arXiv subjects

Jiayuan Chen

Publications and source records attributed to Jiayuan Chen.

At least 19 recordsLinked to original sources

arXiv2026

RAGCell: Retrieval-Augmented Generation as Supervision for Versatile Single-cell Analysis

Single-cell foundation models (scFMs) are transforming computational biology by enabling generalizable, task-agnostic representations for versatile single-cell analysis. Despite their progress in facilitating rapid deployment for downstream tasks, off-the-shelf scFMs still have some overlooked concerns: (I) (Pretraining Cost.) Pretrain-based scFMs necessitate pretraining on a vast volume of cells, rendering it draining resources in applications. (II) (Heterogeneous Gap.) Large Language Models (LLM)-based scFMs ignore the tremendous heterogeneous gap between LLM textual and raw cellular spaces, leading to insufficient capability when facing downstream tasks. To this end, we introduce RAGCell, a versatile single-cell analysis framework that achieves a double-win in both cost-effectiveness and high performance. The success of RAGCell lies in two key aspects: Leveraging LLMs to construct cell-level and feature-level knowledge databases, which serve as supervision signals for training the cell model and significantly reduce the training cost ($>$pretrain-based scFMs). Aligning cell representations with text embeddings from the bi-level knowledge databases, enabling knowledge transfer from textual spaces to cellular spaces and effectively mitigating the heterogeneous gap ($>$LLM-based scFMs). Through extensive experiments on six downstream single-cell analysis tasks, we demonstrate that RAGCell achieves outstanding performance compared to state-of-the-art scFMs while operating at less than $\sim$1/10 the cost of pretrain-based scFMs.

q-bio.GN↗

arXiv2026

Natural-Language Policies to Executable Decisions: An Interpretable Large Language Model Framework

Pricing automation in large-scale tourism is challenging because travel orders are highly unstructured, while pricing policies are complex, rapidly evolving, and inherently open-ended. Traditional rule engines are brittle and costly to maintain, whereas unconstrained LLM agents lack the reliability and auditability required for financial decisions. We present a production-grade LLM-powered pricing system with a strict decision boundary: LLMs perform structured extraction and bounded policy/path selection, while all numeric pricing, including total-price computation, is executed deterministically. Policies are compiled into interpretable condition trees, enabling open-ended support for new clauses and evolving rules without code changes, while exposing auditable artifacts for human-in-the-loop control. Periodic fine-tuning on logged traces further improves tree induction and path matching. Deployed at a municipal state-owned tourism enterprise across 7 scenic sites and 12 business categories with 1,500+ operators and 1,000+ active policies, the system processed 3,960 orders in six months, reduced the order management team from 15-20 to 3, and cut per-order handling time from 10 minutes to <2 minutes.

cs.CL↗

arXiv2026

Beyond Knowledge to Agency: Evaluating Expertise, Autonomy, and Integrity in Finance with CNFinBench

As large language models (LLMs) become high-privilege agents in risk-sensitive settings, they introduce systemic threats beyond hallucination, where minor compliance errors can cause critical data leaks. However, existing benchmarks focus on rule-based QA, lacking agentic execution modeling, overlooking compliance drift in adversarial interactions, and relying on binary safety metrics that fail to capture behavioral degradation. To bridge these gaps, we present CNFinBench, a comprehensive benchmark spanning 29 subtasks grounded in the triad of expertise, autonomy, and integrity. It assesses domain-specific capabilities through certified regulatory corpora and professional financial tasks, reconstructs end-to-end agent workflows from requirement parsing to tool verification, and simulates multi-turn adversarial attacks that induce behavioral compliance drift. To quantify safety degradation, we introduce the Harmful Instruction Compliance Score (HICS), a multi-dimensional safety metric that integrates risk-type-specific deductions, multi-turn consistency tracking, and severity-adjusted penalty scaling based on fine-grained violation triggers. Evaluations over 22 open-/closed-source models reveal: LLMs perform well in applied tasks yet lack robust rule understanding, suffer a 15.4 decline from single modules to full execution chains, and collapse rapidly in multi-turn attacks, with average violations surging by 159.05\% in Round 2. CNFinBench is available at https://cnfinbench.opencompass.org.cn and https://github.com/open-compass/CNFinBench.

