Chang Yu

Jiabei Cheng, Jingbo Zhou, Jun Xia et al.

Simultaneous measurement of multiple omics modalities in single cells enables researchers to gain a more comprehensive understanding of cellular states and regulatory mechanisms. However, due to high experimental costs, significant noise, and incomplete modality coverage, a variety of computational methods for modality translation have emerged in recent years. Despite the development of translation models, there is still a lack of systematic benchmark evaluation in terms of datasets, evaluation metrics, and influencing factors. To address this, we present scTranslation, a comprehensive benchmark for single-cell multi-omics modality translation tasks. It includes diverse translation datasets, integrates state-of-the-art models, and provides a comprehensive evaluation metrics. In addition, we assess model performance under different scenarios, such as feature selection, feature quality, and few-shot settings. These factors significantly affect model performance but have rarely been systematically studied before. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development. The benchmark is open-sourced to facilitate future research. The code is anonymously released at https://github.com/Bunnybeibei/scTranslation.

Xin Jin, Hongyu Zhu, Siyuan Li et al.

As Deep Neural Networks have achieved thrilling breakthroughs in the past decade, data augmentations have garnered increasing attention as regularization techniques when massive labeled data are unavailable. Among existing augmentations, Mixup and relevant data-mixing methods that convexly combine selected samples and the corresponding labels are widely adopted because they yield high performances by generating data-dependent virtual data while easily migrating to various domains. This survey presents a comprehensive review of foundational mixup methods and their applications. We first elaborate on the training pipeline with mixup augmentations as a unified framework containing modules. A reformulated framework could contain various mixup methods and give intuitive operational procedures. Then, we systematically investigate the applications of mixup augmentations on vision downstream tasks, various data modalities, and some analysis \& theorems of mixup. Meanwhile, we conclude the current status and limitations of mixup research and point out further work for effective and efficient mixup augmentations. This survey can provide researchers with the current state of the art in mixup methods and provide some insights and guidance roles in the mixup arena. An online project with this survey is available at https://github.com/Westlake-AI/Awesome-Mixup.

Xiangyu Zhu, Chang Yu, Di Huang et al.

3D Morphable Model (3DMM) fitting has widely benefited face analysis due to its strong 3D priori. However, previous reconstructed 3D faces suffer from degraded visual verisimilitude due to the loss of fine-grained geometry, which is attributed to insufficient ground-truth 3D shapes, unreliable training strategies and limited representation power of 3DMM. To alleviate this issue, this paper proposes a complete solution to capture the personalized shape so that the reconstructed shape looks identical to the corresponding person. Specifically, given a 2D image as the input, we virtually render the image in several calibrated views to normalize pose variations while preserving the original image geometry. A many-to-one hourglass network serves as the encode-decoder to fuse multiview features and generate vertex displacements as the fine-grained geometry. Besides, the neural network is trained by directly optimizing the visual effect, where two 3D shapes are compared by measuring the similarity between the multiview images rendered from the shapes. Finally, we propose to generate the ground-truth 3D shapes by registering RGB-D images followed by pose and shape augmentation, providing sufficient data for network training. Experiments on several challenging protocols demonstrate the superior reconstruction accuracy of our proposal on the face shape.

Chang Yu, Xiangyu Zhu, Xiaomei Zhang et al.

Capsule networks are designed to present the objects by a set of parts and their relationships, which provide an insight into the procedure of visual perception. Although recent works have shown the success of capsule networks on simple objects like digits, the human faces with homologous structures, which are suitable for capsules to describe, have not been explored. In this paper, we propose a Hierarchical Parsing Capsule Network (HP-Capsule) for unsupervised face subpart-part discovery. When browsing large-scale face images without labels, the network first encodes the frequently observed patterns with a set of explainable subpart capsules. Then, the subpart capsules are assembled into part-level capsules through a Transformer-based Parsing Module (TPM) to learn the compositional relations between them. During training, as the face hierarchy is progressively built and refined, the part capsules adaptively encode the face parts with semantic consistency. HP-Capsule extends the application of capsule networks from digits to human faces and takes a step forward to show how the neural networks understand homologous objects without human intervention. Besides, HP-Capsule gives unsupervised face segmentation results by the covered regions of part capsules, enabling qualitative and quantitative evaluation. Experiments on BP4D and Multi-PIE datasets show the effectiveness of our method.

Yehui Yang, Zelin Zang, Changxi Chi et al.

Automated cellular reasoning faces a core dichotomy: supervised methods fall into the Reference Trap and fail to generalize to out-of-distribution cell states, while large language models (LLMs), without grounded biological priors, suffer from a Signal-to-Noise Paradox that produces spurious associations. We propose MAT-Cell, a neuro-symbolic reasoning framework that reframes single-cell analysis from black-box classification into constructive, verifiable proof generation. MAT-Cell injects symbolic constraints through adaptive Retrieval-Augmented Generation (RAG) to ground neural reasoning in biological axioms and reduce transcriptomic noise. It further employs a dialectic verification process with homogeneous rebuttal agents to audit and prune reasoning paths, forming syllogistic derivation trees that enforce logical consistency.Across large-scale and cross-species benchmarks, MAT-Cell significantly outperforms state-of-the-art (SOTA) models and maintains robust per-formance in challenging scenarios where baselinemethods severely degrade. Code is available at https://gith ub.com/jiangliu91/MAT-Cell-A-Mul ti-Agent-Tree-Structured-Reasoni ng-Framework-for-Batch-Level-Sin gle-Cell-Annotation.

