costs: longer outputs increase latency, memory usage, and KV-cache demands. These issues are especially critical in software engineering tasks where concise and deterministic outputs are required. To investigate these trade-offs, we conduct an empirical study based on code generation benchmarks. The results reveal that longer CoT does not always help. Excessive reasoning often causes truncation, accuracy drops, and latency up to five times higher, with failed outputs consistently longer than successful ones. These findings challenge the assumption that longer reasoning is inherently better and highlight the need for adaptive CoT control. Motivated by this, we propose SEER (Self-Enhancing Efficient Reasoning), an adaptive framework that compresses CoT while preserving accuracy. SEER combines Best-of-N sampling with task-aware adaptive filtering, dynamically adjusting thresholds based on pre-inference outputs to reduce verbosity and computational overhead. We then evaluate SEER on three software engineering tasks and one math task. On average, SEER shortens CoT by 42.1%, improves accuracy by reducing truncation, and eliminates most infinite loops. These results demonstrate SEER as a practical method to make CoT-enhanced LLMs more efficient and robust, even under resource constraints.

cs.SE↗

arXiv2025

CREME: Robustness Enhancement of Code LLMs via Layer-Aware Model Editing

Large language models (LLMs) have demonstrated impressive capabilities in code generation, where the natural language prompt plays a crucial role in conveying user intent to the model. However, prior studies have shown that LLMs are highly sensitive to prompt perturbations. Minor modifications in wording, syntax, or formatting can significantly reduce the functional correctness of generated code. As perturbations frequently occur in real-world scenarios, improving the robustness of LLMs to prompt perturbations is essential for ensuring reliable performance in practical code generation. In this paper, we introduce CREME (Code Robustness Enhancement via Model Editing), a novel approach that enhances LLM robustness through targeted parameter updates. CREME first identifies robustness-sensitive layers by comparing hidden states between an original prompt and its perturbed variant. Then, it performs lightweight parameter editing at the identified layer to reduce performance degradation. We evaluate CREME on two widely used code generation benchmarks (HumanEval and MBPP) along with their perturbed counterparts. Experimental results show that CREME improves Pass@1 accuracy by 63% on perturbed prompts while maintaining stable performance on clean inputs, with accuracy deviations within 1%. Further analysis reveals that robustness-sensitive layers are primarily concentrated in the middle and deeper layers of the network, and their locations vary across different model architectures. These insights provide a valuable foundation for developing future robustness-oriented editing strategies.

cs.SE↗

arXiv2024

The Mitochondrial Genome of Cathaya argyrophylla Reaches 18.99 Mb: Analysis of Super-Large Mitochondrial Genomes in Pinaceae

Mitochondrial genomes in the Pinaceae family are notable for their large size and structural complexity. In this study, we sequenced and analyzed the mitochondrial genome of Cathaya argyrophylla, an endangered and endemic Pinaceae species, uncovering a genome size of 18.99 Mb, meaning the largest mitochondrial genome reported to date. To investigate the mechanisms behind this exceptional size, we conducted comparative analyses with other Pinaceae species possessing both large and small mitochondrial genomes, as well as with other gymnosperms. We focused on repeat sequences, transposable element activity, RNA editing events, chloroplast-derived sequence transfers (mtpts), and sequence homology with nuclear genomes. Our findings indicate that while Cathaya argyrophylla and other extremely large Pinaceae mitochondrial genomes contain substantial amounts of repeat sequences and show increased activity of LINEs and LTR retrotransposons, these factors alone do not fully account for the genome expansion. Notably, we observed a significant incorporation of chloroplast-derived sequences in Cathaya argyrophylla and other large mitochondrial genomes, suggesting that extensive plastid-to-mitochondrial DNA transfer may play a crucial role in genome enlargement. Additionally, large mitochondrial genomes exhibited distinct patterns of RNA editing and limited similarity with nuclear genomes compared to smaller genomes. These results suggest that the massive mitochondrial genomes in Pinaceae are likely the result of multiple contributing factors, including repeat sequences, transposon activity, and extensive plastid sequence incorporation. Our study enhances the understanding of mitochondrial genome evolution in plants and provides valuable genetic information for the conservation and study of Cathaya argyrophylla.

q-bio.GN↗

arXiv2023

Key Gene Mining in Transcriptional Regulation for Specific Biological Processes with Small Sample Sizes Using Multi-network pipeline Transformer

Gene mining is an important topic in the field of life sciences, but traditional machine learning methods cannot consider the regulatory relationships between genes. Deep learning methods perform poorly in small sample sizes. This study proposed a deep learning method, called TransGeneSelector, that can mine critical regulatory genes involved in certain life processes using a small-sample transcriptome dataset. The method combines a WGAN-GP data augmentation network, a sample filtering network, and a Transformer classifier network, which successfully classified the state (germinating or dry seeds) of Arabidopsis thaliana seed in a dataset of 79 samples, showing performance comparable to that of Random Forests. Further, through the use of SHapley Additive exPlanations method, TransGeneSelector successfully mined genes involved in seed germination. Through the construction of gene regulatory networks and the enrichment analysis of KEGG, as well as RT-qPCR quantitative analysis, it was confirmed that these genes are at a more upstream regulatory level than those Random Forests mined, and the top 11 genes that were uniquely mined by TransGeneSelector were found to be related to the KAI2 signaling pathway, which is of great regulatory importance for germination-related genes. This study provides a practical tool for life science researchers to mine key genes from transcriptome data.

q-bio.QM↗