cs.CE↗

arXiv2026

SafeMed-R1: Clinician-Audited Safety and Ethics Alignment for Medical Large Language Models

Large language models(LLMs) increasingly match expert performance on licensing examinations, yet routine clinical use remains limited because governance requires auditable reasoning, safety and ethics alignment, and resilience to adversarial misuse. Here we present SafeMed-R1, trained with a traceable Clinical Trust Signals(CTS) pipeline that links each reasoning instance to clinician rubric scores and edit histories, and aligned through safety and ethics supervision and red team stress testing. SafeMed-R1 attains a macro-averaged accuracy of 79.6% across clinical benchmarks. Under adversarial safety testing, it shows the lowest aggregated risk and reduces unsafe outputs by about 3 to 5% relative to its baseline. In a paired expert study of 30 medication safety vignettes, SafeMed-R1 matches PGY1 and PGY2 residents on medical correctness and scores higher for medication safety, guideline consistency, and clinical usefulness. Collectively, these results suggest that clinician-audited supervision provenance, together with domain-tailored safety and ethics alignment, can strengthen governance-relevant evidence without relying on inference-time retrieval or citation grounding.

cs.AI↗

arXiv2026

Intervention-Aware Multiscale Representation Learning from Imaging Phenomics and Perturbation Transcriptomics

Microscopy-based phenotypic profiling is scalable for drug discovery but lacks the mechanistic depth of transcriptomics, which remains costly and scarce. Existing multimodal approaches either use images to support other modalities or naively align representations by sample identity, ignoring cell-type and dose variations in weakly paired data-limiting generalization to unseen interventions. In this paper, we introduce an intervention-aware distillation framework that leverages perturbational transcriptomics to guide image representation learning. A transcriptome-conditioned teacher integrates gene expression and intervention metadata to produce soft distributions over a chemistry-aware codebook organized by drug similarity. The teacher employs a fine-tuned single-cell foundation model to encode cell-type context and disentangle dose effects. An image-only student learns to predict these distributions from microscopy alone, distilling mechanistic knowledge while operating independently at test time. This design emphasizes intervention semantics rather than identity alignment and explicitly handles dose and cell-type mismatches. We provide theoretical guarantees showing that transcriptomic guidance tightens the risk bound for image-based prediction. On Cell Painting and RxRx datasets paired with L1000, our method significantly improves one-shot transfer to unseen interventions and drug-target gene discovery compared to self-supervised and alignment baselines.

cs.CV↗

arXiv2026

Not Search, But Scan: Benchmarking MLLMs on Scan-Oriented Academic Paper Reasoning

With the rapid progress of multimodal large language models (MLLMs), AI already performs well at literature retrieval and certain reasoning tasks, serving as a capable assistant to human researchers, yet it remains far from autonomous research. The fundamental reason is that current work on academic paper reasoning is largely confined to a search-oriented paradigm centered on pre-specified targets, with reasoning grounded in relevance retrieval, which struggles to support researcher-style full-document understanding, reasoning, and verification. To bridge this gap, we propose \textbf{ScholScan}, a new benchmark for academic paper reasoning. ScholScan introduces a scan-oriented task setting that asks models to read and cross-check entire papers like human researchers, scanning the document to identify consistency issues. The benchmark comprises 1,800 carefully annotated questions drawn from nine error categories across 13 natural-science domains and 715 papers, and provides detailed annotations for evidence localization and reasoning traces, together with a unified evaluation protocol. We assessed 15 models across 24 input configurations and conducted a fine-grained analysis of MLLM capabilities for all error categories. Across the board, retrieval-augmented generation (RAG) methods yield no significant improvements, revealing systematic deficiencies of current MLLMs on scan-oriented tasks and underscoring the challenge posed by ScholScan. We expect ScholScan to be the leading and representative work of the scan-oriented task paradigm.

cs.AI↗

arXiv2026

THEMIS: Towards Holistic Evaluation of MLLMs for Scientific Paper Fraud Forensics

