Mingyu Tsoi

Wenxuan Huang, Mingyu Tsoi, Yanhao Huang et al.

Single-cell perturbation studies face dual heterogeneity bottlenecks: (i) semantic heterogeneity--identical biological concepts encoded under incompatible metadata schemas across datasets; and (ii) statistical heterogeneity--distribution shifts from biological variation demanding dataset-specific inductive biases. We propose HarmonyCell, an end-to-end agent framework resolving each challenge through a dedicated mechanism: an LLM-driven Semantic Unifier autonomously maps disparate metadata into a canonical interface without manual intervention; and an adaptive Monte Carlo Tree Search engine operates over a hierarchical action space to synthesize architectures with optimal statistical inductive biases for distribution shifts. Evaluated across diverse perturbation tasks under both semantic and distribution shifts, HarmonyCell achieves a 95% valid execution rate on heterogeneous input datasets (versus 0% for general agents) while matching or even exceeding expert-designed baselines in rigorous out-of-distribution evaluations. This dual-track orchestration enables scalable automatic virtual cell modeling without dataset-specific engineering.

Xue Xia, Chengkai Yao, Mingyu Tsoi et al.

Systematic ablations are essential to attribute performance gains in AI Virtual Cells, yet they are rarely performed because biological repositories are under-standardized and tightly coupled to domain-specific data and formats. While recent coding agents can translate ideas into implementations, they typically stop at producing code and lack a verifier that can reproduce strong baselines and rigorously test which components truly matter. We introduce AblateCell, a reproduce-then-ablate agent for virtual cell repositories that closes this verification gap. AblateCell first reproduces reported baselines end-to-end by auto-configuring environments, resolving dependency and data issues, and rerunning official evaluations while emitting verifiable artifacts. It then conducts closed-loop ablation by generating a graph of isolated repository mutations and adaptively selecting experiments under a reward that trades off performance impact and execution cost. Evaluated on three single-cell perturbation prediction repositories (CPA, GEARS, BioLORD), AblateCell achieves 88.9% (+29.9% to human expert) end-to-end workflow success and 93.3% (+53.3% to heuristic) accuracy in recovering ground-truth critical components. These results enable scalable, repository-grounded verification and attribution directly on biological codebases.

Runxi Huang, Mingxuan Yu, Mingyu Tsoi et al.

Real-time multimodal inference on resource-constrained edge devices is essential for applications such as autonomous driving, human-computer interaction, and mobile health. However, prior work often overlooks the tight coupling between sensing dynamics and model execution, as well as the complex inter-modality dependencies. In this paper, we propose MMEdge, an new on-device multi-modal inference framework based on pipelined sensing and encoding. Instead of waiting for complete sensor inputs, MMEdge decomposes the entire inference process into a sequence of fine-grained sensing and encoding units, allowing computation to proceed incrementally as data arrive. MMEdge also introduces a lightweight but effective temporal aggregation module that captures rich temporal dynamics across different pipelined units to maintain accuracy performance. Such pipelined design also opens up opportunities for fine-grained cross-modal optimization and early decision-making during inference. To further enhance system performance under resource variability and input data complexity, MMEdge incorporates an adaptive multimodal configuration optimizer that dynamically selects optimal sensing and model configurations for each modality under latency constraints, and a cross-modal speculative skipping mechanism that bypasses future units of slower modalities when early predictions reach sufficient confidence. We evaluate MMEdge using two public multimodal datasets and deploy it on a real-world unmanned aerial vehicle (UAV)-based multimodal testbed. The results show that MMEdge significantly reduces end-to-end latency while maintaining high task accuracy across various system and data dynamics.