arXiv subjects

Zhonghui Zhang

Publications and source records attributed to Zhonghui Zhang.

7 recordsLinked to original sources

arXiv2026

GATHER: Convergence-Centric Hyper-Entity Retrieval for Zero-Shot Cell-Type Annotation

Zero-shot single-cell cell-type annotation aims to determine a cell's type from a given set of expressed genes without any training. Existing knowledge-graph-based RAG approaches retrieve evidence by expanding from source entities and relying on iterative LLM reasoning. However, in this setting each query contains tens to hundreds of genes, where no single gene is decisive and the label emerges only from their collective co-occurrence. Such hyper-entity queries fundamentally challenge local, entity-wise exploration strategies, which reason from individual genes, leading to poor scalability and substantial LLM cost. We propose GATHER (Graph-Aware Traversal with Hyper-Entity Retrieval), a convergence-centric retriever tailored to hyper-entity queries. It performs global multi-source graph traversal and identifies topological convergence points -- nodes jointly reachable from many input genes. These convergence nodes act as high-information hyper-entities that capture entity synergy. By incorporating node- and path-importance scoring, GATHER selects informative evidence entirely without LLM involvement during retrieval. Instantiated on a self-constructed cell-centric biological knowledge graph (VCKG), GATHER outperforms strong KG-RAG baselines (ToG, ToG-2, RoG, PoG) on two datasets (Immune and Lung), achieving the highest exact-match accuracy (27.45% and 59.64%) with only a single LLM call per sample, compared to 2--61 calls for KG-RAG baselines. Our results demonstrate that convergence nodes compress multi-entity signals into compact, high-information evidence that conveys more per item than multi-hop paths, providing an efficient global alternative to local entity-wise reasoning.

cs.CL↗

arXiv2026

SC-Arena: A Natural Language Benchmark for Single-Cell Reasoning with Knowledge-Augmented Evaluation

Large language models (LLMs) are increasingly applied in scientific research, offering new capabilities for knowledge discovery and reasoning. In single-cell biology, however, evaluation practices for both general and specialized LLMs remain inadequate: existing benchmarks are fragmented across tasks, adopt formats such as multiple-choice classification that diverge from real-world usage, and rely on metrics lacking interpretability and biological grounding. We present SC-ARENA, a natural language evaluation framework tailored to single-cell foundation models. SC-ARENA formalizes a virtual cell abstraction that unifies evaluation targets by representing both intrinsic attributes and gene-level interactions. Within this paradigm, we define five natural language tasks (cell type annotation, captioning, generation, perturbation prediction, and scientific QA) that probe core reasoning capabilities in cellular biology. To overcome the limitations of brittle string-matching metrics, we introduce knowledge-augmented evaluation, which incorporates external ontologies, marker databases, and scientific literature to support biologically faithful and interpretable judgments. Experiments and analysis across both general-purpose and domain-specialized LLMs demonstrate that (i) under the Virtual Cell unified evaluation paradigm, current models achieve uneven performance on biologically complex tasks, particularly those demanding mechanistic or causal understanding; and (ii) our knowledge-augmented evaluation framework ensures biological correctness, provides interpretable, evidence-grounded rationales, and achieves high discriminative capacity, overcoming the brittleness and opacity of conventional metrics. SC-Arena thus provides a unified and interpretable framework for assessing LLMs in single-cell biology, pointing toward the development of biology-aligned, generalizable foundation models.

cs.AI↗

arXiv2026

DART: Diffusion-Inspired Speculative Decoding for Fast LLM Inference

Speculative decoding is an effective and lossless approach for accelerating LLM inference. However, existing widely adopted model-based draft designs, such as EAGLE3, improve accuracy at the cost of multi-step autoregressive inference, resulting in high drafting latency and ultimately rendering the drafting stage itself a performance bottleneck. Inspired by diffusion-based large language models (dLLMs), we propose DART, which leverages parallel generation to reduce drafting latency. DART predicts logits for multiple future masked positions in parallel within a single forward pass based on hidden states of the target model, thereby eliminating autoregressive rollouts in the draft model while preserving a lightweight design. Based on these parallel logit predictions, we further introduce an efficient tree pruning algorithm that constructs high-quality draft token trees with N-gram-enforced semantic continuity. DART substantially reduces draft-stage overhead while preserving high draft accuracy, leading to significantly improved end-to-end decoding speed. Experimental results demonstrate that DART achieves a 2.03x--3.44x wall-clock time speedup across multiple datasets, surpassing EAGLE3 by 30% on average and offering a practical speculative decoding framework. Code is released at https://github.com/fvliang/DART.

