Huirong Chai

Mansoor Ahmed, Huirong Chai, Haoxin Wang et al.

Antibodies neutralize foreign antigens by binding to specific surface regions called epitopes. Computational epitope prediction is critical for understanding immune recognition and guiding antibody engineering. However, existing methods face three fundamental challenges: antibody-aware models encode each chain independently and combine them only at a late stage, failing to capture co-dependent structural features that define binding interfaces, whereas severe class imbalance and scarcity of known antibody-antigen complexes render standard training objectives ineffective. We propose EpiFormer, a general encoder-decoder framework that addresses these challenges jointly. Our key design principle is interleaved cross-attention within GNN encoding layers, enabling bidirectional antigen-antibody information flow throughout representation learning rather than only at the output. This early-fusion principle is backbone-agnostic, providing consistent gains across GNN architectures from simple GCNs to equivariant models. We further show that sparsity-aware objectives are effective when paired with early-fusion architectures for the epitope prediction task. EpiFormer improves over the previous best method by over 40% in F1 score on standard benchmarks, demonstrating generalizability and cross-dataset transferability. Notably, EpiFormer discovers known biological principles as emergent behaviors of end-to-end training, where the learned cross-attention gates favor antigen-to-antibody information flow, consistent with the asymmetric roles of the two chains at the binding interface, and the model's preference for geometric over evolutionary features aligns with the established finding that epitope residues are not evolutionarily conserved. The source code is available at: https://github.com/mansoor181/epiformer.git

Haoxin Wang, Xiaolong Tu, Hongyu Ke et al.

Large Language Models (LLMs) are increasingly integrated into everyday applications, but their prevalent cloud-based deployment raises growing concerns around data privacy and long-term sustainability. Running LLMs locally on mobile and edge devices (on-device LLMs) offers the promise of enhanced privacy, reliability, and reduced communication costs. However, realizing this vision remains challenging due to substantial memory and compute demands, as well as limited visibility into performance-efficiency trade-offs on resource-constrained hardware. We propose lm-Meter, the first lightweight, online latency profiler tailored for on-device LLM inference. lm-Meter captures fine-grained, real-time latency at both phase (e.g., embedding, prefill, decode, softmax, sampling) and kernel levels without auxiliary devices. We implement lm-Meter on commercial mobile platforms and demonstrate its high profiling accuracy with minimal system overhead, e.g., only 2.58% throughput reduction in prefill and 0.99% in decode under the most constrained Powersave governor. Leveraging lm-Meter, we conduct comprehensive empirical studies revealing phase- and kernel-level bottlenecks in on-device LLM inference, quantifying accuracy-efficiency trade-offs, and identifying systematic optimization opportunities. lm-Meter provides unprecedented visibility into the runtime behavior of LLMs on constrained platforms, laying the foundation for informed optimization and accelerating the democratization of on-device LLM systems. Code and tutorials are available at https://github.com/amai-gsu/LM-Meter.