arXiv subjects

Jiahao Zhao

Publications and source records attributed to Jiahao Zhao.

At least 19 recordsLinked to original sources

arXiv2026

ToolArtist: Tool-Using Unified Multimodal Models for Agentic Image Generation

Text-to-image (T2I) models can produce visually compelling images, yet they remain limited on open-world tasks that require complex semantic understanding, multi-step reasoning, and the integration of external world knowledge. Existing efforts introduce agent capabilities into image generation, but they either prescribe a fixed workflow or place only a subset of the open-world image generation process under agent control. Consequently, reasoning, tool invocation, and image generation are not coordinated by a single policy. We propose ToolArtist, a fully agentic image generation model obtained by post-training a Unified Multimodal Model (UMM). ToolArtist dynamically orchestrates reasoning, external tool use, and native image generation within one unified policy. During Supervised Fine-Tuning (SFT), we equip a teacher agent with search tools alongside an image-generation tool. We then convert the collected trajectories into a UMM compatible format, where the image-generation tool is concealed while the resulting generated images are retained. During Reinforcement Learning (RL), we develop an agentic RL infrastructure for UMMs and introduce Reason-Act-Draw GRPO (RAD-GRPO), which uses complementary intent and quality rewards to jointly optimize the model. Experiments show that placing the entire open-world image-generation process under an agent policy consistently outperforms approaches with fixed pipelines or only partially agent-controlled components. We release the training data and the complete post-training infrastructure.

cs.CV↗

arXiv2026

From Execution to Capability: Scientific Experience Consolidation via Procedural Knowledge Synthesis

Large language models increasingly solve scientific-computing tasks, but executable feedback from one problem rarely becomes durable capability on subsequent problems. We study scientific-computing experience consolidation: converting verified runtime experience into transferable procedural knowledge and persistent model improvement. This setting presents two challenges: trajectory-derived artifacts may encode source-specific repairs rather than cross-task computational mechanisms; and a weaker target model may be unable to operationalize an otherwise valid abstract procedure - an abstraction-execution gap. We introduce SciConsolidate, which contrasts verified successes and failures to induce cross-task procedures, selects them through a development-validation gate, and uses failure-informed, answer-free query synthesis to expand the consolidation data without requiring pre-existing reference answers. Because the target model may not directly execute these abstractions, a stronger model concretizes them into executable code supervision for standard, procedure-free SFT; a matched no-procedure teacher branch isolates the value of procedural guidance. On SciCode, runtime procedure injection improves Qwen3.6-27B by +3.85/+6.26 sub-step/main-problem points, but yields almost no aggregate main-problem gain for Qwen3.5-9B, providing operational evidence of the abstraction-execution gap. After procedure-guided concretization, the 9B student improves under procedure-free deployment by +3.89/+6.25 points over the no-procedure SFT control and by +5.62/+11.25 over the original 9B model. These results establish an experience-to-capability pathway for scientific computing and provide a practical starting point for scaling self-improving scientific assistance.

cs.AI↗

arXiv2026

S1-Omni: A Unified Multimodal Reasoning Model for Scientific Understanding, Prediction, and Generation

We present S1-Omni, a unified multimodal reasoning model for scientific understanding, prediction, and generation. AI for Science (AI4S) has advanced significantly through domain-specific models, tool-augmented LLMs, and scientific language models. However, model capabilities remain highly fragmented, limiting the joint modeling of heterogeneous data, scientific laws, and expert knowledge. S1-Omni addresses this gap by consolidating these capabilities into a single, coherent scientific reasoning model. The architecture of S1-Omni is built upon three core components: unified representation of scientific data, natural-world knowledge alignment, and decoding for domain-specific tasks. First, S1-Omni maps natural-language instructions and scientific objects, including CIF, SMILES, protein sequences, spectra, and scientific images, into a shared representation space. Second, it incorporates scientific laws and expert knowledge into data construction and training, enabling the model to reason from scientific evidence. Third, it performs task-specific decoding to support a broad range of applications, including property prediction, spectrum-to-molecular generation, protein site and structure prediction, and scientific image generation and editing. S1-Omni is trained on S1-Omni-Corpus, which covers 200 scientific tasks and contains millions of reasoning samples, and is evaluated on over 60 scientific benchmarks. It outperforms GPT-5.5 and Gemini-3.1-Pro on most benchmarks and matches or surpasses domain-specific models on several benchmarks. Overall, S1-Omni provides a practical path toward unified scientific modeling.

