arXiv subjects

Bin Feng

Publications and source records attributed to Bin Feng.

At least 19 recordsLinked to original sources

arXiv2026

Apodex Discovery: Reality Benchmarks and Environments for Evaluating and Building Discoverative Artificial Intelligence

Apollo did not reach the Moon merely because its engineers could solve difficult equations. It succeeded by turning a distant ambition into a mission architecture of explicit objectives, simulation, verification, and repeated correction. AI now faces a similar transition: frontier models can solve difficult tasks once the problem, tools, and success criteria are specified, yet consequential real-world challenges rarely arrive in an executable or verifiable form. We introduce Apodex Discovery, a framework for building and evaluating discoverative AI through the heavy-duty solver, a system comprising a foundation model, harness, tools, and control policies that pursues extended, stateful, verifiable investigations. It has three core components. First, a problem-scouting process surveyed 561 industries across 16 sectors, assembled 423 high-value real-world problems, and selected 20 for the initial release. Second, a common environment-task-episode abstraction provides data, tools, constraints, feedback, trajectory recording, and verification of intermediate artifacts and final submissions. Third, HDS6 evaluates Tools, Repair, Alternatives, Coherence, Evidence, and Scope independently of final-task success. In AAV capsid design, Apodex surpassed the published state of the art by 7% across viability, tropism, structure prediction, and generative design. In drug repurposing and reformulation, a task-specific biomedical environment improved the mean normalized prediction score of GPT-5.5 and GPT-5.6-sol by 2.5 and 7.6 points over the same closed-book backbone. Controlled ablations show that the fixed TRACES episode interface enables attribution of performance differences to specific solver components. Apodex Discovery moves AI evaluation beyond predefined benchmarks toward verifiable investigations aimed at genuine discovery.

cs.AI↗

arXiv2026

Density-aware Hierarchical Clustering Based on Element-Categorized Connection Subgraphs

Clustering is a fundamental data mining technique for pattern recognition through unsupervised learning. Among various clustering methods, hierarchical clustering, density-based clustering, and graph clustering stand out as representative approaches. For hierarchical clustering, it can be categorized into agglomerative and divisive modes to construct clusters in a recursive manner. The key aspect of both modes is the calculation of inter-cluster similarity, which determines whether to merge the sub-clusters into one cluster or divide a current cluster into sub-clusters. Traditionally, the similarity is derived from pairwise distances, often overlooking density variations and structural connectivity in graphs. To address this, we propose a density-aware hierarchical clustering method based on element-categorized connection subgraphs (DHC-ECS), which effectively integrates the hierarchical clustering, density-based clustering, and graph clustering. Particularly, a novel inter-cluster similarity metric is introduced that considers not only distances but also the element categorization in the KNN connection subgraphs, kernel density estimation, and local connectivity within sub-clusters. Extensive evaluations on heterogeneous benchmark datasets demonstrate that DHC-ECS exhibits superior overall performance in terms of clustering accuracy and parameter robustness compared with the baseline methods (including AChameleon, RNN-DBSCAN, McDPC, and G-RMS). The work indicates the great potential of the proposed clustering algorithm for low-dimensional datasets by leveraging local density and graph-structured connectivity (i.e., the duality of vertices and edges), as well as the possibility to determine an intrinsic threshold, reducing the reliance on manual parameter tuning.

cs.LG↗

arXiv2026

Sustainable Metal-Organic Framework Water Harvesters in the Artificial Intelligence Era

Metal-organic frameworks (MOFs) are excellent candidates for water harvesting due to their tunable pore environments, which can be precisely engineered to capture and release water in arid conditions. Integrating artificial intelligence (AI) into MOF discovery can further accelerate the design of high-performance sorbents by identifying structural features that enhance atmospheric water harvesting (AWH), stability, and cycling efficiency. In this Perspective, we examine key MOF design principles, including cooperative adsorption, operational relative humidity (RH), uptake capacity, hysteresis, and scalability. We highlight recent design advancements such as multivariate strategies and long-arm linker extension, and examine how these principles tune pore capacity and hydrophilicity, while preserving stability and crystallinity. Furthermore, we discuss how AI, large language models (LLMs), and data mining can accelerate the discovery process through predictive synthesis, inverse design, and elucidating synthesis-structure-property relationships for the next generation of MOF water harvesters.

