Keyan Ding

Xiang Zhuang, Qiang Zhang, Bin Wu et al.

Molecular property is usually observed with a limited number of samples, and researchers have considered property prediction as a few-shot problem. One important fact that has been ignored by prior works is that each molecule can be recorded with several different properties simultaneously. To effectively utilize many-to-many correlations of molecules and properties, we propose a Graph Sampling-based Meta-learning (GS-Meta) framework for few-shot molecular property prediction. First, we construct a Molecule-Property relation Graph (MPG): molecule and properties are nodes, while property labels decide edges. Then, to utilize the topological information of MPG, we reformulate an episode in meta-learning as a subgraph of the MPG, containing a target property node, molecule nodes, and auxiliary property nodes. Third, as episodes in the form of subgraphs are no longer independent of each other, we propose to schedule the subgraph sampling process with a contrastive loss function, which considers the consistency and discrimination of subgraphs. Extensive experiments on 5 commonly-used benchmarks show GS-Meta consistently outperforms state-of-the-art methods by 5.71%-6.93% in ROC-AUC and verify the effectiveness of each proposed module. Our code is available at https://github.com/HICAI-ZJU/GS-Meta.

Xiang Zhuang, Qiang Zhang, Keyan Ding et al.

Molecular representation learning lays the foundation for drug discovery. However, existing methods suffer from poor out-of-distribution (OOD) generalization, particularly when data for training and testing originate from different environments. To address this issue, we propose a new framework for learning molecular representations that exhibit invariance and robustness against distribution shifts. Specifically, we propose a strategy called ``first-encoding-then-separation'' to identify invariant molecule features in the latent space, which deviates from conventional practices. Prior to the separation step, we introduce a residual vector quantization module that mitigates the over-fitting to training data distributions while preserving the expressivity of encoders. Furthermore, we design a task-agnostic self-supervised learning objective to encourage precise invariance identification, which enables our method widely applicable to a variety of tasks, such as regression and multi-label classification. Extensive experiments on 18 real-world molecular datasets demonstrate that our model achieves stronger generalization against state-of-the-art baselines in the presence of various distribution shifts. Our code is available at https://github.com/HICAI-ZJU/iMoLD.

Zeyuan Wang, Qiang Zhang, Keyan Ding et al.

Large Language Models (LLMs) have revolutionized the field of natural language processing, but they fall short in comprehending biological sequences such as proteins. To address this challenge, we propose InstructProtein, an innovative LLM that possesses bidirectional generation capabilities in both human and protein languages: (i) taking a protein sequence as input to predict its textual function description and (ii) using natural language to prompt protein sequence generation. To achieve this, we first pre-train an LLM on both protein and natural language corpora, enabling it to comprehend individual languages. Then supervised instruction tuning is employed to facilitate the alignment of these two distinct languages. Herein, we introduce a knowledge graph-based instruction generation framework to construct a high-quality instruction dataset, addressing annotation imbalance and instruction deficits in existing protein-text corpus. In particular, the instructions inherit the structural relations between proteins and function annotations in knowledge graphs, which empowers our model to engage in the causal modeling of protein functions, akin to the chain-of-thought processes in natural languages. Extensive experiments on bidirectional protein-text generation tasks show that InstructProtein outperforms state-of-the-art LLMs by large margins. Moreover, InstructProtein serves as a pioneering step towards text-based protein function prediction and sequence design, effectively bridging the gap between protein and human language understanding.

Yuhang Zhang, Keyan Ding, Peilin Chen et al.

Enzyme-reaction retrieval is a fundamental problem in computational biology, underpinning enzyme characterization, reaction mechanism elucidation, and the rational design of metabolic pathways and biocatalysts. As a bidirectional task, it entails both enzyme-to-reaction and reaction-to-enzyme mapping. However, existing approaches suffer from poor generalization across tasks and distributions, with performance highly sensitive to dataset splits and substantial asymmetry between retrieval directions. To address these challenges, we present TIGER, a Text-Informed Generalized Enzyme-Reaction Retrieval framework that leverages protein-to-text generation models to distill textual semantic knowledge from enzyme sequences, providing a generalized representation that bridges enzymes and biochemical reactions. To ensure the quality and reliability of textual semantics, we design a Dynamic Gating Network that adaptively fuses text-derived knowledge with sequence features, enabling more consistent and informative enzyme representations, while a Structure-Shared Feature Projector aligns enzyme and reaction representations within a unified latent space. Extensive experiments demonstrate that, under bidirectional retrieval supervision, TIGER significantly outperforms state-of-the-art baselines across diverse distributions and exhibits strong robustness and transferability across tasks.

