Jiayuan Chen

Jinru Ding, Chao Ding, Yidong Jiang et al.

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/VertiAIBench/CNFinBench.

Jiayuan Chen, Yu Wang, Ruining Deng et al.

Podocytes, specialized epithelial cells that envelop the glomerular capillaries, play a pivotal role in maintaining renal health. The current description and quantification of features on pathology slides are limited, prompting the need for innovative solutions to comprehensively assess diverse phenotypic attributes within Whole Slide Images (WSIs). In particular, understanding the morphological characteristics of podocytes, terminally differentiated glomerular epithelial cells, is crucial for studying glomerular injury. This paper introduces the Spatial Pathomics Toolkit (SPT) and applies it to podocyte pathomics. The SPT consists of three main components: (1) instance object segmentation, enabling precise identification of podocyte nuclei; (2) pathomics feature generation, extracting a comprehensive array of quantitative features from the identified nuclei; and (3) robust statistical analyses, facilitating a comprehensive exploration of spatial relationships between morphological and spatial transcriptomics features.The SPT successfully extracted and analyzed morphological and textural features from podocyte nuclei, revealing a multitude of podocyte morphomic features through statistical analysis. Additionally, we demonstrated the SPT's ability to unravel spatial information inherent to podocyte distribution, shedding light on spatial patterns associated with glomerular injury. By disseminating the SPT, our goal is to provide the research community with a powerful and user-friendly resource that advances cellular spatial pathomics in renal pathology. The implementation and its complete source code of the toolkit are made openly accessible at https://github.com/hrlblab/spatial_pathomics.

Jiayuan Chen, Changyan Yi, Hongyang Du et al.

Mobile Artificial Intelligence-Generated Content (AIGC) technology refers to the adoption of AI algorithms deployed at mobile edge networks to automate the information creation process while fulfilling the requirements of end users. Mobile AIGC has recently attracted phenomenal attentions and can be a key enabling technology for an emerging application, called human digital twin (HDT). HDT empowered by the mobile AIGC is expected to revolutionize the personalized healthcare by generating rare disease data, modeling high-fidelity digital twin, building versatile testbeds, and providing 24/7 customized medical services. To promote the development of this new breed of paradigm, in this article, we propose a system architecture of mobile AIGC-driven HDT and highlight the corresponding design requirements and challenges. Moreover, we illustrate two use cases, i.e., mobile AIGC-driven HDT in customized surgery planning and personalized medication. In addition, we conduct an experimental study to prove the effectiveness of the proposed mobile AIGC-driven HDT solution, which shows a particular application in a virtual physical therapy teaching platform. Finally, we conclude this article by briefly discussing several open issues and future directions.

Chao Ding, Mouxiao Bian, Tianbin Li et al.

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.

Jiayuan Chen, Xiang Zhang, Yinfei Xu et al.

Recently, graph-based models designed for downstream tasks have significantly advanced research on graph neural networks (GNNs). GNN baselines based on neural message-passing mechanisms such as GCN and GAT perform worse as the network deepens. Therefore, numerous GNN variants have been proposed to tackle this performance degradation problem, including many deep GNNs. However, a unified framework is still lacking to connect these existing models and interpret their effectiveness at a high level. In this work, we focus on deep GNNs and propose a novel view for understanding them. We establish a theoretical framework via inference on a probabilistic graphical model. Given the fixed point equation (FPE) derived from the variational inference on the Markov random fields, the deep GNNs, including JKNet, GCNII, DGCN, and the classical GNNs, such as GCN, GAT, and APPNP, can be regarded as different approximations of the FPE. Moreover, given this framework, more accurate approximations of FPE are brought, guiding us to design a more powerful GNN: coupling graph neural network (CoGNet). Extensive experiments are carried out on citation networks and natural language processing downstream tasks. The results demonstrate that the CoGNet outperforms the SOTA models.

Tzu-Yen Ma, Bo Zhang, Zichen Tang et al. · princeton

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.

Kangkun Mao, Jinru Ding, Jiayuan Chen et al.

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.

Qi Wu, Chao Fang, Jiayuan Chen et al.

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.

Boyu Zhang, Jiayuan Chen, Yinfei Xu et al.