cond-mat.mtrl-sci↗

arXiv2026

Three-Dimensional Atomic-Scale Structural Transformation in a SrTiO3 Grain Boundary

Grain boundaries (GBs) in complex oxides play critical roles in governing their functional properties, which are intrinsically linked to their three-dimensional (3D) atomic configurations and local chemical environments that can deviate markedly from those of the bulk. However, the 3D atomic structures of GBs remain poorly understood due to the projection limitations of conventional (S)TEM. Here, using multislice electron ptychography, we resolve the 3D atomic structure of a {\Sigma}13(510)/[001] tilt GB in SrTiO3 with simultaneous visualization of both cation and oxygen columns. Depth-resolved reconstruction reveals pronounced structural inhomogeneity along the GB, uncovering a transition from the canonical symmetric configuration (STR1) to an asymmetric configuration (STR2) that is hidden in conventional projection imaging. Quantitative analysis of atomic-column intensities demonstrates that these two GB configurations possess distinct local chemical and vacancy distributions. By further mapping the atomic displacement fields, we reveal that the transformation between STR1 and STR2 proceeds via local atomic shuffling at the GB core and collective shear displacement in the adjoining grains, mediated by the step and dislocation character of the junction, respectively. Moreover, analysis of oxygen octahedral rotations reveals a strong dependence on the local atomic structure with pronounced asymmetry around the STR2 region. These findings establish a direct link among the 3D atomic structure, local chemical composition, and lattice order parameters at the GB, underscoring the critical importance of depth-resolved characterization in understanding and engineering GB-mediated functionalities in complex oxides.

cond-mat.mtrl-sci↗

arXiv2026

SciCustom: A Framework for Custom Evaluation of Scientific Capabilities in Large Language Models

Large language models (LLMs) are increasingly applied to scientific research, yet existing evaluations often fail to reflect the fine-grained capabilities required in practice. Most benchmarks are manually curated or domain-generic, limiting scalability and alignment with real scientific use cases. In this paper, we propose a new framework named SciCustom to address the problem. It enables the custom construction of benchmarks from large-scale scientific data to evaluate application-specific scientific capabilities in LLMs. SciCustom first organizes scientific knowledge into ontology-grounded knowledge units with controlled granularity and trains a tagger to map large-scale data instances into this knowledge space. Given a custom requirement, relevant knowledge units are identified via voting-based multi-model consensus. These units enable relevance-aware benchmark retrieval via binary search, followed by proxy subset selection and data-grounded benchmark generation for efficient evaluation. Experiments in chemistry and healthcare demonstrate that SciCustom reveals fine-grained differences in LLM scientific capabilities that standard benchmarks overlook, while requiring neither expert annotation nor synthetic question generation. This work provides a scalable and application-aware foundation for benchmarking scientific capabilities in LLMs. The source code is available at https://github.com/yjwtheonly/SciCustom.

cs.CL↗

arXiv2026

Pushing Biomolecular Utility-Diversity Frontiers with Supergroup Relative Policy Optimization

Biomolecular generators are often adapted with reward feedback to improve task-specific utility, but pushing utility alone can concentrate generation on a narrow family of candidates. Maintaining diversity is difficult because sample diversity is a set-level property. We introduce Supergroup Relative Policy Optimization (SGRPO), a flexible GRPO-style framework that directly constructs rewards from set-level diversity. For each condition, SGRPO samples a supergroup of candidate sets, compares their diversity under the same condition, and redistributes the group diversity reward to individual rollouts through leave-one-out diversity contributions before combining it with rollout-level utility. This design decouples SGRPO from a particular generator, utility reward, or diversity metric, and allows instantiation with different GRPO-style approaches. We evaluate SGRPO on de novo small-molecule design, pocket-based small-molecule design, and de novo protein design, instantiating it with both GRPO and Coupled-GRPO across autoregressive and discrete diffusion generators. Across decoding sweeps, SGRPO expands the utility-diversity Pareto frontier and achieves the best frontier-level metrics relative to pretrained generators, GRPO, and memory-assisted GRPO when applicable. Our analyses further show that direct set-level diversity rewards remain effective with small groups and help preserve broader generation-distribution coverage during post-training. The code is available at https://github.com/IDEA-XL/SGRPO.