Shuofei Qiao, Yunxiang Wei, Jiazheng Fan et al.

The exponential growth of global academic output has confronted researchers and AI agents with an unprecedented ``information explosion,'' where fragmented and unstructured knowledge organization impedes deep interdisciplinary integration. Current academic retrieval tools predominantly rely on superficial keyword matching or vector-space semantic retrieval, which lack the topological reasoning capabilities required to navigate complex logical connections. Agentic deep-research-based frameworks are often prone to logical hallucinations and consuming high inference costs. To bridge this gap, in this report, we introduce SciAtlas, a large-scale, multi-disciplinary, heterogeneous academic resource knowledge graph designed as a panoramic scientific evolution network. By integrating over 43M papers from 26 disciplines, and a total of 157M entities and 3B triplets, SciAtlas provides a structured topological cognitive substrate that dismantles disciplinary barriers and furnishes AI agents with a global perspective. Furthermore, we develop a neuro-symbolic retrieval algorithm featuring tri-path collaborative recall and graph reranking, achieving a seamless transition from simple semantic matching to deterministic association discovery. We also present key application directions of SciAtlas, including literature review, automated research trend synthesis, idea positioning, and academic trajectory exploration, to demonstrate that SciAtlas can serve as an effective ``cognitive map'' to empower the full loop of automated scientific research while significantly reducing reasoning costs. We have released the interfaces for KG retrieval and various downstream tasks in our GitHub repo.

Kehua Feng, Keyan Ding, Hongzhi Tan et al.

Reliable evaluation of large language models (LLMs) is impeded by two key challenges: objective metrics often fail to reflect human perception of natural language, and exhaustive human labeling is prohibitively expensive. Here, we propose a sample-efficient human evaluation method for LLMs based on the principle of MAximum Discrepancy (MAD) Competition. Our method automatically and adaptively selects a compact set of input instructions that maximize semantic discrepancy between pairs of LLM responses. Human evaluators then perform three-alternative forced choices on these paired responses, which are aggregated into a global ranking using Elo rating. We apply our approach to compare eight widely used LLMs across four tasks: scientific knowledge understanding, mathematical reasoning, creative and functional writing, and code generation and explanation. Experimental results show that our sample-efficient evaluation method recovers "gold-standard" model rankings with a handful of MAD-selected instructions, reveals respective strengths and weaknesses of each LLM, and offers nuanced insights to guide future LLM development. Code is available at https://github.com/weiji-Feng/MAD-Eval .

Xiang Zhuang, Chenyi Zhou, Kehua Feng et al.

Artificial intelligence has demonstrated remarkable capability in predicting scientific properties, yet scientific discovery remains an inherently physical, long-horizon pursuit governed by experimental cycles. Most current computational approaches are misaligned with this reality, framing discovery as isolated, task-specific predictions rather than continuous interaction with the physical world. Here, we argue for embodied science, a paradigm that reframes scientific discovery as a closed loop tightly coupling agentic reasoning with physical execution. We propose a unified Perception-Language-Action-Discovery (PLAD) framework, wherein embodied agents perceive experimental environments, reason over scientific knowledge, execute physical interventions, and internalize outcomes to drive subsequent exploration. By grounding computational reasoning in robust physical feedback, this approach bridges the gap between digital prediction and empirical validation, offering a roadmap for autonomous discovery systems in the life and chemical sciences.

Mingyang Rao, Kehua Feng, Zhihui Zhu et al.

While Large Language Models (LLMs) have revolutionized scientific text processing, they exhibit a significant capability gap when interpreting chemical reaction diagrams. We identify two fundamental bottlenecks restricting current systems: a Visual Deficit, where generic vision encoders struggle to resolve the strict topological connectivity of dense molecular graphs, and a Semantic Disconnect, where standard linear strings, such as SMILES, fail to effectively activate the model's latent chemical reasoning. To bridge these gaps, we propose the Chemical Visual Activation (ChemVA) framework, which employs a Visual Anchor mechanism to ground functional groups via hybrid-granularity detection, followed by a semantic alignment approach that translates visual features into entity names to maximize knowledge activation in LLMs. We evaluate our approach on OCRD-Bench, a newly constructed dataset featuring dense visual-semantic contexts and comprehensive reaction coverage to evaluate the full spectrum from recognition to reasoning. Extensive experiments on OCRD-Bench demonstrate that ChemVA achieves 92.0% structural recognition accuracy. By bridging visual and semantic bottlenecks, our framework delivers a consistent performance gain of approximately 20 percentage points across 9 diverse LLMs, enabling open-weight models to rival proprietary SOTA systems in complex chemical reasoning tasks.

