arXiv subjects

Bin Feng

Publications and source records attributed to Bin Feng.

At least 37 records · Page 2Linked to original sources

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

Rethinking Text-based Protein Understanding: Retrieval or LLM?

In recent years, protein-text models have gained significant attention for their potential in protein generation and understanding. Current approaches focus on integrating protein-related knowledge into large language models through continued pretraining and multi-modal alignment, enabling simultaneous comprehension of textual descriptions and protein sequences. Through a thorough analysis of existing model architectures and text-based protein understanding benchmarks, we identify significant data leakage issues present in current benchmarks. Moreover, conventional metrics derived from natural language processing fail to accurately assess the model's performance in this domain. To address these limitations, we reorganize existing datasets and introduce a novel evaluation framework based on biological entities. Motivated by our observation, we propose a retrieval-enhanced method, which significantly outperforms fine-tuned LLMs for protein-to-text generation and shows accuracy and efficiency in training-free scenarios. Our code and data can be seen at https://github.com/IDEA-XL/RAPM.

cs.CL↗

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↗

arXiv2025

DentVLM: A Multimodal Vision-Language Model for Comprehensive Dental Diagnosis and Enhanced Clinical Practice

Diagnosing and managing oral diseases necessitate advanced visual interpretation across diverse imaging modalities and integrated information synthesis. While current AI models excel at isolated tasks, they often fall short in addressing the complex, multimodal requirements of comprehensive clinical dental practice. Here we introduce DentVLM, a multimodal vision-language model engineered for expert-level oral disease diagnosis. DentVLM was developed using a comprehensive, large-scale, bilingual dataset of 110,447 images and 2.46 million visual question-answering (VQA) pairs. The model is capable of interpreting seven 2D oral imaging modalities across 36 diagnostic tasks, significantly outperforming leading proprietary and open-source models by 19.6% higher accuracy for oral diseases and 27.9% for malocclusions. In a clinical study involving 25 dentists, evaluating 1,946 patients and encompassing 3,105 QA pairs, DentVLM surpassed the diagnostic performance of 13 junior dentists on 21 of 36 tasks and exceeded that of 12 senior dentists on 12 of 36 tasks. When integrated into a collaborative workflow, DentVLM elevated junior dentists' performance to senior levels and reduced diagnostic time for all practitioners by 15-22%. Furthermore, DentVLM exhibited promising performance across three practical utility scenarios, including home-based dental health management, hospital-based intelligent diagnosis and multi-agent collaborative interaction. These findings establish DentVLM as a robust clinical decision support tool, poised to enhance primary dental care, mitigate provider-patient imbalances, and democratize access to specialized medical expertise within the field of dentistry.

cs.CV↗

arXiv2025

CGTGait: Collaborative Graph and Transformer for Gait Emotion Recognition

Skeleton-based gait emotion recognition has received significant attention due to its wide-ranging applications. However, existing methods primarily focus on extracting spatial and local temporal motion information, failing to capture long-range temporal representations. In this paper, we propose \textbf{CGTGait}, a novel framework that collaboratively integrates graph convolution and transformers to extract discriminative spatiotemporal features for gait emotion recognition. Specifically, CGTGait consists of multiple CGT blocks, where each block employs graph convolution to capture frame-level spatial topology and the transformer to model global temporal dependencies. Additionally, we introduce a Bidirectional Cross-Stream Fusion (BCSF) module to effectively aggregate posture and motion spatiotemporal features, facilitating the exchange of complementary information between the two streams. We evaluate our method on two widely used datasets, Emotion-Gait and ELMD, demonstrating that our CGTGait achieves state-of-the-art or at least competitive performance while reducing computational complexity by approximately \textbf{82.2\%} (only requiring 0.34G FLOPs) during testing. Code is available at \small{https://github.com/githubzjj1/CGTGait.}

