arXiv subjects

Chen Li

Publications and source records attributed to Chen Li.

At least 217 records · Page 12Linked to original sources

arXiv2025

Combating the Bucket Effect:Multi-Knowledge Alignment for Medication Recommendation

Medication recommendation is crucial in healthcare, offering effective treatments based on patient's electronic health records (EHR). Previous studies show that integrating more medication-related knowledge improves medication representation accuracy. However, not all medications encompass multiple types of knowledge data simultaneously. For instance, some medications provide only textual descriptions without structured data. This imbalance in data availability limits the performance of existing models, a challenge we term the "bucket effect" in medication recommendation. Our data analysis uncovers the severity of the "bucket effect" in medication recommendation. To fill this gap, we introduce a cross-modal medication encoder capable of seamlessly aligning data from different modalities and propose a medication recommendation framework to integrate Multiple types of Knowledge, named MKMed. Specifically, we first pre-train a cross-modal encoder with contrastive learning on five knowledge modalities, aligning them into a unified space. Then, we combine the multi-knowledge medication representations with patient records for recommendations. Extensive experiments on the MIMIC-III and MIMIC-IV datasets demonstrate that MKMed mitigates the "bucket effect" in data, and significantly outperforms state-of-the-art baselines in recommendation accuracy and safety.

cs.AI↗

arXiv2025

PH2ST:ST-Prompt Guided Histological Hypergraph Learning for Spatial Gene Expression Prediction

Spatial Transcriptomics (ST) reveals the spatial distribution of gene expression in tissues, offering critical insights into biological processes and disease mechanisms. However, the high cost, limited coverage, and technical complexity of current ST technologies restrict their widespread use in clinical and research settings, making obtaining high-resolution transcriptomic profiles across large tissue areas challenging. Predicting ST from H\&E-stained histology images has emerged as a promising alternative to address these limitations but remains challenging due to the heterogeneous relationship between histomorphology and gene expression, which is affected by substantial variability across patients and tissue sections. In response, we propose PH2ST, a prompt-guided hypergraph learning framework, which leverages limited ST signals to guide multi-scale histological representation learning for accurate and robust spatial gene expression prediction. Extensive evaluations on two public ST datasets and multiple prompt sampling strategies simulating real-world scenarios demonstrate that PH2ST not only outperforms existing state-of-the-art methods, but also shows strong potential for practical applications such as imputing missing spots, ST super-resolution, and local-to-global prediction, highlighting its value for scalable and cost-effective spatial gene expression mapping in biomedical contexts.

cs.CV↗

arXiv2025

De Novo Generation of Hit-like Molecules from Gene Expression Profiles via Deep Learning

De novo generation of hit-like molecules is a challenging task in the drug discovery process. Most methods in previous studies learn the semantics and syntax of molecular structures by analyzing molecular graphs or simplified molecular input line entry system (SMILES) strings; however, they do not take into account the drug responses of the biological systems consisting of genes and proteins. In this study we propose a hybrid neural network, HNN2Mol, which utilizes gene expression profiles to generate molecular structures with desirable phenotypes for arbitrary target proteins. In the algorithm, a variational autoencoder is employed as a feature extractor to learn the latent feature distribution of the gene expression profiles. Then, a long short-term memory is leveraged as the chemical generator to produce syntactically valid SMILES strings that satisfy the feature conditions of the gene expression profile extracted by the feature extractor. Experimental results and case studies demonstrate that the proposed HNN2Mol model can produce new molecules with potential bioactivities and drug-like properties.

cs.LG↗

arXiv2025

ContourFormer: Real-Time Contour-Based End-to-End Instance Segmentation Transformer

This paper presents Contourformer, a real-time contour-based instance segmentation algorithm. The method is fully based on the DETR paradigm and achieves end-to-end inference through iterative and progressive mechanisms to optimize contours. To improve efficiency and accuracy, we develop two novel techniques: sub-contour decoupling mechanisms and contour fine-grained distribution refinement. In the sub-contour decoupling mechanism, we propose a deformable attention-based module that adaptively selects sampling regions based on the current predicted contour, enabling more effective capturing of object boundary information. Additionally, we design a multi-stage optimization process to enhance segmentation precision by progressively refining sub-contours. The contour fine-grained distribution refinement technique aims to further improve the ability to express fine details of contours. These innovations enable Contourformer to achieve stable and precise segmentation for each instance while maintaining real-time performance. Extensive experiments demonstrate the superior performance of Contourformer on multiple benchmark datasets, including SBD, COCO, and KINS. We conduct comprehensive evaluations and comparisons with existing state-of-the-art methods, showing significant improvements in both accuracy and inference speed. This work provides a new solution for contour-based instance segmentation tasks and lays a foundation for future research, with the potential to become a strong baseline method in this field.