Chang Yu, Xiangyu Zhu, Xiaomei Zhang et al.

The function of constructing the hierarchy of objects is important to the visual process of the human brain. Previous studies have successfully adopted capsule networks to decompose the digits and faces into parts in an unsupervised manner to investigate the similar perception mechanism of neural networks. However, their descriptions are restricted to the 2D space, limiting their capacities to imitate the intrinsic 3D perception ability of humans. In this paper, we propose an Inverse Graphics Capsule Network (IGC-Net) to learn the hierarchical 3D face representations from large-scale unlabeled images. The core of IGC-Net is a new type of capsule, named graphics capsule, which represents 3D primitives with interpretable parameters in computer graphics (CG), including depth, albedo, and 3D pose. Specifically, IGC-Net first decomposes the objects into a set of semantic-consistent part-level descriptions and then assembles them into object-level descriptions to build the hierarchy. The learned graphics capsules reveal how the neural networks, oriented at visual perception, understand faces as a hierarchy of 3D models. Besides, the discovered parts can be deployed to the unsupervised face segmentation task to evaluate the semantic consistency of our method. Moreover, the part-level descriptions with explicit physical meanings provide insight into the face analysis that originally runs in a black box, such as the importance of shape and texture for face recognition. Experiments on CelebA, BP4D, and Multi-PIE demonstrate the characteristics of our IGC-Net.

Peifeng Ma, Li Chen, Chang Yu et al.

Landslide susceptibility assessment (LSA) is of paramount importance in mitigating landslide risks. Recently, there has been a surge in the utilization of data-driven methods for predicting landslide susceptibility due to the growing availability of aerial and satellite data. Nonetheless, the rapid oscillations within the landslide-inducing environment (LIE), primarily due to significant changes in external triggers such as rainfall, pose difficulties for contemporary data-driven LSA methodologies to accommodate LIEs over diverse timespans. This study presents dynamic landslide susceptibility mapping that simply employs multiple predictive models for annual LSA. In practice, this will inevitably encounter small sample problems due to the limited number of landslide samples in certain years. Another concern arises owing to the majority of the existing LSA approaches train black-box models to fit distinct datasets, yet often failing in generalization and providing comprehensive explanations concerning the interactions between input features and predictions. Accordingly, we proposed to meta-learn representations with fast adaptation ability using a few samples and gradient updates; and apply SHAP for each model interpretation and landslide feature permutation. Additionally, we applied MT-InSAR for LSA result enhancement and validation. The chosen study area is Lantau Island, Hong Kong, where we conducted a comprehensive dynamic LSA spanning from 1992 to 2019. The model interpretation results demonstrate that the primary factors responsible for triggering landslides in Lantau Island are terrain slope and extreme rainfall. The results also indicate that the variation in landslide causes can be primarily attributed to extreme rainfall events, which result from global climate change, and the implementation of the Landslip Prevention and Mitigation Programme (LPMitP) by the Hong Kong government.

Shuang Xu, Chang Yu, Jiangjun Peng et al.

Remote sensing image restoration aims to reconstruct missing or corrupted areas within images. To date, low-rank based models have garnered significant interest in this field. This paper proposes a novel low-rank regularization term, named the Haar nuclear norm (HNN), for efficient and effective remote sensing image restoration. It leverages the low-rank properties of wavelet coefficients derived from the 2-D frontal slice-wise Haar discrete wavelet transform, effectively modeling the low-rank prior for separated coarse-grained structure and fine-grained textures in the image. Experimental evaluations conducted on hyperspectral image inpainting, multi-temporal image cloud removal, and hyperspectral image denoising have revealed the HNN's potential. Typically, HNN achieves a performance improvement of 1-4 dB and a speedup of 10-28x compared to some state-of-the-art methods (e.g., tensor correlated total variation, and fully-connected tensor network) for inpainting tasks.

Jingxuan Wei, Siyuan Li, Yuhang Xu et al.

The construction of World Models capable of learning, simulating, and reasoning about objective physical laws constitutes a foundational challenge in the pursuit of Artificial General Intelligence. Recent advancements represented by video generation models like Sora have demonstrated the potential of data-driven scaling laws to approximate physical dynamics, while the emerging Unified Multimodal Model (UMM) offers a promising architectural paradigm for integrating perception, language, and reasoning. Despite these advances, the field still lacks a principled theoretical framework that defines the essential properties requisite for a General World Model. In this paper, we propose that a World Model must be grounded in the Trinity of Consistency: Modal Consistency as the semantic interface, Spatial Consistency as the geometric basis, and Temporal Consistency as the causal engine. Through this tripartite lens, we systematically review the evolution of multimodal learning, revealing a trajectory from loosely coupled specialized modules toward unified architectures that enable the synergistic emergence of internal world simulators. To complement this conceptual framework, we introduce CoW-Bench, a benchmark centered on multi-frame reasoning and generation scenarios. CoW-Bench evaluates both video generation models and UMMs under a unified evaluation protocol. Our work establishes a principled pathway toward general world models, clarifying both the limitations of current systems and the architectural requirements for future progress.