cs.CV↗

arXiv2025

BioMD: All-atom Generative Model for Biomolecular Dynamics Simulation

Molecular dynamics (MD) simulations are essential tools in computational chemistry and drug discovery, offering crucial insights into dynamic molecular behavior. However, their utility is significantly limited by substantial computational costs, which severely restrict accessible timescales for many biologically relevant processes. Despite the encouraging performance of existing machine learning (ML) methods, they struggle to generate extended biomolecular system trajectories, primarily due to the lack of MD datasets and the large computational demands of modeling long historical trajectories. Here, we introduce BioMD, the first all-atom generative model to simulate long-timescale protein-ligand dynamics using a hierarchical framework of forecasting and interpolation. We demonstrate the effectiveness and versatility of BioMD on the DD-13M (ligand unbinding) and MISATO datasets. For both datasets, BioMD generates highly realistic conformations, showing high physical plausibility and low reconstruction errors. Besides, BioMD successfully generates ligand unbinding paths for 97.1% of the protein-ligand systems within ten attempts, demonstrating its ability to explore critical unbinding pathways. Collectively, these results establish BioMD as a tool for simulating complex biomolecular processes, offering broad applicability for computational chemistry and drug discovery.

physics.chem-ph↗

arXiv2025

Dynamic 2D Gaussians: Geometrically Accurate Radiance Fields for Dynamic Objects

Reconstructing objects and extracting high-quality surfaces play a vital role in the real world. Current 4D representations show the ability to render high-quality novel views for dynamic objects, but cannot reconstruct high-quality meshes due to their implicit or geometrically inaccurate representations. In this paper, we propose a novel representation that can reconstruct accurate meshes from sparse image input, named Dynamic 2D Gaussians (D-2DGS). We adopt 2D Gaussians for basic geometry representation and use sparse-controlled points to capture the 2D Gaussian's deformation. By extracting the object mask from the rendered high-quality image and masking the rendered depth map, we remove floaters that are prone to occur during reconstruction and can extract high-quality dynamic mesh sequences of dynamic objects. Experiments demonstrate that our D-2DGS is outstanding in reconstructing detailed and smooth high-quality meshes from sparse inputs. The code is available at https://github.com/hustvl/Dynamic-2DGS.

cs.CV↗

arXiv2025

V2T-CoT: From Vision to Text Chain-of-Thought for Medical Reasoning and Diagnosis

Recent advances in multimodal techniques have led to significant progress in Medical Visual Question Answering (Med-VQA). However, most existing models focus on global image features rather than localizing disease-specific regions crucial for diagnosis. Additionally, current research tends to emphasize answer accuracy at the expense of the reasoning pathway, yet both are crucial for clinical decision-making. To address these challenges, we propose From Vision to Text Chain-of-Thought (V2T-CoT), a novel approach that automates the localization of preference areas within biomedical images and incorporates this localization into region-level pixel attention as knowledge for Vision CoT. By fine-tuning the vision language model on constructed R-Med 39K dataset, V2T-CoT provides definitive medical reasoning paths. V2T-CoT integrates visual grounding with textual rationale generation to establish precise and explainable diagnostic results. Experimental results across four Med-VQA benchmarks demonstrate state-of-the-art performance, achieving substantial improvements in both performance and interpretability.

cs.CE↗

arXiv2025

SMI-Editor: Edit-based SMILES Language Model with Fragment-level Supervision

SMILES, a crucial textual representation of molecular structures, has garnered significant attention as a foundation for pre-trained language models (LMs). However, most existing pre-trained SMILES LMs focus solely on the single-token level supervision during pre-training, failing to fully leverage the substructural information of molecules. This limitation makes the pre-training task overly simplistic, preventing the models from capturing richer molecular semantic information. Moreover, during pre-training, these SMILES LMs only process corrupted SMILES inputs, never encountering any valid SMILES, which leads to a train-inference mismatch. To address these challenges, we propose SMI-Editor, a novel edit-based pre-trained SMILES LM. SMI-Editor disrupts substructures within a molecule at random and feeds the resulting SMILES back into the model, which then attempts to restore the original SMILES through an editing process. This approach not only introduces fragment-level training signals, but also enables the use of valid SMILES as inputs, allowing the model to learn how to reconstruct complete molecules from these incomplete structures. As a result, the model demonstrates improved scalability and an enhanced ability to capture fragment-level molecular information. Experimental results show that SMI-Editor achieves state-of-the-art performance across multiple downstream molecular tasks, and even outperforming several 3D molecular representation models.