cs.CL↗

arXiv2025

Accelerating Mixture-of-Experts Inference by Hiding Offloading Latency with Speculative Decoding

Recent advancements in Mixture of Experts (MoE) models have significantly increased their parameter scale as well as model performance. Extensive offloading techniques have been proposed to address the GPU memory limitations of MoE inference. However, due to the I/O bottleneck and sparse computation of MoE models, existing offloading techniques still suffer from low hardware utilization. To fully utilize the hardware resources, we propose SpecMoEOff, which employs the speculative decoding technique to enlarge the workload of each expert. SpecMoEOff orchestrates the GPU and CPU by both theoretical and empirical roofline analysis. In addition, we develop a dedicated CPU chunked attention verification kernel to fit the speculative decoding in offloading scenarios as well as minimizing the additional overhead led by draft models. SpecMoEOff further integrates an optimizer to automatically tune the hyperparameters of speculative decoding under given hardware and workload. Experimental results show that SpecMoEOff achieves up to 2.5x decode throughput improvement over the state-of-the-art MoE offloading techniques.

cs.DC↗

arXiv2025

CoDec: Prefix-Shared Decoding Kernel for LLMs

Prefix-sharing among multiple prompts presents opportunities to combine the operations of the shared prefix, while attention computation in the decode stage, which becomes a critical bottleneck with increasing context lengths, is a memory-intensive process requiring heavy memory access on the key-value (KV) cache of the prefixes. Therefore, in this paper, we explore the potential of prefix-sharing in the attention computation of the decode stage. However, the tree structure of the prefix-sharing mechanism presents significant challenges for attention computation in efficiently processing shared KV cache access patterns while managing complex dependencies and balancing irregular workloads. To address the above challenges, we propose a dedicated attention kernel to combine the memory access of shared prefixes in the decoding stage, namely CoDec. CoDec delivers two key innovations: a novel shared-prefix attention kernel that optimizes memory hierarchy and exploits both intra-block and inter-block parallelism, and a comprehensive workload balancing mechanism that efficiently estimates cost, divides tasks, and schedules execution. Experimental results show that CoDec achieves an average $1.9\times$ speedup and $120.9\times$ memory access reduction compared to the state-of-the-art FlashDecoding kernel regarding attention computation in the decode stage and $3.8\times$ end-to-end time per output token compared to the vLLM.

cs.LG↗

arXiv2025

Echo: Efficient Co-Scheduling of Hybrid Online-Offline Tasks for Large Language Model Serving

Large language models have been widely deployed in various applications, encompassing both interactive online tasks and batched offline tasks. Given the burstiness and latency sensitivity of online tasks, over-provisioning resources is common practice. This allows for the integration of latency-insensitive offline tasks during periods of low online load, enhancing resource utilization. However, strategically serving online and offline tasks through a preemption mechanism fails to fully leverage the flexibility of offline tasks and suffers from KV cache recomputation and irregular workloads. In this paper, we introduce Echo, a collaborative online-offline task serving system, including a scheduler, a KV cache manager, and estimation toolkits. The scheduler and KV cache manager work tightly to maximize the throughput of offline tasks, while the estimator further predicts execution time to ensure online task SLOs. The scheduler leverages the batch information of last iteration to reduce the search space for finding the optimal schedule. The KV cache manager sets the priority of the KV cache based on the type of tasks and the opportunity of prefix sharing to reduce the recomputation. Finally, the estimation toolkits predict the execution time, future memory consumption, and the throughput of offline tasks to guide the scheduler, KV cache manager, and the system deployer. Evaluation based on real-world workloads demonstrates that Echo can increase offline task throughput by up to $3.3\times$, while satisfying online task SLOs.

cs.DC↗

arXiv2024

Revisiting Service Level Objectives and System Level Metrics in Large Language Model Serving

User experience is a critical factor Large Language Model (LLM) serving systems must consider, where service level objectives (SLOs) considering the experience of individual requests and system level metrics (SLMs) considering the overall system performance are two key performance measures. However, we observe two notable issues in existing metrics: 1) manually delaying the delivery of some tokens can improve SLOs, and 2) actively abandoning requests that do not meet SLOs can improve SLMs, both of which are counterintuitive. In this paper, we revisit SLOs and SLMs in LLM serving, and propose a new SLO that aligns with user experience. Based on the SLO, we propose a comprehensive metric framework called smooth goodput, which integrates SLOs and SLMs to reflect the nature of user experience in LLM serving. Through this unified framework, we reassess the performance of different LLM serving systems under multiple workloads. Evaluation results show that our metric framework provides a more comprehensive view of token delivery and request processing, and effectively captures the optimal point of user experience and system performance with different serving strategies.

cs.LG↗