cs.CE↗

arXiv2026

Predicting Scale-Up of Metal-Organic Framework Syntheses with Large Language Models

Scalable synthesis remains the gate between MOF discovery and industrial deployment, as scale-up know-how is fragmented across disparate reports. We introduce ScaleMOF, a literature-mined dataset and a positive-unlabeled learning strategy that fine-tunes large language models. Achieving 93.5% accuracy, this proof-of-concept serves as a literature-grounded ranking tool prioritizing plausible scale-up candidates.

cond-mat.mtrl-sci↗

arXiv2026

ReactBench: A Benchmark for Topological Reasoning in MLLMs on Chemical Reaction Diagrams

Multimodal Large Language Models (MLLMs) excel at recognizing individual visual elements and reasoning over simple linear diagrams. However, when faced with complex topological structures involving branching paths, converging flows, and cyclic dependencies, their reasoning capabilities degrade sharply, even on tasks as basic as counting endpoints. Existing benchmarks fail to probe this gap, focusing on semantic comprehension rather than structural reasoning. We introduce ReactBench, a benchmark that reveals fundamental limitations in structural reasoning through chemical reaction diagrams. These real-world scientific diagrams offer an ideal testbed because they naturally span diverse structures from linear chains to cyclic graphs, while requiring both precise local recognition and coherent global reasoning. Our benchmark comprises 1,618 expert-annotated QA pairs across four hierarchical task dimensions. Extensive evaluation across 24 MLLMs reveals a significant performance gap exceeding 30% between anchor-based tasks and holistic structural reasoning tasks. Controlled ablations confirm this bottleneck lies in reasoning, not perception. These findings expose a fundamental deficit in structural understanding and establish directions for advancing visual reasoning.

cs.AI↗

arXiv2026

Bridging the Skill Gap in Clinical CBCT Interpretation with CBCTRepD

Generative AI has advanced rapidly in medical report generation; however, its application to oral and maxillofacial CBCT reporting remains limited, largely because of the scarcity of high-quality paired CBCT-report data and the intrinsic complexity of volumetric CBCT interpretation. To address this, we introduce CBCTRepD, a bilingual oral and maxillofacial CBCT report-generation system designed for integration into routine radiologist-AI co-authoring workflows. We curated a large-scale, high-quality paired CBCT-report dataset comprising approximately 7,408 studies, covering 55 oral disease entities across diverse acquisition settings, and used it to develop the system. We further established a clinically grounded, multi-level evaluation framework that assesses both direct AI-generated drafts and radiologist-edited collaboration reports using automatic metrics together with radiologist- and clinician-centered evaluation. Using this framework, we show that CBCTRepD achieves superior report-generation performance and produces drafts with writing quality and standardization comparable to those of intermediate radiologists. More importantly, in radiologist-AI collaboration, CBCTRepD provides consistent and clinically meaningful benefits across experience levels: it helps novice radiologists improve toward intermediate-level reporting, enables intermediate radiologists to approach senior-level performance, and even assists senior radiologists by reducing omission-related errors, including clinically important missed lesions. By improving report structure, reducing omissions, and promoting attention to co-existing lesions across anatomical regions, CBCTRepD shows strong and reliable potential as a practical assistant for real-world CBCT reporting across multi-level care settings.