cs.LG↗

arXiv2025

ExLM: Rethinking the Impact of [MASK] Tokens in Masked Language Models

Masked Language Models (MLMs) have achieved remarkable success in many self-supervised representation learning tasks. MLMs are trained by randomly masking portions of the input sequences with [MASK] tokens and learning to reconstruct the original content based on the remaining context. This paper explores the impact of [MASK] tokens on MLMs. Analytical studies show that masking tokens can introduce the corrupted semantics problem, wherein the corrupted context may convey multiple, ambiguous meanings. This problem is also a key factor affecting the performance of MLMs on downstream tasks. Based on these findings, we propose a novel enhanced-context MLM, ExLM. Our approach expands [MASK] tokens in the input context and models the dependencies between these expanded states. This enhancement increases context capacity and enables the model to capture richer semantic information, effectively mitigating the corrupted semantics problem during pre-training. Experimental results demonstrate that ExLM achieves significant performance improvements in both text modeling and SMILES modeling tasks. Further analysis confirms that ExLM enriches semantic representations through context enhancement, and effectively reduces the semantic multimodality commonly observed in MLMs.

cs.CL↗

arXiv2025

STP4D: Spatio-Temporal-Prompt Consistent Modeling for Text-to-4D Gaussian Splatting

Text-to-4D generation is rapidly developing and widely applied in various scenarios. However, existing methods often fail to incorporate adequate spatio-temporal modeling and prompt alignment within a unified framework, resulting in temporal inconsistencies, geometric distortions, or low-quality 4D content that deviates from the provided texts. Therefore, we propose STP4D, a novel approach that aims to integrate comprehensive spatio-temporal-prompt consistency modeling for high-quality text-to-4D generation. Specifically, STP4D employs three carefully designed modules: Time-varying Prompt Embedding, Geometric Information Enhancement, and Temporal Extension Deformation, which collaborate to accomplish this goal. Furthermore, STP4D is among the first methods to exploit the Diffusion model to generate 4D Gaussians, combining the fine-grained modeling capabilities and the real-time rendering process of 4DGS with the rapid inference speed of the Diffusion model. Extensive experiments demonstrate that STP4D excels in generating high-fidelity 4D content with exceptional efficiency (approximately 4.6s per asset), surpassing existing methods in both quality and speed.

cs.CV↗

arXiv2025

RCCFormer: A Robust Crowd Counting Network Based on Transformer

Crowd counting, which is a key computer vision task, has emerged as a fundamental technology in crowd analysis and public safety management. However, challenges such as scale variations and complex backgrounds significantly impact the accuracy of crowd counting. To mitigate these issues, this paper proposes a robust Transformer-based crowd counting network, termed RCCFormer, specifically designed for background suppression and scale awareness. The proposed method incorporates a Multi-level Feature Fusion Module (MFFM), which meticulously integrates features extracted at diverse stages of the backbone architecture. It establishes a strong baseline capable of capturing intricate and comprehensive feature representations, surpassing traditional baselines. Furthermore, the introduced Detail-Embedded Attention Block (DEAB) captures contextual information and local details through global self-attention and local attention along with a learnable manner for efficient fusion. This enhances the model's ability to focus on foreground regions while effectively mitigating background noise interference. Additionally, we develop an Adaptive Scale-Aware Module (ASAM), with our novel Input-dependent Deformable Convolution (IDConv) as its fundamental building block. This module dynamically adapts to changes in head target shapes and scales, significantly improving the network's capability to accommodate large-scale variations. The effectiveness of the proposed method is validated on the ShanghaiTech Part_A and Part_B, NWPU-Crowd, and QNRF datasets. The results demonstrate that our RCCFormer achieves excellent performance across all four datasets, showcasing state-of-the-art outcomes.