cs.CV↗

arXiv2025

FreeDOM: Online Dynamic Object Removal Framework for Static Map Construction Based on Conservative Free Space Estimation

Online map construction is essential for autonomous robots to navigate in unknown environments. However, the presence of dynamic objects may introduce artifacts into the map, which can significantly degrade the performance of localization and path planning. To tackle this problem, a novel online dynamic object removal framework for static map construction based on conservative free space estimation (FreeDOM) is proposed, consisting of a scan-removal front-end and a map-refinement back-end. First, we propose a multi-resolution map structure for fast computation and effective map representation. In the scan-removal front-end, we employ raycast enhancement to improve free space estimation and segment the LiDAR scan based on the estimated free space. In the map-refinement back-end, we further eliminate residual dynamic objects in the map by leveraging incremental free space information. As experimentally verified on SemanticKITTI, HeLiMOS, and indoor datasets with various sensors, our proposed framework overcomes the limitations of visibility-based methods and outperforms state-of-the-art methods with an average F1-score improvement of 9.7%.

cs.RO↗

arXiv2025

Extending ring polymer molecular dynamics rate theory to reactions with non-separable reactants

The ring polymer molecular dynamics (RPMD) rate theory is an efficient and accurate method for estimating rate coefficients of chemical reactions affected by nuclear quantum effects. The commonly used RPMD treatment of gas-phase bimolecular reactions adopts two dividing surfaces, one at the transition state and another in the reactant asymptote, where partition functions of separated reactants can be readily obtained. With some exceptions, however, this strategy is difficult to implement for processes on surfaces or in liquids, because the reactants are often strongly coupled with the extended medium (surface or solvent) and thus non-separable. Under such circumstances, the RPMD rate theory with a single dividing surface (SDS) is better suited. However, most of its implementations adopted Cartesian forms of the reaction coordinate, which, in many cases, are not ideal for describing complex reactions. Here, we present a SDS-based RPMD implementation, which are able to tackle the aforementioned challenges. This approach is demonstrated in four representative reactions, including the gas phase H + H2 exchange reaction, gas phase CH3NC isomerization, H recombinative desorption from Pt(111), and NO desorption from Pd(111). This implementation, which is applicable to both uni- and bi-molecular reactions, offers a unified treatment of gas-phase and surface reaction rate calculations on the same footing.

physics.chem-ph↗

arXiv2025

DiHuR: Diffusion-Guided Generalizable Human Reconstruction

We introduce DiHuR, a novel Diffusion-guided model for generalizable Human 3D Reconstruction and view synthesis from sparse, minimally overlapping images. While existing generalizable human radiance fields excel at novel view synthesis, they often struggle with comprehensive 3D reconstruction. Similarly, directly optimizing implicit Signed Distance Function (SDF) fields from sparse-view images typically yields poor results due to limited overlap. To enhance 3D reconstruction quality, we propose using learnable tokens associated with SMPL vertices to aggregate sparse view features and then to guide SDF prediction. These tokens learn a generalizable prior across different identities in training datasets, leveraging the consistent projection of SMPL vertices onto similar semantic areas across various human identities. This consistency enables effective knowledge transfer to unseen identities during inference. Recognizing SMPL's limitations in capturing clothing details, we incorporate a diffusion model as an additional prior to fill in missing information, particularly for complex clothing geometries. Our method integrates two key priors in a coherent manner: the prior from generalizable feed-forward models and the 2D diffusion prior, and it requires only multi-view image training, without 3D supervision. DiHuR demonstrates superior performance in both within-dataset and cross-dataset generalization settings, as validated on THuman, ZJU-MoCap, and HuMMan datasets compared to existing methods.

cs.CV↗

arXiv2025

Stacking Brick by Brick: Aligned Feature Isolation for Incremental Face Forgery Detection

