arXiv subjects

Jie Chen

Publications and source records attributed to Jie Chen.

At least 199 records · Page 11Linked to original sources

arXiv2025

Patho-R1: A Multimodal Reinforcement Learning-Based Pathology Expert Reasoner

Recent advances in vision language models (VLMs) have enabled broad progress in the general medical field. However, pathology still remains a more challenging subdomain, with current pathology specific VLMs exhibiting limitations in both diagnostic accuracy and reasoning plausibility. Such shortcomings are largely attributable to the nature of current pathology datasets, which are primarily composed of image description pairs that lack the depth and structured diagnostic paradigms employed by real world pathologists. In this study, we leverage pathology textbooks and real world pathology experts to construct high-quality, reasoning-oriented datasets. Building on this, we introduce Patho-R1, a multimodal RL-based pathology Reasoner, trained through a three-stage pipeline: (1) continued pretraining on 3.5 million image-text pairs for knowledge infusion; (2) supervised fine-tuning on 500k high-quality Chain-of-Thought samples for reasoning incentivizing; (3) reinforcement learning using Group Relative Policy Optimization and Decoupled Clip and Dynamic sAmpling Policy Optimization strategies for multimodal reasoning quality refinement. To further assess the alignment quality of our dataset, we propose Patho-CLIP, trained on the same figure-caption corpus used for continued pretraining. Comprehensive experimental results demonstrate that both Patho-CLIP and Patho-R1 achieve robust performance across a wide range of pathology-related tasks, including zero-shot classification, cross-modal retrieval, Visual Question Answering, and Multiple Choice Question. Our project is available at the Patho-R1 repository: https://github.com/Wenchuan-Zhang/Patho-R1.

cs.CV↗

arXiv2025

Toward a Graph Foundation Model: Pre-Training Transformers With Random Walks

A foundation model like GPT elicits many emergent abilities, owing to the pre-training with broad inclusion of data and the use of the powerful Transformer architecture. While foundation models in natural languages are prevalent, can we build similar models for graphs? This paper describes an approach toward a graph foundation model that is pre-trained with diverse graph datasets by adapting the Transformer backbone. A central challenge toward this end is how a sequence model encodes graphs of varying sizes and from different domains. We propose representing a node as multiple random walks, such that the Transformer can extract node representations from sequences, which in turn form edge and graph representations. We develop a novel context prediction loss for these random walks and theoretically analyze their expressive power in distinguishing neighborhoods and graphs. We also demonstrate the pre-training of our model and its adaptation to downstream tasks, showcasing its potential as a foundation for processing and reasoning with graph-structured data.

cs.LG↗

arXiv2025

Rethinking Generative Human Video Coding with Implicit Motion Transformation

Beyond traditional hybrid-based video codec, generative video codec could achieve promising compression performance by evolving high-dimensional signals into compact feature representations for bitstream compactness at the encoder side and developing explicit motion fields as intermediate supervision for high-quality reconstruction at the decoder side. This paradigm has achieved significant success in face video compression. However, compared to facial videos, human body videos pose greater challenges due to their more complex and diverse motion patterns, i.e., when using explicit motion guidance for Generative Human Video Coding (GHVC), the reconstruction results could suffer severe distortions and inaccurate motion. As such, this paper highlights the limitations of explicit motion-based approaches for human body video compression and investigates the GHVC performance improvement with the aid of Implicit Motion Transformation, namely IMT. In particular, we propose to characterize complex human body signal into compact visual features and transform these features into implicit motion guidance for signal reconstruction. Experimental results demonstrate the effectiveness of the proposed IMT paradigm, which can facilitate GHVC to achieve high-efficiency compression and high-fidelity synthesis.

cs.CV↗

arXiv2025

Digital quantum simulation of squeezed states via enhanced bosonic encoding in a superconducting quantum processor