cs.CV↗

arXiv2025

Mask-Adapter: The Devil is in the Masks for Open-Vocabulary Segmentation

Recent open-vocabulary segmentation methods adopt mask generators to predict segmentation masks and leverage pre-trained vision-language models, e.g., CLIP, to classify these masks via mask pooling. Although these approaches show promising results, it is counterintuitive that accurate masks often fail to yield accurate classification results through pooling CLIP image embeddings within the mask regions. In this paper, we reveal the performance limitations of mask pooling and introduce Mask-Adapter, a simple yet effective method to address these challenges in open-vocabulary segmentation. Compared to directly using proposal masks, our proposed Mask-Adapter extracts semantic activation maps from proposal masks, providing richer contextual information and ensuring alignment between masks and CLIP. Additionally, we propose a mask consistency loss that encourages proposal masks with similar IoUs to obtain similar CLIP embeddings to enhance models' robustness to varying predicted masks. Mask-Adapter integrates seamlessly into open-vocabulary segmentation methods based on mask pooling in a plug-and-play manner, delivering more accurate classification results. Extensive experiments across several zero-shot benchmarks demonstrate significant performance gains for the proposed Mask-Adapter on several well-established methods. Notably, Mask-Adapter also extends effectively to SAM and achieves impressive results on several open-vocabulary segmentation datasets. Code and models are available at https://github.com/hustvl/MaskAdapter.

cs.CV↗

arXiv2025

SentiFormer: Metadata Enhanced Transformer for Image Sentiment Analysis

As more and more internet users post images online to express their daily emotions, image sentiment analysis has attracted increasing attention. Recently, researchers generally tend to design different neural networks to extract visual features from images for sentiment analysis. Despite the significant progress, metadata, the data (e.g., text descriptions and keyword tags) for describing the image, has not been sufficiently explored in this task. In this paper, we propose a novel Metadata Enhanced Transformer for sentiment analysis (SentiFormer) to fuse multiple metadata and the corresponding image into a unified framework. Specifically, we first obtain multiple metadata of the image and unify the representations of diverse data. To adaptively learn the appropriate weights for each metadata, we then design an adaptive relevance learning module to highlight more effective information while suppressing weaker ones. Moreover, we further develop a cross-modal fusion module to fuse the adaptively learned representations and make the final prediction. Extensive experiments on three publicly available datasets demonstrate the superiority and rationality of our proposed method.

cs.CV↗

arXiv2025

IPP-Net: A Generalizable Deep Neural Network Model for Indoor Pathloss Radio Map Prediction

In this paper, we propose a generalizable deep neural network model for indoor pathloss radio map prediction (termed as IPP-Net). IPP-Net is based on a UNet architecture and learned from both large-scale ray tracing simulation data and a modified 3GPP indoor hotspot model. The performance of IPP-Net is evaluated in the First Indoor Pathloss Radio Map Prediction Challenge in ICASSP 2025. The evaluation results show that IPP-Net achieves a weighted root mean square error of 9.501 dB on three competition tasks and obtains the second overall ranking.

eess.SP↗

arXiv2024

An accelerate Prediction Strategy for Dynamic Multi-Objective Optimization

This paper addresses the challenge of dynamic multi-objective optimization problems (DMOPs) by introducing novel approaches for accelerating prediction strategies within the evolutionary algorithm framework. Since the objectives of DMOPs evolve over time, both the Pareto optimal set (PS) and the Pareto optimal front (PF) are dynamic. To effectively track the changes in the PS and PF in both decision and objective spaces, we propose an adaptive prediction strategy that incorporates second-order derivatives to predict and adjust the algorithms search behavior. This strategy enhances the algorithm's ability to anticipate changes in the environment, allowing for more efficient population re-initialization. We evaluate the performance of the proposed method against four state-of-the-art algorithms using standard DMOPs benchmark problems. Experimental results demonstrate that the proposed approach significantly outperforms the other algorithms across most test problems.

cs.NE↗