The rapid advancement of face forgery techniques has introduced a growing variety of forgeries. Incremental Face Forgery Detection (IFFD), involving gradually adding new forgery data to fine-tune the previously trained model, has been introduced as a promising strategy to deal with evolving forgery methods. However, a naively trained IFFD model is prone to catastrophic forgetting when new forgeries are integrated, as treating all forgeries as a single ''Fake" class in the Real/Fake classification can cause different forgery types overriding one another, thereby resulting in the forgetting of unique characteristics from earlier tasks and limiting the model's effectiveness in learning forgery specificity and generality. In this paper, we propose to stack the latent feature distributions of previous and new tasks brick by brick, $\textit{i.e.}$, achieving $\textbf{aligned feature isolation}$. In this manner, we aim to preserve learned forgery information and accumulate new knowledge by minimizing distribution overriding, thereby mitigating catastrophic forgetting. To achieve this, we first introduce Sparse Uniform Replay (SUR) to obtain the representative subsets that could be treated as the uniformly sparse versions of the previous global distributions. We then propose a Latent-space Incremental Detector (LID) that leverages SUR data to isolate and align distributions. For evaluation, we construct a more advanced and comprehensive benchmark tailored for IFFD. The leading experimental results validate the superiority of our method.

cs.CV↗

arXiv2025

TopoCellGen: Generating Histopathology Cell Topology with a Diffusion Model

Accurately modeling multi-class cell topology is crucial in digital pathology, as it provides critical insights into tissue structure and pathology. The synthetic generation of cell topology enables realistic simulations of complex tissue environments, enhances downstream tasks by augmenting training data, aligns more closely with pathologists' domain knowledge, and offers new opportunities for controlling and generalizing the tumor microenvironment. In this paper, we propose a novel approach that integrates topological constraints into a diffusion model to improve the generation of realistic, contextually accurate cell topologies. Our method refines the simulation of cell distributions and interactions, increasing the precision and interpretability of results in downstream tasks such as cell detection and classification. To assess the topological fidelity of generated layouts, we introduce a new metric, Topological Frechet Distance (TopoFD), which overcomes the limitations of traditional metrics like FID in evaluating topological structure. Experimental results demonstrate the effectiveness of our approach in generating multi-class cell layouts that capture intricate topological relationships. Code is available at https://github.com/Melon-Xu/TopoCellGen.

eess.IV↗

arXiv2025

HunyuanProver: A Scalable Data Synthesis Framework and Guided Tree Search for Automated Theorem Proving

We introduce HunyuanProver, an language model finetuned from the Hunyuan 7B for interactive automatic theorem proving with LEAN4. To alleviate the data sparsity issue, we design a scalable framework to iterative synthesize data with low cost. Besides, guided tree search algorithms are designed to enable effective ``system 2 thinking`` of the prover. HunyuanProver achieves state-of-the-art (SOTA) performances on major benchmarks. Specifically, it achieves a pass of 68.4% on the miniF2F-test compared to 65.9%, the current SOTA results. It proves 4 IMO statements (imo_1960_p2, imo_1962_p2}, imo_1964_p2 and imo_1983_p6) in miniF2F-test. To benefit the community, we will open-source a dataset of 30k synthesized instances, where each instance contains the original question in natural language, the converted statement by autoformalization, and the proof by HunyuanProver.

cs.AI↗

arXiv2025

NeuSG: Neural Implicit Surface Reconstruction with 3D Gaussian Splatting Guidance

Existing neural implicit surface reconstruction methods have achieved impressive performance in multi-view 3D reconstruction by leveraging explicit geometry priors such as depth maps or point clouds as regularization. However, the reconstruction results still lack fine details because of the over-smoothed depth map or sparse point cloud. In this work, we propose a neural implicit surface reconstruction pipeline with guidance from 3D Gaussian Splatting to recover highly detailed surfaces. The advantage of 3D Gaussian Splatting is that it can generate dense point clouds with detailed structure. Nonetheless, a naive adoption of 3D Gaussian Splatting can fail since the generated points are the centers of 3D Gaussians that do not necessarily lie on the surface. We thus introduce a scale regularizer to pull the centers close to the surface by enforcing the 3D Gaussians to be extremely thin. Moreover, we propose to refine the point cloud from 3D Gaussians Splatting with the normal priors from the surface predicted by neural implicit models instead of using a fixed set of points as guidance. Consequently, the quality of surface reconstruction improves from the guidance of the more accurate 3D Gaussian splatting. By jointly optimizing the 3D Gaussian Splatting and the neural implicit model, our approach benefits from both representations and generates complete surfaces with intricate details. Experiments on Tanks and Temples verify the effectiveness of our proposed method.