Shuofei Qiao, Yunxiang Wei, Xuehai Wang et al.

The rapid evolution of Large Language Models has catalyzed a surge in scientific idea production, yet this leap has not been accompanied by a matching advance in idea evaluation. The fundamental nature of scientific evaluation needs knowledgeable grounding, collective deliberation, and multi-criteria decision-making. However, existing idea evaluation methods often suffer from narrow knowledge horizons, flattened evaluation dimensions, and the inherent bias in LLM-as-a-Judge. To address these, we regard idea evaluation as a knowledge-grounded, multi-perspective reasoning problem and introduce InnoEval, a deep innovation evaluation framework designed to emulate human-level idea assessment. We apply a heterogeneous deep knowledge search engine that retrieves and grounds dynamic evidence from diverse online sources. We further achieve review consensus with an innovation review board containing reviewers with distinct academic backgrounds, enabling a multi-dimensional decoupled evaluation across multiple metrics. We construct comprehensive datasets derived from authoritative peer-reviewed submissions to benchmark InnoEval. Experiments demonstrate that InnoEval can consistently outperform baselines in point-wise, pair-wise, and group-wise evaluation tasks, exhibiting judgment patterns and consensus highly aligned with human experts.

Tianwen Lyu, Xiang Zhuang, Keyan Ding et al.

Understanding complex biomolecular mechanisms requires multi-step reasoning across molecular interactions, signaling cascades, and metabolic pathways. While large language models(LLMs) show promise in such tasks, their application to biomolecular problems is hindered by logical inconsistencies and the lack of grounding in domain knowledge. Existing approaches often exacerbate these issues: reasoning steps may deviate from biological facts or fail to capture long mechanistic dependencies. To address these challenges, we propose a Knowledge-Augmented Long-CoT Reasoning framework that integrates LLMs with knowledge graph-based multi-hop reasoning chains. The framework constructs mechanistic chains via guided multi-hop traversal and pruning on the knowledge graph; these chains are then incorporated into supervised fine-tuning to improve factual grounding and further refined with reinforcement learning to enhance reasoning reliability and consistency. Furthermore, to overcome the shortcomings of existing benchmarks, which are often restricted in scale and scope and lack annotations for deep reasoning chains, we introduce PrimeKGQA, a comprehensive benchmark for biomolecular question answering. Experimental results on both PrimeKGQA and existing datasets demonstrate that although larger closed-source models still perform well on relatively simple tasks, our method demonstrates clear advantages as reasoning depth increases, achieving state-of-the-art performance on multi-hop tasks that demand traversal of structured biological knowledge. These findings highlight the effectiveness of combining structured knowledge with advanced reasoning strategies for reliable and interpretable biomolecular reasoning.

Yiwen Zhang, Keyan Ding, Yihang Wu et al.

Retrieving molecular structures from tandem mass spectra is a crucial step in rapid compound identification. Existing retrieval methods, such as traditional mass spectral library matching, suffer from limited spectral library coverage, while recent cross-modal representation learning frameworks often encounter modality misalignment, resulting in suboptimal retrieval accuracy and generalization. To address these limitations, we propose GLMR, a Generative Language Model-based Retrieval framework that mitigates the cross-modal misalignment through a two-stage process. In the pre-retrieval stage, a contrastive learning-based model identifies top candidate molecules as contextual priors for the input mass spectrum. In the generative retrieval stage, these candidate molecules are integrated with the input mass spectrum to guide a generative model in producing refined molecular structures, which are then used to re-rank the candidates based on molecular similarity. Experiments on both MassSpecGym and the proposed MassRET-20k dataset demonstrate that GLMR significantly outperforms existing methods, achieving over 40% improvement in top-1 accuracy and exhibiting strong generalizability.

Shunyang Luo, Peibei Cao, Zhihui Zhu et al.