cs.CV↗

arXiv2026

Mozi: Governed Autonomy for Drug Discovery LLM Agents

Tool-augmented large language model (LLM) agents promise to unify scientific reasoning with computation, yet their deployment in high-stakes domains like drug discovery is bottlenecked by two critical barriers: unconstrained tool-use governance and poor long-horizon reliability. In dependency-heavy pharmaceutical pipelines, autonomous agents often drift into irreproducible trajectories, where early-stage hallucinations multiplicatively compound into downstream failures. To overcome this, we present Mozi, a dual-layer architecture that bridges the flexibility of generative AI with the deterministic rigor of computational biology. Layer A (Control Plane) establishes a governed supervisor--worker hierarchy that enforces role-based tool isolation, limits execution to constrained action spaces, and drives reflection-based replanning. Layer B (Workflow Plane) operationalizes canonical drug discovery stages -- from Target Identification to Lead Optimization -- as stateful, composable skill graphs. This layer integrates strict data contracts and strategic human-in-the-loop (HITL) checkpoints to safeguard scientific validity at high-uncertainty decision boundaries. Operating on the design principle of ``free-form reasoning for safe tasks, structured execution for long-horizon pipelines,'' Mozi provides built-in robustness mechanisms and trace-level audibility to completely mitigate error accumulation. We evaluate Mozi on PharmaBench, a curated benchmark for biomedical agents, demonstrating superior orchestration accuracy over existing baselines. Furthermore, through end-to-end therapeutic case studies, we demonstrate Mozi's ability to navigate massive chemical spaces, enforce stringent toxicity filters, and generate highly competitive in silico candidates, effectively transforming the LLM from a fragile conversationalist into a reliable, governed co-scientist.

cs.AI↗

arXiv2026

TriC-Motion: Tri-Domain Causal Modeling Grounded Text-to-Motion Generation

Text-to-motion generation, a rapidly evolving field in computer vision, aims to produce realistic and text-aligned motion sequences. Current methods primarily focus on spatial-temporal modeling or independent frequency domain analysis, lacking a unified framework for joint optimization across spatial, temporal, and frequency domains. This limitation hinders the model's ability to leverage information from all domains simultaneously, leading to suboptimal generation quality. Additionally, in motion generation frameworks, motion-irrelevant cues caused by noise are often entangled with features that contribute positively to generation, thereby leading to motion distortion. To address these issues, we propose Tri-Domain Causal Text-to-Motion Generation (TriC-Motion), a novel diffusion-based framework integrating spatial-temporal-frequency-domain modeling with causal intervention. TriC-Motion includes three core modeling modules for domain-specific modeling, namely Temporal Motion Encoding, Spatial Topology Modeling, and Hybrid Frequency Analysis. After comprehensive modeling, a Score-guided Tri-domain Fusion module integrates valuable information from the triple domains, simultaneously ensuring temporal consistency, spatial topology, motion trends, and dynamics. Moreover, the Causality-based Counterfactual Motion Disentangler is meticulously designed to expose motion-irrelevant cues to eliminate noise, disentangling the real modeling contributions of each domain for superior generation. Extensive experimental results validate that TriC-Motion achieves superior performance compared to state-of-the-art methods, attaining an outstanding R@1 of 0.612 on the HumanML3D dataset. These results demonstrate its capability to generate high-fidelity, coherent, diverse, and text-aligned motion sequences. Code is available at: https://caoyiyang1105.github.io/TriC-Motion/.

cs.CV↗

arXiv2026

Human Identification at a Distance: Challenges, Methods and Results on the Competition HID 2025

Human identification at a distance (HID) is challenging because traditional biometric modalities such as face and fingerprints are often difficult to acquire in real-world scenarios. Gait recognition provides a practical alternative, as it can be captured reliably at a distance. To promote progress in gait recognition and provide a fair evaluation platform, the International Competition on Human Identification at a Distance (HID) has been organized annually since 2020. Since 2023, the competition has adopted the challenging SUSTech-Competition dataset, which features substantial variations in clothing, carried objects, and view angles. No dedicated training data are provided, requiring participants to train their models using external datasets. Each year, the competition applies a different random seed to generate distinct evaluation splits, which reduces the risk of overfitting and supports a fair assessment of cross-domain generalization. While HID 2023 and HID 2024 already used this dataset, HID 2025 explicitly examined whether algorithmic advances could surpass the accuracy limits observed previously. Despite the heightened difficulty, participants achieved further improvements, and the best-performing method reached 94.2% accuracy, setting a new benchmark on this dataset. We also analyze key technical trends and outline potential directions for future research in gait recognition.