Haoran Yu, Chang Yu, Zihan Wang et al.

In recent years, the application of Large Language Models (LLMs) in healthcare has shown significant promise in improving the accessibility and dissemination of medical knowledge. This paper presents a detailed study of various LLMs trained on the MedQuAD medical question-answering dataset, with a focus on identifying the most effective model for providing accurate medical information. Among the models tested, the Sentence-t5 combined with Mistral 7B demonstrated superior performance, achieving a precision score of 0.762. This model's enhanced capabilities are attributed to its advanced pretraining techniques, robust architecture, and effective prompt construction methodologies. By leveraging these strengths, the Sentence-t5 + Mistral 7B model excels in understanding and generating precise medical answers. Our findings highlight the potential of integrating sophisticated LLMs in medical contexts to facilitate efficient and accurate medical knowledge retrieval, thus significantly enhancing patient education and support.

Chang Yu, Yixin Jin, Qianwen Xing et al.

Bank credit risk is a significant challenge in modern financial transactions, and the ability to identify qualified credit card holders among a large number of applicants is crucial for the profitability of a bank'sbank's credit card business. In the past, screening applicants'applicants' conditions often required a significant amount of manual labor, which was time-consuming and labor-intensive. Although the accuracy and reliability of previously used ML models have been continuously improving, the pursuit of more reliable and powerful AI intelligent models is undoubtedly the unremitting pursuit by major banks in the financial industry. In this study, we used a dataset of over 40,000 records provided by a commercial bank as the research object. We compared various dimensionality reduction techniques such as PCA and T-SNE for preprocessing high-dimensional datasets and performed in-depth adaptation and tuning of distributed models such as LightGBM and XGBoost, as well as deep models like Tabnet. After a series of research and processing, we obtained excellent research results by combining SMOTEENN with these techniques. The experiments demonstrated that LightGBM combined with PCA and SMOTEENN techniques can assist banks in accurately predicting potential high-quality customers, showing relatively outstanding performance compared to other models.

Liheng Jiang, Xuechun yang, Chang Yu et al.

Trauma is a significant cause of mortality and disability, particularly among individuals under forty. Traditional diagnostic methods for traumatic injuries, such as X-rays, CT scans, and MRI, are often time-consuming and dependent on medical expertise, which can delay critical interventions. This study explores the application of artificial intelligence (AI) and machine learning (ML) to improve the speed and accuracy of abdominal trauma diagnosis. We developed an advanced AI-based model combining 3D segmentation, 2D Convolutional Neural Networks (CNN), and Recurrent Neural Networks (RNN) to enhance diagnostic performance. Our model processes abdominal CT scans to provide real-time, precise assessments, thereby improving clinical decision-making and patient outcomes. Comprehensive experiments demonstrated that our approach significantly outperforms traditional diagnostic methods, as evidenced by rigorous evaluation metrics. This research sets a new benchmark for automated trauma detection, leveraging the strengths of AI and ML to revolutionize trauma care.

Qianwen Xing, Chang Yu, Sining Huang et al.

In contemporary economic society, credit scores are crucial for every participant. A robust credit evaluation system is essential for the profitability of core businesses such as credit cards, loans, and investments for commercial banks and the financial sector. This paper combines high-performance models like XGBoost and LightGBM, already widely used in modern banking systems, with the powerful TabNet model. We have developed a potent model capable of accurately determining credit score levels by integrating Random Forest, XGBoost, and TabNet, and through the stacking technique in ensemble modeling. This approach surpasses the limitations of single models and significantly advances the precise credit score prediction. In the following sections, we will explain the techniques we used and thoroughly validate our approach by comprehensively comparing a series of metrics such as Precision, Recall, F1, and AUC. By integrating Random Forest, XGBoost, and with the TabNet deep learning architecture, these models complement each other, demonstrating exceptionally strong overall performance.

Xichen Yan, Zelin Zang, Changxi Chi et al.

A critical challenge in single-cell RNA sequencing (scRNA-seq) integration is resolving the tension between eliminating batch effects and maintaining biological fidelity. While recent evidence indicates that batch effects manifest heterogeneously across genes, most existing methods process the transcriptome uniformly, frequently resulting in over-correction and loss of subtle biological signals. To address this, we present scHelix, a dataset-adaptive framework that fundamentally changes how features are processed by explicitly partitioning genes into domain-invariant Anchors and domain-sensitive Variants at the input level. scHelix utilizes a dual-stream sparse diffusion encoder equipped with stop-gradient graph caching to efficiently learn multi-scale structural representations. The core of our approach is a novel asymmetric Align-Refine-Fuse protocol: the unstable Variant stream is first aligned to the robust topology of the Anchor stream, followed by a conservative refinement phase where the Anchor stream absorbs denoised details via bounded residual gating. This divide-and-conquer architecture prevents shortcut learning and ensures robust batch removal without compromising the integrity of biological clusters. Extensive benchmarking demonstrates that scHelix outperforms state-of-the-art methods.

Sining Huang, Yukun Song, Yixiao Kang et al.