We present THEMIS, a novel multi-task benchmark designed to comprehensively evaluate multimodal large language models (MLLMs) on visual fraud reasoning within real-world academic scenarios. Compared to existing benchmarks, THEMIS introduces three major advances. (1) Real-World Scenarios and Complexity: Our benchmark comprises over 4,000 questions spanning seven scenarios, derived from authentic retracted-paper cases and carefully curated multimodal synthetic data. With 60.47% complex-texture images, THEMIS bridges the critical gap between existing benchmarks and the complexity of real-world academic fraud. (2) Fraud-Type Diversity and Granularity: THEMIS systematically covers five challenging fraud types and introduces 16 fine-grained manipulation operations. On average, each sample undergoes multiple stacked manipulation operations, with the diversity and difficulty of these manipulations demanding a high level of visual fraud reasoning from the models. (3) Multi-Dimensional Capability Evaluation: We establish a mapping from fraud types to five core visual fraud reasoning capabilities, thereby enabling an evaluation that reveals the distinct strengths and specific weaknesses of different models across these core capabilities. Experiments on 16 leading MLLMs show that even the best-performing model, GPT-5, achieves an overall performance of only 56.15%, demonstrating that our benchmark presents a stringent test. We expect THEMIS to advance the development of MLLMs for complex, real-world fraud reasoning tasks.

cs.CV↗

arXiv2026

A Scheduling Framework for Efficient MoE Inference on Edge GPU-NDP Systems

Mixture-of-Experts (MoE) models facilitate edge deployment by decoupling model capacity from active computation, yet their large memory footprint drives the need for GPU systems with near-data processing (NDP) capabilities that offload experts to dedicated processing units. However, deploying MoE models on such edge-based GPU-NDP systems faces three critical challenges: 1) severe load imbalance across NDP units due to non-uniform expert selection and expert parallelism, 2) insufficient GPU utilization during expert computation within NDP units, and 3) extensive data pre-profiling necessitated by unpredictable expert activation patterns for pre-fetching. To address these challenges, this paper proposes an efficient inference framework featuring three key optimizations. First, the underexplored tensor parallelism in MoE inference is exploited to partition and compute large expert parameters across multiple NDP units simultaneously towards edge low-batch scenarios. Second, a load-balancing-aware scheduling algorithm distributes expert computations across NDP units and GPU to maximize resource utilization. Third, a dataset-free pre-fetching strategy proactively loads frequently accessed experts to minimize activation delays. Experimental results show that our framework enables GPU-NDP systems to achieve 2.41x on average and up to 2.56x speedup in end-to-end latency compared to state-of-the-art approaches, significantly enhancing MoE inference efficiency in resource-constrained environments.

cs.DC↗

arXiv2025

MedBench v4: A Robust and Scalable Benchmark for Evaluating Chinese Medical Language Models, Multimodal Models, and Intelligent Agents

Recent advances in medical large language models (LLMs), multimodal models, and agents demand evaluation frameworks that reflect real clinical workflows and safety constraints. We present MedBench v4, a nationwide, cloud-based benchmarking infrastructure comprising over 700,000 expert-curated tasks spanning 24 primary and 91 secondary specialties, with dedicated tracks for LLMs, multimodal models, and agents. Items undergo multi-stage refinement and multi-round review by clinicians from more than 500 institutions, and open-ended responses are scored by an LLM-as-a-judge calibrated to human ratings. We evaluate 15 frontier models. Base LLMs reach a mean overall score of 54.1/100 (best: Claude Sonnet 4.5, 62.5/100), but safety and ethics remain low (18.4/100). Multimodal models perform worse overall (mean 47.5/100; best: GPT-5, 54.9/100), with solid perception yet weaker cross-modal reasoning. Agents built on the same backbones substantially improve end-to-end performance (mean 79.8/100), with Claude Sonnet 4.5-based agents achieving up to 85.3/100 overall and 88.9/100 on safety tasks. MedBench v4 thus reveals persisting gaps in multimodal reasoning and safety for base models, while showing that governance-aware agentic orchestration can markedly enhance benchmarked clinical readiness without sacrificing capability. By aligning tasks with Chinese clinical guidelines and regulatory priorities, the platform offers a practical reference for hospitals, developers, and policymakers auditing medical AI.