cs.CV↗

arXiv2026

Agentic reinforcement learning empowers next-generation chemical language models for molecular design and synthesis

Language models are revolutionizing the biochemistry domain, assisting scientists in drug design and chemical synthesis with high efficiency. Yet current approaches struggle between small language models prone to hallucination and limited knowledge retention, and large cloud-based language models plagued by privacy risks and high inference costs. To bridge this gap, we introduce ChemCRAFT, a novel framework leveraging agentic reinforcement learning to decouple chemical reasoning from knowledge storage. Instead of forcing the model to memorize vast chemical data, our approach empowers the language model to interact with a sandbox for precise information retrieval. This externalization of knowledge allows a locally deployable small model to achieve superior performance with minimal inference costs. To enable small language models for agent-calling ability, we build an agentic trajectory construction pipeline and a comprehensive chemical-agent sandbox. Based on sandbox interactions, we constructed ChemToolDataset, the first large-scale chemical tool trajectory dataset. Simultaneously, we propose SMILES-GRPO to build a dense chemical reward function, promoting the model's ability to call chemical agents. Evaluations across diverse aspects of drug design show that ChemCRAFT outperforms current cloud-based LLMs in molecular structure analysis, molecular optimization, and synthesis pathway prediction, demonstrating that scientific reasoning is not solely an emergent ability of model scale, but a learnable policy of tool orchestration. This work establishes a cost-effective and privacy-preserving paradigm for AI-aided chemistry, opening new avenues for accelerating molecular discovery with locally deployable agents. Code available at https://github.com/HowardLi1984/ChemCraft.

cs.LG↗

arXiv2026

GO-MLVTON: Garment Occlusion-Aware Multi-Layer Virtual Try-On with Diffusion Models

Existing image-based virtual try-on (VTON) methods primarily focus on single-layer or multi-garment VTON, neglecting multi-layer VTON (ML-VTON), which involves dressing multiple layers of garments onto the human body with realistic deformation and layering to generate visually plausible outcomes. The main challenge lies in accurately modeling occlusion relationships between inner and outer garments to reduce interference from redundant inner garment features. To address this, we propose GO-MLVTON, the first multi-layer VTON method, introducing the Garment Occlusion Learning module to learn occlusion relationships and the StableDiffusion-based Garment Morphing & Fitting module to deform and fit garments onto the human body, producing high-quality multi-layer try-on results. Additionally, we present the MLG dataset for this task and propose a new metric named Layered Appearance Coherence Difference (LACD) for evaluation. Extensive experiments demonstrate the state-of-the-art performance of GO-MLVTON. Project page: https://upyuyang.github.io/go-mlvton/.

cs.CV↗

arXiv2025

MolSight: Optical Chemical Structure Recognition with SMILES Pretraining, Multi-Granularity Learning and Reinforcement Learning

Optical Chemical Structure Recognition (OCSR) plays a pivotal role in modern chemical informatics, enabling the automated conversion of chemical structure images from scientific literature, patents, and educational materials into machine-readable molecular representations. This capability is essential for large-scale chemical data mining, drug discovery pipelines, and Large Language Model (LLM) applications in related domains. However, existing OCSR systems face significant challenges in accurately recognizing stereochemical information due to the subtle visual cues that distinguish stereoisomers, such as wedge and dash bonds, ring conformations, and spatial arrangements. To address these challenges, we propose MolSight, a comprehensive learning framework for OCSR that employs a three-stage training paradigm. In the first stage, we conduct pre-training on large-scale but noisy datasets to endow the model with fundamental perception capabilities for chemical structure images. In the second stage, we perform multi-granularity fine-tuning using datasets with richer supervisory signals, systematically exploring how auxiliary tasks-specifically chemical bond classification and atom localization-contribute to molecular formula recognition. Finally, we employ reinforcement learning for post-training optimization and introduce a novel stereochemical structure dataset. Remarkably, we find that even with MolSight's relatively compact parameter size, the Group Relative Policy Optimization (GRPO) algorithm can further enhance the model's performance on stereomolecular. Through extensive experiments across diverse datasets, our results demonstrate that MolSight achieves state-of-the-art performance in (stereo)chemical optical structure recognition.

