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.

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.

FlashForge: Ultra-Efficient Prefix-Aware Attention for LLM Decoding

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 FlashForge. FlashForge 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 FlashForge achieves an average 1.9x speedup and 120.9x memory access reduction compared to the state-of-the-art FlashDecoding kernel regarding attention computation in the decode stage and 3.8x end-to-end time per output token compared to the vLLM.