cs.AI↗

arXiv2026

Scientific Logicality Enriched Methodology for LLM Reasoning: A Practice in Physics

With the continuous advancement of reasoning abilities in Large Language Models (LLMs), their application to scientific reasoning tasks has gained significant research attention. Current research primarily emphasizes boosting LLMs' performance on scientific QA benchmarks by training on larger, more comprehensive datasets with extended reasoning chains. However, these approaches neglect the essence of the scientific reasoning process -- logicality, which is the rational foundation to ensure the validity of reasoning steps leading to reliable conclusions. In this work, we make the first systematic investigation into the internal logicality underlying LLM scientific reasoning, and develop a scientific logicality-enriched methodology, including a set of assessment criteria and data sampling methods for logicality-guided training, to improve the logical faithfulness as well as task performance. Further, we take physics, characterized by its diverse logical structures and formalisms, as an exemplar discipline to practise the above methodology. For data construction, we extract scientific problems from academic literature and sample a high-quality dataset exhibiting strong logicality. Experiments based on three different backbone LLMs reveal that: 1) the training data we constructed can effectively improve the scientific logicality in LLM reasoning; and 2) the enriched scientific logicality plays a critical role in solving scientific problems. Code is available at \href{https://github.com/ScienceOne-AI/PhysLogic}{https://github.com/ScienceOne-AI/PhysLogic}.

cs.AI↗

arXiv2026

A Step to Decouple Optimization in 3DGS

3D Gaussian Splatting (3DGS) has emerged as a powerful technique for real-time novel view synthesis. As an explicit representation optimized through gradient propagation among primitives, optimization widely accepted in deep neural networks (DNNs) is actually adopted in 3DGS, such as synchronous weight updating and Adam with the adaptive gradient. However, considering the physical significance and specific design in 3DGS, there are two overlooked details in the optimization of 3DGS: (i) update step coupling, which induces optimizer state rescaling and costly attribute updates outside the viewpoints, and (ii) gradient coupling in the moment, which may lead to under- or over-effective regularization. Nevertheless, such a complex coupling is under-explored. After revisiting the optimization of 3DGS, we take a step to decouple it and recompose the process into: Sparse Adam, Re-State Regularization and Decoupled Attribute Regularization. Taking a large number of experiments under the 3DGS and 3DGS-MCMC frameworks, our work provides a deeper understanding of these components. Finally, based on the empirical analysis, we re-design the optimization and propose AdamW-GS by re-coupling the beneficial components, under which better optimization efficiency and representation effectiveness are achieved simultaneously.

cs.CV↗

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

MeasHalu: Mitigation of Scientific Measurement Hallucinations for Large Language Models with Enhanced Reasoning

The accurate extraction of scientific measurements from literature is a critical yet challenging task in AI4Science, enabling large-scale analysis and integration of quantitative research findings. However, Large Language Models (LLMs) frequently exhibit severe hallucinations, which significantly undermine the reliability of automated scientific document understanding systems. To address this problem, we propose MeasHalu, a novel framework for mitigating scientific measurement hallucinations through enhanced reasoning and targeted optimization. We first present a fine-grained taxonomy of measurement-specific hallucinations, categorizing errors across quantities, units, modifiers, and relations. Our approach incorporates a two-stage reasoning-aware fine-tuning strategy using augmented scientific data and process-based supervision. Furthermore, we introduce a progressive reward curriculum designed to penalize specific hallucination types, significantly improving extraction faithfulness. Experimental results demonstrate that MeasHalu substantially reduces hallucination rates and improves overall accuracy on the MeasEval benchmark. This work provides a targeted solution to a key bottleneck in automated scientific knowledge extraction, facilitating more trustworthy and scalable machine-assisted scientific literature analysis.

cs.CL↗

arXiv2026

Skip-Connected Policy Optimization for Implicit Advantage

Group Relative Policy Optimization (GRPO) has proven effective in RLVR by using outcome-based rewards. While fine-grained dense rewards can theoretically improve performance, we reveal that under practical sampling budgets, Monte Carlo estimation yields high-variance and sign-inconsistent advantages for early reasoning tokens, paradoxically underperforming outcome-only GRPO. We propose Skip-Connected Optimization (SKPO), which decomposes reasoning into upstream and downstream phases: upstream receives dense rewards from downstream Monte Carlo sampling with single-stream optimization; downstream maintains group-relative optimization, where a skip connection concatenates the upstream segment with the original problem, enabling the model to leverage helpful upstream reasoning while preserving the freedom to bypass flawed reasoning through direct problem access. Experiments demonstrate improvements of 3.91% and 6.17% relative gains over the strongest baselines on Qwen2.5-Math-7B and Llama-3.2-3B respectively across mathematical benchmarks and out-of-domain tasks including general reasoning and code generation. Further analysis reveals an implicit advantage: SKPO generates trajectories with higher intermediate-step quality even when matched for final correctness.