We present a fully digital approach for simulating single-mode squeezed states on a superconducting quantum processor using an enhanced bosonic encoding strategy. By mapping up to 2^{n} photonic Fock states onto n qubits, our framework leverages Gray-code-based encodings to reduce gate overhead compared to conventional one-hot or binary mappings. We further optimize resource usage by restricting the simulation on Fock states with even number of photons only, effectively doubling the range of photon numbers that can be represented for a given number of qubits. To overcome noise and finite coherence in current hardware, we employ a variational quantum simulation protocol, which adapts shallow, parameterized circuits through iterative optimization. Implemented on the Zuchongzhi-2 superconducting platform, our method demonstrates squeezed-state dynamics across a parameter sweep from vacuum state preparation (r=0) to squeezing levels exceeding the Fock space truncation limit (r>1.63). Experimental results, corroborated by quantum state tomography and Wigner-function analysis, confirm high-fidelity state preparation and demonstrate the potential of Gray-code-inspired techniques for realizing continuous-variable physics on near-term, qubit-based quantum processors.

quant-ph↗

arXiv2025

MTPNet: Multi-Grained Target Perception for Unified Activity Cliff Prediction

Activity cliff prediction is a critical task in drug discovery and material design. Existing computational methods are limited to handling single binding targets, which restricts the applicability of these prediction models. In this paper, we present the Multi-Grained Target Perception network (MTPNet) to incorporate the prior knowledge of interactions between the molecules and their target proteins. Specifically, MTPNet is a unified framework for activity cliff prediction, which consists of two components: Macro-level Target Semantic (MTS) guidance and Micro-level Pocket Semantic (MPS) guidance. By this way, MTPNet dynamically optimizes molecular representations through multi-grained protein semantic conditions. To our knowledge, it is the first time to employ the receptor proteins as guiding information to effectively capture critical interaction details. Extensive experiments on 30 representative activity cliff datasets demonstrate that MTPNet significantly outperforms previous approaches, achieving an average RMSE improvement of 18.95% on top of several mainstream GNN architectures. Overall, MTPNet internalizes interaction patterns through conditional deep learning to achieve unified predictions of activity cliffs, helping to accelerate compound optimization and design. Codes are available at: https://github.com/ZishanShu/MTPNet.

cs.LG↗

arXiv2025

PseudoVC: Improving One-shot Voice Conversion with Pseudo Paired Data

As parallel training data is scarce for one-shot voice conversion (VC) tasks, waveform reconstruction is typically performed by various VC systems. A typical one-shot VC system comprises a content encoder and a speaker encoder. However, two types of mismatches arise: one for the inputs to the content encoder during training and inference, and another for the inputs to the speaker encoder. To address these mismatches, we propose a novel VC training method called \textit{PseudoVC} in this paper. First, we introduce an innovative information perturbation approach named \textit{Pseudo Conversion} to tackle the first mismatch problem. This approach leverages pretrained VC models to convert the source utterance into a perturbed utterance, which is fed into the content encoder during training. Second, we propose an approach termed \textit{Speaker Sampling} to resolve the second mismatch problem, which will substitute the input to the speaker encoder by another utterance from the same speaker during training. Experimental results demonstrate that our proposed \textit{Pseudo Conversion} outperforms previous information perturbation methods, and the overall \textit{PseudoVC} method surpasses publicly available VC models. Audio examples are available.

eess.AS↗

arXiv2025

Foundation Molecular Grammar: Multi-Modal Foundation Models Induce Interpretable Molecular Graph Languages

Recent data-efficient molecular generation approaches exploit graph grammars to introduce interpretability into the generative models. However, grammar learning therein relies on expert annotation or unreliable heuristics for algorithmic inference. We propose Foundation Molecular Grammar (FMG), which leverages multi-modal foundation models (MMFMs) to induce an interpretable molecular language. By exploiting the chemical knowledge of an MMFM, FMG renders molecules as images, describes them as text, and aligns information across modalities using prompt learning. FMG can be used as a drop-in replacement for the prior grammar learning approaches in molecular generation and property prediction. We show that FMG not only excels in synthesizability, diversity, and data efficiency but also offers built-in chemical interpretability for automated molecular discovery workflows. Code is available at https://github.com/shiningsunnyday/induction.