Reward models (RMs) are central to aligning large language models, yet their practical effectiveness hinges on generalization to unseen prompts and shifting distributions. Most existing RM evaluations rely on static, pre-annotated preference datasets, which provide limited coverage and often fail to faithfully assess generalization in open-world settings. We introduce Pairwise Maximum Discrepancy Competition (PMDC), a dynamic and annotation-efficient framework for evaluating RM generalization using a large, unlabeled, open-domain prompt pool. PMDC actively selects prompt--response pairs that maximize disagreement between two RMs, yielding a compact set of highly contentious test cases. These cases are adjudicated by an oracle, and the resulting outcomes are aggregated via a Bradley--Terry model to produce a global ranking and pairwise win-rate landscape of RMs. We apply PMDC to re-evaluate 10 representative RMs and observe substantial rank reshuffling compared with conventional benchmarks. Qualitative analyses further uncover systematic generalization failures, providing valuable insights for improving reward modeling.

Yuqi Tang, Jing Yu, Zichang Su et al.

Clinical diagnosis begins with doctor-patient interaction, during which physicians iteratively gather information, determine examination and refine differential diagnosis through patients' response. This dynamic clinical-reasoning process is poorly represented by existing LLM benchmarks that focus on static question-answering. To mitigate these gaps, recent methods explore dynamic medical frameworks involving interactive clinical dialogues. Although effective, they often rely on limited, contamination-prone datasets and lack granular, multi-level evaluation. In this work, we propose ClinDEF, a dynamic framework for assessing clinical reasoning in LLMs through simulated diagnostic dialogues. Grounded in a disease knowledge graph, our method dynamically generates patient cases and facilitates multi-turn interactions between an LLM-based doctor and an automated patient agent. Our evaluation protocol goes beyond diagnostic accuracy by incorporating fine-grained efficiency analysis and rubric-based assessment of diagnostic quality. Experiments show that ClinDEF effectively exposes critical clinical reasoning gaps in state-of-the-art LLMs, offering a more nuanced and clinically meaningful evaluation paradigm.

Kehua Feng, Keyan Ding, Yuhao Wang et al.

Recent advancements in large language models (LLMs) have accelerated progress toward artificial general intelligence, yet their potential to generate harmful content poses critical safety challenges. Existing alignment methods often struggle to cover diverse safety scenarios and remain vulnerable to adversarial attacks. In this work, we propose SAFER, a framework for Safety Alignment via eFficient Ex-Ante Reasoning. Our approach instantiates structured Ex-Ante reasoning through initial assessment, rule verification, and path calibration, and embeds predefined safety rules to provide transparent and verifiable safety judgments. Specifically, our approach consists of two training stages: (1) supervised fine-tuning with synthetic traces to teach the multi-stage Ex-Ante reasoning, and (2) step-level reasoning preference optimization to jointly enhance safety, utility, and efficiency. Experiments on multiple open-source LLMs demonstrate that SAFER significantly enhances safety performance while maintaining helpfulness and response efficiency.

Xiang Zhuang, Bin Wu, Jiyu Cui et al.

Molecular structure elucidation involves deducing a molecule's structure from various types of spectral data, which is crucial in chemical experimental analysis. While large language models (LLMs) have shown remarkable proficiency in analyzing and reasoning through complex tasks, they still encounter substantial challenges in molecular structure elucidation. We identify that these challenges largely stem from LLMs' limited grasp of specialized chemical knowledge. In this work, we introduce a Knowledge-enhanced reasoning framework for Molecular Structure Elucidation (K-MSE), leveraging Monte Carlo Tree Search for test-time scaling as a plugin. Specifically, we construct an external molecular substructure knowledge base to extend the LLMs' coverage of the chemical structure space. Furthermore, we design a specialized molecule-spectrum scorer to act as a reward model for the reasoning process, addressing the issue of inaccurate solution evaluation in LLMs. Experimental results show that our approach significantly boosts performance, particularly gaining more than 20% improvement on both GPT-4o-mini and GPT-4o. Our code is available at https://github.com/HICAI-ZJU/K-MSE.

Yongrui Chen, Zhiqiang Liu, Jing Yu et al.