cs.LG↗

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

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

cs.AI↗

arXiv2025

Cognitive-YOLO: LLM-Driven Architecture Synthesis from First Principles of Data for Object Detection

General-purpose object detection algorithms face a domain-shift bottleneck when deployed in vertical scenarios, and manually customizing a network architecture relies heavily on expert experience with high trial-and-error cost. To address these problems, we present \textbf{Cognitive-YOLO}, an adaptive object-detection model synthesis system driven by a large language model (LLM) collaborating with an autonomous agent. Cognitive-YOLO builds a fully automated \emph{Analyze--Synthesize--Compile} pipeline. First, a data-profiling module quantitatively extracts dataset features, guiding a ReAct-paradigm agent to autonomously retrieve matching network modules from a curated component library. Second, the LLM performs logical reasoning and topological assembly conditioned on the data features, producing a specification-compliant neural architecture description. Finally, a backend hybrid compiler dynamically instantiates the model, closing the loop with end-to-end training and evaluation scheduling. Cross-validation on datasets including rail-surface defects and rice diseases shows that the lightweight models synthesized by Cognitive-YOLO markedly compress the parameter count (down to 1.9M) while matching or surpassing mainstream baselines such as YOLOv11n in mAP@0.5:0.95, effectively balancing model compactness and feature-representation capability.

cs.CV↗

arXiv2025

SurveyEval: Towards Comprehensive Evaluation of LLM-Generated Academic Surveys

LLM-based automatic survey systems are transforming how users acquire information from the web by integrating retrieval, organization, and content synthesis into end-to-end generation pipelines. While recent works focus on developing new generation pipelines, how to evaluate such complex systems remains a significant challenge. To this end, we introduce SurveyEval, a comprehensive benchmark that evaluates automatically generated surveys across three dimensions: overall quality, outline coherence, and reference accuracy. We extend the evaluation across 7 subjects and augment the LLM-as-a-Judge framework with human references to strengthen evaluation-human alignment. Evaluation results show that while general long-text or paper-writing systems tend to produce lower-quality surveys, specialized survey-generation systems are able to deliver substantially higher-quality results. We envision SurveyEval as a scalable testbed to understand and improve automatic survey systems across diverse subjects and evaluation criteria.

cs.CL↗

arXiv2025

RxSafeBench: Identifying Medication Safety Issues of Large Language Models in Simulated Consultation

Numerous medical systems powered by Large Language Models (LLMs) have achieved remarkable progress in diverse healthcare tasks. However, research on their medication safety remains limited due to the lack of real world datasets, constrained by privacy and accessibility issues. Moreover, evaluation of LLMs in realistic clinical consultation settings, particularly regarding medication safety, is still underexplored. To address these gaps, we propose a framework that simulates and evaluates clinical consultations to systematically assess the medication safety capabilities of LLMs. Within this framework, we generate inquiry diagnosis dialogues with embedded medication risks and construct a dedicated medication safety database, RxRisk DB, containing 6,725 contraindications, 28,781 drug interactions, and 14,906 indication-drug pairs. A two-stage filtering strategy ensures clinical realism and professional quality, resulting in the benchmark RxSafeBench with 2,443 high-quality consultation scenarios. We evaluate leading open-source and proprietary LLMs using structured multiple choice questions that test their ability to recommend safe medications under simulated patient contexts. Results show that current LLMs struggle to integrate contraindication and interaction knowledge, especially when risks are implied rather than explicit. Our findings highlight key challenges in ensuring medication safety in LLM-based systems and provide insights into improving reliability through better prompting and task-specific tuning. RxSafeBench offers the first comprehensive benchmark for evaluating medication safety in LLMs, advancing safer and more trustworthy AI-driven clinical decision support.

cs.AI↗

arXiv2025

ABC-Eval: Benchmarking Large Language Models on Symbolic Music Understanding and Instruction Following