cs.AI↗

arXiv2025

Directed Graph Grammars for Sequence-based Learning

Directed acyclic graphs (DAGs) are a class of graphs commonly used in practice, with examples that include electronic circuits, Bayesian networks, and neural architectures. While many effective encoders exist for DAGs, it remains challenging to decode them in a principled manner, because the nodes of a DAG can have many different topological orders. In this work, we propose a grammar-based approach to constructing a principled, compact and equivalent sequential representation of a DAG. Specifically, we view a graph as derivations over an unambiguous grammar, where the DAG corresponds to a unique sequence of production rules. Equivalently, the procedure to construct such a description can be viewed as a lossless compression of the data. Such a representation has many uses, including building a generative model for graph generation, learning a latent space for property prediction, and leveraging the sequence representational continuity for Bayesian Optimization over structured data. Code is available at https://github.com/shiningsunnyday/induction.

cs.LG↗

arXiv2025

Denoising Mutual Knowledge Distillation in Bi-Directional Multiple Instance Learning

Multiple Instance Learning is the predominant method for Whole Slide Image classification in digital pathology, enabling the use of slide-level labels to supervise model training. Although MIL eliminates the tedious fine-grained annotation process for supervised learning, whether it can learn accurate bag- and instance-level classifiers remains a question. To address the issue, instance-level classifiers and instance masks were incorporated to ground the prediction on supporting patches. These methods, while practically improving the performance of MIL methods, may potentially introduce noisy labels. We propose to bridge the gap between commonly used MIL and fully supervised learning by augmenting both the bag- and instance-level learning processes with pseudo-label correction capabilities elicited from weak to strong generalization techniques. The proposed algorithm improves the performance of dual-level MIL algorithms on both bag- and instance-level predictions. Experiments on public pathology datasets showcase the advantage of the proposed methods.

cs.CV↗

arXiv2025

Enhancing Visual Grounding for GUI Agents via Self-Evolutionary Reinforcement Learning

Graphical User Interface (GUI) agents have made substantial strides in understanding and executing user instructions across diverse platforms. Yet, grounding these instructions to precise interface elements remains challenging, especially in complex, high-resolution, professional environments. Traditional supervised finetuning (SFT) methods often require large volumes of diverse data and exhibit weak generalization. To overcome these limitations, we introduce a reinforcement learning (RL) based framework that incorporates three core strategies: (1) seed data curation to ensure high quality training samples, (2) a dense policy gradient that provides continuous feedback based on prediction accuracy, and (3) a self evolutionary reinforcement finetuning mechanism that iteratively refines the model using attention maps. With only 3k training samples, our 7B-parameter model achieves state-of-the-art results among similarly sized models on three grounding benchmarks. Notably, it attains 47.3\% accuracy on the ScreenSpot-Pro dataset, outperforming much larger models, such as UI-TARS-72B, by a margin of 24.2\%. These findings underscore the effectiveness of RL-based approaches in enhancing GUI agent performance, particularly in high-resolution, complex environments.

cs.AI↗

arXiv2025

Compressing Human Body Video with Interactive Semantics: A Generative Approach

In this paper, we propose to compress human body video with interactive semantics, which can facilitate video coding to be interactive and controllable by manipulating semantic-level representations embedded in the coded bitstream. In particular, the proposed encoder employs a 3D human model to disentangle nonlinear dynamics and complex motion of human body signal into a series of configurable embeddings, which are controllably edited, compactly compressed, and efficiently transmitted. Moreover, the proposed decoder can evolve the mesh-based motion fields from these decoded semantics to realize the high-quality human body video reconstruction. Experimental results illustrate that the proposed framework can achieve promising compression performance for human body videos at ultra-low bitrate ranges compared with the state-of-the-art video coding standard Versatile Video Coding (VVC) and the latest generative compression schemes. Furthermore, the proposed framework enables interactive human body video coding without any additional pre-/post-manipulation processes, which is expected to shed light on metaverse-related digital human communication in the future.