In the field of spatial computing, one of the most essential tasks is the pose estimation of 3D objects. While rigid transformations of arbitrary 3D objects are relatively hard to detect due to varying environment introducing factors like insufficient lighting or even occlusion, objects with pre-defined shapes are often easy to track, leveraging geometric constraints. Curved images, with flexible dimensions but a confined shape, are essential shapes often targeted in 3D tracking. Traditionally, proprietary algorithms often require specific curvature measures as the input along with the original flattened images to enable pose estimation for a single image target. In this paper, we propose a pipeline that can detect several logo images simultaneously and only requires the original images as the input, unlocking more effects in downstream fields such as Augmented Reality (AR).

Jingbo Zhou, Jun Xia, Siyuan Li et al.

Graph Transformer has demonstrated impressive capabilities in the field of graph representation learning. However, existing approaches face two critical challenges: (1) most models suffer from exponentially increasing computational complexity, making it difficult to scale to large graphs; (2) attention mechanisms based on node-level operations limit the flexibility of the model and result in poor generalization performance in out-of-distribution (OOD) scenarios. To address these issues, we propose \textbf{VecFormer} (the \textbf{Vec}tor Quantized Graph Trans\textbf{former}), an efficient and highly generalizable model for node classification, particularly under OOD settings. VecFormer adopts a two-stage training paradigm. In the first stage, two codebooks are used to reconstruct the node features and the graph structure, aiming to learn the rich semantic \texttt{Graph Codes}. In the second stage, attention mechanisms are performed at the \texttt{Graph Token} level based on the transformed cross codebook, reducing computational complexity while enhancing the model's generalization capability. Extensive experiments on datasets of various sizes demonstrate that VecFormer outperforms the existing Graph Transformer in both performance and speed.

Ying Jiang, Chang Yu, Tianyi Xie et al.

As consumer Virtual Reality (VR) and Mixed Reality (MR) technologies gain momentum, there's a growing focus on the development of engagements with 3D virtual content. Unfortunately, traditional techniques for content creation, editing, and interaction within these virtual spaces are fraught with difficulties. They tend to be not only engineering-intensive but also require extensive expertise, which adds to the frustration and inefficiency in virtual object manipulation. Our proposed VR-GS system represents a leap forward in human-centered 3D content interaction, offering a seamless and intuitive user experience. By developing a physical dynamics-aware interactive Gaussian Splatting in a Virtual Reality setting, and constructing a highly efficient two-level embedding strategy alongside deformable body simulations, VR-GS ensures real-time execution with highly realistic dynamic responses. The components of our Virtual Reality system are designed for high efficiency and effectiveness, starting from detailed scene reconstruction and object segmentation, advancing through multi-view image in-painting, and extending to interactive physics-based editing. The system also incorporates real-time deformation embedding and dynamic shadow casting, ensuring a comprehensive and engaging virtual experience.Our project page is available at: https://yingjiang96.github.io/VR-GS/.

Yutao Feng, Xiang Feng, Yintong Shang et al.

We demonstrate the feasibility of integrating physics-based animations of solids and fluids with 3D Gaussian Splatting (3DGS) to create novel effects in virtual scenes reconstructed using 3DGS. Leveraging the coherence of the Gaussian Splatting and Position-Based Dynamics (PBD) in the underlying representation, we manage rendering, view synthesis, and the dynamics of solids and fluids in a cohesive manner. Similar to GaussianShader, we enhance each Gaussian kernel with an added normal, aligning the kernel's orientation with the surface normal to refine the PBD simulation. This approach effectively eliminates spiky noises that arise from rotational deformation in solids. It also allows us to integrate physically based rendering to augment the dynamic surface reflections on fluids. Consequently, our framework is capable of realistically reproducing surface highlights on dynamic fluids and facilitating interactions between scene objects and fluids from new views. For more information, please visit our project page at \url{https://gaussiansplashing.github.io/}.

Xiang Feng, Chang Yu, Zoubin Bi et al.

Recent image-to-3D reconstruction models have greatly advanced geometry generation, but they still struggle to faithfully generate realistic appearance. To address this, we introduce ARM, a novel method that reconstructs high-quality 3D meshes and realistic appearance from sparse-view images. The core of ARM lies in decoupling geometry from appearance, processing appearance within the UV texture space. Unlike previous methods, ARM improves texture quality by explicitly back-projecting measurements onto the texture map and processing them in a UV space module with a global receptive field. To resolve ambiguities between material and illumination in input images, ARM introduces a material prior that encodes semantic appearance information, enhancing the robustness of appearance decomposition. Trained on just 8 H100 GPUs, ARM outperforms existing methods both quantitatively and qualitatively.

Siyuan Li, Luyuan Zhang, Zedong Wang et al.

Masked Image Modeling (MIM) with Vector Quantization (VQ) has achieved great success in both self-supervised pre-training and image generation. However, most existing methods struggle to address the trade-off in shared latent space for generation quality vs. representation learning and efficiency. To push the limits of this paradigm, we propose MergeVQ, which incorporates token merging techniques into VQ-based generative models to bridge the gap between image generation and visual representation learning in a unified architecture. During pre-training, MergeVQ decouples top-k semantics from latent space with the token merge module after self-attention blocks in the encoder for subsequent Look-up Free Quantization (LFQ) and global alignment and recovers their fine-grained details through cross-attention in the decoder for reconstruction. As for the second-stage generation, we introduce MergeAR, which performs KV Cache compression for efficient raster-order prediction. Extensive experiments on ImageNet verify that MergeVQ as an AR generative model achieves competitive performance in both visual representation learning and image generation tasks while maintaining favorable token efficiency and inference speed. The code and model will be available at https://apexgen-x.github.io/MergeVQ.