Large Language Models (LLMs) have demonstrated substantial progress on reasoning tasks involving unstructured text, yet their capabilities significantly deteriorate when reasoning requires integrating structured external knowledge such as knowledge graphs, code snippets, or formal logic. This limitation is partly due to the absence of benchmarks capable of systematically evaluating LLM performance across diverse structured knowledge modalities. To address this gap, we introduce \textbf{\textsc{OneEval}}, a comprehensive benchmark explicitly designed to assess the knowledge-intensive reasoning capabilities of LLMs across four structured knowledge modalities, unstructured text, knowledge graphs, code, and formal logic, and five critical domains (general knowledge, government, science, law, and programming). \textsc{OneEval} comprises 4,019 carefully curated instances and includes a challenging subset, \textsc{OneEval}\textsubscript{Hard}, consisting of 1,285 particularly difficult cases. Through extensive evaluation of 18 state-of-the-art open-source and proprietary LLMs, we establish three core findings: a) \emph{persistent limitations in structured reasoning}, with even the strongest model achieving only 32.2\% accuracy on \textsc{OneEval}\textsubscript{Hard}; b) \emph{performance consistently declines as the structural complexity of the knowledge base increases}, with accuracy dropping sharply from 53\% (textual reasoning) to 25\% (formal logic); and c) \emph{diminishing returns from extended reasoning chains}, highlighting the critical need for models to adapt reasoning depth appropriately to task complexity. We release the \textsc{OneEval} datasets, evaluation scripts, and baseline results publicly, accompanied by a leaderboard to facilitate ongoing advancements in structured knowledge reasoning.

Kehua Feng, Xinyi Shen, Weijie Wang et al.

Large language models (LLMs) are playing an increasingly important role in scientific research, yet there remains a lack of comprehensive benchmarks to evaluate the breadth and depth of scientific knowledge embedded in these models. To address this gap, we introduce SciKnowEval, a large-scale dataset designed to systematically assess LLMs across five progressive levels of scientific understanding: memory, comprehension, reasoning, discernment, and application. SciKnowEval comprises 28K multi-level questions and solutions spanning biology, chemistry, physics, and materials science. Using this benchmark, we evaluate 20 leading open-source and proprietary LLMs. The results show that while proprietary models often achieve state-of-the-art performance, substantial challenges remain -- particularly in scientific reasoning and real-world application. We envision SciKnowEval as a standard benchmark for evaluating scientific capabilities in LLMs and as a catalyst for advancing more capable and reliable scientific language models.

Keyan Ding, Kede Ma, Shiqi Wang et al.

Objective measures of image quality generally operate by comparing pixels of a "degraded" image to those of the original. Relative to human observers, these measures are overly sensitive to resampling of texture regions (e.g., replacing one patch of grass with another). Here, we develop the first full-reference image quality model with explicit tolerance to texture resampling. Using a convolutional neural network, we construct an injective and differentiable function that transforms images to multi-scale overcomplete representations. We demonstrate empirically that the spatial averages of the feature maps in this representation capture texture appearance, in that they provide a set of sufficient statistical constraints to synthesize a wide variety of texture patterns. We then describe an image quality method that combines correlations of these spatial averages ("texture similarity") with correlations of the feature maps ("structure similarity"). The parameters of the proposed measure are jointly optimized to match human ratings of image quality, while minimizing the reported distances between subimages cropped from the same texture images. Experiments show that the optimized method explains human perceptual scores, both on conventional image quality databases, as well as on texture databases. The measure also offers competitive performance on related tasks such as texture classification and retrieval. Finally, we show that our method is relatively insensitive to geometric transformations (e.g., translation and dilation), without use of any specialized training or data augmentation. Code is available at https://github.com/dingkeyan93/DISTS.

Yuan Liang, Ruobin Zhong, Haoming Xu et al.

Current AI agents can flexibly invoke tools and execute complex tasks, yet their long-term advancement is hindered by the lack of systematic accumulation and transfer of skills. Without a unified mechanism for skill consolidation, agents frequently ``reinvent the wheel'', rediscovering solutions in isolated contexts without leveraging prior strategies. To overcome this limitation, we introduce SkillNet, an open infrastructure designed to create, evaluate, and organize AI skills at scale. SkillNet structures skills within a unified ontology that supports creating skills from heterogeneous sources, establishing rich relational connections, and performing multi-dimensional evaluation across Safety, Completeness, Executability, Maintainability, and Cost-awareness. Our infrastructure integrates a repository of over 200,000 skills, an interactive platform, and a versatile Python toolkit. Experimental evaluations on ALFWorld, WebShop, and ScienceWorld demonstrate that SkillNet significantly enhances agent performance, improving average rewards by 40% and reducing execution steps by 30% across multiple backbone models. By formalizing skills as evolving, composable assets, SkillNet provides a robust foundation for agents to move from transient experience to durable mastery.