eess.IV↗

arXiv2025

An Information Theory-inspired Strategy for Automatic Network Pruning

Despite superior performance on many computer vision tasks, deep convolution neural networks are well known to be compressed on devices that have resource constraints. Most existing network pruning methods require laborious human efforts and prohibitive computation resources, especially when the constraints are changed. This practically limits the application of model compression when the model needs to be deployed on a wide range of devices. Besides, existing methods are still challenged by the missing theoretical guidance. In this paper we propose an information theory-inspired strategy for automatic model compression. The principle behind our method is the information bottleneck theory, i.e., the hidden representation should compress information with each other. We thus introduce the normalized Hilbert-Schmidt Independence Criterion (nHSIC) on network activations as a stable and generalized indicator of layer importance. When a certain resource constraint is given, we integrate the HSIC indicator with the constraint to transform the architecture search problem into a linear programming problem with quadratic constraints. Such a problem is easily solved by a convex optimization method with a few seconds. We also provide a rigorous proof to reveal that optimizing the normalized HSIC simultaneously minimizes the mutual information between different layers. Without any search process, our method achieves better compression tradeoffs comparing to the state-of-the-art compression algorithms. For instance, with ResNet-50, we achieve a 45.3%-FLOPs reduction, with a 75.75 top-1 accuracy on ImageNet. Codes are avaliable at https://github.com/MAC-AutoML/ITPruner/tree/master.

cs.CV↗

arXiv2025

Dual-Balancing for Physics-Informed Neural Networks

Physics-informed neural networks (PINNs) have emerged as a new learning paradigm for solving partial differential equations (PDEs) by enforcing the constraints of physical equations, boundary conditions (BCs), and initial conditions (ICs) into the loss function. Despite their successes, vanilla PINNs still suffer from poor accuracy and slow convergence due to the intractable multi-objective optimization issue. In this paper, we propose a novel Dual-Balanced PINN (DB-PINN), which dynamically adjusts loss weights by integrating inter-balancing and intra-balancing to alleviate two imbalance issues in PINNs. Inter-balancing aims to mitigate the gradient imbalance between PDE residual loss and condition-fitting losses by determining an aggregated weight that offsets their gradient distribution discrepancies. Intra-balancing acts on condition-fitting losses to tackle the imbalance in fitting difficulty across diverse conditions. By evaluating the fitting difficulty based on the loss records, intra-balancing can allocate the aggregated weight proportionally to each condition loss according to its fitting difficulty level. We further introduce a robust weight update strategy to prevent abrupt spikes and arithmetic overflow in instantaneous weight values caused by large loss variances, enabling smooth weight updating and stable training. Extensive experiments demonstrate that DB-PINN achieves significantly superior performance than those popular gradient-based weighting methods in terms of convergence speed and prediction accuracy. Our code and supplementary material are available at https://github.com/chenhong-zhou/DualBalanced-PINNs.

cs.LG↗

arXiv2025

iSegMan: Interactive Segment-and-Manipulate 3D Gaussians

The efficient rendering and explicit nature of 3DGS promote the advancement of 3D scene manipulation. However, existing methods typically encounter challenges in controlling the manipulation region and are unable to furnish the user with interactive feedback, which inevitably leads to unexpected results. Intuitively, incorporating interactive 3D segmentation tools can compensate for this deficiency. Nevertheless, existing segmentation frameworks impose a pre-processing step of scene-specific parameter training, which limits the efficiency and flexibility of scene manipulation. To deliver a 3D region control module that is well-suited for scene manipulation with reliable efficiency, we propose interactive Segment-and-Manipulate 3D Gaussians (iSegMan), an interactive segmentation and manipulation framework that only requires simple 2D user interactions in any view. To propagate user interactions to other views, we propose Epipolar-guided Interaction Propagation (EIP), which innovatively exploits epipolar constraint for efficient and robust interaction matching. To avoid scene-specific training to maintain efficiency, we further propose the novel Visibility-based Gaussian Voting (VGV), which obtains 2D segmentations from SAM and models the region extraction as a voting game between 2D Pixels and 3D Gaussians based on Gaussian visibility. Taking advantage of the efficient and precise region control of EIP and VGV, we put forth a Manipulation Toolbox to implement various functions on selected regions, enhancing the controllability, flexibility and practicality of scene manipulation. Extensive results on 3D scene manipulation and segmentation tasks fully demonstrate the significant advantages of iSegMan. Project page is available at https://zhao-yian.github.io/iSegMan.

