Jiahao Zhao
Publications
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.
DLLM-Searcher: Adapting Diffusion Large Language Model for Search Agents
Recently, Diffusion Large Language Models (dLLMs) have demonstrated unique efficiency advantages, enabled by their inherently parallel decoding mechanism and flexible generation paradigm. Meanwhile, despite the rapid advancement of Search Agents, their practical deployment is constrained by a fundamental limitation, termed as 1) Latency Challenge: the serial execution of multi-round reasoning, tool calling, and tool response waiting under the ReAct agent paradigm induces severe end-to-end latency. Intuitively, dLLMs can leverage their distinctive strengths to optimize the operational efficiency of agents under the ReAct agent paradigm. Practically, existing dLLM backbones face the 2) Agent Ability Challenge. That is, existing dLLMs exhibit remarkably weak reasoning and tool-calling capabilities, preventing these advantages from being effectively realized in practice. In this paper, we propose DLLM-Searcher, an optimization framework for dLLM-based Search Agents. To solve the Agent Ability Challenge, we design a two-stage post-training pipeline encompassing Agentic Supervised Fine-Tuning (Agentic SFT) and Agentic Variance-Reduced Preference Optimization Agentic VRPO, which enhances the backbone dLLM's information seeking and reasoning capabilities. To mitigate the Latency Challenge, we leverage the flexible generation mechanism of dLLMs and propose a novel agent paradigm termed Parallel-Reasoning and Acting P-ReAct. P-ReAct guides the model to prioritize decoding tool_call instructions, thereby allowing the model to keep thinking while waiting for the tool's return. Experimental results demonstrate that DLLM-Searcher achieves performance comparable to mainstream LLM-based search agents and P-ReAct delivers approximately 15% inference acceleration. Our code is available at https://anonymous.4open.science/r/DLLM-Searcher-553C