Junhui Wu

Juntong Wu, Zijing Liu, He Cao et al.

In recent years, protein-text models have gained significant attention for their potential in protein generation and understanding. Current approaches focus on integrating protein-related knowledge into large language models through continued pretraining and multi-modal alignment, enabling simultaneous comprehension of textual descriptions and protein sequences. Through a thorough analysis of existing model architectures and text-based protein understanding benchmarks, we identify significant data leakage issues present in current benchmarks. Moreover, conventional metrics derived from natural language processing fail to accurately assess the model's performance in this domain. To address these limitations, we reorganize existing datasets and introduce a novel evaluation framework based on biological entities. Motivated by our observation, we propose a retrieval-enhanced method, which significantly outperforms fine-tuned LLMs for protein-to-text generation and shows accuracy and efficiency in training-free scenarios. Our code and data can be seen at https://github.com/IDEA-XL/RAPM.

Yifei Liu, Juntong Wu, Yang Liu et al.

In retrieval augmented generation (RAG) and agentic LLM serving, prompts are assembled from independent segments into long contexts, making the prefill stage dominate the per-request computation cost. To this cost, two directions have emerged in parallel: position-independent caching (PIC) admits KV reuse for non-contiguous segments shared across different requests, while hybrid-attention models reduce computation complexity by replacing most full-attention layers with linear attention. However, they cannot coexist: applying PIC to hybrid-attention models breaks down because per-token KV-cache reuse primitives do not transfer to the per-request recurrent state. In this work, we present Hypic, the first serving system for hybrid-attention LLMs with position-independent caching. For linear-attention layers, we identify the segment-cumulative transition operator as the missing algebraic primitive, and cache it alongside each segment's zero-start end-state, enabling near-exact and constant-time state composition of independently cached segments. For the remaining full-attention layers, existing PIC methods also fail as linear layers do not expose the per-token hidden states for selective recomputation. We show that the most significant attention deviation concentrates at segment boundaries, so recomputing only a small seam window at each boundary suffices to restore cross-segment lookback. Finally, Hypic exploits segment-level self-containment to parallelize cache-miss prefill across instances, turning long cold requests -- a major tail-latency contributor under both prefix caching and prior PIC -- into an accelerable workload. Evaluated across four hybrid-attention models and five workloads, Hypic reduces time-to-first-token (TTFT) by 2.45x on average and improves peak throughput by up to 2.0x over existing systems, while staying within 3.3 points of full-recompute accuracy.