The action quality assessment (AQA) of videos is a challenging vision task since the relation between videos and action scores is difficult to model. Thus, AQA has been widely studied in the literature. Traditionally, AQA is treated as a regression problem to learn the underlying mappings between videos and action scores. But previous methods ignored data uncertainty in AQA dataset. To address aleatoric uncertainty, we further develop a plug-and-play module Distribution Auto-Encoder (DAE). Specifically, it encodes videos into distributions and uses the reparameterization trick in variational auto-encoders (VAE) to sample scores, which establishes a more accurate mapping between videos and scores. Meanwhile, a likelihood loss is used to learn the uncertainty parameters. We plug our DAE approach into MUSDL and CoRe. Experimental results on public datasets demonstrate that our method achieves state-of-the-art on AQA-7, MTL-AQA, and JIGSAWS datasets. Our code is available at https://github.com/InfoX-SEU/DAE-AQA.

Rongjin Li, Zichen Tang, Xianghe Wang et al.

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.

Jiayuan Chen, You Shi, Changyan Yi et al.

The Internet of things (IoT) can significantly enhance the quality of human life, specifically in healthcare, attracting extensive attentions to IoT-healthcare services. Meanwhile, the human digital twin (HDT) is proposed as an innovative paradigm that can comprehensively characterize the replication of the individual human body in the digital world and reflect its physical status in real time. Naturally, HDT is envisioned to empower IoT-healthcare beyond the application of healthcare monitoring by acting as a versatile and vivid human digital testbed, simulating the outcomes and guiding the practical treatments. However, successfully establishing HDT requires high-fidelity virtual modeling and strong information interactions but possibly with scarce, biased and noisy data. Fortunately, a recent popular technology called generative artificial intelligence (GAI) may be a promising solution because it can leverage advanced AI algorithms to automatically create, manipulate, and modify valuable while diverse data. This survey particularly focuses on the implementation of GAI-driven HDT in IoT-healthcare. We start by introducing the background of IoT-healthcare and the potential of GAI-driven HDT. Then, we delve into the fundamental techniques and present the overall framework of GAI-driven HDT. After that, we explore the realization of GAI-driven HDT in detail, including GAI-enabled data acquisition, communication, data management, digital modeling, and data analysis. Besides, we discuss typical IoT-healthcare applications that can be revolutionized by GAI-driven HDT, namely personalized health monitoring and diagnosis, personalized prescription, and personalized rehabilitation. Finally, we conclude this survey by highlighting some future research directions.

Jiayuan Chen, Changchang Yin, Yuanlong Wang et al.

Deep learning-based predictive models, leveraging Electronic Health Records (EHR), are receiving increasing attention in healthcare. An effective representation of a patient's EHR should hierarchically encompass both the temporal relationships between historical visits and medical events, and the inherent structural information within these elements. Existing patient representation methods can be roughly categorized into sequential representation and graphical representation. The sequential representation methods focus only on the temporal relationships among longitudinal visits. On the other hand, the graphical representation approaches, while adept at extracting the graph-structured relationships between various medical events, fall short in effectively integrate temporal information. To capture both types of information, we model a patient's EHR as a novel temporal heterogeneous graph. This graph includes historical visits nodes and medical events nodes. It propagates structured information from medical event nodes to visit nodes and utilizes time-aware visit nodes to capture changes in the patient's health status. Furthermore, we introduce a novel temporal graph transformer (TRANS) that integrates temporal edge features, global positional encoding, and local structural encoding into heterogeneous graph convolution, capturing both temporal and structural information. We validate the effectiveness of TRANS through extensive experiments on three real-world datasets. The results show that our proposed approach achieves state-of-the-art performance.

Xiang Chen, Wenjie Zhu, Jiayuan Chen et al.

This paper proposes a novel edge computing enabled real-time video analysis system for intelligent visual devices. The proposed system consists of a tracking-assisted object detection module (TAODM) and a region of interesting module (ROIM). TAODM adaptively determines the offloading decision to process each video frame locally with a tracking algorithm or to offload it to the edge server inferred by an object detection model. ROIM determines each offloading frame's resolution and detection model configuration to ensure that the analysis results can return in time. TAODM and ROIM interact jointly to filter the repetitive spatial-temporal semantic information to maximize the processing rate while ensuring high video analysis accuracy. Unlike most existing works, this paper investigates the real-time video analysis systems where the intelligent visual device connects to the edge server through a wireless network with fluctuating network conditions. We decompose the real-time video analysis problem into the offloading decision and configurations selection sub-problems. To solve these two sub-problems, we introduce a double deep Q network (DDQN) based offloading approach and a contextual multi-armed bandit (CMAB) based adaptive configurations selection approach, respectively. A DDQN-CMAB reinforcement learning (DCRL) training framework is further developed to integrate these two approaches to improve the overall video analyzing performance. Extensive simulations are conducted to evaluate the performance of the proposed solution, and demonstrate its superiority over counterparts.