cs.CV↗

arXiv2025

Leveraging Deep Neural Networks for Aspect-Based Sentiment Classification

Aspect-based sentiment analysis seeks to determine sentiment with a high level of detail. While graph convolutional networks (GCNs) are commonly used for extracting sentiment features, their straightforward use in syntactic feature extraction can lead to a loss of crucial information. This paper presents a novel edge-enhanced GCN, called EEGCN, which improves performance by preserving feature integrity as it processes syntactic graphs. We incorporate a bidirectional long short-term memory (Bi-LSTM) network alongside a self-attention-based transformer for effective text encoding, ensuring the retention of long-range dependencies. A bidirectional GCN (Bi-GCN) with message passing then captures the relationships between entities, while an aspect-specific masking technique removes extraneous information. Extensive evaluations and ablation studies on four benchmark datasets show that EEGCN significantly enhances aspect-based sentiment analysis, overcoming issues with syntactic feature extraction and advancing the field's methodologies.

cs.CL↗

arXiv2025

A Reinforcement Learning-Driven Transformer GAN for Molecular Generation

Generating molecules with desired chemical properties presents a critical challenge in fields such as chemical synthesis and drug discovery. Recent advancements in artificial intelligence (AI) and deep learning have significantly contributed to data-driven molecular generation. However, challenges persist due to the inherent sensitivity of simplified molecular input line entry system (SMILES) representations and the difficulties in applying generative adversarial networks (GANs) to discrete data. This study introduces RL-MolGAN, a novel Transformer-based discrete GAN framework designed to address these challenges. Unlike traditional Transformer architectures, RL-MolGAN utilizes a first-decoder-then-encoder structure, facilitating the generation of drug-like molecules from both $de~novo$ and scaffold-based designs. In addition, RL-MolGAN integrates reinforcement learning (RL) and Monte Carlo tree search (MCTS) techniques to enhance the stability of GAN training and optimize the chemical properties of the generated molecules. To further improve the model's performance, RL-MolWGAN, an extension of RL-MolGAN, incorporates Wasserstein distance and mini-batch discrimination, which together enhance the stability of the GAN. Experimental results on two widely used molecular datasets, QM9 and ZINC, validate the effectiveness of our models in generating high-quality molecular structures with diverse and desirable chemical properties.

cs.LG↗

arXiv2025

WeGen: A Unified Model for Interactive Multimodal Generation as We Chat

Existing multimodal generative models fall short as qualified design copilots, as they often struggle to generate imaginative outputs once instructions are less detailed or lack the ability to maintain consistency with the provided references. In this work, we introduce WeGen, a model that unifies multimodal generation and understanding, and promotes their interplay in iterative generation. It can generate diverse results with high creativity for less detailed instructions. And it can progressively refine prior generation results or integrating specific contents from references following the instructions in its chat with users. During this process, it is capable of preserving consistency in the parts that the user is already satisfied with. To this end, we curate a large-scale dataset, extracted from Internet videos, containing rich object dynamics and auto-labeled dynamics descriptions by advanced foundation models to date. These two information are interleaved into a single sequence to enable WeGen to learn consistency-aware generation where the specified dynamics are generated while the consistency of unspecified content is preserved aligned with instructions. Besides, we introduce a prompt self-rewriting mechanism to enhance generation diversity. Extensive experiments demonstrate the effectiveness of unifying multimodal understanding and generation in WeGen and show it achieves state-of-the-art performance across various visual generation benchmarks. These also demonstrate the potential of WeGen as a user-friendly design copilot as desired. The code and models will be available at https://github.com/hzphzp/WeGen.

cs.CV↗

arXiv2025

TimeStep Master: Asymmetrical Mixture of Timestep LoRA Experts for Versatile and Efficient Diffusion Models in Vision