cs.CL↗

arXiv2025

Evaluating the Ability of Large Language Models to Identify Adherence to CONSORT Reporting Guidelines in Randomized Controlled Trials: A Methodological Evaluation Study

The Consolidated Standards of Reporting Trials statement is the global benchmark for transparent and high-quality reporting of randomized controlled trials. Manual verification of CONSORT adherence is a laborious, time-intensive process that constitutes a significant bottleneck in peer review and evidence synthesis. This study aimed to systematically evaluate the accuracy and reliability of contemporary LLMs in identifying the adherence of published RCTs to the CONSORT 2010 statement under a zero-shot setting. We constructed a golden standard dataset of 150 published RCTs spanning diverse medical specialties. The primary outcome was the macro-averaged F1-score for the three-class classification task, supplemented by item-wise performance metrics and qualitative error analysis. Overall model performance was modest. The top-performing models, Gemini-2.5-Flash and DeepSeek-R1, achieved nearly identical macro F1 scores of 0.634 and Cohen's Kappa coefficients of 0.280 and 0.282, respectively, indicating only fair agreement with expert consensus. A striking performance disparity was observed across classes: while most models could identify compliant items with high accuracy (F1 score > 0.850), they struggled profoundly with identifying non-compliant and not applicable items, where F1 scores rarely exceeded 0.400. Notably, some high-profile models like GPT-4o underperformed, achieving a macro F1-score of only 0.521. LLMs show potential as preliminary screening assistants for CONSORT checks, capably identifying well-reported items. However, their current inability to reliably detect reporting omissions or methodological flaws makes them unsuitable for replacing human expertise in the critical appraisal of trial quality.

cs.CL↗

arXiv2025

TCM-5CEval: Extended Deep Evaluation Benchmark for LLM's Comprehensive Clinical Research Competence in Traditional Chinese Medicine

Large language models (LLMs) have demonstrated exceptional capabilities in general domains, yet their application in highly specialized and culturally-rich fields like Traditional Chinese Medicine (TCM) requires rigorous and nuanced evaluation. Building upon prior foundational work such as TCM-3CEval, which highlighted systemic knowledge gaps and the importance of cultural-contextual alignment, we introduce TCM-5CEval, a more granular and comprehensive benchmark. TCM-5CEval is designed to assess LLMs across five critical dimensions: (1) Core Knowledge (TCM-Exam), (2) Classical Literacy (TCM-LitQA), (3) Clinical Decision-making (TCM-MRCD), (4) Chinese Materia Medica (TCM-CMM), and (5) Clinical Non-pharmacological Therapy (TCM-ClinNPT). We conducted a thorough evaluation of fifteen prominent LLMs, revealing significant performance disparities and identifying top-performing models like deepseek\_r1 and gemini\_2\_5\_pro. Our findings show that while models exhibit proficiency in recalling foundational knowledge, they struggle with the interpretative complexities of classical texts. Critically, permutation-based consistency testing reveals widespread fragilities in model inference. All evaluated models, including the highest-scoring ones, displayed a substantial performance degradation when faced with varied question option ordering, indicating a pervasive sensitivity to positional bias and a lack of robust understanding. TCM-5CEval not only provides a more detailed diagnostic tool for LLM capabilities in TCM but aldso exposes fundamental weaknesses in their reasoning stability. To promote further research and standardized comparison, TCM-5CEval has been uploaded to the Medbench platform, joining its predecessor in the "In-depth Challenge for Comprehensive TCM Abilities" special track.

cs.CL↗

arXiv2025

MedCalc-Eval and MedCalc-Env: Advancing Medical Calculation Capabilities of Large Language Models