Chang Yu, Junran Peng, Xiangyu Zhu et al.

The text-to-image synthesis by diffusion models has recently shown remarkable performance in generating high-quality images. Although performs well for simple texts, the models may get confused when faced with complex texts that contain multiple objects or spatial relationships. To get the desired images, a feasible way is to manually adjust the textual descriptions, i.e., narrating the texts or adding some words, which is labor-consuming. In this paper, we propose a framework to learn the proper textual descriptions for diffusion models through prompt learning. By utilizing the quality guidance and the semantic guidance derived from the pre-trained diffusion model, our method can effectively learn the prompts to improve the matches between the input text and the generated images. Extensive experiments and analyses have validated the effectiveness of the proposed method.

Yuyang Li, Wenxin Du, Chang Yu et al.

Tactile sensing is crucial for achieving human-level robotic capabilities in manipulation tasks. As a promising solution, Vision-Based Tactile Sensors (VBTSs) offer high spatial resolution and cost-effectiveness, but present unique challenges in robotics for their complex physical characteristics and visual signal processing requirements. The lack of efficient and accurate simulation tools for VBTSs has significantly limited the scale and scope of tactile robotics research. We present Taccel, a high-performance simulation platform that integrates IPC and ABD to model robots, tactile sensors, and objects with both accuracy and unprecedented speed, achieving an 18-fold acceleration over real-time across thousands of parallel environments. Unlike previous simulators that operate at sub-real-time speeds with limited parallelization, Taccel provides precise physics simulation and realistic tactile signals while supporting flexible robot-sensor configurations through user-friendly APIs. Through extensive validation in object recognition, robotic grasping, and articulated object manipulation, we demonstrate precise simulation and successful sim-to-real transfer. These capabilities position Taccel as a powerful tool for scaling up tactile robotics research and development, potentially transforming how robots interact with and understand their physical environment.

Zicheng Liu, Siyuan Li, Zhiyuan Chen et al.

The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. Although modern biological pre-trained models have achieved great success in analyzing these macromolecules individually, their interconnected nature remains underexplored. This paper follows the guidance of the central dogma to redesign both the data and model pipeline and offers a comprehensive framework, Life-Code, that spans different biological functions. As for data flow, we propose a unified pipeline to integrate multi-omics data by reverse-transcribing RNA and reverse-translating amino acids into nucleotide-based sequences. As for the model, we design a codon tokenizer and a hybrid long-sequence architecture to encode the interactions between coding and non-coding regions through masked modeling pre-training. To model the translation and folding process with coding sequences, Life-Code learns protein structures of the corresponding amino acids by knowledge distillation from off-the-shelf protein language models. Such designs enable Life-Code to capture complex interactions within genetic sequences, providing a more comprehensive understanding of multi-omics with the central dogma. Extensive experiments show that Life-Code achieves state-of-the-art results on various tasks across three omics, highlighting its potential for advancing multi-omics analysis and interpretation.

Huanyu Liu, Jia Li, Chang Yu et al. · pku

Reinforcement learning with verifiable reward (RLVR) has become a promising paradigm for post-training large language models (LLMs) to improve their reasoning capability. However, when the rollout accuracy is low on hard problems, the reward becomes sparse, limiting learning efficiency and causing exploration bottlenecks. Existing approaches either rely on teacher models for distillation or filter out difficult problems, which limits scalability or restricts reasoning improvement through exploration. We propose EvoCoT, a self-evolving curriculum learning framework based on two-stage chain-of-thought (CoT) reasoning optimization. EvoCoT constrains the exploration space by self-generating and verifying CoT trajectories, then gradually shortens CoT steps to expand the space in a controlled way. The framework enables LLMs to stably learn from initially unsolved hard problems under sparse rewards. We apply EvoCoT to multiple LLM families, including Qwen, DeepSeek, and Llama. Experiments show that EvoCoT enables LLMs to solve previously unsolved problems, improves reasoning capability without external CoT supervision, and is compatible with various RL fine-tuning methods. We release the source code to support future research.

Chang Yu, Fang Liu, Jie Zhu et al. · amazon-science

This paper proposes a hybrid framework combining LSTM (Long Short-Term Memory) networks with LightGBM and CatBoost for stock price prediction. The framework processes time-series financial data and evaluates performance using seven models: Artificial Neural Networks (ANNs), Convolutional Neural Networks (CNNs), Bidirectional LSTM (BiLSTM), vanilla LSTM, XGBoost, LightGBM, and standard Neural Networks (NNs). Key metrics, including MAE, R-squared, MSE, and RMSE, are used to establish benchmarks across different time scales. Building on these benchmarks, we develop an ensemble model that combines the strengths of sequential and tree-based approaches. Experimental results show that the proposed framework improves accuracy by 10 to 15 percent compared to individual models and reduces error during market changes. This study highlights the potential of ensemble methods for financial forecasting and provides a flexible design for integrating new machine learning techniques.