Keyan Ding, Jing Yu, Junjie Huang et al.

Scientific research increasingly relies on specialized computational tools, yet effectively utilizing these tools demands substantial domain expertise. While Large Language Models (LLMs) show promise in tool automation, they struggle to seamlessly integrate and orchestrate multiple tools for complex scientific workflows. Here, we present SciToolAgent, an LLM-powered agent that automates hundreds of scientific tools across biology, chemistry, and materials science. At its core, SciToolAgent leverages a scientific tool knowledge graph that enables intelligent tool selection and execution through graph-based retrieval-augmented generation. The agent also incorporates a comprehensive safety-checking module to ensure responsible and ethical tool usage. Extensive evaluations on a curated benchmark demonstrate that SciToolAgent significantly outperforms existing approaches. Case studies in protein engineering, chemical reactivity prediction, chemical synthesis, and metal-organic framework screening further demonstrate SciToolAgent's capability to automate complex scientific workflows, making advanced research tools accessible to both experts and non-experts.

Yuhao Wang, Keyan Ding, Kehua Feng et al.

Protein language models have emerged as powerful tools for sequence generation, offering substantial advantages in functional optimization and denovo design. However, these models also present significant risks of generating harmful protein sequences, such as those that enhance viral transmissibility or evade immune responses. These concerns underscore critical biosafety and ethical challenges. To address these issues, we propose a Knowledge-guided Preference Optimization (KPO) framework that integrates prior knowledge via a Protein Safety Knowledge Graph. This framework utilizes an efficient graph pruning strategy to identify preferred sequences and employs reinforcement learning to minimize the risk of generating harmful proteins. Experimental results demonstrate that KPO effectively reduces the likelihood of producing hazardous sequences while maintaining high functionality, offering a robust safety assurance framework for applying generative models in biotechnology.

Kehua Feng, Keyan Ding, Zhihui Zhu et al.

While chain-of-thought (CoT) distillation from advanced large language models (LLMs) has proven effective in general reasoning tasks, it struggles in scientific domains where even advanced models often produce incorrect or superficial reasoning due to high complexity and specialized knowledge requirements. Directly distilling from such flawed outputs results in low-quality training data and limits the performance of smaller student models. To overcome this, we propose CoT-Evo, an evolutionary CoT distillation framework. It begins by constructing a diverse pool of reasoning trajectories from multiple LLM thinkers, enriches them with automatically retrieved domain knowledge, and iteratively refines the trajectories using novelty-driven selection, reflective recombination and mutation. The refinement is guided by a fitness function that evaluates answer correctness, coherence, and effective knowledge utilization. This results in a high-quality CoT dataset tailored for scientific reasoning. We employ this evolved dataset to fine-tune a compact model, which achieves state-of-the-art performance on scientific reasoning benchmarks. Our work establishes a scalable approach to synthesizing high-fidelity scientific reasoning data from diverse and fallible LLMs.

Hanwei Zhu, Yu Tian, Keyan Ding et al.

Image quality assessment (IQA) is inherently complex, as it reflects both the quantification and interpretation of perceptual quality rooted in the human visual system. Conventional approaches typically rely on fixed models to output scalar scores, limiting their adaptability to diverse distortions, user-specific queries, and interpretability needs. Furthermore, scoring and interpretation are often treated as independent processes, despite their interdependence: interpretation identifies perceptual degradations, while scoring abstracts them into a compact metric. To address these limitations, we propose AgenticIQA, a modular agentic framework that integrates vision-language models (VLMs) with traditional IQA tools in a dynamic, query-aware manner. AgenticIQA decomposes IQA into four subtasks -- distortion detection, distortion analysis, tool selection, and tool execution -- coordinated by a planner, executor, and summarizer. The planner formulates task-specific strategies, the executor collects perceptual evidence via tool invocation, and the summarizer integrates this evidence to produce accurate scores with human-aligned explanations. To support training and evaluation, we introduce AgenticIQA-200K, a large-scale instruction dataset tailored for IQA agents, and AgenticIQA-Eval, the first benchmark for assessing the planning, execution, and summarization capabilities of VLM-based IQA agents. Extensive experiments across diverse IQA datasets demonstrate that AgenticIQA consistently surpasses strong baselines in both scoring accuracy and explanatory alignment.