As large language models (LLMs) enter the medical domain, most benchmarks evaluate them on question answering or descriptive reasoning, overlooking quantitative reasoning critical to clinical decision-making. Existing datasets like MedCalc-Bench cover few calculation tasks and fail to reflect real-world computational scenarios. We introduce MedCalc-Eval, the largest benchmark for assessing LLMs' medical calculation abilities, comprising 700+ tasks across two types: equation-based (e.g., Cockcroft-Gault, BMI, BSA) and rule-based scoring systems (e.g., Apgar, Glasgow Coma Scale). These tasks span diverse specialties including internal medicine, surgery, pediatrics, and cardiology, offering a broader and more challenging evaluation setting. To improve performance, we further develop MedCalc-Env, a reinforcement learning environment built on the InternBootcamp framework, enabling multi-step clinical reasoning and planning. Fine-tuning a Qwen2.5-32B model within this environment achieves state-of-the-art results on MedCalc-Eval, with notable gains in numerical sensitivity, formula selection, and reasoning robustness. Remaining challenges include unit conversion, multi-condition logic, and contextual understanding. Code and datasets are available at https://github.com/maokangkun/MedCalc-Eval.

cs.CL↗

arXiv2025

The Boundaries of Fair AI in Medical Image Prognosis: A Causal Perspective

As machine learning (ML) algorithms are increasingly used in medical image analysis, concerns have emerged about their potential biases against certain social groups. Although many approaches have been proposed to ensure the fairness of ML models, most existing works focus only on medical image diagnosis tasks, such as image classification and segmentation, and overlooked prognosis scenarios, which involve predicting the likely outcome or progression of a medical condition over time. To address this gap, we introduce FairTTE, the first comprehensive framework for assessing fairness in time-to-event (TTE) prediction in medical imaging. FairTTE encompasses a diverse range of imaging modalities and TTE outcomes, integrating cutting-edge TTE prediction and fairness algorithms to enable systematic and fine-grained analysis of fairness in medical image prognosis. Leveraging causal analysis techniques, FairTTE uncovers and quantifies distinct sources of bias embedded within medical imaging datasets. Our large-scale evaluation reveals that bias is pervasive across different imaging modalities and that current fairness methods offer limited mitigation. We further demonstrate a strong association between underlying bias sources and model disparities, emphasizing the need for holistic approaches that target all forms of bias. Notably, we find that fairness becomes increasingly difficult to maintain under distribution shifts, underscoring the limitations of existing solutions and the pressing need for more robust, equitable prognostic models.

cs.LG↗

arXiv2025

Enriching Object-Centric Event Data with Process Scopes: A Framework for Aggregation and Analysis

Object-Centric Process Mining enables the analysis of complex operational behavior by capturing interactions among multiple business objects (e.g., orders, items, deliveries). These interactions are recorded using Object-Centric Event Data (OCED) formats, such as the Object-Centric Event Log (OCEL). However, existing formats lack explicit definitions of process scopes, which restricts analysis to individual processes and limits insights to a low level of granularity. In practice, OCED often spans multiple interrelated processes, as shared objects connect events across organizational functions. This structure reflects how value is created along the organizational value chain, but introduces challenges for interpretation when process boundaries are not clearly defined. Moreover, process definitions are typically subjective and context-dependent; they vary across organizations, roles, and analytical goals, and cannot always be discovered automatically. To address these challenges, we propose a method for embedding analyst-defined process scopes into OCEL. This enables the structured representation of multiple coexisting processes, supports the aggregation of event data across scopes, and facilitates analysis at varying levels of abstraction. We demonstrate the applicability of our approach using a publicly available OCEL log and provide supporting tools for scope definition and analysis.

cs.DB↗

arXiv2025

Integrating Biological Knowledge for Robust Microscopy Image Profiling on De Novo Cell Lines

High-throughput screening techniques, such as microscopy imaging of cellular responses to genetic and chemical perturbations, play a crucial role in drug discovery and biomedical research. However, robust perturbation screening for \textit{de novo} cell lines remains challenging due to the significant morphological and biological heterogeneity across cell lines. To address this, we propose a novel framework that integrates external biological knowledge into existing pretraining strategies to enhance microscopy image profiling models. Our approach explicitly disentangles perturbation-specific and cell line-specific representations using external biological information. Specifically, we construct a knowledge graph leveraging protein interaction data from STRING and Hetionet databases to guide models toward perturbation-specific features during pretraining. Additionally, we incorporate transcriptomic features from single-cell foundation models to capture cell line-specific representations. By learning these disentangled features, our method improves the generalization of imaging models to \textit{de novo} cell lines. We evaluate our framework on the RxRx database through one-shot fine-tuning on an RxRx1 cell line and few-shot fine-tuning on cell lines from the RxRx19a dataset. Experimental results demonstrate that our method enhances microscopy image profiling for \textit{de novo} cell lines, highlighting its effectiveness in real-world phenotype-based drug discovery applications.