Changxi Chi, Jun Xia, Jingbo Zhou et al.

Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene regulatory networks (GRN) is essential to understand and predict the effects of genetic perturbations. However, current methods fail to fully leverage gene-related information, and solely rely on simple evaluation metrics to construct coarse-grained GRN. More importantly, they ignore functional differences between biotypes, limiting the ability to capture potential gene interactions. In this work, we leverage pre-trained large language model and DNA sequence model to extract features from gene descriptions and DNA sequence data, respectively, which serve as the initialization for gene representations. Additionally, we introduce gene biotype information for the first time in genetic perturbation, simulating the distinct roles of genes with different biotypes in regulating cellular processes, while capturing implicit gene relationships through graph structure learning (GSL). We propose GRAPE, a heterogeneous graph neural network (HGNN) that leverages gene representations initialized with features from descriptions and sequences, models the distinct roles of genes with different biotypes, and dynamically refines the GRN through GSL. The results on publicly available datasets show that our method achieves state-of-the-art performance.

Chang Yu, Yisi Luo, Kai Ye et al.

Implicit neural representation (INR) has emerged as a powerful paradigm for visual data representation. However, classical INR methods represent data in the original space mixed with different frequency components, and several feature encoding parameters (e.g., the frequency parameter $ω$ or the rank $R$) need manual configurations. In this work, we propose a self-evolving cross-frequency INR using the Haar wavelet transform (termed CF-INR), which decouples data into four frequency components and employs INRs in the wavelet space. CF-INR allows the characterization of different frequency components separately, thus enabling higher accuracy for data representation. To more precisely characterize cross-frequency components, we propose a cross-frequency tensor decomposition paradigm for CF-INR with self-evolving parameters, which automatically updates the rank parameter $R$ and the frequency parameter $ω$ for each frequency component through self-evolving optimization. This self-evolution paradigm eliminates the laborious manual tuning of these parameters, and learns a customized cross-frequency feature encoding configuration for each dataset. We evaluate CF-INR on a variety of visual data representation and recovery tasks, including image regression, inpainting, denoising, and cloud removal. Extensive experiments demonstrate that CF-INR outperforms state-of-the-art methods in each case.

Changxi Chi, Jun Xia, Yufei Huang et al.

Estimating single-cell responses across various perturbations facilitates the identification of key genes and enhances drug screening, significantly boosting experimental efficiency. However, single-cell sequencing is a destructive process, making it impossible to capture the same cell's phenotype before and after perturbation. Consequently, data collected under perturbed and unperturbed conditions are inherently unpaired. Existing methods either attempt to forcibly pair unpaired data using random sampling, or neglect the inherent relationship between unperturbed and perturbed cells during the modeling. In this work, we propose a framework based on Dual Diffusion Implicit Bridges (DDIB) to learn the mapping between different data distributions, effectively addressing the challenge of unpaired data. We further interpret this framework as a form of data augmentation. We integrate gene regulatory network (GRN) information to propagate perturbation signals in a biologically meaningful way, and further incorporate a masking mechanism to predict silent genes, improving the quality of generated profiles. Moreover, gene expression under the same perturbation often varies significantly across cells, frequently exhibiting a bimodal distribution that reflects intrinsic heterogeneity. To capture this, we introduce a more suitable evaluation metric. We propose Unlasting, dual conditional diffusion models that overcome the problem of unpaired single-cell perturbation data and strengthen the model's insight into perturbations under the guidance of the GRN, with a dedicated mask model designed to improve generation quality by predicting silent genes. In addition, we introduce a biologically grounded evaluation metric that better reflects the inherent heterogeneity in single-cell responses.

Shuang Xu, Zixiang Zhao, Haowen Bai et al.

Hyperspectral images (HSIs) are frequently noisy and of low resolution due to the constraints of imaging devices. Recently launched satellites can concurrently acquire HSIs and panchromatic (PAN) images, enabling the restoration of HSIs to generate clean and high-resolution imagery through fusing PAN images for denoising and super-resolution. However, previous studies treated these two tasks as independent processes, resulting in accumulated errors. This paper introduces \textbf{H}yperspectral \textbf{I}mage Joint \textbf{Pand}enoising \textbf{a}nd Pan\textbf{s}harpening (Hipandas), a novel learning paradigm that reconstructs HRHS images from noisy low-resolution HSIs (LRHS) and high-resolution PAN images. The proposed zero-shot Hipandas framework consists of a guided denoising network, a guided super-resolution network, and a PAN reconstruction network, utilizing an HSI low-rank prior and a newly introduced detail-oriented low-rank prior. The interconnection of these networks complicates the training process, necessitating a two-stage training strategy to ensure effective training. Experimental results on both simulated and real-world datasets indicate that the proposed method surpasses state-of-the-art algorithms, yielding more accurate and visually pleasing HRHS images.

Siyuan Li, Kai Yu, Anna Wang et al.