cs.CV↗

arXiv2025

A Comparative Review of RNA Language Models

Given usefulness of protein language models (LMs) in structure and functional inference, RNA LMs have received increased attentions in the last few years. However, these RNA models are often not compared against the same standard. Here, we divided RNA LMs into three classes (pretrained on multiple RNA types (especially noncoding RNAs), specific-purpose RNAs, and LMs that unify RNA with DNA or proteins or both) and compared 13 RNA LMs along with 3 DNA and 1 protein LMs as controls in zero-shot prediction of RNA secondary structure and functional classification. Results shows that the models doing well on secondary structure prediction often perform worse in function classification or vice versa, suggesting that more balanced unsupervised training is needed.

q-bio.BM↗

arXiv2025

Data-driven Internal Model Control for Output Regulation

Output regulation is a fundamental problem in control theory, extensively studied since the 1970s. Traditionally, research has primarily addressed scenarios where the system model is explicitly known, leaving the problem in the absence of a system model less explored. Leveraging the recent advancements in Willems et al.'s fundamental lemma, data-driven control has emerged as a powerful tool for stabilizing unknown systems. This paper tackles the output regulation problem for unknown single and multi-agent systems (MASs) using noisy data. Previous approaches have attempted to solve data-based output regulation equations (OREs), which are inadequate for achieving zero tracking error with noisy data. To circumvent the need for solving data-based OREs, we propose an internal model-based data-driven controller that reformulates the output regulation problem into a stabilization problem. This method is first applied to linear time-invariant (LTI) systems, demonstrating exact solution capabilities, i.e., zero tracking error, through solving a straightforward data-based linear matrix inequality (LMI). Furthermore, we extend our approach to solve the $k$th-order output regulation problem for nonlinear systems. Extensions to both linear and nonlinear MASs are discussed. Finally, numerical tests validate the effectiveness and correctness of the proposed controllers.

eess.SY↗

arXiv2025

FullStack Bench: Evaluating LLMs as Full Stack Coders

As the capabilities of code large language models (LLMs) continue to expand, their applications across diverse code intelligence domains are rapidly increasing. However, most existing datasets only evaluate limited application domains. To address this gap, we have developed a comprehensive code evaluation dataset FullStack Bench focusing on full-stack programming, which encompasses a wide range of application domains (e.g., basic programming, data analysis, software engineering, mathematics, and machine learning). Besides, to assess multilingual programming capabilities, in FullStack Bench, we design real-world instructions and corresponding unit test cases from 16 widely-used programming languages to reflect real-world usage scenarios rather than simple translations. Moreover, we also release an effective code sandbox execution tool (i.e., SandboxFusion) supporting various programming languages and packages to evaluate the performance of our FullStack Bench efficiently. Comprehensive experimental results on our FullStack Bench demonstrate the necessity and effectiveness of our FullStack Bench and SandboxFusion.

cs.AI↗

arXiv2025

Mixed Precision Orthogonalization-Free Projection Methods for Eigenvalue and Singular Value Problems

Mixed-precision arithmetic offers significant computational advantages for large-scale matrix computation tasks, yet preserving accuracy and stability in eigenvalue problems and the singular value decomposition (SVD) remains challenging. This paper introduces an approach that eliminates orthogonalization requirements in traditional Rayleigh-Ritz projection methods. The proposed method employs non-orthogonal bases computed at reduced precision, resulting in bases computed without inner-products. A primary focus is on maintaining the linear independence of the basis vectors. Through extensive evaluation with both synthetic test cases and real-world applications, we demonstrate that the proposed approach achieves the desired accuracy while fully taking advantage of mixed-precision arithmetic.

math.NA↗