Runwen Hu, Peilin Chen, Keyan Ding et al.

Artificial intelligence (AI) revolutionizes molecule generation in bioengineering and biological research, significantly accelerating discovery processes. However, this advancement introduces critical concerns regarding intellectual property protection. To address these challenges, we propose the first robust watermarking method designed for molecules, which utilizes atom-level features to preserve molecular integrity and invariant features to ensure robustness against affine transformations. Comprehensive experiments validate the effectiveness of our method using the datasets QM9 and GEOM-DRUG, and generative models GeoBFN and GeoLDM. We demonstrate the feasibility of embedding watermarks, maintaining basic properties higher than 90.00\% while achieving watermark accuracy greater than 95.00\%. Furthermore, downstream docking simulations reveal comparable performance between original and watermarked molecules, with binding affinities reaching -6.00 kcal/mol and root mean square deviations below 1.602 Å. These results confirm that our watermarking technique effectively safeguards molecular intellectual property without compromising scientific utility, enabling secure and responsible AI integration in molecular discovery and research applications.

Yuqi Tang, Kehua Feng, Yunfeng Wang et al.

Evaluating the conversational abilities of large language models (LLMs) remains a challenging task. Current mainstream approaches primarily rely on the "LLM-as-a-judge" paradigm, where an LLM is prompted to serve as an evaluator to assess dialogue quality. However, such methods often suffer from various biases, which undermine the reliability and consistency of the evaluation results. To mitigate these biases, recent methods employ multiple LLMs as judges and aggregate their judgments to select the optimal assessment. Although effective, this multi-judge approach incurs significant computational overhead during inference. In this paper, we propose an efficient multi-turn dialogue evaluator that captures the collective wisdom of multiple LLM judges by aggregating their preference knowledge into a single model. Our approach preserves the advantages of diverse multi-judge feedback while drastically reducing the evaluation cost, enabling fast and flexible dialogue quality assessment. Extensive experiments on seven single rating and pairwise comparison dialogue evaluation benchmarks demonstrate that our method outperforms existing baselines across diverse scenarios, showcasing its efficiency and robustness.

Han Liu, Keyan Ding, Peilin Chen et al.

Accurate prediction of protein-ligand binding affinity is critical for drug discovery. While recent deep learning approaches have demonstrated promising results, they often rely solely on structural features of proteins and ligands, overlooking their valuable biochemical knowledge associated with binding affinity. To address this limitation, we propose KEPLA, a novel deep learning framework that explicitly integrates prior knowledge from Gene Ontology and ligand properties to enhance prediction performance. KEPLA takes protein sequences and ligand molecular graphs as input and optimizes two complementary objectives: (1) aligning global representations with knowledge graph relations to capture domain-specific biochemical insights, and (2) leveraging cross attention between local representations to construct fine-grained joint embeddings for prediction. Experiments on two benchmark datasets across both in-domain and cross-domain scenarios demonstrate that KEPLA consistently outperforms state-of-the-art baselines. Furthermore, interpretability analyses based on knowledge graph relations and cross attention maps provide valuable insights into the underlying predictive mechanisms.

Jing Yu, Yuqi Tang, Kehua Feng et al.

Large Language Models (LLMs) have shown impressive capabilities in contextual understanding and reasoning. However, evaluating their performance across diverse scientific domains remains underexplored, as existing benchmarks primarily focus on general domains and fail to capture the intricate complexity of scientific data. To bridge this gap, we construct SciCUEval, a comprehensive benchmark dataset tailored to assess the scientific context understanding capability of LLMs. It comprises ten domain-specific sub-datasets spanning biology, chemistry, physics, biomedicine, and materials science, integrating diverse data modalities including structured tables, knowledge graphs, and unstructured texts. SciCUEval systematically evaluates four core competencies: Relevant information identification, Information-absence detection, Multi-source information integration, and Context-aware inference, through a variety of question formats. We conduct extensive evaluations of state-of-the-art LLMs on SciCUEval, providing a fine-grained analysis of their strengths and limitations in scientific context understanding, and offering valuable insights for the future development of scientific-domain LLMs.

Yixuan Li, Peilin Chen, Hanwei Zhu et al.

