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.

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.

Beyond Chemical QA: Evaluating LLM's Chemical Reasoning with Modular Chemical Operations

While large language models (LLMs) with Chain-of-Thought (CoT) reasoning excel in mathematics and coding, their potential for systematic reasoning in chemistry, a domain demanding rigorous structural analysis for real-world tasks like drug design and reaction engineering, remains untapped. Current benchmarks focus on simple knowledge retrieval, neglecting step-by-step reasoning required for complex tasks such as molecular optimization and reaction prediction. To address this, we introduce ChemCoTBench, a reasoning framework that bridges molecular structure understanding with arithmetic-inspired operations, including addition, deletion, and substitution, to formalize chemical problem-solving into transparent, step-by-step workflows. By treating molecular transformations as modular "chemical operations", the framework enables slow-thinking reasoning, mirroring the logic of mathematical proofs while grounding solutions in real-world chemical constraints. We evaluate models on two high-impact tasks: Molecular Property Optimization and Chemical Reaction Prediction. These tasks mirror real-world challenges while providing structured evaluability. By providing annotated datasets, a reasoning taxonomy, and baseline evaluations, ChemCoTBench bridges the gap between abstract reasoning methods and practical chemical discovery, establishing a foundation for advancing LLMs as tools for AI-driven scientific innovation.

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.

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.

Enhanced Sampling, Public Dataset and Generative Model for Drug-Protein Dissociation Dynamics

Drug-protein binding and dissociation dynamics are fundamental to understanding molecular interactions in biological systems. While many tools for drug-protein interaction studies have emerged, especially artificial intelligence (AI)-based generative models, predictive tools on binding/dissociation kinetics and dynamics are still limited. We propose a novel research paradigm that combines molecular dynamics (MD) simulations, enhanced sampling, and AI generative models to address this issue. We propose an enhanced sampling strategy to efficiently implement the drug-protein dissociation process in MD simulations and estimate the free energy surface (FES). We constructed a program pipeline of MD simulations based on this sampling strategy, thus generating a dataset including 26,612 drug-protein dissociation trajectories containing about 13 million frames. We named this dissociation dynamics dataset DD-13M and used it to train a deep equivariant generative model UnbindingFlow, which can generate collision-free dissociation trajectories. The DD-13M database and UnbindingFlow model represent a significant advancement in computational structural biology, and we anticipate its broad applicability in machine learning studies of drug-protein interactions. Our ongoing efforts focus on expanding this methodology to encompass a broader spectrum of drug-protein complexes and exploring novel applications in pathway prediction.

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.

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.

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.

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.