Yuhua Zheng
Publications
In Search of Lost DNA Sequence Pretraining
DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have overwhelmingly emphasized pretraining scale and custom downstream evaluation datasets, while neglecting some essential components of the pretraining paradigm. In this paper, we reveal three critical yet heretofore overlooked problems in DNA pretraining: inappropriate downstream datasets, inherent flaws in the neighbor-masking strategy, and the lack of detailed discussion on vocabulary. Therefore, we undertake comprehensive investigations and propose principled guidelines, including selection criteria for evaluation datasets, guiding task design, and in-depth vocabulary analysis. Extensive experiments validate the significance of our identified problems and support the rationale behind our recommendations. Finally, we introduce a standardized testbed that enables reproducible and rigorous benchmarking of DNA pretraining methods to advance the development of genomic foundation models.
Spatial Transcriptomics as Images for Large-Scale Pretraining
Spatial Transcriptomics (ST) profiles thousands of gene expression values at discrete spots with precise coordinates on tissue sections, preserving spatial context essential for clinical and pathological studies. With rising sequencing throughput and advancing platforms, the expanding data volumes motivate large-scale ST pretraining. However, the fundamental unit for pretraining, i.e., what constitutes a single training sample, remains ill-posed. Existing choices fall into two camps: (1) treating each spot as an independent sample, which discards spatial dependencies and collapses ST into single-cell transcriptomics; and (2) treating an entire slide as a single sample, which produces prohibitively large inputs and drastically fewer training examples, undermining effective pretraining. To address this gap, we propose treating spatial transcriptomics as croppable images. Specifically, we define a multi-channel image representation with fixed spatial size by cropping patches from raw slides, thereby preserving spatial context while substantially increasing the number of training samples. Along the channel dimension, we define gene subset selection rules to control input dimensionality and improve pretraining stability. Extensive experiments show that the proposed image-like dataset construction for ST pretraining consistently improves downstream performance, outperforming conventional pretraining schemes. Ablation studies verify that both spatial patching and channel design are necessary, establishing a unified, practical paradigm for organizing ST data and enabling large-scale pretraining.
MobileKernelBench: Can LLMs Write Efficient Kernels for Mobile Devices?
Large language models (LLMs) have demonstrated remarkable capabilities in code generation, yet their potential for generating kernels specifically for mobile de- vices remains largely unexplored. In this work, we extend the scope of automated kernel generation to the mobile domain to investigate the central question: Can LLMs write efficient kernels for mobile devices? To enable systematic investigation, we introduce MobileKernelBench, a comprehensive evaluation framework comprising a benchmark prioritizing operator diversity and cross-framework interoperability, coupled with an automated pipeline that bridges the host-device gap for on-device verification. Leveraging this framework, we conduct extensive evaluation on the CPU backend of Mobile Neural Network (MNN), revealing that current LLMs struggle with the engineering complexity and data scarcity inher-ent to mobile frameworks; standard models and even fine-tuned variants exhibit high compilation failure rates (over 54%) and negligible performance gains due to hallucinations and a lack of domain-specific grounding. To overcome these limitations, we propose the Mobile K ernel A gent (MoKA), a multi-agent system equipped with repository-aware reasoning and a plan-and-execute paradigm.Validated on MobileKernelBench, MoKA achieves state-of-the-art performance, boosting compilation success to 93.7% and enabling 27.4% of generated kernelsto deliver measurable speedups over native libraries.