Diffusion models have driven the advancement of vision generation over the past years. However, it is often difficult to apply these large models in downstream tasks, due to massive fine-tuning cost. Recently, Low-Rank Adaptation (LoRA) has been applied for efficient tuning of diffusion models. Unfortunately, the capabilities of LoRA-tuned diffusion models are limited, since the same LoRA is used for different timesteps of the diffusion process. To tackle this problem, we introduce a general and concise TimeStep Master (TSM) paradigm with two key fine-tuning stages. In the fostering stage (1-stage), we apply different LoRAs to fine-tune the diffusion model at different timestep intervals. This results in different TimeStep LoRA experts that can effectively capture different noise levels. In the assembling stage (2-stage), we design a novel asymmetrical mixture of TimeStep LoRA experts, via core-context collaboration of experts at multi-scale intervals. For each timestep, we leverage TimeStep LoRA expert within the smallest interval as the core expert without gating, and use experts within the bigger intervals as the context experts with time-dependent gating. Consequently, our TSM can effectively model the noise level via the expert in the finest interval, and adaptively integrate contexts from the experts of other scales, boosting the versatility of diffusion models. To show the effectiveness of our TSM paradigm, we conduct extensive experiments on three typical and popular LoRA-related tasks of diffusion models, including domain adaptation, post-pretraining, and model distillation. Our TSM achieves the state-of-the-art results on all these tasks, throughout various model structures (UNet, DiT and MM-DiT) and visual data modalities (Image, Video), showing its remarkable generalization capacity.

cs.CV↗

arXiv2025

Get In Video: Add Anything You Want to the Video

Video editing increasingly demands the ability to incorporate specific real-world instances into existing footage, yet current approaches fundamentally fail to capture the unique visual characteristics of particular subjects and ensure natural instance/scene interactions. We formalize this overlooked yet critical editing paradigm as "Get-In-Video Editing", where users provide reference images to precisely specify visual elements they wish to incorporate into videos. Addressing this task's dual challenges, severe training data scarcity and technical challenges in maintaining spatiotemporal coherence, we introduce three key contributions. First, we develop GetIn-1M dataset created through our automated Recognize-Track-Erase pipeline, which sequentially performs video captioning, salient instance identification, object detection, temporal tracking, and instance removal to generate high-quality video editing pairs with comprehensive annotations (reference image, tracking mask, instance prompt). Second, we present GetInVideo, a novel end-to-end framework that leverages a diffusion transformer architecture with 3D full attention to process reference images, condition videos, and masks simultaneously, maintaining temporal coherence, preserving visual identity, and ensuring natural scene interactions when integrating reference objects into videos. Finally, we establish GetInBench, the first comprehensive benchmark for Get-In-Video Editing scenario, demonstrating our approach's superior performance through extensive evaluations. Our work enables accessible, high-quality incorporation of specific real-world subjects into videos, significantly advancing personalized video editing capabilities.

cs.CV↗

arXiv2025

Reinforcement Learning Within the Classical Robotics Stack: A Case Study in Robot Soccer

Robot decision-making in partially observable, real-time, dynamic, and multi-agent environments remains a difficult and unsolved challenge. Model-free reinforcement learning (RL) is a promising approach to learning decision-making in such domains, however, end-to-end RL in complex environments is often intractable. To address this challenge in the RoboCup Standard Platform League (SPL) domain, we developed a novel architecture integrating RL within a classical robotics stack, while employing a multi-fidelity sim2real approach and decomposing behavior into learned sub-behaviors with heuristic selection. Our architecture led to victory in the 2024 RoboCup SPL Challenge Shield Division. In this work, we fully describe our system's architecture and empirically analyze key design decisions that contributed to its success. Our approach demonstrates how RL-based behaviors can be integrated into complete robot behavior architectures.

cs.RO↗

arXiv2025

Surface-dominant transport in Weyl semimetal NbAs nanowires for next-generation interconnects

Ongoing demands for smaller and more energy efficient electronic devices necessitate alternative interconnect materials with lower electrical resistivity at reduced dimensions. Despite the emergence of many promising candidates, synthesizing high quality nanostructures remains a major bottleneck in evaluating their performance. Here, we report the successful synthesis of Weyl semimetal NbAs nanowires via thermomechanical nanomolding, achieving single crystallinity and controlled diameters as small as 40 nm. Our NbAs nanowires exhibit a remarkably low room-temperature resistivity of 9.7 +/- 1.6 microOhm-cm, which is three to four times lower than their bulk counterpart. Theoretical calculations corroborate the experimental observations, attributing this exceptional resistivity reduction to surface dominant conduction with long carrier lifetime at finite temperatures. Further characterization of NbAs nanowires and bulk single crystals reveals high breakdown current density, robust stability, and superior thermal conductivity. Collectively, these properties highlight the strong potential of NbAs nanowires as next-generation interconnects, which can surpass the limitations of current copper-based interconnects. Technologically, our findings present a practical application of topological materials, while scientifically showcasing the fundamental properties uniquely accessible in nanoscale platforms.

cond-mat.mes-hall↗