Tianai Huang, Lu Lu, Jiayuan Chen et al.

Large language models (LLMs) excel in various NLP tasks and modern medicine, but their evaluation in traditional Chinese medicine (TCM) is underexplored. To address this, we introduce TCM3CEval, a benchmark assessing LLMs in TCM across three dimensions: core knowledge mastery, classical text understanding, and clinical decision-making. We evaluate diverse models, including international (e.g., GPT-4o), Chinese (e.g., InternLM), and medical-specific (e.g., PLUSE). Results show a performance hierarchy: all models have limitations in specialized subdomains like Meridian & Acupoint theory and Various TCM Schools, revealing gaps between current capabilities and clinical needs. Models with Chinese linguistic and cultural priors perform better in classical text interpretation and clinical reasoning. TCM-3CEval sets a standard for AI evaluation in TCM, offering insights for optimizing LLMs in culturally grounded medical domains. The benchmark is available on Medbench's TCM track, aiming to assess LLMs' TCM capabilities in basic knowledge, classic texts, and clinical decision-making through multidimensional questions and real cases.

Jiayuan Chen, Ruoqi Liu, Zishan Gu et al.

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.

Chao Ding, Mouxiao Bian, Pengcheng Chen et al.

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.

Jinru Ding, Lu Lu, Chao Ding et al.

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.

Tianai Huang, Jiayuan Chen, Lu Lu et al.

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.

Zhichao He, Mouxiao Bian, Jianhong Zhu et al.

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.

Thai-Hoang Pham, Jiayuan Chen, Seungyeon Lee et al.

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.

Jiayuan Chen, Thai-Hoang Pham, Yuanlong Wang et al.

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.

Jiayuan Chen, Yuxiang Li, Changyan Yi et al.

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.

Luyi Jiang, Jiayuan Chen, Lu Lu et al.

The evaluation and improvement of medical large language models (LLMs) are critical for their real-world deployment, particularly in ensuring accuracy, safety, and ethical alignment. Existing frameworks inadequately dissect domain-specific error patterns or address cross-modal challenges. This study introduces a granular error taxonomy through systematic analysis of top 10 models on MedBench, categorizing incorrect responses into eight types: Omissions, Hallucination, Format Mismatch, Causal Reasoning Deficiency, Contextual Inconsistency, Unanswered, Output Error, and Deficiency in Medical Language Generation. Evaluation of 10 leading models reveals vulnerabilities: despite achieving 0.86 accuracy in medical knowledge recall, critical reasoning tasks show 96.3% omission, while safety ethics evaluations expose alarming inconsistency (robustness score: 0.79) under option shuffled. Our analysis uncovers systemic weaknesses in knowledge boundary enforcement and multi-step reasoning. To address these, we propose a tiered optimization strategy spanning four levels, from prompt engineering and knowledge-augmented retrieval to hybrid neuro-symbolic architectures and causal reasoning frameworks. This work establishes an actionable roadmap for developing clinically robust LLMs while redefining evaluation paradigms through error-driven insights, ultimately advancing the safety and trustworthiness of AI in high-stakes medical environments.

Jiayuan Chen, Boyu Zhang, Yinfei Xu et al.

Recently, text classification model based on graph neural network (GNN) has attracted more and more attention. Most of these models adopt a similar network paradigm, that is, using pre-training node embedding initialization and two-layer graph convolution. In this work, we propose TextRGNN, an improved GNN structure that introduces residual connection to deepen the convolution network depth. Our structure can obtain a wider node receptive field and effectively suppress the over-smoothing of node features. In addition, we integrate the probabilistic language model into the initialization of graph node embedding, so that the non-graph semantic information of can be better extracted. The experimental results show that our model is general and efficient. It can significantly improve the classification accuracy whether in corpus level or text level, and achieve SOTA performance on a wide range of text classification datasets.

Jianchao Lee, Qiannan Duan, Sifan Bi et al.

The spectroscopy measurement is one of main pathways for exploring and understanding the nature. Today, it seems that racing artificial intelligence will remould its styles. The algorithms contained in huge neural networks are capable of substituting many of expensive and complex components of spectrum instruments. In this work, we presented a smart machine learning strategy on the measurement of absorbance curves, and also initially verified that an exceedingly-simplified equipment is sufficient to meet the needs for this strategy. Further, with its simplicity, the setup is expected to infiltrate into many scientific areas in versatile forms.