cs.CV↗

arXiv2025

Generative AI-Aided QoE Maximization for RIS-Assisted Digital Twin Interaction

In this paper, we investigate a quality of experience (QoE)-aware resource allocation problem for reconfigurable intelligent surface (RIS)-assisted digital twin (DT) interaction with uncertain evolution. In the considered system, mobile users are expected to interact with a DT model maintained on a DT server that is deployed on a base station, via effective uplink and downlink channels assisted by an RIS. Our goal is to maximize the sum of all mobile users' joint subjective and objective QoE in DT interactions across various DT scenes, by jointly optimizing phase shift matrix, receive/transmit beamforming matrix, rendering resolution configuration and computing resource allocation. While solving this problem is challenging mainly due to the uncertain evolution of the DT model, which leads to multiple scene-specific problems, and require us to constantly re-solve each of them whenever DT model evolves. To this end, leveraging the dynamic optimization capabilities of decision transformers and the generalization strengths of generative artificial intelligence (GAI), we propose a novel GAI-aided approach, called the prompt-guided decision transformer integrated with zero-forcing optimization (PG-ZFO). Simulations are conducted to evaluate the proposed PG-ZFO, demonstrating its effectiveness and superiority over counterparts.

cs.NI↗

arXiv2025

Distributionally Robust Optimization for Digital Twin Service Provisioning over Edge Computing

Digital Twin (DT) is a transformative technology poised to revolutionize a wide range of applications. This advancement has led to the emergence of digital twin as a service (DTaaS), enabling users to interact with DT models that accurately reflect the real-time status of their physical counterparts. Quality of DTaaS primarily depends on the freshness of DT data, which can be quantified by the age of information (AoI). The reliance on remote cloud servers solely for DTaaS provisioning presents significant challenges for latency-sensitive applications with strict AoI demands. Edge computing, as a promising paradigm, is expected to enable the AoI-aware provision of real-time DTaaS for users. In this paper, we study the joint optimization of DT model deployment and DT model selection for DTaaS provisioning over edge computing, with the objective of maximizing the quality of DTaaS. To address the uncertainties of DT interactions imposed on DTaaS provisioning, we propose a novel distributionally robust optimization (DRO)-based approach, called Wasserstein DRO (WDRO), where we first reformulate the original problem to a robust optimization problem, with the objective of maximizing the quality of DTaaS under the unforeseen extreme request conditions. Then, we leverage multi-level dual transformations based on Wasserstein distance to derive a robust solution. Simulations are conducted to evaluate the performance of the proposed WDRO, and the results demonstrate its superiority over counterparts.

cs.NI↗

arXiv2025

Building a Human-Verified Clinical Reasoning Dataset via a Human LLM Hybrid Pipeline for Trustworthy Medical AI

Despite strong performance in medical question-answering, the clinical adoption of Large Language Models (LLMs) is critically hampered by their opaque 'black-box' reasoning, limiting clinician trust. This challenge is compounded by the predominant reliance of current medical LLMs on corpora from scientific literature or synthetic data, which often lack the granular expert validation and high clinical relevance essential for advancing their specialized medical capabilities. To address these critical gaps, we introduce a highly clinically relevant dataset with 31,247 medical question-answer pairs, each accompanied by expert-validated chain-of-thought (CoT) explanations. This resource, spanning multiple clinical domains, was curated via a scalable human-LLM hybrid pipeline: LLM-generated rationales were iteratively reviewed, scored, and refined by medical experts against a structured rubric, with substandard outputs revised through human effort or guided LLM regeneration until expert consensus. This publicly available dataset provides a vital source for the development of medical LLMs that capable of transparent and verifiable reasoning, thereby advancing safer and more interpretable AI in medicine.

cs.CV↗