Modeling genomic sequences faces two unsolved challenges: the information density varies widely across different regions, while there is no clearly defined minimum vocabulary unit. Relying on either four primitive bases or independently designed DNA tokenizers, existing approaches with naive masked language modeling pre-training often fail to adapt to the varying complexities of genomic sequences. Leveraging Token Merging techniques, this paper introduces a hierarchical architecture that jointly optimizes a dynamic genomic tokenizer and latent Transformers with context-aware pre-training tasks. As for network structures, the tokenization module automatically chunks adjacent bases into words by stacking multiple layers of the differentiable token merging blocks with local-window constraints, then a Latent Encoder captures the global context of these merged words by full-attention blocks. Symmetrically employing a Latent Decoder and a Local Decoder, MergeDNA learns with two pre-training tasks: Merged Token Reconstruction simultaneously trains the dynamic tokenization module and adaptively filters important tokens, while Adaptive Masked Token Modeling learns to predict these filtered tokens to capture informative contents. Extensive experiments show that MergeDNA achieves superior performance on three popular DNA benchmarks and several multi-omics tasks with fine-tuning or zero-shot evaluation, outperforming typical tokenization methods and large-scale DNA foundation models.

Zelin Zang, WenZhe Li, Fei Chen et al.

In single-cell research, tracing and analyzing high-throughput single-cell differentiation trajectories is crucial for understanding complex biological processes. Key to this is the modeling and generation of hierarchical data that represents the intrinsic structure within datasets. Traditional methods face limitations in terms of computational cost, performance, generative capacity, and stability. Recent VAEs based approaches have made strides in addressing these challenges but still require specialized network modules for each tree branch, limiting their stability and ability to capture deep hierarchical relationships. To overcome these challenges, we introduce diffusion-based approach called HDTree. HDTree captures tree relationships within a hierarchical latent space using a unified hierarchical codebook and quantized diffusion processes to model tree node transitions. This method improves stability by eliminating branch-specific modules and enhancing generative capacity through gradual hierarchical changes simulated by the diffusion process. HDTree's effectiveness is demonstrated through comparisons on both general-purpose and single-cell datasets, where it outperforms existing methods in terms of accuracy and performance. These contributions provide a new tool for hierarchical lineage analysis, enabling more accurate and efficient modeling of cellular differentiation paths and offering insights for downstream biological tasks. The code of HDTree is available at anonymous link https://anonymous.4open.science/r/code_HDTree_review-A8DB.

Xin Chen, Jason M. Klusowski, Yan Shuo Tan et al.

Combining randomized estimators in an ensemble, such as via random forests, has become a fundamental technique in modern data science, but can be computationally expensive. Furthermore, the mechanism by which this improves predictive performance is poorly understood. We address these issues in the context of sparse linear regression by proposing and analyzing an ensemble of greedy forward selection estimators that are randomized by feature subsampling -- at each iteration, the best feature is selected from within a random subset. We design a novel implementation based on dynamic programming that greatly improves its computational efficiency. Furthermore, we show via careful numerical experiments that our method can outperform popular methods such as lasso and elastic net across a wide range of settings. Next, contrary to prevailing belief that randomized ensembling is analogous to shrinkage, we show via numerical experiments that it can simultaneously reduce training error and degrees of freedom, thereby shifting the entire bias-variance trade-off curve of the base estimator. We prove this fact rigorously in the setting of orthogonal features, in which case, the ensemble estimator rescales the ordinary least squares coefficients with a two-parameter family of logistic weights, thereby enlarging the model search space. These results enhance our understanding of random forests and suggest that implicit regularization in general may have more complicated effects than explicit regularization.

Xuan Li, Chang Yu, Wenxin Du et al.

Recent advances in large models have significantly advanced image-to-3D reconstruction. However, the generated models are often fused into a single piece, limiting their applicability in downstream tasks. This paper focuses on 3D garment generation, a key area for applications like virtual try-on with dynamic garment animations, which require garments to be separable and simulation-ready. We introduce Dress-1-to-3, a novel pipeline that reconstructs physics-plausible, simulation-ready separated garments with sewing patterns and humans from an in-the-wild image. Starting with the image, our approach combines a pre-trained image-to-sewing pattern generation model for creating coarse sewing patterns with a pre-trained multi-view diffusion model to produce multi-view images. The sewing pattern is further refined using a differentiable garment simulator based on the generated multi-view images. Versatile experiments demonstrate that our optimization approach substantially enhances the geometric alignment of the reconstructed 3D garments and humans with the input image. Furthermore, by integrating a texture generation module and a human motion generation module, we produce customized physics-plausible and realistic dynamic garment demonstrations. Project page: https://dress-1-to-3.github.io/

Xiangyu Zhu, Chang Yu, Jiankuo Zhao et al.

David Marr's seminal theory of vision proposes that the human visual system operates through a sequence of three stages, known as the 2D sketch, the 2.5D sketch, and the 3D model. In recent years, Deep Neural Networks (DNN) have been widely thought to have reached a level comparable to human vision. However, the mechanisms by which DNNs accomplish this and whether they adhere to Marr's 2D--2.5D--3D construction theory remain unexplored. In this paper, we delve into the perception task to explore these questions and find evidence supporting Marr's theory. We introduce a graphics probe, a sub-network crafted to reconstruct the original image from the network's intermediate layers. The key to the graphics probe is its flexible architecture that supports image in both 2D and 3D formats, as well as in a transitional state between them. By injecting graphics probes into neural networks, and analyzing their behavior in reconstructing images, we find that DNNs initially encode images as 2D representations in low-level layers, and finally construct 3D representations in high-level layers. Intriguingly, in mid-level layers, DNNs exhibit a hybrid state, building a geometric representation that s sur normals within a narrow depth range, akin to the appearance of a low-relief sculpture. This stage resembles the 2.5D representations, providing a view of how DNNs evolve from 2D to 3D in the perception process. The graphics probe therefore serves as a tool for peering into the mechanisms of DNN, providing empirical support for Marr's theory.