cs.CV↗

arXiv2025

From Static Structures to Ensembles: Studying and Harnessing Protein Structure Tokenization

Protein structure tokenization converts 3D structures into discrete or vectorized representations, enabling the integration of structural and sequence data. Despite many recent works on structure tokenization, the properties of the underlying discrete representations are not well understood. In this work, we first demonstrate that the successful utilization of structural tokens in a language model for structure prediction depends on using rich, pre-trained sequence embeddings to bridge the semantic gap between the sequence and structural "language". The analysis of the structural vocabulary itself then reveals significant semantic redundancy, where multiple distinct tokens correspond to nearly identical local geometries, acting as "structural synonyms". This redundancy, rather than being a flaw, can be exploited with a simple "synonym swap" strategy to generate diverse conformational ensembles by perturbing a predicted structure with its structural synonyms. This computationally lightweight method accurately recapitulates protein flexibility, performing competitively with state-of-the-art models. Our study provides fundamental insights into the nature of discrete protein structure representations and introduces a powerful, near-instantaneous method for modeling protein dynamics. Source code is available in https://github.com/IDEA-XL/TokenMD.

cs.LG↗

arXiv2025

Gait Recognition via Collaborating Discriminative and Generative Diffusion Models

Gait recognition offers a non-intrusive biometric solution by identifying individuals through their walking patterns. Although discriminative models have achieved notable success in this domain, the full potential of generative models remains largely underexplored. In this paper, we introduce \textbf{CoD$^2$}, a novel framework that combines the data distribution modeling capabilities of diffusion models with the semantic representation learning strengths of discriminative models to extract robust gait features. We propose a Multi-level Conditional Control strategy that incorporates both high-level identity-aware semantic conditions and low-level visual details. Specifically, the high-level condition, extracted by the discriminative extractor, guides the generation of identity-consistent gait sequences, whereas low-level visual details, such as appearance and motion, are preserved to enhance consistency. Furthermore, the generated sequences facilitate the discriminative extractor's learning, enabling it to capture more comprehensive high-level semantic features. Extensive experiments on four datasets (SUSTech1K, CCPG, GREW, and Gait3D) demonstrate that CoD$^2$ achieves state-of-the-art performance and can be seamlessly integrated with existing discriminative methods, yielding consistent improvements.

cs.CV↗

arXiv2025

Hulu-Med: A Transparent Generalist Model towards Holistic Medical Vision-Language Understanding

Real-world clinical decision-making requires integrating heterogeneous data, including medical text, 2D images, 3D volumes, and videos, while existing AI systems fail to unify all these signals, limiting their utility. In this paper, we introduce Hulu-Med, a transparent, generalist medical Vision-Language Model (VLM) designed to unify language-only, 2D/3D vision-language, and video understanding within a single architecture. Hulu-Med is trained on a curated corpus of 16.7 million samples, comprising exclusively public or synthetic data, spanning 12 major anatomical systems and 14 medical imaging modalities. Hulu-Med employs a medical-aware token-reduction strategy that prunes redundant visual tokens, achieving up to a 55% reduction for 3D and video inputs, improving cross-modal efficiency, and enabling training at 7B-32B parameter scales in approximately 4,000-40,000 GPU hours. Across 30 public in-domain and out-of-domain medical benchmarks-covering text reasoning, visual question answering, report generation, multilingual dialogue, video understanding, and rare disease diagnosis-Hulu-Med surpasses existing open-source models on 27 of 30 benchmarks and outperforms proprietary systems such as GPT-4o on 16 benchmarks. Despite being a VLM, Hulu-Med outperforms GPT-4o and matches GPT-o1 on the text-only HealthBench. For the first time in the community, we provide a fully transparent, reproducible and cost-effective pipeline for holistic medical vision-language understanding by releasing our end-to-end data curation, training procedures, and model parameters. Code and models are available at https://github.com/ZJUI-AI4H/Hulu-Med.

cs.CV↗