Opinion-Unaware Blind Image Quality Assessment (OU-BIQA) models aim to predict image quality without training on reference images and subjective quality scores. Thereinto, image statistical comparison is a classic paradigm, while the performance is limited by the representation ability of visual descriptors. Deep features as visual descriptors have advanced IQA in recent research, but they are discovered to be highly texture-biased and lack of shape-bias. On this basis, we find out that image shape and texture cues respond differently towards distortions, and the absence of either one results in an incomplete image representation. Therefore, to formulate a well-round statistical description for images, we utilize the shapebiased and texture-biased deep features produced by Deep Neural Networks (DNNs) simultaneously. More specifically, we design a Shape-Texture Adaptive Fusion (STAF) module to merge shape and texture information, based on which we formulate qualityrelevant image statistics. The perceptual quality is quantified by the variant Mahalanobis Distance between the inner and outer Shape-Texture Statistics (DSTS), wherein the inner and outer statistics respectively describe the quality fingerprints of the distorted image and natural images. The proposed DSTS delicately utilizes shape-texture statistical relations between different data scales in the deep domain, and achieves state-of-the-art (SOTA) quality prediction performance on images with artificial and authentic distortions.

Keyan Ding, Yi Liu, Xueyi Zou et al.

The latest advances in full-reference image quality assessment (IQA) involve unifying structure and texture similarity based on deep representations. The resulting Deep Image Structure and Texture Similarity (DISTS) metric, however, makes rather global quality measurements, ignoring the fact that natural photographic images are locally structured and textured across space and scale. In this paper, we describe a locally adaptive structure and texture similarity index for full-reference IQA, which we term A-DISTS. Specifically, we rely on a single statistical feature, namely the dispersion index, to localize texture regions at different scales. The estimated probability (of one patch being texture) is in turn used to adaptively pool local structure and texture measurements. The resulting A-DISTS is adapted to local image content, and is free of expensive human perceptual scores for supervised training. We demonstrate the advantages of A-DISTS in terms of correlation with human data on ten IQA databases and optimization of single image super-resolution methods.

Keyan Ding, Kede Ma, Shiqi Wang et al.

The performance of objective image quality assessment (IQA) models has been evaluated primarily by comparing model predictions to human quality judgments. Perceptual datasets gathered for this purpose have provided useful benchmarks for improving IQA methods, but their heavy use creates a risk of overfitting. Here, we perform a large-scale comparison of IQA models in terms of their use as objectives for the optimization of image processing algorithms. Specifically, we use eleven full-reference IQA models to train deep neural networks for four low-level vision tasks: denoising, deblurring, super-resolution, and compression. Subjective testing on the optimized images allows us to rank the competing models in terms of their perceptual performance, elucidate their relative advantages and disadvantages in these tasks, and propose a set of desirable properties for incorporation into future IQA models.

Keyan Ding, Kede Ma, Shiqi Wang

The goal of research in automatic image popularity assessment (IPA) is to develop computational models that can accurately predict the potential of a social image to go viral on the Internet. Here, we aim to single out the contribution of visual content to image popularity, i.e., intrinsic image popularity. Specifically, we first describe a probabilistic method to generate massive popularity-discriminable image pairs, based on which the first large-scale image database for intrinsic IPA (I$^2$PA) is established. We then develop computational models for I$^2$PA based on deep neural networks, optimizing for ranking consistency with millions of popularity-discriminable image pairs. Experiments on Instagram and other social platforms demonstrate that the optimized model performs favorably against existing methods, exhibits reasonable generalizability on different databases, and even surpasses human-level performance on Instagram. In addition, we conduct a psychophysical experiment to analyze various aspects of human behavior in I$^2$PA.

Keyan Ding, Linfang Xiao

Active contour models based on local region fitting energy can segment images with intensity inhomogeneity effectively, but their segmentation results are easy to error if the initial contour is inappropriate. In this paper, we present a simple and universal method of improving the robustness of initial contour for these local fitting-based models. The core idea of proposed method is exchanging the fitting values on the two sides of contour, so that the fitting values inside the contour are always larger (or smaller) than the values outside the contour in the process of curve evolution. In this way, the whole curve will evolve along the inner (or outer) boundaries of object, and less likely to be stuck in the object or background. Experimental results have proved that using the proposed method can enhance the robustness of initial contour and meanwhile keep the original advantages in the local fitting-based models.