As large language models continue to develop, the feasibility and significance of text-based symbolic music tasks have become increasingly prominent. While symbolic music has been widely used in generation tasks, LLM capabilities in understanding and reasoning about symbolic music remain largely underexplored. To address this gap, we propose ABC-Eval, the first open-source benchmark dedicated to the understanding and instruction-following capabilities in text-based ABC notation scores. It comprises 1,086 test samples spanning 10 sub-tasks, covering scenarios from basic musical syntax comprehension to complex sequence-level reasoning. Such a diverse scope poses substantial challenges to models' ability to handle symbolic music tasks. We evaluated seven state-of-the-art LLMs on ABC-Eval, and the results reveal notable limitations in existing models' symbolic music processing capabilities. Furthermore, the consistent performance of individual baselines across different sub-tasks supports the reliability of our benchmark.

cs.SD↗

arXiv2025

Meow: End-to-End Outline Writing for Automatic Academic Survey

As academic paper publication numbers grow exponentially, conducting in-depth surveys with LLMs automatically has become an inevitable trend. Outline writing, which aims to systematically organize related works, is critical for automated survey generation. Yet existing automatic survey methods treat outline writing as mere workflow steps in the overall pipeline. Such template-based workflows produce outlines that lack in-depth understanding of the survey topic and fine-grained styles. To address these limitations, we propose Meow, the first metadata-driven outline writing framework that produces organized and faithful outlines efficiently. Specifically, we first formulate outline writing as an end-to-end task that generates hierarchical structured outlines from paper metadata. We then curate a high-quality dataset of surveys from arXiv, bioRxiv, and medRxiv, and establish systematic evaluation metrics for outline quality assessment. Finally, we employ a two-stage training approach combining supervised fine-tuning and reinforcement learning. Our 8B reasoning model demonstrates strong performance with high structural fidelity and stylistic coherence.

cs.CL↗

arXiv2025

HingeNet: A Harmonic-Aware Fine-Tuning Approach for Beat Tracking

Fine-tuning pre-trained foundation models has made significant progress in music information retrieval. However, applying these models to beat tracking tasks remains unexplored as the limited annotated data renders conventional fine-tuning methods ineffective. To address this challenge, we propose HingeNet, a novel and general parameter-efficient fine-tuning method specifically designed for beat tracking tasks. HingeNet is a lightweight and separable network, visually resembling a hinge, designed to tightly interface with pre-trained foundation models by using their intermediate feature representations as input. This unique architecture grants HingeNet broad generalizability, enabling effective integration with various pre-trained foundation models. Furthermore, considering the significance of harmonics in beat tracking, we introduce harmonic-aware mechanism during the fine-tuning process to better capture and emphasize the harmonic structures in musical signals. Experiments on benchmark datasets demonstrate that HingeNet achieves state-of-the-art performance in beat and downbeat tracking

cs.SD↗

arXiv2025

BeatFM: Improving Beat Tracking with Pre-trained Music Foundation Model

Beat tracking is a widely researched topic in music information retrieval. However, current beat tracking methods face challenges due to the scarcity of labeled data, which limits their ability to generalize across diverse musical styles and accurately capture complex rhythmic structures. To overcome these challenges, we propose a novel beat tracking paradigm BeatFM, which introduces a pre-trained music foundation model and leverages its rich semantic knowledge to improve beat tracking performance. Pre-training on diverse music datasets endows music foundation models with a robust understanding of music, thereby effectively addressing these challenges. To further adapt it for beat tracking, we design a plug-and-play multi-dimensional semantic aggregation module, which is composed of three parallel sub-modules, each focusing on semantic aggregation in the temporal, frequency, and channel domains, respectively. Extensive experiments demonstrate that our method achieves state-of-the-art performance in beat and downbeat tracking across multiple benchmark datasets.

cs.SD↗

arXiv2025

Jinx: Unlimited LLMs for Probing Alignment Failures

Unlimited, or so-called helpful-only language models are trained without safety alignment constraints and never refuse user queries. They are widely used by leading AI companies as internal tools for red teaming and alignment evaluation. For example, if a safety-aligned model produces harmful outputs similar to an unlimited model, this indicates alignment failures that require further attention. Despite their essential role in assessing alignment, such models are not available to the research community. We introduce Jinx, a helpful-only variant of popular open-weight LLMs. Jinx responds to all queries without refusals or safety filtering, while preserving the base model's capabilities in reasoning and instruction following. It provides researchers with an accessible tool for probing alignment failures, evaluating safety boundaries, and systematically studying failure modes in language model safety.

cs.CL↗