Kangtong Mo, Wenyan Liu, Xuanzhen Xu et al.

In this study, we explore the application of sentiment analysis on financial news headlines to understand investor sentiment. By leveraging Natural Language Processing (NLP) and Large Language Models (LLM), we analyze sentiment from the perspective of retail investors. The FinancialPhraseBank dataset, which contains categorized sentiments of financial news headlines, serves as the basis for our analysis. We fine-tuned several models, including distilbert-base-uncased, Llama, and gemma-7b, to evaluate their effectiveness in sentiment classification. Our experiments demonstrate that the fine-tuned gemma-7b model outperforms others, achieving the highest precision, recall, and F1 score. Specifically, the gemma-7b model showed significant improvements in accuracy after fine-tuning, indicating its robustness in capturing the nuances of financial sentiment. This model can be instrumental in providing market insights, risk management, and aiding investment decisions by accurately predicting the sentiment of financial news. The results highlight the potential of advanced LLMs in transforming how we analyze and interpret financial information, offering a powerful tool for stakeholders in the financial industry.

Qi Zheng, Chang Yu, Jin Cao et al.

With the rise of various online and mobile payment systems, transaction fraud has become a significant threat to financial security. This study explores the application of advanced machine learning models, specifically based on XGBoost and LightGBM, for developing a more accurate and robust Payment Security Protection Model. To enhance data reliability, we meticulously processed the data sources and applied SMOTE (Synthetic Minority Over-sampling Technique) to address class imbalance and improve data representation. By selecting highly correlated features, we aimed to strengthen the training process and boost model performance. We conducted thorough performance evaluations of our proposed models, comparing them against traditional methods including Random Forest, Neural Network, and Logistic Regression. Using metrics such as Precision, Recall, and F1 Score, we rigorously assessed their effectiveness. Our detailed analyses and comparisons reveal that the combination of SMOTE with XGBoost and LightGBM offers a highly efficient and powerful mechanism for payment security protection. Moreover, the integration of XGBoost and LightGBM in a Local Ensemble model further demonstrated outstanding performance. After incorporating SMOTE, the new combined model achieved a significant improvement of nearly 6\% over traditional models and around 5\% over its sub-models, showcasing remarkable results.

Chang Yu, Yongshun Xu, Jin Cao et al.

With the proliferation of various online and mobile payment systems, credit card fraud has emerged as a significant threat to financial security. This study focuses on innovative applications of the latest Transformer models for more robust and precise fraud detection. To ensure the reliability of the data, we meticulously processed the data sources, balancing the dataset to address the issue of data sparsity significantly. We also selected highly correlated vectors to strengthen the training process.To guarantee the reliability and practicality of the new Transformer model, we conducted performance comparisons with several widely adopted models, including Support Vector Machine (SVM), Random Forest, Neural Network, and Logistic Regression. We rigorously compared these models using metrics such as Precision, Recall, and F1 Score. Through these detailed analyses and comparisons, we present to the readers a highly efficient and powerful anti-fraud mechanism with promising prospects. The results demonstrate that the Transformer model not only excels in traditional applications but also shows great potential in niche areas like fraud detection, offering a substantial advancement in the field.

Cailey I. Kerley, Leon Y. Cai, Chang Yu et al.

Mild traumatic brain injury (mTBI) is a complex syndrome that affects up to 600 per 100,000 individuals, with a particular concentration among military personnel. About half of all mTBI patients experience a diverse array of chronic symptoms which persist long after the acute injury. Hence, there is an urgent need for better understanding of the white matter and gray matter pathologies associated with mTBI to map which specific brain systems are impacted and identify courses of intervention. Previous works have linked mTBI to disruptions in white matter pathways and cortical surface abnormalities. Herein, we examine these hypothesized links in an exploratory study of joint structural connectivity and cortical surface changes associated with mTBI and its chronic symptoms. Briefly, we consider a cohort of 12 mTBI and 26 control subjects. A set of 588 cortical surface metrics and 4,753 structural connectivity metrics were extracted from cortical surface regions and diffusion weighted magnetic resonance imaging in each subject. Principal component analysis (PCA) was used to reduce the dimensionality of each metric set. We then applied independent component analysis (ICA) both to each PCA space individually and together in a joint ICA approach. We identified a stable independent component across the connectivity-only and joint ICAs which presented significant group differences in subject loadings (p<0.05, corrected). Additionally, we found that two mTBI symptoms, slowed thinking and forgetfulness, were significantly correlated (p<0.05, corrected) with mTBI subject loadings in a surface-only ICA. These surface-only loadings captured an increase in bilateral cortical thickness.